[0001] This application claims the benefit of U.S. Provisional Application No. 62/443247, filed January 6, 2017, the disclosure of which is incorporated herein by reference in its entirety.

Field of the Invention

[0002] The present invention relates to tubulin binding compounds and methods of using the compounds to inhibit proliferative disorders. Specifically, the tubulin binding compounds can be useful for inhibiting the growth of a cancer cell or a neoplastic cell or inducing tubulin depolymerization and activating GEF-H1.

Description of the Related Art

[0003] Currently, cancer therapy involves surgery, chemotherapy and/or radiation treatment to eradicate neoplastic cells in a patient. All of these approaches pose significant drawbacks for the patient. Surgery, for example, may be contraindicated due to the health of the patient or may be unacceptable to the patient. Additionally, surgery may not completely remove the neoplastic tissue. Radiation therapy is effective only when the irradiated neoplastic tissue exhibits a higher sensitivity to radiation than normal tissue, and radiation therapy can also often elicit serious side effects. With respect to chemotherapy, there are a variety of chemotherapeutic agents available for treatment of neoplastic disease. However, despite the availability of a variety of chemotherapeutic agents, chemotherapy has many drawbacks. Many chemotherapeutic agents are toxic, and chemotherapy causes significant, and often dangerous, side effects. Additionally, many tumor cells are resistant or develop resistance to chemotherapeutic agents through multi-drug resistance. Thus, there is a need for additional chemotherapeutic agents.

SUMMARY OF THE INVENTION

[0004] Some embodiments relate to a compound or a pharmaceutically acceptable salt, prodrug, or ester thereof, for use in inhibiting tubulin polymerization, the compound comprising at least four moieties selected from L _A , L _B , L _C , L _D , and L _E , wherein: LA is an optionally substituted C6-io aryl or optionally substituted five to ten membered heteroaryl positioned to interact with one or more first tubulin residues selected from the list consisting of

and wherein the distance between at least one atom of the first tubulin

residues and at least one atom of the aryl or heteroaryl of the LA moiety is less than 5 A:

LB IS an optionally substituted Ce-io aryl or optionally substituted five to ten membered heteroaryl positioned to interact with one or more second tubulin residues selected from the list consisting of wherein the distance between at least one atom of the second tubulin residues and at least one atom of the aryl or heteroaryl of the LB moiety is less than 5 A;

Lc is a moiety configured to hydrogen bond with one or more third tubulin residues selected from and wherein

the distance between at least an atom of the third tubulin residues and at least one atom of the hydrogen bonding atom of the Lc moiety is less than 5 A;

LD is a moiety configured to hydrogen bond with one or more fourth tubulin residues selected from and wherein

the distance between at least one atom of the fourth tubulin residues and the hydrogen bonding atom of the LD moiety is less than 5 A; and

LE is a moiety configured to form a hydrophobic interaction with one or more fifth tubulin residues selected from αΤ179, βΤ353, βί248, βί255, βΑ354, βΑ31ό, βΑ317, and βΙ318, wherein the distance between at least one atom of the fifth tubulin residues and at least one atom of the LE moiety is less than 5 A.

[0005] Some embodiments relate to a compound or a pharmaceutically acceptable salt, prodrug, ester thereof!, comprising at least three moieties selected from Lc, LD, LF, or LG, wherein:

Lc is a moiety configured to hydrogen bond with a tubulin βΕ200 oxygen atom, wherein the distance between the oxygen atom and the hydrogen bonding atom of the Lc moiety is less than 4 A; L _D is a moiety configured to hydrogen bond with a tubulin EV238 oxygen atom, wherein the distance between the tubulin EV238 oxygen atom and the hydrogen bonding atom of the L _D moiety is less than 4 Å;

L _F is a moiety configured to hydrogen bond with a tubulin DT179 oxygen atom, wherein the distance between the tubulin DT179 oxygen atom and the hydrogen bonding atom of L _F is less than 8 Å; and

L _G is a moiety configured to hydrogen bond with a tubulin EG237 oxygen atom, wherein the distance between the tubulin EG237 oxygen atom and the hydrogen bonding atom of L _G is less than 8 Å.

[0006] Some embodiments relate to a pharmaceutical composition comprising the compound described herein.

[0007] Some embodiments relate to a method of treating proliferative disease, disorder, or condition, comprising administering he compound or composition described herein.

[0008] Some embodiments relate to a method of treating a cancer, comprising administering the compound or composition described herein.

[0009] Some embodiments relate to a method of inhibiting tubulin polymerization, comprising administering the compound or composition described herein.

BRIEF DESCRIPTION OF THE DRAWINGS

[0010] Figure 1 is a pharmacophore model used for screening the tubulin compounds.

[0011] Figure 2 is a flowchart showing the steps for screening compounds that can bind to tubulin based on the pharmacophore model.

[0012] Figure 3 shows the interacting residues seen in the tubulin-plinabulin complex.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT

[0013] Microtubules are made of Įȕ-tubulin heterodimers that assemble into protofilaments in a head-to-tail fashion, and the straight and parallel protofilaments interact laterally to form the microtubule hollow cylinder. The compounds disclosed herein can bind to tubulin and interfere with microtubule dynamics. There can be five binding sites for exogenous agents on tubulin, namely the taxane, vinca alkaloid, colchicine, laulimalide, and maytansine domains. The compounds described herein can target one or more of these binding sites. Specifically, the compounds described herein can target the colchicine binding site.

[0014] The binding of the compounds described herein may not affect the global conformation of tubulin, nor of the T2R complex. The rmsd for approximately 2000 Ca atoms is less than 0.5Å for all pairwise comparisons of tubulin–ligand complexes. The major conformational changes may involve two loops near the colchicine binding site, bT7 and aT5. The nomenclature of tubulin secondary structure elements and loops can be found in Lowe J, Li H, Downing KH & Nogales E (2001), J Mol Biol 313, 1045–1057, which is incorporated herein by reference for this purpose in its entirety.

Definitions

[0015] A“prodrug” refers to an agent that is converted into the parent drug in vivo. Prodrugs are often useful because, in some situations, they may be easier to administer than the parent drug. They may, for instance, be bioavailable by oral administration whereas the parent is not. The prodrug may also have improved solubility in pharmaceutical compositions over the parent drug. An example, without limitation, of a prodrug would be a compound which is administered as an ester (the“prodrug”) to facilitate transmittal across a cell membrane where water solubility is detrimental to mobility but which then is metabolically hydrolyzed to the carboxylic acid, the active entity, once inside the cell where water-solubility is beneficial. A further example of a prodrug might be a short peptide (polyaminoacid) bonded to an acid group where the peptide is metabolized to reveal the active moiety. Conventional procedures for the selection and preparation of suitable prodrug derivatives are described, for example, in Design of Prodrugs, (ed. H. Bundgaard, Elsevier, 1985), which is hereby incorporated herein by reference in its entirety.

[0016] The term“pro-drug ester” refers to derivatives of the compounds disclosed herein formed by the addition of any of several ester-forming groups that are hydrolyzed under physiological conditions. Examples of pro-drug ester groups include pivoyloxymethyl, acetoxymethyl, phthalidyl, indanyl and methoxymethyl, as well as other such groups known in the art, including a (5-R-2-oxo-1,3-dioxolen-4-yl)methyl group. Other examples of pro- drug ester groups can be found in, for example, T. Higuchi and V. Stella, in "Pro-drugs as Novel Delivery Systems", Vol.14, A.C.S. Symposium Series, American Chemical Society (1975); and "Bioreversible Carriers in Drug Design: Theory and Application", edited by E. B. Roche, Pergamon Press: New York, 14-21 (1987) (providing examples of esters useful as prodrugs for compounds containing carboxyl groups). Each of the above-mentioned references is herein incorporated by reference in their entirety.

[0017] “Metabolites” of the compounds disclosed herein include active species that are produced upon introduction of the compounds into the biological milieu.

[0018] “Solvate” refers to the compound formed by the interaction of a solvent and a compound described herein, a metabolite, or salt thereof. Suitable solvates are pharmaceutically acceptable solvates including hydrates.

[0019] The term“pharmaceutically acceptable salt” refers to salts that retain the biological effectiveness and properties of a compound, which are not biologically or otherwise undesirable for use in a pharmaceutical. In many cases, the compounds herein are capable of forming acid and/or base salts by virtue of the presence of amino and/or carboxyl groups or groups similar thereto. Pharmaceutically acceptable acid addition salts can be formed with inorganic acids and organic acids. Inorganic acids from which salts can be derived include, for example, hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, and the like. Organic acids from which salts can be derived include, for example, acetic acid, propionic acid, glycolic acid, pyruvic acid, oxalic acid, maleic acid, malonic acid, succinic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, p-toluenesulfonic acid, salicylic acid, and the like. Pharmaceutically acceptable base addition salts can be formed with inorganic and organic bases. Inorganic bases from which salts can be derived include, for example, sodium, potassium, lithium, ammonium, calcium, magnesium, iron, zinc, copper, manganese, aluminum, and the like; particularly preferred are the ammonium, potassium, sodium, calcium and magnesium salts. Organic bases from which salts can be derived include, for example, primary, secondary, and tertiary amines, substituted amines including naturally occurring substituted amines, cyclic amines, basic ion exchange resins, and the like, specifically such as isopropylamine, trimethylamine, diethylamine, triethylamine, tripropylamine, and ethanolamine. Many such salts are known in the art, as described in WO 87/05297, Johnston et al., published September 11, 1987 (incorporated by reference herein in its entirety).

[0020] As used herein,“C _a to C _b ” or“C _a-b ” in which“a” and“b” are integers refer to the number of carbon atoms in the specified group. That is, the group can contain from “a” to“b”, inclusive, carbon atoms. Thus, for example, a“C ₁ to C ₄ alkyl” or“C _1-4 alkyl” group refers to all alkyl groups having from 1 to 4 carbons, that is, CH ₃ -, CH ₃ CH ₂ -, CH ₃ CH ₂ CH ₂ -, (CH ₃ ) ₂ CH-, CH ₃ CH ₂ CH ₂ CH ₂ -, CH ₃ CH ₂ CH(CH ₃ )- and (CH ₃ ) ₃ C-.

[0021] The term“halogen” or“halo,” as used herein, means any one of the radio- stable atoms of column 7 of the Periodic Table of the Elements, e.g., fluorine, chlorine, bromine, or iodine, with fluorine and chlorine being preferred.

[0022] As used herein,“alkyl” refers to a straight or branched hydrocarbon chain that is fully saturated (i.e., contains no double or triple bonds). The alkyl group may have 1 to 20 carbon atoms (whenever it appears herein, a numerical range such as“1 to 20” refers to each integer in the given range; e.g.,“1 to 20 carbon atoms” means that the alkyl group may consist of 1 carbon atom, 2 carbon atoms, 3 carbon atoms, etc., up to and including 20 carbon atoms, although the present definition also covers the occurrence of the term“alkyl” where no numerical range is designated). The alkyl group may also be a medium size alkyl having 1 to 9 carbon atoms. The alkyl group could also be a lower alkyl having 1 to 4 carbon atoms. The alkyl group of the compounds may be designated as“C _1-4 alkyl” or similar designations. By way of example only,“C _1-4 alkyl” indicates that there are one to four carbon atoms in the alkyl chain, i.e., the alkyl chain is selected from the group consisting of methyl, ethyl, propyl, iso-propyl, n-butyl, iso-butyl, sec-butyl, and t-butyl. Typical alkyl groups include, but are in no way limited to, methyl, ethyl, propyl, isopropyl, butyl, isobutyl, tertiary butyl, pentyl, hexyl, and the like.

[0023] As used herein,“alkoxy” refers to the formula–OR wherein R is an alkyl as is defined above, such as“C _1-9 alkoxy”, including but not limited to methoxy, ethoxy, n- propoxy, 1-methylethoxy (isopropoxy), n-butoxy, iso-butoxy, sec-butoxy, and tert-butoxy, and the like. [0024] As used herein,“alkylthio” refers to the formula–SR wherein R is an alkyl as is defined above, such as“C _1-9 alkylthio” and the like, including but not limited to methylmercapto, ethylmercapto, n-propylmercapto, 1-methylethylmercapto (isopropylmercapto), n-butylmercapto, iso-butylmercapto, sec-butylmercapto, tert- butylmercapto, and the like.

[0025] As used herein,“alkenyl” refers to a straight or branched hydrocarbon chain containing one or more double bonds. The alkenyl group may have 2 to 20 carbon atoms, although the present definition also covers the occurrence of the term“alkenyl” where no numerical range is designated. The alkenyl group may also be a medium size alkenyl having 2 to 9 carbon atoms. The alkenyl group could also be a lower alkenyl having 2 to 4 carbon atoms. The alkenyl group of the compounds may be designated as“C _2-4 alkenyl” or similar designations. By way of example only,“C _2-4 alkenyl” indicates that there are two to four carbon atoms in the alkenyl chain, i.e., the alkenyl chain is selected from the group consisting of ethenyl, propen-1-yl, propen-2-yl, propen-3-yl, buten-1-yl, buten-2-yl, buten-3- yl, buten-4-yl, 1-methyl-propen-1-yl, 2-methyl-propen-1-yl, 1-ethyl-ethen-1-yl, 2-methyl- propen-3-yl, buta-1,3-dienyl, buta-1,2,-dienyl, and buta-1,2-dien-4-yl. Typical alkenyl groups include, but are in no way limited to, ethenyl, propenyl, butenyl, pentenyl, and hexenyl, and the like.

[0026] As used herein,“alkynyl” refers to a straight or branched hydrocarbon chain containing one or more triple bonds. The alkynyl group may have 2 to 20 carbon atoms, although the present definition also covers the occurrence of the term“alkynyl” where no numerical range is designated. The alkynyl group may also be a medium size alkynyl having 2 to 9 carbon atoms. The alkynyl group could also be a lower alkynyl having 2 to 4 carbon atoms. The alkynyl group of the compounds may be designated as“C _2-4 alkynyl” or similar designations. By way of example only,“C _2-4 alkynyl” indicates that there are two to four carbon atoms in the alkynyl chain, i.e., the alkynyl chain is selected from the group consisting of ethynyl, propyn-1-yl, propyn-2-yl, butyn-1-yl, butyn-3-yl, butyn-4-yl, and 2- butynyl. Typical alkynyl groups include, but are in no way limited to, ethynyl, propynyl, butynyl, pentynyl, and hexynyl, and the like. [0027] As used herein,“heteroalkyl” refers to a straight or branched hydrocarbon chain containing one or more heteroatoms, that is, an element other than carbon, including but not limited to, nitrogen, oxygen and sulfur, in the chain backbone. The heteroalkyl group may have 1 to 20 carbon atoms although the present definition also covers the occurrence of the term“heteroalkyl” where no numerical range is designated. The heteroalkyl group may also be a medium size heteroalkyl having 1 to 9 carbon atoms. The heteroalkyl group could also be a lower heteroalkyl having 1 to 4 carbon atoms. The heteroalkyl group of the compounds may be designated as“C _1-4 heteroalkyl” or similar designations. The heteroalkyl group may contain one or more heteroatoms. By way of example only,“C _1-4 heteroalkyl” indicates that there are one to four carbon atoms in the heteroalkyl chain and additionally one or more heteroatoms in the backbone of the chain.

[0028] The term“aromatic” refers to a ring or ring system having a conjugated pi electron system and includes both carbocyclic aromatic (e.g., phenyl) and heterocyclic aromatic groups (e.g., pyridine). The term includes monocyclic or fused-ring polycyclic (i.e., rings which share adjacent pairs of atoms) groups provided that the entire ring system is aromatic.

[0029] As used herein,“aryl” refers to an aromatic ring or ring system (i.e., two or more fused rings that share two adjacent carbon atoms) containing only carbon in the ring backbone. When the aryl is a ring system, every ring in the system is aromatic. The aryl group may have 6 to 18 carbon atoms, although the present definition also covers the occurrence of the term“aryl” where no numerical range is designated. In some embodiments, the aryl group has 6 to 10 carbon atoms. The aryl group may be designated as“C _6-10 aryl,” “C6 or C10 aryl,” or similar designations. Examples of aryl groups include, but are not limited to, phenyl, naphthyl, azulenyl, and anthracenyl.

[0030] As used herein,“aryloxy” and“arylthio” refers to RO- and RS-, in which R is an aryl as is defined above, , such as“C _6-10 aryloxy” or“C _6-10 arylthio” and the like, includingbut not limited to phenyloxy.

[0031] An“aralkyl” or“arylalkyl” is an aryl group connected, as a substituent, via an alkylene group, such“C _7-14 aralkyl” and the like, including but not limited to benzyl, 2- phenylethyl, 3-phenylpropyl, and naphthylalkyl. In some cases, the alkylene group is a lower alkylene group (i.e., a C _1-4 alkylene group).

[0032] As used herein,“heteroaryl” refers to an aromatic ring or ring system (i.e., two or more fused rings that share two adjacent atoms) that contain(s) one or more heteroatoms, that is, an element other than carbon, including but not limited to, nitrogen, oxygen and sulfur, in the ring backbone. When the heteroaryl is a ring system, every ring in the system is aromatic. The heteroaryl group may have 5-18 ring members (i.e., the number of atoms making up the ring backbone, including carbon atoms and heteroatoms), although the present definition also covers the occurrence of the term“heteroaryl” where no numerical range is designated. In some embodiments, the heteroaryl group has 5 to 10 ring members or 5 to 7 ring members. The heteroaryl group may be designated as“5-7 membered heteroaryl,” “5-10 membered heteroaryl,” or similar designations. Examples of heteroaryl rings include, but are not limited to, furyl, thienyl, phthalazinyl, pyrrolyl, oxazolyl, thiazolyl, imidazolyl, pyrazolyl, isoxazolyl, isothiazolyl, triazolyl, thiadiazolyl, pyridinyl, pyridazinyl, pyrimidinyl, pyrazinyl, triazinyl, quinolinyl, isoquinlinyl, benzimidazolyl, benzoxazolyl, benzothiazolyl, indolyl, isoindolyl, and benzothienyl.

[0033] A“heteroaralkyl” or“heteroarylalkyl” is heteroaryl group connected, as a substituent, via an alkylene group. Examples include but are not limited to 2-thienylmethyl, 3-thienylmethyl, furylmethyl, thienylethyl, pyrrolylalkyl, pyridylalkyl, isoxazollylalkyl, and imidazolylalkyl. In some cases, the alkylene group is a lower alkylene group (i.e., a C _1-4 alkylene group).

[0034] As used herein,“carbocyclyl” means a non-aromatic cyclic ring or ring system containing only carbon atoms in the ring system backbone. When the carbocyclyl is a ring system, two or more rings may be joined together in a fused, bridged or spiro-connected fashion. Carbocyclyls may have any degree of saturation provided that at least one ring in a ring system is not aromatic. Thus, carbocyclyls include cycloalkyls, cycloalkenyls, and cycloalkynyls. The carbocyclyl group may have 3 to 20 carbon atoms, although the present definition also covers the occurrence of the term“carbocyclyl” where no numerical range is designated. The carbocyclyl group may also be a medium size carbocyclyl having 3 to 10 carbon atoms. The carbocyclyl group could also be a carbocyclyl having 3 to 6 carbon atoms. The carbocyclyl group may be designated as“C3-6 carbocyclyl” or similar designations. Examples of carbocyclyl rings include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cyclohexenyl, 2,3-dihydro-indene, bicycle[2.2.2]octanyl, adamantyl, and spiro[4.4]nonanyl.

[0035] A“(carbocyclyl)alkyl” is a carbocyclyl group connected, as a substituent, via an alkylene group, such as“C _4-10 (carbocyclyl)alkyl” and the like, including but not limited to, cyclopropylmethyl, cyclobutylmethyl, cyclopropylethyl, cyclopropylbutyl, cyclobutylethyl, cyclopropylisopropyl, cyclopentylmethyl, cyclopentylethyl, cyclohexylmethyl, cyclohexylethyl, cycloheptylmethyl, and the like. In some cases, the alkylene group is a lower alkylene group.

[0036] As used herein,“cycloalkyl” means a fully saturated carbocyclyl ring or ring system. Examples include cyclopropyl, cyclobutyl, cyclopentyl, and cyclohexyl.

[0037] As used herein,“cycloalkenyl” means a carbocyclyl ring or ring system having at least one double bond, wherein no ring in the ring system is aromatic. An example is cyclohexenyl.

[0038] As used herein,“heterocyclyl” means a non-aromatic cyclic ring or ring system containing at least one heteroatom in the ring backbone. Heterocyclyls may be joined together in a fused, bridged or spiro-connected fashion. Heterocyclyls may have any degree of saturation provided that at least one ring in the ring system is not aromatic. The heteroatom(s) may be present in either a non-aromatic or aromatic ring in the ring system. The heterocyclyl group may have 3 to 20 ring members (i.e., the number of atoms making up the ring backbone, including carbon atoms and heteroatoms), although the present definition also covers the occurrence of the term“heterocyclyl” where no numerical range is designated. The heterocyclyl group may also be a medium size heterocyclyl having 3 to 10 ring members. The heterocyclyl group could also be a heterocyclyl having 3 to 6 ring members. The heterocyclyl group may be designated as “3-6 membered heterocyclyl” or similar designations. In preferred six membered monocyclic heterocyclyls, the heteroatom(s) are selected from one up to three of O, N or S, and in preferred five membered monocyclic heterocyclyls, the heteroatom(s) are selected from one or two heteroatoms selected from O, N, or S. Examples of heterocyclyl rings include, but are not limited to, azepinyl, acridinyl, carbazolyl, cinnolinyl, dioxolanyl, imidazolinyl, imidazolidinyl, morpholinyl, oxiranyl, oxepanyl, thiepanyl, piperidinyl, piperazinyl, dioxopiperazinyl, pyrrolidinyl, pyrrolidonyl, pyrrolidionyl, 4-piperidonyl, pyrazolinyl, pyrazolidinyl, 1,3-dioxinyl, 1,3-dioxanyl, 1,4- dioxinyl, 1,4-dioxanyl, 1,3-oxathianyl, 1,4-oxathiinyl, 1,4-oxathianyl, 2H-1,2-oxazinyl, trioxanyl, hexahydro-1,3,5-triazinyl, 1,3-dioxolyl, 1,3-dioxolanyl, 1,3-dithiolyl, 1,3- dithiolanyl, isoxazolinyl, isoxazolidinyl, oxazolinyl, oxazolidinyl, oxazolidinonyl, thiazolinyl, thiazolidinyl, 1,3-oxathiolanyl, indolinyl, isoindolinyl, tetrahydrofuranyl, tetrahydropyranyl, tetrahydrothiophenyl, tetrahydrothiopyranyl, tetrahydro-1,4-thiazinyl, thiamorpholinyl, dihydrobenzofuranyl, benzimidazolidinyl, and tetrahydroquinoline.

[0039] A“(heterocyclyl)alkyl” is a heterocyclyl group connected, as a substituent, via an alkylene group. Examples include, but are not limited to, imidazolinylmethyl and indolinylethyl.

[0040] As used herein,“acyl” refers to–C(=O)R, wherein R is hydrogen, C _1-6 alkyl, C _2-6 alkenyl, C _2-6 alkynyl, C _3-7 carbocyclyl, aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein. Non-limiting examples include formyl, acetyl, propanoyl, benzoyl, and acryl.

[0041] An“O-carboxy” group refers to a“-OC(=O)R” group in which R is selected from hydrogen, C _1-6 alkyl, C _2-6 alkenyl, C _2-6 alkynyl, C _3-7 carbocyclyl, aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein.

[0042] A“C-carboxy” group refers to a“-C(=O)OR” group in which R is selected from hydrogen, C _1-6 alkyl, C _2-6 alkenyl, C _2-6 alkynyl, C _3-7 carbocyclyl, aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein. A non-limiting example includes carboxyl (i.e., -C(=O)OH).

[0043] A“cyano” group refers to a“-CN” group.

[0044] A“cyanato” group refers to an“-OCN” group.

[0045] An“isocyanato” group refers to a“-NCO” group.

[0046] A“thiocyanato” group refers to a“-SCN” group.

[0047] An“isothiocyanato” group refers to an“-NCS” group. [0048] A“sulfinyl” group refers to an“-S(=O)R” group in which R is selected from hydrogen, C _1-6 alkyl, C _2-6 alkenyl, C _2-6 alkynyl, C _3-7 carbocyclyl, C _6-10 aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein.

[0049] A“sulfonyl” group refers to an“-SO ₂ R” group in which R is selected from hydrogen, C _1-6 alkyl, C _2-6 alkenyl, C _2-6 alkynyl, C _3-7 carbocyclyl, C _6-10 aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein.

[0050] An“S-sulfonamido” group refers to a“-SO ₂ NR _A R _B ” group in which R _A and R _B are each independently selected from hydrogen, C _1-6 alkyl, C _2-6 alkenyl, C _2-6 alkynyl, C _3-7 carbocyclyl, C _6-10 aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein.

[0051] An“N-sulfonamido” group refers to a“-N(R _A )SO ₂ R _B ” group in which R _A and R _b are each independently selected from hydrogen, C _1-6 alkyl, C _2-6 alkenyl, C _2-6 alkynyl, C _3-7 carbocyclyl, C _6-10 aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein.

[0052] An“O-carbamyl” group refers to a“-OC(=O)NR _A R _B ” group in which R _A and R _B are each independently selected from hydrogen, C _1-6 alkyl, C _2-6 alkenyl, C _2-6 alkynyl, C _3-7 carbocyclyl, C _6-10 aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein.

[0053] An“N-carbamyl” group refers to an“-N(R _A )OC(=O)R _B ” group in which R _A and R _B are each independently selected from hydrogen, C _1-6 alkyl, C _2-6 alkenyl, C _2-6 alkynyl, C _3-7 carbocyclyl, C _6-10 aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein.

[0054] An“O-thiocarbamyl” group refers to a“-OC(=S)NR _A R _B ” group in which R _A and R _B are each independently selected from hydrogen, C _1-6 alkyl, C _2-6 alkenyl, C _2-6 alkynyl, C _3-7 carbocyclyl, aC _6-10 ryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein.

[0055] An“N-thiocarbamyl” group refers to an“-N(R _A )OC(=S)R _B ” group in which R _A and R _B are each independently selected from hydrogen, C _1-6 alkyl, C _2-6 alkenyl, C _{2- 6} alkynyl, C _3-7 carbocyclyl, C _6-10 aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein. [0056] A“C-amido” group refers to a“-C(=O)NR _A R _B ” group in which R _A and R _B are each independently selected from hydrogen, C _1-6 alkyl, C _2-6 alkenyl, C _2-6 alkynyl, C _3-7 carbocyclyl, C _6-10 aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein.

[0057] An“N-amido” group refers to a“-N(R _A )C(=O)R _B ” group in which R _A and R _B are each independently selected from hydrogen, C _1-6 alkyl, C _2-6 alkenyl, C _2-6 alkynyl, C _3-7 carbocyclyl, C _6-10 aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein.

[0058] An“amino” group refers to a“-NR _A R _B ” group in which R _A and R _B are each independently selected from hydrogen, C _1-6 alkyl, C _2-6 alkenyl, C _2-6 alkynyl, C _3-7 carbocyclyl, C _6-10 aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein.

[0059] An“aminoalkyl” group refers to an amino group connected via an alkylene group.

[0060] An“alkoxyalkyl” group refers to an alkoxy group connected via an alkylene group, such as a“C _2-8 alkoxyalkyl” and the like.

[0061] As used herein, a substituted group is derived from the unsubstituted parent group in which there has been an exchange of one or more hydrogen atoms for another atom or group. Unless otherwise indicated, when a group is deemed to be“substituted,” it is meant that the group is substituted with one or more subsitutents independently selected from C ₁ -C ₆ alkyl, C ₁ -C ₆ alkenyl, C ₁ -C ₆ alkynyl, C ₁ -C ₆ heteroalkyl, C ₃ -C ₇ carbocyclyl (optionally substituted with halo, C ₁ -C ₆ alkyl, C ₁ -C ₆ alkoxy, C ₁ -C ₆ haloalkyl, and C ₁ -C ₆ haloalkoxy), C ₃ - C ₇ -carbocyclyl-C ₁ -C ₆ -alkyl (optionally substituted with halo, C ₁ -C ₆ alkyl, C ₁ -C ₆ alkoxy, C ₁ - C ₆ haloalkyl, and C ₁ -C ₆ haloalkoxy), 5-10 membered heterocyclyl (optionally substituted with halo, C1-C6 alkyl, C1-C6 alkoxy, C1-C6 haloalkyl, and C1-C6 haloalkoxy), 5-10 membered heterocyclyl-C ₁ -C ₆ -alkyl (optionally substituted with halo, C ₁ -C ₆ alkyl, C ₁ -C ₆ alkoxy, C ₁ -C ₆ haloalkyl, and C ₁ -C ₆ haloalkoxy), aryl (optionally substituted with halo, C ₁ -C ₆ alkyl, C ₁ -C ₆ alkoxy, C ₁ -C ₆ haloalkyl, and C ₁ -C ₆ haloalkoxy), aryl(C ₁ -C ₆ )alkyl (optionally substituted with halo, C ₁ -C ₆ alkyl, C ₁ -C ₆ alkoxy, C ₁ -C ₆ haloalkyl, and C ₁ -C ₆ haloalkoxy), 5- 10 membered heteroaryl (optionally substituted with halo, C ₁ -C ₆ alkyl, C ₁ -C ₆ alkoxy, C ₁ -C ₆ haloalkyl, and haloalkoxy), membered heteroaryl(C1-C6)alkyl (optionally substituted with halo,

halo, cyano, hydroxy, aryloxy,

sulfhydryl (mercapto),

alkylthio, arylthio, amino, nitro, O-carbamyl, N-carbamyl, O-

thiocarbamyl, N-thiocarbamyl, C-amido, N-amido, S-sulfonamido, N-sulfonamido, C- carboxy, O-carboxy, acyl, cyanato, isocyanato, thiocyanato, isothiocyanato, sulfinyl, sulfonyl, and oxo (=O). Wherever a group is described as“optionally substituted” that group can be substituted with the above substituents.

[0062] In some embodiments, substituted group(s) is (are) substituted with one or more substituent(s) individually and independently selected from C ₁ -C ₄ alkyl, amino, hydroxy, and halogen.

[0063] It is to be understood that certain radical naming conventions can include either a mono-radical or a di-radical, depending on the context. For example, where a substituent requires two points of attachment to the rest of the molecule, it is understood that the substituent is a di-radical. For example, a substituent identified as alkyl that requires two points of attachment includes di-radicals such as

and the like. Other radical naming conventions clearly indicate that the radical is a di-radical such as“alkylene” or“alkenylene.”

[0064] As used herein,“alkylene” means a branched, or straight chain fully saturated di-radical chemical group containing only carbon and hydrogenthat is attached to the rest of the molecule via two points of attachment (i.e., an alkanediyl). The alkylene group may have 1 to 20 carbon atoms, although the present definition also covers the occurrence of the term alkylene where no numerical range is designated. The alkylene group may also be a medium size alkylene having 1 to 9 carbon atoms. The alkylene group could also be a lower alkylene having 1 to 4 carbon atoms. The alkylene group may be designated as“C _1-4 alkylene” or similar designations. By way of example only,“C _1-4 alkylene” indicates that there are one to four carbon atoms in the alkylene chain, i.e., the alkylene chain is selected from the group consisting of methylene, ethylene, ethan-1,1-diyl, propylene, propan-1,1-diyl, propan-2,2-diyl, 1-methyl-ethylene, butylene, butan-1,1-diyl, butan-2,2-diyl, 2-methyl- propan-1,1-diyl, 1-methyl-propylene, 2-methyl-propylene, 1,1-dimethyl-ethylene, 1,2- dimethyl-ethylene, and 1-ethyl-ethylene.

[0065] As used herein,“alkenylene” means a straight or branched chain di-radical chemical group containing only carbon and hydrogen and containing at least one carbon- carbon double bond that is attached to the rest of the molecule via two points of attachment. The alkenylene group may have 2 to 20 carbon atoms, although the present definition also covers the occurrence of the term alkenylene where no numerical range is designated. The alkenylene group may also be a medium size alkenylene having 2 to 9 carbon atoms. The alkenylene group could also be a lower alkenylene having 2 to 4 carbon atoms. The alkenylene group may be designated as“C _2-4 alkenylene” or similar designations. By way of example only,“C _2-4 alkenylene” indicates that there are two to four carbon atoms in the alkenylene chain, i.e., the alkenylene chain is selected from the group consisting of ethenylene, ethen-1,1-diyl, propenylene, propen-1,1-diyl, prop-2-en-1,1-diyl, 1-methyl- ethenylene, but-1-enylene, but-2-enylene, but-1,3-dienylene, buten-1,1-diyl, but-1,3-dien-1,1- diyl, but-2-en-1,1-diyl, but-3-en-1,1-diyl, 1-methyl-prop-2-en-1,1-diyl, 2-methyl-prop-2-en- 1,1-diyl, 1-ethyl-ethenylene, 1,2-dimethyl-ethenylene, 1-methyl-propenylene, 2-methyl- propenylene, 3-methyl-propenylene, 2-methyl-propen-1,1-diyl, and 2,2-dimethyl-ethen-1,1- diyl.

[0066] The term“agent” or“test agent” includes any substance, molecule, element, compound, entity, or a combination thereof. It includes, but is not limited to, e.g., protein, polypeptide, peptide or mimetic, small organic molecule, polysaccharide, polynucleotide, and the like. It can be a natural product, a synthetic compound, or a chemical compound, or a combination of two or more substances. Unless otherwise specified, the terms“agent”,“substance”, and“compound” are used interchangeably herein.

[0067] The term“analog” or“derivative” is used herein to refer to a molecule that structurally resembles a reference molecule but which has been modified in a targeted and controlled manner, by replacing a specific substituent of the reference molecule with an alternate substituent. Compared to the reference molecule, an analog would be expected, by one skilled in the art, to exhibit the same, similar, or improved utility. Synthesis and screening of analogs, to identify variants of known compounds having improved characteristics (such as higher binding affinity for a target molecule) is an approach that is well known in pharmaceutical chemistry.

[0068] The term“mammal” is used in its usual biological sense. Thus, it specifically includes, but is not limited to, primates, including simians (chimpanzees, apes, monkeys) and humans, cattle, horses, sheep, goats, swine, rabbits, dogs, cats, rats and mice but also includes many other species.

[0069] The term “pharmaceutically acceptable carrier” or“pharmaceutically acceptable excipient” includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents and the like. The use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredient, its use in the therapeutic compositions is contemplated. In addition, various adjuvants such as are commonly used in the art may be included. Considerations for the inclusion of various components in pharmaceutical compositions are described, e.g., in Gilman et al. (Eds.) (1990); Goodman and Gilman’s: The Pharmacological Basis of Therapeutics, 8th Ed., Pergamon Press, which is incorporated herein by reference in its entirety. The pharmaceutically acceptable excipient can be a monosaccharide or monosaccharide derivative.

[0070] “Subject” as used herein, means a human or a non-human mammal, e.g., a dog, a cat, a mouse, a rat, a cow, a sheep, a pig, a goat, a non-human primate or a bird, e.g., a chicken, as well as any other vertebrate or invertebrate.

[0071] An“effective amount” or a“therapeutically effective amount” as used herein refers to an amount of a therapeutic agent that is effective to relieve, to some extent, or to reduce the likelihood of onset of, one or more of the symptoms of a disease or condition, and includes curing a disease or condition.“Curing” means that the symptoms of a disease or condition are eliminated; however, certain long-term or permanent effects may exist even after a cure is obtained (such as extensive tissue damage).

[0072] “Treat,”“treatment,” or“treating,” as used herein refers to administering a pharmaceutical composition for prophylactic and/or therapeutic purposes. The term “prophylactic treatment” refers to treating a subject who does not yet exhibit symptoms of a disease or condition, but who is susceptible to, or otherwise at risk of, a particular disease or condition, whereby the treatment reduces the likelihood that the patient will develop the disease or condition. The term "therapeutic treatment" refers to administering treatment to a subject already suffering from a disease or condition.

Compound and Pharmacophore

[0073] Microtubules, which are noncovalently linked polymers formed by the a- and β-tubulin heterodimers, are a major component of the cytoskeleton with an important role in a variety of cellular functions, such as cell shape maintenance, intracellular transport, polarity, cell signaling, and mitosis. Compounds possessing tubulin-depolymerizing activity, such as plinabulin were recognized as effective anti-tumor/anti-cancer agents. The effect of tubulin depolymerization can lead to a loss of blood supply and eventual contraction of the tumor. The compounds described herein can bind to tubulin and cause tubulin- depolymerization, and thus can be used to effectively treat cancer and tumor.

[0074] Human β-tubulin can have nine isoforms, including TUBBl, TUBB2a, TUBB2b, TUBB3, TUBB4a, TUBB4b, TUBB5 (TUBB), TUBB6, TUBB8. Human β-tubulin TUBBl, TUBB3 and TUBB6 contain a serine residue within close proximity to plinabulin binding, whereas TUBB2A, TUBB2B, TUBB4A, TUBB4B and TUBB 5 contain a cysteine residue. The substitution of a serine for a cysteine amino acid residue may provide a difference in binding affinity due to the presence or absence of a sulfide bonding residue. In some embodiments, the human β-tubulm can be a tubulin isoform having a cysteine at the 241 position. In some embodiments, the human β-tubulin can be TUBB 2a, TUBB2b, TUBB4a, TUBB4b, or TUBB5 isoforms. In some embodiments, the human β-tubulin has a serine at the 241 position. In some embodiments, the human β-tubulin be TUBBl, TUBB3 or TUBB 6 isoform. In some embodiments, the compound described herein can bind stronger to a tubulin isoform (e.g., TUBBl, TUBB3 or TUBB6) wherein the C241 is substituted by a S241.

[0075] In some embodiments, the compounds described herein includes only one of the Lc or the LD moiety. In some embodiments, the compounds described herein includes both the Lc moiety or the LD moiety. [0076] In some embodiments, the distance between at least one atom of the first tubulin residues and at least one atom of the aryl or heteroaryl of the LA moiety is less than 4 A. In some embodiments, distance between at least one atom of the first tubulin residues and at least one atom of the aryl or heteroaryl of the LA moiety is less than 3 A.

[0077] In some embodiments, the distance between at least one atom of the second tubulin residues and at least one atom of the aryl or heteroaryl of the LB moiety is less than 4 A. In some embodiments, wherein the distance between at least one atom of the second tubulin residues and at least one atom of the aryl or heteroaryl of the LB moiety is less than 3

A,

[0078] In some embodiments, the distance between at least an atom of the third tubulin residues and at least one atom of the hydrogen bonding atom of the Lc moiety is less than 4 A. In some embodiments, the distance between at least an atom of the third tubulin residues and at least one atom of the hydrogen bonding atom of the Lc moiety is less than 3

A.

[0079] In some embodiments, the distance between at least an atom of the third tubulin residues and at least one atom of the hydrogen bonding atom of the LD moiety is less than 4 A. In some embodiments, the distance between at least an atom of the third tubuim residues and at least one atom of the hydrogen bonding atom of the LD moiety is less than 3

A.

[0080] The compound of any one of claims 1 to 5, wherein the distance between at least one atom of the fifth tubulin residues and at least one atom of the LE moiety is less than 4 A. The compound of any one of claims 1 to 5, wherein the distance between at least one atom of the fifth tubulin residues and at least one atom of the LE moiety is less than 3 A,

[0081] In some embodiments, at least one atom of the LA moiety is positioned withm 4A from at least one atom of one or more tubulin residues selected from βΝ167, PQ136, and βΕ200. In some embodiments, at least one atom of the LB moiety is positioned within 4A from at least one atom of one or more tubulin residues selected from βΝ258 and βΚ352. In some embodiments, at least one atom of the Lc moiety is positioned within 4A from at least one atom of one or more tubulin residues selected from βΙ318, (3L255, pL242, βΜ259, βΡ268, βΑ316, and βΙ378. In some embodiments, at least one atom of the LD moiety is positioned within 4 A from at least one atom of one or more tubulin residues selected from βI 318, βL255, βL .2-11 βΜ259, βΤ268, βΑ316, and βΙ378. In some embodiments, at least one atom of the LE moiety is positioned within 4 A from at least one atom of one or more tubulin residues selected from β8241 , βΙ376, βΤ239, and βΚ352.

[0082] In some embodiments, the interaction between the moiety of LA and the first residues is a Pi bond interaction. In some embodiments, the interaction between the moiety of LB and the second residues is a Pi bond interaction.

[0083] In some embodiments, LE comprises an optionally substituted -Ci-Cealkyi, halogenated

halogenated or cyano.

[0084] In some embodiments, the compound described herein can have the structure selected from compounds A-l to A-51 in Table 1. In some embodiments, the compounds comprises LA, LB, LC, LD, and LE moieties. In some embodiments, the compounds in Table 1 comprises LA, LB, LC, LD, and LE moieties.

[0085] In some embodiments, the compound described herein can have a structure selected from compounds B-1 to B-293 in Table 2. In some embodiments, the compounds listed comprises L _A , L _B , L _C , and L _E moieties and does not contain L _C moiety. In some embodiments, the compounds comprises L _A , L _B , L _D , and L _E moieties and does not contain L _D moiety. In some embodiments, the compounds in Table 2 comprises L _A , L _B , L _E and only one of L _C and L _E moiety.

[0086] In some embodiments, the compound described herein can have the structure selected from compounds C-1 to C-9 in Table 3. In some embodiments, the compound comprises L _A , L _B , L _C , and L _D moieties and does not contain L _E moiety. In some embodiments, the compound in Table 3 comprises L _A , L _B , L _C , and L _D moieties and does not contain L _E moiety.

Table 3.

[0087] Some embodiments relate to a compound or a pharmaceutically acceptable salt, prodrug, ester thereof, comprising at least three moieties selected from L _C , L _D , L _F , or L _G , wherein:

L _C is a moiety configured to hydrogen bond with a tubulin EE200 oxygen atom, wherein the distance between the oxygen atom and the hydrogen bonding atom of the L _C moiety is less than 4 Å;

L _D is a moiety configured to hydrogen bond with a tubulin EV238 oxygen atom, wherein the distance between the tubulin EV238 side chain and the hydrogen bonding atom of the L _D moiety is less than 4 Å;

L _F is a moiety configured to hydrogen bond with a tubulin DT179 oxygen atom, wherein the distance between the oxygen of the tubulin DT179 amide and the hydrogen bonding atom of L _F is less than 8 Å; and

L _G is a moiety configured to hydrogen bond with a tubulin EG237 oxygen atom, wherein the distance between the oxygen of the tubulin EG237 and the hydrogen bonding atom of L _G is less than 8 Å.

[0088] Some embodiments relate to a compound or a pharmaceutically acceptable salt, prodrug, ester thereof, comprising at least three moieties selected from L _C , L _D , L _F , or L _G , wherein:

L _C is a moiety configured to hydrogen bond with a tubulin EE200 oxygen atom, wherein the distance between the oxygen atom and the hydrogen atom bonding atom of the L _C moiety is less than 4 Å;

L _D is a moiety configured to hydrogen bond with a tubulin EV238 side chain, wherein the distance between the tubulin EV238 side chain and the hydrogen atom bonding atom of the L _D moiety is less than 4 Å;

L _F is a moiety configured to hydrogen bond with a water molecule, wherein the water molecule in turn hydrogen bonds with a tubulin DT179 oxygen atom, wherein the distance between the oxygen of the tubulin DT179 amide and the hydrogen atom bonding atom of LF is less than 8 Å, preferably less than 4 Å;

L _G is a moiety configured to hydrogen bond with a water molecule, wherein the water molecule in turn hydrogen bonds with a tubulin EG237 oxygen atom, wherein the distance between the oxygen of the tubulin EG237 and the hydrogen atom bonding atom of L _G is less than 8 Å, preferably less than 4 Å.

In some embodiments, the compounds described herein include a structure of formula (I) wherein:

L _A is an optionally substituted C _5-10 aryl or optionally substituted five to ten membered heteroaryl,

X ₁ is an organic spacer having one or more chain atoms selected from C, O, N, and S, wherein three or more the adjacent atoms of the chain may optionally form an optionally substituted C _5-10 aryl or optionally substituted five to ten membered heteroaryl or form a four to ten membered heterocyclyl ring with the atoms on A ₁ , X ₂ is absent or an organic linker comprising 1 to 4 chain atoms selected from C, O, N, and S, and

L _B is a substituted C _5-10 aryl or substituted five to ten membered heteroaryl.

[0089] In some embodiments, L _A is an optionally substituted C _5-10 aryl or optionally substituted five to ten membered heteroaryl selected from the group consisting of pyrimidine, pyrrolidine, piperazine, piperidine, morpholino, hexahydroazepine, cyclohexene, piperideino, tetrahydroquinoline, tetrahydroisoquinoline, dihydropyrrole, phenyl, naphthyl, furane, pyrrole, thiophene, oxazole, isoxazole, imidazole, thiazole, oxadiazole, thiadiazole, triazole, pyridine, pyrimidine, pyridazine, pyrazine, quinoline, isoquinoline, benzothiazole, benzoimidazole and benzoxazole.

[0090] In some embodiments, L _B is an optionally substituted C _5-10 aryl or optionally substituted five to ten membered heteroaryl selected from the group consisting of pyrimidine, pyrrolidine, piperazine, piperidine, morpholino, hexahydroazepine, cyclohexene, piperideino, tetrahydroquinoline, tetrahydroisoquinoline, dihydropyrrole, phenyl, naphthyl, furane, pyrrole, thiophene, oxazole, isoxazole, imidazole, thiazole, oxadiazole, thiadiazole, triazole, pyridine, pyrimidine, pyridazine, pyrazine, quinoline, isoquinoline, benzothiazole, benzoimidazole, isoindoline, 1,3-dihydroisobenzofuran, and benzoxazole. [0091] In some embodiments, at least one of L _A and L _B is optionally substituted with one or more substituents selected from the group consisting of -C ₁ -C ₆ alkyl, -C ₂ - C ₆ alkenyl, -C ₂ -C ₆ alkynyl, C _1- C ₆ heteroalkyl, C _6- C ₁₀ aryl, five to tem mmbered heteroaryl, halogenated C ₁ -C ₆ alkyl, C _3-10 carbocyclyl, 3-10 membered heterocyclyl, -O-C ₁ -C ₆ alkyl, -O- halogenated C ₁ -C ₆ alkyl, -C ₁ -C ₆ alkyl-O-C ₁ -C ₆ alkyl, -S-C ₁ -C ₆ alkyl, amino, -C ₁ -C ₆ alkylelen- amino, -C(O)H, -CO-C ₁ -C ₆ alkyl, -C(O)-amino, -S(O) ₂ -amino, -COO-C ₁ -C ₆ alkyl, -C ₁ - C ₆ alkylene—amide, -N(C ₁ -C ₆ alkyl)(CO-C ₁ -C ₆ alkyl), -NH(CO-C ₁ -C ₆ alkyl),hydroxy, cyano, azido, nitro, -CH ₂ CH(CH ₃ ) ₂ OCH ₂ -, -OCH ₂ O-, -O(CH ₂ ) ₂ O-, and halogen.

[0092] In some embodiments, at least one of L _A and L _B is optionally substituted with one or more substituents, and the one or more subsisutents together with the atoms on L _A or L _B form a C _3-10 cycloalkyl ring or three to ten membered heterocyclic ring.

[0093] In some embodiments, the X ₁ is a cyclic or acyclic linker having a molecular weight less than 250 g/mol.

[0094] In some embodiments, the X ₁ comprises one or more fragments selected from the group consisitng of -C(O)-NH-, -C1-6 alkylene, -S-, -O-, -(CH2)0-6-NH-, -CH(OH)-, -C(CN)=CH-, -CH=N-, optionally substituted phenylene, optionally subtituted four to ten membered heterocyclylene, and optionally substituted five to tem membered heteroarylene.

[0095] In some embodiments, the X ₂ comprises one or more fragments selected from the group consisitng of -C(O)-NH-, -C _1-6 alkylene, -S-, -O-, -(CH ₂ ) _0-6 -NH-, -CH(OH)-, - C(CN)=CH-, and -CH=N-, and X ₂ has a molecular weight that is in the range of 10 g/mol to about 250 g/mol.

[0096] The compound described herein have microtubule depolymerizing activity and can be effective chemotherapeutic agents. In some embodiments, the compounds described herein can reside in a deeper position in E-tubulin, making hydrogen bonds with EE200 on S6 and ȕV238 on H7, and also interacting with ȕG237 on H7 and with ĮT179 on T5 via water molecules.

[0097] The colchicine domain is a big pocket surrounded by two D-helices (H7 and H8) and by strands of the two tubulin E-sheets (S1-S4-S5-S6 and S7-S10-S8-S9) from the E subunit and is capped by two loops (ET7 and DT5). In some embodiments, ES7 paired with both ES6 and ES10 via its N-terminus and C-terminus, respectively, thus bridging the two E-sheets into a super E-sheet.

[0098] In some embodiments, the compound described herein includes a pharmacophore that comprise two or three hydrophobic moieties and at least two hydrogen bond moieties L _C and L _F (either hydrogen bond acceptor or donor). In some embodiments, the compound comprises a large hydrophobic group fitting into the hydrophobic core of the colchicine domain. In some embodiments, two extended hydrophobic pockets in the colchicine domain accommodate two other hydrophobic moieties: one is buried deeply in b- tubulin and the other one is located at the interface of the D/E tubulin heterodimer. In some embodiments, the hydrophilic groups (e.g., L _C and L _F ) may form hydrogen bonds with tubulin. In some embodiments, the pharmacophore can include two additional hydrogen bond moieties L _D and L _G that may form hydrogen bond with tubulin.

[0099] The compounds described herein may bind to E-tubulin. E-tubulin isotypes have a varied distribution in different cell types and modulate the cell sensitivity to chemotherapeutic drugs. Tumor cells may show differences in the expression of tubulin isotypes. The compounds described herein targeting tubulin may differentiate between different cell types, thus the undesirable side effects associated with current chemotherapeutic treatments may be reduced.

[0100] Regulation of the actin cytoskeleton by microtubules is mediated by the Rho family GTPases. The Rho guanine nucleotide exchange factor (GEF-H1) is regulated by an interaction with microtubules. GEF-H1 mutants that are deficient in microtubule binding have higher activity levels than microtubule–bound forms. These mutants also induce Rho- dependent changes in cell morphology and actin organization. Furthermore, drug-induced microtubule depolymerization induces changes in cell morphology and gene expression that are similar to the changes induced by the expression of active forms of GEF-H1. Furthermore, these effects may be inhibited by dominant- negative versions of GEF-H1. Thus, GEF-H1 links may change in microtubule integrity to Rho-dependent regulation of the actin cytoskeleton.

[0101] GEF-H1 is a microtubule-associated nucleotide exchange factor that is a member of the Dbl family of proteins. The N- or C-terminal portions of GEF-H1 may be involved in the interaction with microtubules and/or MAPs. A combination of N- or C- terminal protein domains may be necessary for microtubule binding. In some embodiments, the zinc finger domain may be involved in the interaction of GEF-H1 with microtubules. In some embodiments, the PH domain may be involved in the interaction of GEF-H1 with microtubules.

[0102] In some embodiments, GEF-H1 is inactive when bound to microtubules or tubulins and becomes activated when microtubules or tubulins are depolymerized, either as a result of inherent instability or after treatment with microtubule-depolymerizing drugs. Activated GEF-H1 promotes the binding of GTP to Rho, resulting in the activation of Rho, which in turn induces the upregulation of myosin II contractility, stress fiber assembly and SRE-regulated gene expression.

[0103] The expression of GEF-H1 constructs deficient in microtubule binding may induce changes in cell morphology, including cell retraction and the formation of actin stress fibers. This may be reminiscent of the changes induced by constitutively active RhoA. The expression of non-microtubule-associated GEF-H1 may result in the activation of RhoA. GEF-H1 can promote nucleotide exchange on RhoA, but not Rac or Cdc4, in cells expressing GEF-H1 constructs. GEF-H1 is a nucleotide exchange factor for Rho and are in a good agreement with the observation that Lfc, the mouse homologue of GEF-H1, is also specific for Rho25. The effects of GEF-H1 on cell morphology and gene expression are mediated by Rho, but not by Rac or Cdc42.

[0104] Microtubule depolymerization can activate Rho by increasing the amount of free, active GEF-H1, whereas microtubule assembly downregulates Rho by sequestering and inactivating GEF-H1. In migrating cells, microtubule depolymerization may locally activate Rho in the cell body, resulting in high myosin II activity and thus promoting tail retraction during locomotion. The prevalence of growing microtubules near the leading edge would result in low Rho activity at the front of the cell, allowing expansion of the leading edge to proceed without being hindered by myosin contractility. The inactivation of GEF-H1 by microtubule polymerization caused by the compounds described herein may also be utilized for treating proliferative disorders and other types of diseases or conditions described herein. [0105] In some embodiments, the distance between the tubulin EE200 oxygen atom and the hydrogen bonding atom of the L _C moiety is less than about 2 Å, 2.5 Å, 2.8 Å, 3 Å, 3.2 Å, 3.5 Å, 4 Å, 5 Å, 6 Å, 7 Å, 8 Å, 9 Å, or10 Å. In some embodiments, the distance between the tubulin EE200 oxygen atom and the hydrogen bonding atom of the L _C moiety is greater than about 0.5 Å, 1 Å, 1.25 Å, 1.5 Å, 1.8 Å, 2 Å, 2.5 Å, 2.8 Å, 3 Å, 3.2 Å, 3.5 Å, 4 Å, 5 Å, or 6 Å. In some embodiments, the tubulin EE200 distance between the oxygen atom and the hydrogen bonding atom of the L _C moiety is about 2 Å, 2.1 Å, 2.2 Å, 2.3 Å, 2.4 Å, 2.5 Å, 2.6 Å, 2.7 Å, 2.8 Å, 2.9 Å, 3 Å, 3.2 Å, 3.5 Å, 4 Å, 5 Å, 6 Å, or 7 Å. In some embodiments, the tubulin EE200 distance between the oxygen atom and the hydrogen bonding atom of the L _C moiety is in the range of about 0.5 Å-10 Å, 0.5 Å-9 Å, 0.5 Å-8 Å, 0.5 Å-7 Å, 0.5 Å-6 Å, 0.5 Å-5 Å, 0.5 Å-4 Å, 0.5 Å-3 Å, 0.5 Å-2.8 Å, 0.5 Å-2.5 Å, 0.5 Å-2 Å, 1 Å-10 Å, 1 Å-9 Å, 1Å-8 Å, 1 Å-7 Å, 1 Å-6 Å, 1 Å-5 Å, 1 Å-4 Å, 1 Å-3 Å, 1 Å-2.8 Å, 1 Å-2.5 Å, 1 Å-2 Å, 1.5 Å-10 Å, 1.5 Å-9 Å, 1.5 Å-8 Å, 1.5 Å-7 Å, 1.5 Å-6 Å, 1.5 Å-5 Å, 1.5 Å-4 Å, 1.5 Å-3 Å, 1.5 Å-2.8 Å, 1.5 Å-2.5 Å, 1.5 Å-2 Å, 2 Å-10 Å, 2 Å-9 Å, 2Å-8 Å, 2 Å-7 Å, 2 Å-6 Å, 2 Å-5 Å, 2Å-4 Å, 2 Å-3 Å, 2 Å-2.8 Å, 2 Å- 2.5 Å, 2.5 Å-10 Å, 2.5 Å-9 Å, 2.5Å-8 Å, 2.5 Å-7 Å, 2.5 Å-6 Å, 2.5 Å-5 Å, 2.5Å-4 Å, 2.5 Å-3 Å, or 2.5 Å-2.8 Å. In some embodiments, the tubulin EE200 oxygen atom is an oxygen on the carboxyl group of the Glutamic acid side chain.

[0106] In some embodiments, the distance between the tubulin EV238 oxygen and the hydrogen bonding atom of the L _D moiety is less than about 2 Å, 2.5 Å, 2.8 Å, 3 Å, 3.2 Å, 3.5 Å, 4 Å, 5 Å, 6 Å, 7 Å, 8 Å, 9 Å, or 10 Å. In some embodiments, the distance between the tubulin EV238 oxygen and the hydrogen bonding atom of the L _D moiety is greater than about 0.5 Å, 1 Å, 1.25 Å, 1.5 Å, 1.8 Å, 2 Å, 2.5 Å, 2.9 Å, 3 Å, 3.2 Å, 3.5 Å, 4 Å, 5 Å, or 6 Å. In some embodiments, the distance between the tubulin EV238 oxygen and the hydrogen bonding atom of the L _D moiety is about 2 Å, 2.1 Å, 2.2 Å, 2.3 Å, 2.4 Å, 2.5 Å, 2.6 Å, 2.7 Å, 2.8 Å, 2.9 Å, 3 Å, 3.2 Å, 3.5 Å, 4 Å, 5 Å, 6 Å, or 7 Å. In some embodiments, the distance between the tubulin EV238 oxygen and the hydrogen bonding atom of the L _D moiety is in the range of about 0.5 Å-10 Å, 0.5 Å-9 Å, 0.5 Å-8 Å, 0.5 Å-7 Å, 0.5 Å-6 Å, 0.5 Å-5 Å, 0.5 Å-4 Å, 0.5 Å-3 Å, 0.5 Å-2.9 Å, 0.5 Å-2.5 Å, 0.5 Å-2 Å, 1 Å-10 Å, 1 Å-9 Å, 1Å-8 Å, 1 Å-7 Å, 1 Å-6 Å, 1 Å-5 Å, 1 Å- 4 Å, 1 Å-3 Å, 1 Å-2.9 Å, 1 Å-2.5 Å, 1 Å-2 Å, 1.5 Å-10 Å, 1.5 Å-9 Å, 1.5 Å-8 Å, 1.5 Å-7 Å, 1.5 Å-6 Å, 1.5 Å-5 Å, 1.5 Å-4 Å, 1.5 Å-3 Å, 1.5 Å-2.9 Å, 1.5 Å-2.5 Å, 1.5 Å-2 Å, 2 Å-10 Å, 2 Å-9 Å, 2Å-8 Å, 2 Å-7 Å, 2 Å-6 Å, 2 Å-5 Å, 2Å-4 Å, 2 Å-3 Å, 2 Å-2.9 Å, 2 Å-2.5 Å, 2.5 Å-10 Å, 2.5 Å-9 Å, 2.5Å-8 Å, 2.5 Å-7 Å, 2.5 Å-6 Å, 2.5 Å-5 Å, 2.5Å-4 Å, 2.5 Å-3 Å, or 2.5 Å-2.9 Å. In some embodiments, the tubulin EV238 oxygen atom is the oxygen atom of the amide group. In some embodiments, the amide group is part of the peptide backbone.

[0107] In some embodiments, the distance between the oxygen of the tubulin DT179 and the hydrogen bonding atom of L _F is less than 8 Å. In some embodiments, the distance between the oxygen of the tubulin DT179 and the hydrogen bonding atom of L _F is less than about 2 Å, 2.5 Å, 2.8 Å, 3 Å, 3.2 Å, 3.5 Å, 3.8 Å, 4 Å, 4.2 Å, 4.5 Å, 4.8 Å, 5 Å, 5.2 Å, 5.5 Å, 5.8 Å, 6 Å, 6.2 Å, 6.5 Å, 6.8 Å, 7 Å, 8 Å, 9 Å, or 10 Å. . In some embodiments, the distance between the oxygen of the tubulin DT179 and the hydrogen bonding atom of L _F is greater than about 0.5 Å, 1 Å, 1.25 Å, 1.5 Å, 1.8 Å, 2 Å, 2.5 Å, 2.9 Å, 3 Å, 3.2 Å, 3.5 Å, 4 Å, 5 Å, or 6 Å. In some embodiments, the distance between the oxygen of the tubulin DT179 and the hydrogen bonding atom of L _F is in the range of about 0.5 Å-10 Å, 0.5 Å-9 Å, 0.5 Å-8 Å, 0.5 Å-7 Å, 0.5 Å-6 Å, 0.5 Å-5 Å, 0.5 Å-4.5 Å, 0.5 Å- 4Å, 0.5 Å-3.5 Å, 0.5 Å-3 Å, 0.5 Å-2 Å, 1 Å-10 Å, 1 Å-9 Å, 1Å-8 Å, 1 Å-7 Å, 1 Å-6 Å, 1 Å-5.5 Å, 1 Å-5 Å, 1 Å-4.5 Å, 1 Å-4Å, 1 Å-3 Å, 1 Å-2 Å, 1.5 Å-10 Å, 1.5 Å-9 Å, 1.5 Å-8 Å, 1.5 Å-7 Å, 1.5 Å-6 Å, 1.5 Å-5.5 Å, 1.5 Å-5 Å, 1.5 Å-4.5 Å, 1.5 Å-4 Å, 1.5 Å-3 Å, 1.5 Å-2 Å, 2 Å-10 Å, 2 Å-9 Å, 2Å-8 Å, 2 Å-7 Å, 2 Å-6 Å, 2 Å-5.5 Å, 2Å-5 Å, 2 Å-4.5 Å, 2 Å-4 Å, 2 Å-3.5 Å, 2 Å-3 Å, 2.5 Å-10 Å, 2.5 Å-9 Å, 2.5Å-8 Å, 2.5 Å-7 Å, 2.5 Å-6 Å, 2.5 Å-5.5 Å, 2.5 Å-5 Å, 2.5Å-4 Å, 2.5 Å-3 Å, 3 Å-10 Å, 3 Å-9 Å, 3Å-8 Å, 3 Å-7 Å, 3 Å-6 Å, 3 Å- 5.5 Å, 3Å-5 Å, 3 Å-4.5 Å, 3 Å-4 Å, 3 Å-3.5 Å, 3.5 Å-10 Å, 3.5 Å-9 Å, 3.5Å-8 Å, 3.5 Å-7 Å, 3.5 Å-6 Å, 3.5 Å-5.5 Å, 3.5 Å-5 Å, 3.5Å-4 Å, 3.5 Å-3 Å, 4 Å-10 Å, 4 Å-9 Å, 4Å-8 Å, 4 Å-7 Å, 4 Å-6 Å, 4 Å-5.5 Å, 4Å-5 Å, or 4 Å-4.5 Å. In some embodiments, the oxygen of the tubulin DT179 is the oxygen of the amide group. In some embodiments, the amide group is part of the peptide backbone.

[0108] In some embodiments, the distance between the oxygen of the tubulin EG237 and the hydrogen bonding atom of L _G is less than 8. In some embodiments, the distance between the oxygen of the tubulin EG237 and the hydrogen bonding atom of L _G is less than 2 Å, 2.5 Å, 2.8 Å, 3 Å, 3.2 Å, 3.5 Å, 3.8 Å, 4 Å, 4.2 Å, 4.5 Å, 4.8 Å, 5 Å, 5.2 Å, 5.5 Å, 5.8 Å, 6 Å, 6.2 Å, 6.5 Å, 6.8 Å, 7 Å, 8 Å, 9 Å, or 10 Å. In some embodiments, the distance between the oxygen of the tubulin EG237 and the hydrogen bonding atom of L _G is greater than about 0.5 Å, 1 Å, 1.25 Å, 1.5 Å, 1.8 Å, 2 Å, 2.5 Å, 2.9 Å, 3 Å, 3.2 Å, 3.5 Å, 4 Å, 5 Å, or 6 Å. In some embodiments, the distance between the oxygen of the tubulin EG237 and the hydrogen bonding atom of L _G is in the range of about 0.5 Å-10 Å, 0.5 Å-9 Å, 0.5 Å-8 Å, 0.5 Å- 7 Å, 0.5 Å-6 Å, 0.5 Å-5 Å, 0.5 Å-4.5 Å, 0.5 Å- 4Å, 0.5 Å-3.5 Å, 0.5 Å-3 Å, 0.5 Å-2 Å, 1 Å-10 Å, 1 Å-9 Å, 1Å-8 Å, 1 Å-7 Å, 1 Å-6 Å, 1 Å-5.5 Å, 1 Å-5 Å, 1 Å-4.5 Å, 1 Å-4Å, 1 Å-3 Å, 1 Å-2 Å, 1.5 Å-10 Å, 1.5 Å-9 Å, 1.5 Å-8 Å, 1.5 Å-7 Å, 1.5 Å-6 Å, 1.5 Å-5.5 Å, 1.5 Å-5 Å, 1.5 Å-4.5 Å, 1.5 Å-4 Å, 1.5 Å-3 Å, 1.5 Å-2 Å, 2 Å-10 Å, 2 Å-9 Å, 2Å-8 Å, 2 Å-7 Å, 2 Å-6 Å, 2 Å-5.5 Å, 2Å-5 Å, 2 Å-4.5 Å, 2 Å-4 Å, 2 Å-3.5 Å, 2 Å-3 Å, 2.5 Å-10 Å, 2.5 Å-9 Å, 2.5Å-8 Å, 2.5 Å-7 Å, 2.5 Å-6 Å, 2.5 Å-5.5 Å, 2.5 Å-5 Å, 2.5Å-4 Å, 2.5 Å-3 Å, 3 Å-10 Å, 3 Å-9 Å, 3Å-8 Å, 3 Å-7 Å, 3 Å-6 Å, 3 Å- 5.5 Å, 3Å-5 Å, 3 Å-4.5 Å, 3 Å-4 Å, 3 Å-3.5 Å, 3.5 Å-10 Å, 3.5 Å-9 Å, 3.5Å-8 Å, 3.5 Å-7 Å, 3.5 Å-6 Å, 3.5 Å-5.5 Å, 3.5 Å-5 Å, 3.5Å-4 Å, 3.5 Å-3 Å, 4 Å-10 Å, 4 Å-9 Å, 4Å-8 Å, 4 Å-7 Å, 4 Å-6 Å, 4 Å-5.5 Å, 4Å-5 Å, or 4 Å-4.5 Å. In some embodiments, the oxygen of the tubulin EG237 is the oxygen of the amide group. In some embodiments, the amide group is part of the peptide backbone.

[0109] In some embodiments, L _C is a hydrophilic atom or hydrophilic functional group having a molecular weight or less than 200, 150, 100, 80, or between 14 and 200 g/mol. In some embodiments, L _C is a nitrogen atom or a functional group containing at least one nitrogen atom.

[0110] In some embodiments, L _D is a hydrophilic atom or hydrophilic functional group having a molecular weight or less than 200, 150, 100, 80, or between 14 and 200 g/mol. In some embodiments, L _D is an oxygen atom or a functional group containing at least one oxygen atom.

[0111] In some embodiments, LF is a hydrophilic atom or hydrophilic functional group having a molecular weight or less than 200, 150, 100, 80, or between 14 and 200 g/mol. In some embodiments, L _F is a nitrogen atom or a functional group containing at least one nitrogen atom.

[0112] In some embodiments, L _G is a hydrophilic atom or hydrophilic functional group having a molecular weight or less than 200, 150, 100, 80, or between 14 and 200 g/mol. In some embodiments, L _G is a nitrogen atom or a functional group containing at least one nitrogen atom. [0113] In some embodiments, the hydrophilic atom or functional group within L _C , L _D , L _F , or L _G is selected from C(O), NH, N, CHX, CH2X, CX2, CX3, OH, SO2, SH, C(S), SO3, and PO3, wherein each X is independently a halogen.

[0114] In some embodiments, the hydrogen bond between L _F and the tubulin DT179 comprises a water bridge (L _F hydrogen bonds with a water molecule and the water molecule in turn hydrogen bonds with the tubulin DT179).

[0115] In some embodiments, the hydrogen bond between L _G and the tubulin EG237 comprises a water bridge (L _G hydrogen bonds with a water molecule and the water molecule in turn hydrogen bonds with the tubulin EG237).

[0116] In some embodiments, the hydrogen bond between LD and EV238 comprises a water bridge. In some embodiments, the hydrogen bond of L _D does not have a water bridge.

[0117] In some embodiments, the hydrogen bond between L _D and the tubulin EE200 comprises a water bridge. In some embodiments, the hydrogen bond of L _D does not comprise a water bridge.

[0118] In some embodiments, the compound described herein further comprises a hydrophobic moiety. In some embodiments, the hydrophobic moiety can be a C _1-20 alkyl; C ₂ - 6 alkenyl; C _2-6 alkynyl; C _1-6 heteroalkyl; C _3-7 carbocyclyl; 4-10 membered heterocyclyl; C _6-10 aryl; 3-10 membered heteroaryl, each optionally subsitutetd with one or more substituents. In some embodiments, the hydrophobic moiety can be a C _6-10 aryl optionally subsitutetd with one or more substituents. In some embodiments, the hydrophobic moiety can be an optionally substituted phenyl group. In some embodiments, the hydrophobic moiety is selected from C _3- benzyl, and benzylidene.

[0119] In some embodiments, the compound described herein further comprises a first moiety that interacts with one or more domains of GEF-H1.

[0120] In some embodiments, the tubulin, upon binding of the compound, comprises a second moiety that interacts with one or more domains of GEF-H1.

[0121] In some embodiments, the tubulin, upon binding of the compound, activates the GEF-H1. [0122] In some embodiments, the first moiety of the compound interacts with a N-terminal zinc finger domain of the GEF-H1. In some embodiments, the compound interacts with C53 of the GEF-H1.

[0123] In some embodiments, the second moiety of the tubulin interacts with a N- terminal zinc finger domain of the GEF-H1. In some embodiments, the tubulin interacts with C53 of the GEF-H1.

[0124] In some embodiments, the first moiety of the compound interacts with a C-terminal of the GEF-H1.

[0125] In some embodiments, the second moiety of the tubulin interacts with a C- terminal of the GEF-H1.

[0126] In some embodiments, the compound has a structure of formula (II)

or a pharmaceutically acceptable salt, prodrug, ester thereof, wherein:

;

each of R ₁ , R ₂ , R ₃ , R ₄ , R ₆ , R ₇ , R ₉ , R ₁₀ , R ₁₂ , R ₁₃ , R ₁₅ , and R ₁₆ is independently a bond or an organic moiety having a molecular weight between 14 g/mol and 200 g/mol; and

each of R ₅ , R ₈ , R ₁₁ , and R ₁₄ , is independently an organic moiety having a molecular weight between 14 g/mol and 200 g/mol.

In some embodiments, the compound has the structure of formula (II):

or a pharmaceutically acceptable salt, prodrug, ester thereof.

[0127] In some embodiments, one or more of R ₁ , R ₂ , R ₃ , R ₄ , R ₆ , R ₇ , R ₉ , R ₁₀ , R ₁₂ , R ₁₃ , R ₁₅ , and R ₁₆ is a hydrophobic moiety. In some embodiments, R ⁴ and R ¹⁶ are hydrophobic moieties.

[0128] In some embodiments, one or more of R ₁ , R ₂ , R ₃ , R ₄ , R ₆ , R ₇ , R ₉ , R ₁₀ , R ₁₂ , R ₁₃ , R ₁₅ , and R ₁₆ is a moiety that interacts with one or more domains of GEF-H1. In some embodiments, the one or more domains is a zinc finger domain. In some embodiments, one or more of R ₁ , R ₂ , R ₃ , R ₄ , R ₆ , R ₇ , R ₉ , R ₁₀ , R ₁₂ , R ₁₃ , R ₁₅ , and R ₁₆ is a moiety that interacts with C53 of GEF-H1.

[0129] In some embodiments, the compound described herein comprises the proviso that the compound is not a compound having the structure of formula (III)

(IV)

Wherein:

R’ ₂ and R’ ₃ are each separately selected from the group consisting of a hydrogen atom; a halogen atom; mono-substituted; poly-substituted or unsubstituted, straight or branched chain variants of the following residues: C ₁ -C ₁₂ alkyl, C ₂ -C ₁₂ alkenyl, and alkoxy; and mono-substituted, poly-substituted or unsubstituted variants of the following residues: cycloalkyl, cycloalkoxy, aryl, heteroaryl, amino, and nitro;

R’ ₄ and R’ ₆ are each separately selected from the group consisting of hydrogen; halogen; hydroxyl; mono-substituted, poly-substituted or unsubstituted, straight or branched chain variants of the following residues: C ₁ -C ₂₄ alkyl, C ₂ -C ₂₄ alkenyl, C ₂ -C ₂₄ alkynyl, alkoxy, arylalkyl, heteroarylalkyl, alkyloxycarbonyloxy, alkylcarbonyloxyalkyl, arylcarbonyloxyalkyl, arylalkoxy, alkoxy, and alkylthio; mono-substituted, poly-substituted or unsubstituted variants of the following residues: aryloxycarbonyloxy, cycloalkyl, cycloalkenyl, cycloalkoxy, aryl, heteroaryl, aryloxy, arylcarbonyl, heterocycloalkyl, amino, aminocarbonyl, amide, aminocarbonyloxy, nitro, azido, phenyl, hydroxyl, thio, alkylthio, arylthio, thiophenyl, carboxy, and cyano;

X ₁ and X ₂ are separately selected from the group consisting of an oxygen atom, a sulfur atom, and a nitrogen atom substituted with a R’ ₅ group;

R’ ₅ is selected from the group consisting of a hydrogen atom, a halogen atom, and saturated C ₁ -C ₁₂ alkyl, unsaturated C ₂ -C ₁₂ alkenyl, cycloalkyl, alkoxy, cycloalkoxy, aryl, substituted aryl, heteroaryl, substituted heteroaryl, amino, substituted amino, nitro, and substituted nitro groups;

Y is selected from the group consisting of an oxygen atom, a sulfur atom, an oxidized sulfur atom, and a nitrogen atom substituted with an R’ ₅ group;

n is 0, 1, 2, 3, or 4; and

Ar is a cyclic or polycyclic aryl or heteroaryl ring system comprising between one and three rings, wherein:

each ring in said system is separately a 5, 6, 7, or 8 membered ring;

each ring in said system separately comprises 0, 1, 2, 3, or 4 heteroatoms selected from the group consisting of oxygen, sulfur, and nitrogen; and each ring in said system is optionally substituted with one or more substituents selected from the group consisting of hydrogen; halogen; hydroxyl; mono-substituted, poly-substituted or unsubstituted, straight or branched chain variants of the following residues: C ₁ -C ₂₄ alkyl, C ₂ -C ₂₄ alkenyl, C ₂ -C ₂₄ alkynyl, alkoxy, arylalkyl, heteroarylalkyl, alkyloxycarbonyloxy, alkylcarbonyloxyalkyl, arylcarbonyloxyalkyl, arylalkoxy, alkoxy, and alkylthio; mono-substituted, poly-substituted or unsubstituted variants of the following residues: aryloxycarbonyloxy, cycloalkyl, cycloalkenyl, cycloalkoxy, aryl, heteroaryl, aryloxy, arylcarbonyl, heterocycloalkyl, amino, aminocarbonyl, amide, aminocarbonyloxy, nitro, azido, phenyl, hydroxyl, thio, alkylthio, arylthio, thiophenyl, carboxy, and cyano; and an optionally substituted fused ring selected from the group consisting of dioxole, dithiole, oxathiole, dioxine, dithiine, and oxathiine.

[0130] In some embodiments, the compound described herein is not plinabulin. In some embodiments, the compound is not dehydrophenylahistin, phenylahistin, or t-butyl- phenylahistin. In some embodiments, the compound is not a dehydrophenylahistin, or phenylahistin derivatives.

[0131] In some embodiments, the compound described herein is not any of the compounds listed in Table A or Table B below.

Table A. Phenylahistin and dehydrophenylahistin derivatives

Table B. Additional dehdrohenlahistin derivatives

[0132] More examples of phenylahistin and dehydrophenylahistin derivatives can be found in US 20050090667, which is incorporated herein for reference for this purpose in its entirety.

[0133] Some embodiments relate to a compound having a structure of formula (IV)

or a pharmaceutically acceptable salt, prodrug, ester thereof, wherein A is selected from C _1-20 alkyl; C _2-6 alkenyl; C _2-6 alkynyl; C _1-6 heteroalkyl; C _3-7 carbocyclyl; 4-10 membered heterocyclyl; C _6-10 aryl; 3-10 membered heteroaryl; C ₁ -C ₆ alkoxy(C ₁ -C ₆ )alkyl; aryloxy; or sulfhydryl; each optionally substituted with one or more substituents.

Pharmaceutical Composition and Administration

[0134] Some embodiments relate to a pharmaceutical composition comprising the compound described herein.

[0135] The compounds are administered at a therapeutically effective dosage. While human dosage levels have yet to be optimized for the compounds described herein, generally, a daily dose may be from about 0.25 mg/kg to about 120 mg/kg or more of body weight, from about 0.5 mg/kg or less to about 70 mg/kg, from about 1.0 mg/kg to about 50 mg/kg of body weight, or from about 1.5 mg/kg to about 10 mg/kg of body weight. Thus, for administration to a 70 kg person, the dosage range would be from about 17 mg per day to about 8000 mg per day, from about 35 mg per day or less to about 7000 mg per day or more, from about 70 mg per day to about 6000 mg per day, from about 100 mg per day to about 5000 mg per day, or from about 200 mg to about 3000 mg per day. The amount of active compound administered will, of course, be dependent on the subject and disease state being treated, the severity of the affliction, the manner and schedule of administration and the judgment of the prescribing physician.

[0136] Administration of the compounds disclosed herein or the pharmaceutically acceptable salts thereof can be via any of the accepted modes of administration for agents that serve similar utilities including, but not limited to, orally, subcutaneously, intravenously, intranasally, topically, transdermally, intraperitoneally, intramuscularly, intrapulmonarilly, vaginally, rectally, or intraocularly. Oral and parenteral administrations are customary in treating the indications that are the subject of the preferred embodiments. [0137] The compounds useful as described above can be formulated into pharmaceutical compositions for use in treatment of these conditions. Standard pharmaceutical formulation techniques are used, such as those disclosed in Remington's The Science and Practice of Pharmacy, 21st Ed., Lippincott Williams & Wilkins (2005), incorporated by reference in its entirety. Accordingly, some embodiments include pharmaceutical compositions comprising: (a) a safe and therapeutically effective amount of a compound described herein (including enantiomers, diastereoisomers, tautomers, polymorphs, and solvates thereof), or pharmaceutically acceptable salts thereof; and (b) a pharmaceutically acceptable carrier, diluent, excipient or combination thereof.

[0138] In addition to the selected compound useful as described above, come embodiments include compositions containing a pharmaceutically-acceptable carrier. The term “pharmaceutically acceptable carrier” or “pharmaceutically acceptable excipient” includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents and the like. The use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredient, its use in the therapeutic compositions is contemplated. In addition, various adjuvants such as are commonly used in the art may be included. Considerations for the inclusion of various components in pharmaceutical compositions are described, e.g., in Gilman et al. (Eds.) (1990); Goodman and Gilman’s: The Pharmacological Basis of Therapeutics, 8th Ed., Pergamon Press, which is incorporated herein by reference in its entirety.

[0139] Some examples of substances, which can serve as pharmaceutically- acceptable carriers or components thereof, are sugars, such as lactose, glucose and sucrose; starches, such as corn starch and potato starch; cellulose and its derivatives, such as sodium carboxymethyl cellulose, ethyl cellulose, and methyl cellulose; powdered tragacanth; malt; gelatin; talc; solid lubricants, such as stearic acid and magnesium stearate; calcium sulfate; vegetable oils, such as peanut oil, cottonseed oil, sesame oil, olive oil, corn oil and oil of theobroma; polyols such as propylene glycol, glycerine, sorbitol, mannitol, and polyethylene glycol; alginic acid; emulsifiers, such as the TWEENS; wetting agents, such sodium lauryl sulfate; coloring agents; flavoring agents; tableting agents, stabilizers; antioxidants; preservatives; pyrogen-free water; isotonic saline; and phosphate buffer solutions.

[0140] The choice of a pharmaceutically-acceptable carrier to be used in conjunction with the subject compound is basically determined by the way the compound is to be administered.

[0141] The compositions described herein are preferably provided in unit dosage form. As used herein, a "unit dosage form" is a composition containing an amount of a compound that is suitable for administration to an animal, preferably mammal subject, in a single dose, according to good medical practice. The preparation of a single or unit dosage form however, does not imply that the dosage form is administered once per day or once per course of therapy. Such dosage forms are contemplated to be administered once, twice, thrice or more per day and may be administered as infusion over a period of time (e.g., from about 30 minutes to about 2-6 hours), or administered as a continuous infusion, and may be given more than once during a course of therapy, though a single administration is not specifically excluded. The skilled artisan will recognize that the formulation does not specifically contemplate the entire course of therapy and such decisions are left for those skilled in the art of treatment rather than formulation.

[0142] The compositions useful as described above may be in any of a variety of suitable forms for a variety of routes for administration, for example, for oral, nasal, rectal, topical (including transdermal), ocular, intracerebral, intracranial, intrathecal, intra-arterial, intravenous, intramuscular, or other parental routes of administration. The skilled artisan will appreciate that oral and nasal compositions comprise compositions that are administered by inhalation, and made using available methodologies. Depending upon the particular route of administration desired, a variety of pharmaceutically-acceptable carriers well-known in the art may be used. Pharmaceutically-acceptable carriers include, for example, solid or liquid fillers, diluents, hydrotropies, surface-active agents, and encapsulating substances. Optional pharmaceutically-active materials may be included, which do not substantially interfere with the inhibitory activity of the compound. The amount of carrier employed in conjunction with the compound is sufficient to provide a practical quantity of material for administration per unit dose of the compound. Techniques and compositions for making dosage forms useful in the methods described herein are described in the following references, all incorporated by reference herein: Modern Pharmaceutics, 4th Ed., Chapters 9 and 10 (Banker & Rhodes, editors, 2002); Lieberman et al., Pharmaceutical Dosage Forms: Tablets (1989); and Ansel, Introduction to Pharmaceutical Dosage Forms 8th Edition (2004).

[0143] Various oral dosage forms can be used, including such solid forms as tablets, capsules, granules and bulk powders. Tablets can be compressed, tablet triturates, enteric-coated, sugar-coated, film-coated, or multiple-compressed, containing suitable binders, lubricants, diluents, disintegrating agents, coloring agents, flavoring agents, flow- inducing agents, and melting agents. Liquid oral dosage forms include aqueous solutions, emulsions, suspensions, solutions and/or suspensions reconstituted from non-effervescent granules, and effervescent preparations reconstituted from effervescent granules, containing suitable solvents, preservatives, emulsifying agents, suspending agents, diluents, sweeteners, melting agents, coloring agents and flavoring agents.

[0144] The pharmaceutically-acceptable carrier suitable for the preparation of unit dosage forms for peroral administration is well-known in the art. Tablets typically comprise conventional pharmaceutically-compatible adjuvants as inert diluents, such as calcium carbonate, sodium carbonate, mannitol, lactose and cellulose; binders such as starch, gelatin and sucrose; disintegrants such as starch, alginic acid and croscarmelose; lubricants such as magnesium stearate, stearic acid and talc. Glidants such as silicon dioxide can be used to improve flow characteristics of the powder mixture. Coloring agents, such as the FD&C dyes, can be added for appearance. Sweeteners and flavoring agents, such as aspartame, saccharin, menthol, peppermint, and fruit flavors, are useful adjuvants for chewable tablets. Capsules typically comprise one or more solid diluents disclosed above. The selection of carrier components depends on secondary considerations like taste, cost, and shelf stability, which are not critical, and can be readily made by a person skilled in the art.

[0145] Peroral compositions also include liquid solutions, emulsions, suspensions, and the like. The pharmaceutically-acceptable carriers suitable for preparation of such compositions are well known in the art. Typical components of carriers for syrups, elixirs, emulsions and suspensions include ethanol, glycerol, propylene glycol, polyethylene glycol, liquid sucrose, sorbitol and water. For a suspension, typical suspending agents include methyl cellulose, sodium carboxymethyl cellulose, AVICEL RC-591, tragacanth and sodium alginate; typical wetting agents include lecithin and polysorbate 80; and typical preservatives include methyl paraben and sodium benzoate. Peroral liquid compositions may also contain one or more components such as sweeteners, flavoring agents and colorants disclosed above.

[0146] Such compositions may also be coated by conventional methods, typically with pH or time-dependent coatings, such that the subject compound is released in the gastrointestinal tract in the vicinity of the desired topical application, or at various times to extend the desired action. Such dosage forms typically include, but are not limited to, one or more of cellulose acetate phthalate, polyvinylacetate phthalate, hydroxypropyl methyl cellulose phthalate, ethyl cellulose, Eudragit coatings, waxes and shellac.

[0147] Compositions described herein may optionally include other drug actives.

[0148] Other compositions useful for attaining systemic delivery of the subject compounds include sublingual, buccal and nasal dosage forms. Such compositions typically comprise one or more of soluble filler substances such as sucrose, sorbitol and mannitol; and binders such as acacia, microcrystalline cellulose, carboxymethyl cellulose and hydroxypropyl methyl cellulose. Glidants, lubricants, sweeteners, colorants, antioxidants and flavoring agents disclosed above may also be included.

[0149] A liquid composition, which is formulated for topical ophthalmic use, is formulated such that it can be administered topically to the eye. The comfort should be maximized as much as possible, although sometimes formulation considerations (e.g. drug stability) may necessitate less than optimal comfort. In the case that comfort cannot be maximized, the liquid should be formulated such that the liquid is tolerable to the patient for topical ophthalmic use. Additionally, an ophthalmically acceptable liquid should either be packaged for single use, or contain a preservative to prevent contamination over multiple uses.

[0150] For ophthalmic application, solutions or medicaments are often prepared using a physiological saline solution as a major vehicle. Ophthalmic solutions should preferably be maintained at a comfortable pH with an appropriate buffer system. The formulations may also contain conventional, pharmaceutically acceptable preservatives, stabilizers and surfactants.

[0151] Preservatives that may be used in the pharmaceutical compositions disclosed herein include, but are not limited to, benzalkonium chloride, PHMB, chlorobutanol, thimerosal, phenylmercuric, acetate and phenylmercuric nitrate. A useful surfactant is, for example, Tween 80. Likewise, various useful vehicles may be used in the ophthalmic preparations disclosed herein. These vehicles include, but are not limited to, polyvinyl alcohol, povidone, hydroxypropyl methyl cellulose, poloxamers, carboxymethyl cellulose, hydroxyethyl cellulose and purified water.

[0152] Tonicity adjustors may be added as needed or convenient. They include, but are not limited to, salts, particularly sodium chloride, potassium chloride, mannitol and glycerin, or any other suitable ophthalmically acceptable tonicity adjustor.

[0153] Various buffers and means for adjusting pH may be used so long as the resulting preparation is ophthalmically acceptable. For many compositions, the pH will be between 4 and 9. Accordingly, buffers include acetate buffers, citrate buffers, phosphate buffers and borate buffers. Acids or bases may be used to adjust the pH of these formulations as needed.

[0154] In a similar vein, an ophthalmically acceptable antioxidant includes, but is not limited to, sodium metabisulfite, sodium thiosulfate, acetylcysteine, butylated hydroxyanisole and butylated hydroxytoluene.

[0155] Other excipient components, which may be included in the ophthalmic preparations, are chelating agents. A useful chelating agent is edetate disodium, although other chelating agents may also be used in place or in conjunction with it.

[0156] For topical use, creams, ointments, gels, solutions or suspensions, etc., containing the compound disclosed herein are employed. Topical formulations may generally be comprised of a pharmaceutical carrier, co-solvent, emulsifier, penetration enhancer, preservative system, and emollient.

[0157] For intravenous administration, the compounds and compositions described herein may be dissolved or dispersed in a pharmaceutically acceptable diluent, such as a saline or dextrose solution. Suitable excipients may be included to achieve the desired pH, including but not limited to NaOH, sodium carbonate, sodium acetate, HCl, and citric acid. In various embodiments, the pH of the final composition ranges from 2 to 8, or preferably from 4 to 7. Antioxidant excipients may include sodium bisulfite, acetone sodium bisulfite, sodium formaldehyde, sulfoxylate, thiourea, and EDTA. Other non-limiting examples of suitable excipients found in the final intravenous composition may include sodium or potassium phosphates, citric acid, tartaric acid, gelatin, and carbohydrates such as dextrose, mannitol, and dextran. Further acceptable excipients are described in Powell, et al., Compendium of Excipients for Parenteral Formulations, PDA J Pharm Sci and Tech 1998, 52 238-311 and Nema et al., Excipients and Their Role in Approved Injectable Products: Current Usage and Future Directions, PDA J Pharm Sci and Tech 2011, 65287-332, both of which are incorporated herein by reference in their entirety. Antimicrobial agents may also be included to achieve a bacteriostatic or fungistatic solution, including but not limited to phenylmercuric nitrate, thimerosal, benzethonium chloride, benzalkonium chloride, phenol, cresol, and chlorobutanol.

[0158] The compositions for intravenous administration may be provided to caregivers in the form of one more solids that are reconstituted with a suitable diluent such as sterile water, saline or dextrose in water shortly prior to administration. In other embodiments, the compositions are provided in solution ready to administer parenterally. In still other embodiments, the compositions are provided in a solution that is further diluted prior to administration. In embodiments that include administering a combination of a compound described herein and another agent, the combination may be provided to caregivers as a mixture, or the caregivers may mix the two agents prior to administration, or the two agents may be administered separately.

[0159] The actual dose of the active compounds described herein depends on the specific compound, and on the condition to be treated; the selection of the appropriate dose is well within the knowledge of the skilled artisan.

[0160] In some embodiments, the composition can further include one or more pharmaceutically acceptable diluents. In some embodiments, the pharmaceutically acceptable diluent can include Kolliphor HS15® (Polyoxyl (15)-hydroxystearate). In some embodiments, the pharmaceutically acceptable diluent can include propylene glycol. In some embodiments, the pharmaceutically acceptable diluents can include kolliphor and propylene glycol. In some embodiments, the pharmaceutically acceptable diluents can include kolliphor and propylene glycol, wherein the kolliphor is about 40% by weight and propylene glycol is about 60% by weight based on the total weight of the diluents. In some embodiments, the composition can further include one or more other pharmaceutically acceptable excipients.

[0161] Standard pharmaceutical formulation techniques can be used to make the pharmaceutical compositions described herein, such as those disclosed in Remington's The Science and Practice of Pharmacy, 21st Ed., Lippincott Williams & Wilkins (2005), incorporated herein by reference in its entirety. Accordingly, some embodiments include pharmaceutical compositions comprising: (a) a safe and therapeutically effective amount of the compound described herein or pharmaceutically acceptable salts thereof; (b) a pharmaceutically acceptable carrier, diluent, excipient or combination thereof.

[0162] The actual dose of the active compounds described herein depends on the specific compound, and on the condition to be treated; the selection of the appropriate dose is well within the knowledge of the skilled artisan. In some embodiments, a daily dose of the compound described herein may be from about 0.01 mg/kg to about 250 mg/kg of body weight, from about 0.1 mg/kg to about 200 mg/kg of body weight, from about 0.25 mg/kg to about 120 mg/kg of body weight, from about 0.5 mg/kg to about 70 mg/kg of body weight, from about 1.0 mg/kg to about 50 mg/kg of body weight, from about 1.0 mg/kg to about 15 mg/kg of body weight, from about 2.0 mg/kg to about 15 mg/kg of body weight, from about 3.0 mg/kg to about 12 mg/kg of body weight, or from about 5.0 mg/kg to about 10 mg/kg of body weight. In some embodiments, a daily dose of the compound described herein may be about 15 mg/kg, 12 mg/kg, 10 mg/kg, 8 mg/kg, 5 mg/kg, 2.5 mg/kg, 1.5 mg/kg,1.0 mg/kg, 0.8 mg/kg, 0.5 mg/kg, or 0.1 mg.kg of body weight. Thus, for administration to a 70 kg person, the dosage range may be from about 17 mg per day to about 8000 mg per day, from about 35 mg per day or less to about 7000 mg per day or more, from about 70 mg per day to about 6000 mg per day, from about 70 mg per day to about 1000 mg per day, from about 70 mg to about 800 mg per day, from about 350 mg to about 700 mg per day.

[0163] In some embodiments, a daily dose of the compound described herein may be from about 0.25 mg/kg to about 120 mg/kg or more of body weight, from about 0.5 mg/kg or less to about 70 mg/kg, from about 1.0 mg/kg to about 50 mg/kg of body weight, or from about 1.5 mg/kg to about 10 mg/kg of body weight. Thus, for administration to a 70 kg person, the dosage range may be from about 17 mg per day to about 8000 mg per day, from about 35 mg per day or less to about 7000 mg per day or more, from about 70 mg per day to about 6000 mg per day, from about 100 mg per day to about 5000 mg per day, or from about 200 mg to about 3000 mg per day.

Method of Treatment

[0164] Some embodiments relate to a method of treating a proliferative disease, disorder, or condition comprising administering to a subject in need thereof the compound or the composition described herein.

[0165] Some embodiments relate to a method of treating a cancer comprising administering to a subject in need thereof the compound or the composition described herein.

[0166] Some embodiments relate to a use of a therapeutically effective amount of a compound or the composition described herein in the preparation of a medicament for treating or inhibiting progression of cancer.

[0167] Some embodiments relate to a therapeutically effective amount of a compound of a therapeutically effective amount of a compound or for use in the treatment of or inhibition of progression of cancer.

[0168] In some embodiments, the cancer is head and neck cancer, lung cancer, stomach cancer, colon cancer, pancreatic cancer, prostate cancer, breast cancer, kidney cancer, bladder cancer, ovary cancer, cervical cancer, melanoma, glioblastoma, myeloma, lymphoma, or leukemia. In some embodiments, the cancer is renal cell carcinoma, malignant melanoma, non-small cell lung cancer (NSCLC), ovarian cancer, Hodgkin’s lymphoma or squamous cell carcinoma. In some embodiments, the cancer is selected from breast cancer, colon cancer, rectal cancer, lung cancer, prostate cancer, melanoma, leukemia, ovarian cancer, gastric cancer, renal cell carcinoma, liver cancer, pancreatic cancer, lymphomas and myeloma. In some embodiments, the cancer is a solid tumor or hematological cancer.

[0169] In some embodiments, the cancer is selected from breast cancer, colon cancer, rectal cancer, lung cancer, prostate cancer, melanoma, leukemia, ovarian cancer, gastric cancer, renal cell carcinoma, liver cancer, pancreatic cancer, lymphomas and myeloma. In some embodiments, the cancer is a solid tumor or hematological cancer. In some embodiments, the cancer is the cancer is selected from colon cancer, breast cancer, lung cancer, pancreas cancer, prostate cancer, colorectal adenocarcinoma, a non-small cell lung cancer, a melanoma, a pancreatic cancer, leukemia, ovarian cancer, gastric cancer, renal cell carcinoma, liver cancer, pancreatic cancer, lymphomas and myeloma.

[0170] In some embodiments, the subject is a mammal. In some embodiments, the subject is a human.

EXAMPLES

Example 1

[0171] Screening Protocols: Molecular modeling and screening operations were performed in the Maestro modeling suite (v11.4; Schrödinger), running on iMac workstations running macOS v10.13. A set of over 35 million purchasable compounds from MCULE (https://mcule.com), was curated based on drug-likeness (rule of five parameters) and structural diversity criteria. After curation, approximately 1 million compounds remained (Mcule_Purchasable_In_Stock_Ro5_Diverse_1M_8Dec-2016_v1), of which half were used for first virtual screening campaign. The 2D SMILES of the compounds were converted into 3D structures after adding hydrogens, and energy optimized using LigPrep program. This process generated approximately 15 million conformers. The steps for screening the compounds based on this pharmacophore is shown in Figure 2.

[0172] A pharmacophore query was generated to capture sites or features (binding interactions) present in a set of known active molecules (Plinabulin and its more potent analogs), for use in virtual screening to bias the screening towards these‘active interaction’ extracted from known active molecules.

[0173] Figure 1 shows the structure of the pharmacophore used for screening. In Figure 1, the residules around Residues around R11 (Phenyl ring in Plinabulin) includes: 3Å residues: N167, T239, L242, L252; and 4Å residues: I4, Y52, Q136, F169, E200, Y202, V238; Residues around Right R10 (Imidazole ring in Plinabulin): 3Å residues: L255, M259, A316; and 4Å residues: T179 (A chain), N258, I318, K352; Residues around H8 (t-butyl on Imidazole ring of Plinabulin): 3Å residues: T179 (A chain), T353; and 4Å residues: S241, L248, L255, K352, A354, A316, A317, I318; Residues around D4/D6 H-bond donor sites (Central piperazinedione ring in Plinabulin): 3Å residues: S241, V238 (backbone), I318, L255, E200, Y202; and 4Å residues: L242, M259, F268, A316, I378. The bold residues indicate possible hydrophobic (including pi-) and H-bond interactions with particular pharmacophore site.

[0174] Plinabulin analogs were sketched within Plinabulin/Colchicine binding site of tubulin from 1.5 Å resolution crystal structure (see Example 2) and energy optimized to relieve additional functional groups on core Plinabulin structure within binding pocket. Visual inspection of the tubulin-plinabulin complex structure indicated that plinabulin may bind stronger to beta3-tubulin where betaCys241 is substituted by a serine residue; the side chain of a serine at position 241 may allow for the formation of a stronger hydrogen bond with the O20 atom of plinabulin compared to the one of cysteine. Additionally, excluded volume based on actual receptor’s binding site residues was used to help restrict the hits’ exploration space to actual ligand binding site boundary, which can be useful during next step of structure-based screening workflow. The conformers of every molecule were generated on- the-fly during the pharmacophore screen using the DDHRR pharmacophore query, which represented 2 terminal aromatic rings (RR), 2 hydrogen-bond donors (DD), and a hydrophobic site (H). A‘fitness score’ from pharmacophore screen was used as a ranking parameter, which consists of an alignment score, vector score and volume score. Only hits that matched at least 4 out of 5 sites (hits matching more sites are better), and a fitness score equal to, or greater than 1.6 were considered for structure-based docking screen. The pharmacophore screening led to approximately 9,000 hits that passed the above criteria and were evaluated in the tubulin binding pocket.

[0175] Structure-based virtual screening (SBVS) was conducted on the approximately 9,000 hits. Docking screened was performed using‘refine only’ as ligand sampling method in Glide’s extra-precision (XP) scoring in which a quick optimization of each ligand from its input coordinates is performed. This was used to relieve any steric clashes of ‘pharmacophore-aligned ligand-pose’ with binding site residues, and form additional hydrogen bonding and hydrophobic interactions with nearby residues. In this step the ligand was free to move, while the protein was treated as rigid, except for hydroxyl groups in Serine residues which were flexible. The energy optimized ligand-receptor complexes were then scored using the more accurate Glide XP scoring function, which was reported to filter out false positive hits and enrich the success of screening campaign (Glide score is an estimate of the binding affinity, but it is only accurate to a few kcal/mol). Out of 9,000 pharmacophore hits evaluated in this step, there were 1,212 hits with a docking score higher than -10.3, which matched either 4 or 5 pharmacophore sites, or had lower docking score between -10.3 and -7.0, but matched all 5 pharmacophore sites.

[0176] Binding energy prediction for rank-ordering of potential hits: Prime MM- GBSA involves molecular mechanics optimization of ligand-protein complexes, in which the ligand and 5 A binding site residues are flexible during energy optimization. The MM-GBSA dGbind score is expected to agree reasonably well with ranking based on experimental binding affinity, and has been developed for rank-ordering congeneric series of ligands (MM- GBSA binding energies are approximate free energies of binding, a more negative value indicates stronger binding). Plinabulin and two of its nanomolar anlaogs were included in this evaluation as positive controls, and all hits with dGbind better than Plinabulin's dGbind score were selected for further analysis. Out of 1,212 hits evaluated in this computationally highly expensive step, 353 hits ranked better than Plinabulin, and their binding poses were visually inspected. Further analysis of 353 hits revealed that only 5 hits as shown in Table 1 matched all the five (DDHRR) pharmacophore sites, 293 hits as shown Table 2 matched only four (DHRR) sites (one of the H-bond donors missing), and 9 hits as shown in Table 3 matched (DDRR) sites (hydrophobic site missing).

[0177] Finally, a consensus score (CSCORE) based on fitness score, GlideXP docking score, and MM-GBSA dGbind score was developed, with 0.5, 0.5, and 1.0 weightage respectively, so that more accurate dGbind scoring got full weightage, while uniquely important but less accurate pharmacophore and docking scores received half weightage:

CSCORE= (0.5*DockingScore) - (0.5*FitnessScore) + (1.0*dGbindScore).

[0178] Note: Negative sign to FitnessScore was applied to maintain the overall analysis that lower (i.e., more -ve) the score value better will be its ranking, because

FitnessScore is the only +ve score (better +ve valuer, higher the ranking) among the scores.

Example 2

[0179] The 1.5 A resolution crystal structure of the tubulin-plinabulin complex was solved. Proteins and crystals of the TD1 complex (a protein complex containing one αβ-tubulin dimer and the tubulin-binding Darpin Dl ), as described in Pecqueur, L., et al., Proc. Natl. Acad. Sci. (2012) 109, 12011-12016 (coordinates deposited in the Protein Data Bank (PDB ID 4DRX)), both of which are incorporated herein for reference in their entireties, were prepared (the amino acid residue numbering used herein for β-tubuiin differs by two relative to that in PDB ID 4DRX). Briefly, co-crystallization experiments were performed by diluting a freshly prepared 50 mM piinabulin stock solution (in 100% DMSO) to 5 mM with the crystallization solution (100 mM Bis-TrisMethane pH 5.5, 200 mM Ammonium Sulfate, 25% PEG3350). 1 jxL of TDl at 15 mg/mL was mixed to 1 ,uL of the 5 mM plmabulm solution and equilibrated against 400 μL of the crystallization solution (hanging drop method).

[0180] Crystals appeared overnight and were flash frozen in liquid nitrogen and used directly for Xray diffraction experiments at 100K at the X06DA beamline of the Swiss Light Source (Paul Scherrer Institut, Villigen, Switzerland). Data processing was performed using the XDS software package. The TDl -piinabulin complex crystallized in space group P1211 with a single complex in the asymmetric unit. Structure solution was performed by molecular replacement method using the tubulin-darpin complex structure (PDB ID 4DRX) in the absence of any ligands and solvent as a model using the PHASER program in the ΡΗΕΝΓΧ software package. Piinabulin was added to the model using eLBOW in ΡΗΕΝΓΧ. The resulting model was improved through iterative rounds of model rebuilding in Coot and refinement in ΡΗΕΝIΧ. The quality of the structure was assessed with MolProbity. Data collection and refinement statistics are presented in Table 4. Figures were prepared using PyMOL (The PyMOL Molecular Graphics System, Version 1.4.1. Schrodinger).

Table 4. X-ray data collection and refinement statistics

[0181 ] The TDl -plinabulin complex structure was determined at 1.5 A resolution. Unambiguous difference electron density for plinabulin was observed on the β-tubulin subunits in the TDl-plinabulin complex allowing the modeling of the plinabulin. Plinabulin binds at the colchicine site on tubulin, which is located at the interface between the a- and β-tubulin subunits. It was formed by strands pSl , β84, β8ό, β87, β88, β89, and β810, loop βΤ7, and helices βΗ7 and βΗ8 of β-tubulin, as well as the loop aT5 of a-tubulin. The overall structure of tubulin in the TDl -plinabulin complex could be readily superimposed with the one obtained in the absence of any iigand (PDB ID 4DRX, rmsd of 0.28 A over 684 Cα atoms). This result suggested that binding of plmabuim did not affect the global conformation of the tubulin dimer. The interacting residues seen in the tubulin-plinabulin complex is shown in Figure 3.

[0182] Plmabulin binding was established by hydrogen bond interactions with βΕ200 and βV238 and with J3G237, βC241 and aT179 mediated via water molecules. Interestingly, the side chain of βC241 was present in two alternate conformations, one of which makes a hydrogen bond with plinabulin. The additional β-tubulin residues lining the plinabulin binding site (residues within 4 A of plinabulin) are: βΙ4, βΥ52, βζ)136, βΥ202, βΤ169, βΝ167, βϊ.,252, βL255, βΜ259, βΤ268, βΙ376, βΐ.242, βΤ239, βΑ3Ι6, βΑ317, βΙ318, βΑ354, PL248, βΤ353, βΙ378 and βΚ352.

[0183] A comparison of the β-tubulin subunit between apo TDl and TDl -plinabulin shows that the βΤ7 loop residues βL248 and βΝ249 occupy the pliiiabuiin-binding site in the apo structure. Therefore, to accommodate plinabulin in its binding site the βΤ7 loop has to flip outwards. Similar conformational changes have been observed upon binding of other colchicine site ligands to tubulin. However, in contrast to the colchicine bound tubulin, aT5 loop of α-tubulin in the TD1-plinabulin complex structure maintains its conformation similar to apo tubulin. Since plinabulin belongs to the class of colchicine site binders that are structurally unrelated to colchicine, the beta tubulin from T2R-TTL-colchicine structure (PDB ID 402B) was superimposed onto the TDl -plmabulin structure. The overall conformation of beta tubulin remained unchanged between the two structures (rmsd of 0.37 over 370 Ca atoms). Despite sharing the same binding pocket, plinabulin binds at a site with little overlap with colchicine but with a partial overlap with nocodazole. We compared the binding mode of plinabulin with tubulin to the crystal structures of other known colchicine site binding ligands using LigPlot. Almost all the tubulin residues lining the tubulin dimer in the TDl -plmabulin structure assumes the "curved" conformation characteristic of free tubulin, in contrast with the "straight" tubulin structure that is found in microtubules. To assess whether the binding of plinabulin is compatible with the straight tubulm conformation present in microtubules, we compared the structures of tubulin in the curved and straight conformational states.

[0184] In straight tubulin, the plinabulm binding site was occluded by the βΤ7 loop of β-tubulin, resulting in severe clashes between the βΤ7 loop residues with the plinabulin molecule in the straight tubulin structure. Therefore, the plinabulin-binding site was not accessible in the straight tubulin subunits incorporated into the microtubule lattice. Plinabulin thus acts as microtubule destabilize!" by binding to curved tubulin in solution and/or microtubule ends and preventing the "curved to- straight" structural transition required for microtubule formation. Table 5 lists the binding distance within 4 A of plinabulin in tubulin structure.

Table 5. Distances within 4 A of plinabulin in TD1 structure

Example 3

[0185] A microtubule pelleting assay is used to test in vitro the direct effect of the tubulin binding compounds described herein such as the compounds listed in Tables 1, 2, and 3. The effect of the test compounds in Tables 1, 2, and 3 are compared with several microtubulin depolymerizing agents (MDA) (plinabulin, colchicine and ansamitocin) and one MSA (taxol). Freshly polymerised/depolymerised bovine brain tubulin is supplemented with 34% Glycerol and 1 mM GTP and adjusted to a concentration of 4 mg/mL. Polymerization into microtubule is achieved by incubating the tubulin at 37°C for 30min.

[0186] To assess the effect of the compounds tested, a final concentration of 100 PM is added to the warm microtubules diluted at 2 mg/mL and after a 30 min incubation at 37°C, the reaction mixture is added on top of a glycerol cushion. After high speed centrifugation at 80,000 rpm for 15 min, the microtubule pellet fractions are separated from the supernatant fractions and analyzHG^E\^6'6^3$*(^^ ,Q^ WKH^SUHVHQFH^RI^ WKH^^^0'$V^^ WKH^ tubulin band is observed in the pellet fractions, which indicates the depolymerizing effect of these compounds. In contrast, taxol, which has a strong stabilizing effect on microtubules, increases the amount of tubulin observed in the pellet fraction. The test compounds generally show destabilizing effect on microtubules.