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Title:
NEW AMINOGLYCOSIDE ANTIBIOTICS TARGETING BACTERIAL 16S RIBOSOMAL RNA LACKING OTOTOXICITY
Document Type and Number:
WIPO Patent Application WO/2013/170985
Kind Code:
A1
Abstract:
The present invention relates to paromamine-/neamine-based compounds according to formula I or II having selective antimicrobial activity directed at ribosomal 16S RNA and lacking ototoxicity. Furthermore, the invention is directed to the use of said compounds for preparing a medicament, pharmaceutical preparations, and methods for preparing said compounds.

Inventors:
BOETTGER ERIK C (CH)
VASELLA ANDREA (CH)
Application Number:
PCT/EP2013/055957
Publication Date:
November 21, 2013
Filing Date:
March 21, 2013
Export Citation:
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Assignee:
BOETTGER ERIK C (CH)
International Classes:
C07H15/232; A61K31/7036; A61P31/04
Domestic Patent References:
WO2008092690A12008-08-07
WO2005060573A22005-07-07
WO2005060573A22005-07-07
WO2008092690A12008-08-07
Foreign References:
US20060211634A12006-09-21
US0121860W2001-07-11
USPP31352701P2001-08-20
USPP33924901P2001-12-11
Other References:
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LI ET AL: "Application of glycodiversification: expedient synthesis and antibacterial evaluation of a library of Kanamycin B analogues", ORGANIC LETTERS, AMERICAN CHEMICAL SOCIETY, US, vol. 6, no. 9, 1 January 2004 (2004-01-01), pages 1381 - 1384, XP002380373, ISSN: 1523-7060, DOI: 10.1021/OL0497685
FU-SEN LIANG ET AL: "Targeting RNAs with Tobramycin Analogues", ANGEWANDTE CHEMIE INTERNATIONAL EDITION, vol. 43, no. 47, 3 December 2004 (2004-12-03), pages 6496 - 6500, XP055067845, ISSN: 1433-7851, DOI: 10.1002/anie.200460558
PORTER V R ET AL: "Dissecting the cosubstrate structure requirements of the Staphylococcus aureus aminoglycoside resistance enzyme ANT(4')", BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, ACADEMIC PRESS INC. ORLANDO, FL, US, vol. 403, no. 1, 3 December 2010 (2010-12-03), pages 85 - 90, XP027536766, ISSN: 0006-291X, [retrieved on 20101030], DOI: 10.1016/J.BBRC.2010.10.119
CLAUDINE M. KLEMM ET AL: "Short and Efficient Synthesis of Alkyne-Modified Amino Glycoside Building Blocks", EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, vol. 2009, no. 17, 1 June 2009 (2009-06-01), pages 2788 - 2794, XP055067850, ISSN: 1434-193X, DOI: 10.1002/ejoc.200900076
NUDELMAN I ET AL: "Redesign of aminoglycosides for treatment of human genetic diseases caused by premature stop mutations", BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, PERGAMON, ELSEVIER SCIENCE, GB, vol. 16, no. 24, 15 December 2006 (2006-12-15), pages 6310 - 6315, XP027966012, ISSN: 0960-894X, [retrieved on 20061215]
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Attorney, Agent or Firm:
KASCHE, Dr. André (Resirain 1, Zollikerberg, CH)
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Claims:
Claims

Compounds of formula (I):

or formula (II):

wherein:

X denotes -O-, -S- or CH2, preferably -O-;

Y denotes -O-, -S-, -CH2-, -NH- or -NR1 -, preferably -O-;

R1 and R1 denote in each case independently of one another hydrogen, linear or branched, substituted or non-substituted alkyl, alkenyl, alkynyl or alkylidene, or alternatively R1 and R1 together form part of a heterocyclic ring, preferably selected from the group consisting of aziridin, azetidin, pyrrolidin, piperidin, piperazin, morpholin;

(i) Z denotes -O-, -NH-, -S-, substituted or non-substituted -CH2- or a direct bond to R2,

R2 denotes a substituted or non-substituted heterocyclic ring directly or indirectly linked to Z,

and R3Z1 denotes hydrogen, amino, aminoalkyl or hydroxyl; or YR1 and ZR2 together form a substituted or non-substituted cycloalkyl or heterocyclic ring linked directly or indirectly to a heterocyclic ring, and R3Z1 denotes hydrogen, amino, aminoalkyl or hydroxyl; or

(ii) Z1 denotes -O-, -NH-, -S-, substituted or non-substituted -CH2- or a direct bond to R3,

R3 denotes a substituted or non-substituted heterocyclic ring directly or indirectly linked to Z1, and

R2Z denotes hydrogen, amino, aminoalkyl or hydroxyl;

(iii) R7 denotes a substituted or non-substituted, directly or indirectly linked

heterocyclic ring, and R3 denotes hydrogen, amino, aminoalkyl or hydroxyl;

R4 denotes in each case, independently of one another, hydrogen, amino, aminoalkyl or hydroxyl;

R5 denotes hydrogen, a mono- or oligosaccharide, preferably a mono-, di- or trisaccharide, more preferably a mono- or disaccharide, most preferably a disaccharide, especially preferred a 2,6-diamino-2,6-dideoxy-p-L- idopyranosyl-(1→3)-p-D-ribofuranosyl moiety, a 3-amino-3-deoxy-a-D- glucopyranosyl moiety or a β-D-ribofuranosyl moiety;

R6 denotes hydrogen or glycosyl residues;

R8 denotes hydrogen, halogen, linear or branched, substituted or non- substituted alkyl, preferably hydrogen or CH3;

R11 or R12 denote in each case, independently of one another, hydrogen, linear or branched, substituted or non-substituted alkyl or acyl, preferably linear or branched, substituted or non-substituted acyl;

and their diastereoisomers or enantiomers in the form of their bases or salts of physiologically compatible acids.

2. Compounds according to claim 1 , wherein R1 and R1 denote independently of one another hydrogen, linear or branched, substituted or non-substituted C1-C6 alkyl, C3-C6 alkenyl, C3-C7 cycloalkyl, C3-C6 heterocyclic, C3-C6 heteroaryl, C6 aryl, preferably aralkyl, more preferably Ce aryl C1-C6 alkyl.

3. Compounds according to claim 1 or 2, wherein R denotes halogen, linear or branched, substituted or non-substituted C Cs, preferably C1-C 6, more preferably Ci-C 4 alkyl, most preferably H or CH3.

4. Compounds according to any one of claims 1 to 3, wherein YR1 denotes a

substituted or non-substituted, primary or secondary amine, alcohol or amino- alcohol, preferably selected from the group consisting of -NH-(CH2)iH, -NH-O- (CH2)iH, -NH-(CH2)i-OH, -NH-O-(CH2)-(CH2)i-OH, wherein i is 0 to 6, preferably 0, 1 or 2, with the proviso that for -NH-(CH2)rOH i is not 1 and for -NH-0-(CH2)- (CH2)rOH i is not O.

5. Compounds according to any of claims 1 to 4, wherein R2, R3 or R7 denotes a substituted or non-substituted, saturated or unsaturated 3 to 8-, preferably 4 to 7-, more preferably 5 or 6-membered heterocyclic ring linked directly or indirectly via a Linker to Z or Z1, wherein the heterocyclic ring has one or two heteroatoms selected independently from N, O, and S.

6. Compounds according to claim 5, wherein R2, R3 or R7 denotes a hexose or pentose moiety, preferably furanosyl- or pyranosyl moiety, more preferably a glycosyl moiety selected from D or L, alpha or beta, gluco, ido, alio, manno, galacto, talo, altro, or gu/o-configurated hexopyranosyl, or D or L, alpha or beta, arabino, xylo, ribo, or /yxo-configurated pentopyranosyl or pentofuranosyl residues, wherein all C-substituents are OH or alternatively one or two OH groups are substituted by NH2, NHCH3, NHCH2CH3, NH-cyclopropyl,

NHCH2CH2OH, N(CH3)2 groups, preferably by NH2 groups, and more preferably with one NH2 group being at position 4 of pyranosyl or at position 5 of furanosyl moieties and also alternatively one or two OH groups are substituted by halogen, preferably chlorine, bromine, fluorine or iodine, more preferably a fluorine.

7. Compounds according to claim 6, wherein R2, R3 or R7 denotes alpha-D-4- amino-4-desoxy-glucopyranosyl.

8. Compounds according to any of claims 1 to 7, wherein ZR2 or Z1R3 denotes a moiety selected from the group consisting of -O-CH2-glycosyl, -CH2-O-glycosyl, -O-glycosyl, -CH2-glycosyl and -S-glycosyl.

9. Compounds according to claim 7, wherein ZR2 or Z1R3 denotes a -CH2-NH2- glycosyl, wherein the glycosyl moiety is selected from D or L, alfa or beta ribo, arabino, xylo or /yxo-configu rated 1 -hexulopyranosyl derivatives (so-called Amadori products), wherein C-substituents are all OH or alternatively one or two OH groups are substituted by NH2, NHCH3, NHCH2CH3, NH-cyclopropyl, NHCH2CH2OH, or N(CH3)2 groups, preferably substituted by NH2 groups, and more preferably one OH being substituted with NH2 group at position 4.

10. Compounds according to any of claims 6, 8 and 9, wherein the glycosyl

derivative has no substitutents at positions 2 and 3 or 3 and 4, and optionally one additional bond between C2 and C3 or between C3 and C4, respectively.

1 1 . Compounds according to any of claims 6 and 8 to 10, wherein the glycosyl derivativ is of formula (III) or (IV)

wherein the hashed line indicates an (R) or (S) configuration; each of Q1, Q2, Q3, Q4, Q5 and Q6 are selected independently of one another from the group consisting of H, -OH, -NH2, -NHMe, -NHEt or NMe2; J1 denotes H, -CH2OH, -CH2NH2, -CH2NHMe, -CH2NHEt, CH2N(CH3)2, CHNH-cyclopropyl, or CH3; J2 denotes H or -CH2OH; L is a linker, preferably selected from the group consisting of (a) -(CH2)r for i = 1 to 5, preferably 1 to 3, more preferably 1 or 2; (b) -(CH2)rNH- for i = 0 to 5, preferably 0 to 3; (c) -(CH2) NR13- for i = 0 to 5, preferably 0 to 3, wherein R13 is a linear or branched, unsubstituted or substituted alkyl, preferably a linear or branched, unsubstituted or substituted Ci-6 alkyl, preferably substituted by -OH, -CH3, or -CH2CH2OH; (d) -(CH2)i-S(0)j for j = 0 to 2 and i = 0 to 3; and (e) -(CH2)i-0- for i= 0 to 5, preferably 0 to 3.

12. Connpounds according to any of claims 1 to 1 1 , wherein Y and Z are oxygen, preferably X, Y and Z are oxygen.

13. Compounds according to any one of claims 1 to 12, wherein YR1 and ZR2

together form a substituted or non-substituted (hetero)cycloalkyl ring, more preferably YR1 and ZR2 together form a 6-membered 4',6'-(hetero)cycloalkyl or substituted 4',6'-(hetero)cycloalkyl ring, preferably an alkyl substituted 4', 6'- (hetero)cycloalkyl ring, wherein the alkyl component is preferably a C1-C6 alkyl.

14. Compounds according to any one of claims 1 to 13, wherein R1 or R8 comprises, preferably is, a substituted or non-substituted (C1-C5 alkyl)aryl group and R2 denotes a hexose or pentose moiety, preferably furanosyl- or pyranosyl moiety, more preferably a glycosyl moiety selected from D or L, alpha or beta, gluco, ido, alio, manno, galacto, talo, altro or gulo- configurated hexopyranosyl, or D or L, alpha or beta, arabino, xylo, ribo or /yxo-configurated pentopyranosyl or pentofuranosyl residues, wherein all C-substituents are OH or alternatively one or two OH groups are substituted by NH2, NHCH3, NHCH2CH3, NH-cyclo- propyl, NHCH2CH2OH or N(CH3)2 groups, preferably by NH2 groups, and more preferably with one NH2 group being at position 4 of pyranosyl or at position 5 of furanosyl derivatives.

15. Compounds according to any one of claims 1 to 14, wherein R3 is hydroxyl and/or R4 is amino.

16. Compounds according to any one of claims 1 to 15, wherein R5 is selected from the group consisting of mono- or oligosaccharides, preferably a mono-, di- or trisaccharide, more preferably a mono- or disaccharide, most preferably a disaccharide, especially preferred a 2,6-diamino-2,6-dideoxy- -L-idopyranosyl- (1→3)-p-D-ribofuranosyl moiety, a 3-amino-3-deoxy-a-D-glucopyranosyl moiety or a β-D-ribofuranosyl moiety.

17. Compounds according to any one of claims 1 to 15, wherein R5 denotes hydrogen if R6 denotes a glycosyl, preferably a β-D-ribofuranosyl residue or R6 denotes hydrogen if R5 denotes a glycosyl residue, preferably a β-D- ribofuranosyl residue.

18. Compounds according to any one of claims 1 to 17, wherein for the compound of formula (II) R8 denotes hydrogen, chlorine, bromine, fluorine, iodine, a linear or branched, preferably linear, substituted or non-substituted Ci-Cs alkyl, preferably a substituted linear Ci-C3 alkyl, more preferably an aryl-substituted C1-C3 alkyl, most preferably an aryl-substituted ethyl group.

19. Compounds according to any of claims 1 to 18, wherein R7 preferably

comprises a halogen, preferably a chlorine, bromine, fluorine or iodine, more preferably a fluorine.

20 Compounds according to any one of claims 1 to 19 selected from the group consisting of:

4'-(2-Amino-2-deoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-paromomycin,

4'-(3-Amino-3-deoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-paromomycin,

4'-(4-Amino-4-deoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-paromomycin,

4'-(6-Amino-6-deoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-paromomycin,

4'-(2,3-Diamino-2,3-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-paromo- mycin,

4'-(2,4-Diamino-2,4-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-paromo- mycin,

4'-(2,6-Diamino-2,6-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-paromo- mycin,

4'-(3,4-Diamino-3,4-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-paromo- mycin,

4'-(3,6-Diamino-3,6-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-paromo- mycin,

4'-(4,6-Diamino-4,6-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-paromo- mycin, 4'-(2-Amino-2,3-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-paromo- mycin,

4'-(2-Amino-2,4-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-paromo- mycin,

4'-(2-Amino-2,6-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-paromo- mycin,

4'-(3-Amino-2,3-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-paromo- mycin,

4'-(3-Amino-3,4-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-paromo- mycin,

4'-(3-Amino-3,6-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-paromo- mycin,

4'-(4-Amino-2,4-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-paromo- mycin,

4'-(4-Amino-3,4-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-paromo- mycin,

4'-(4-Amino-4,6-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-paromo- mycin,

4'-(6-Amino-2,6-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-paromo- mycin,

4'-(6-Amino-3,6-dideoxy-alfa-D-glucopyranosyloxynnethyl)-4'-deoxy- paromonnycin,

4'-(6-Amino-4,6-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-paromo- mycin,

4'-(2-Amino-2-deoxy-beta-D-glucopyranosyloxymethyl)-4'-deoxy-paromomycin,

4'-(3-Amino-3-deoxy-beta-D-glucopyranosyloxymethyl)-4'-deoxy-paromomycin,

4'-(4-Amino-4-deoxy-beta-D-glucopyranosyloxymethyl)-4'-deoxy-paromomycin,

4'-(6-Amino-6-deoxy-beta-D-glucopyranosyloxymethyl)-4'-deoxy-paromomycin,

4'-(2,3-Diannino-2,3-dideoxy-beta-D-glucopyranosyloxynnethyl)-4'-deoxy-paro- monnycin,

4'-(2,4-Diannino-2,4-dideoxy-beta-D-glucopyranosyloxynnethyl)-4'-deoxy-paro- monnycin,

4'-(2,6-Diannino-2,6-dideoxy-beta-D-glucopyranosyloxynnethyl)-4'-deoxy-paro- monnycin, 4'-(3,4-Diannino-3,4-dideoxy-beta-D-glucopyranosyloxynnethyl)-4'-deoxy-paro- momycin,

4'-(3,6-Diannino-3,6-dideoxy-beta-D-glucopyranosyloxynnethyl)-4'-deoxy-paro- momycin,

4'-(4,6-Diannino-4,6-dideoxy-beta-D-glucopyranosyloxynnethyl)-4'-deoxy-paro- momycin,

4'-(2-Amino-2,3-dideoxy-beta-D-glucopyranosyloxymethyl)-4'-deoxy-paromo- mycin,

4'-(2-Amino-2,4-dideoxy-beta-D-glucopyranosyloxynnethyl)-4'-deoxy-paromo- mycin,

4'-(2-Amino-2,6-dideoxy-beta-D-glucopyranosyloxynnethyl)-4'-deoxy-paronno- mycin,

4'-(3-Amino-2,3-dideoxy-beta-D-glucopyranosyloxymethyl)-4'-deoxy-paromo- mycin,

4'-(3-Annino-3,4-dideoxy-beta-D-glucopyranosyloxynnethyl)-4'-deoxy-paromo- mycin,

4'-(3-Amino-3,6-dideoxy-beta-D-glucopyranosyloxynnethyl)-4'-deoxy-paronno- mycin,

4'-(4-Amino-2,4-dideoxy-beta-D-glucopyranosyloxymethyl)-4'-deoxy-paromo- mycin,

4'-(4-Amino-3,4-dideoxy-beta-D-glucopyranosyloxymethyl)-4'-deoxy-paromo- mycin,

4'-(4-Amino-4,6-dideoxy-beta-D-glucopyranosyloxynnethyl)-4'-deoxy-paromo- mycin,

4'-(6-Amino-2,6-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-paromo- mycin,

4'-(6-Amino-3,6-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-paromo- mycin,

4'-(6-Annino-4,6-dideoxy-alfa-D-glucopyranosyloxynnethyl)-4'-deoxy-paromo- mycin,

4'-O-(5-Amino-2,6-anhydro-1 ,5-deoxy-D-g'/ycero-D-g'u/o-heptit-1 -yl)-paromo- mycin,

4'-O-(4-Amino-2,6-anhydro-1 ,4-deoxy-D-g/ycero-D-g't//o-heptit-1 -yl)-paromo- mycin, 4'-O-(5-Amino-2,6-anhydro-1 ,5-deoxy-D-g/ycero-D-/'do-heptit-1 -yl)-paromomycin 4'-O-(4-Amino-2,6-anhydro-4-deoxy-D-g/ycero-D-/'do-heptit-1 -yl)-paromomycin, 4',6'-0-[(R)-(1 (R)-4-amino-1 ,6-anhydro-4-deoxy-glucit-1 -yl)methylene]-paro- monnycin,

4',6'-0-[(R)-(1 (R)-3-amino-1 ,6-anhydro-3-deoxy-glucit-1 -yl)methylene]-paronno- mycin,

4'/V-(1 -deoxy-beta-D-fructos-1 -yl)-4'-amino-4'-deoxyparomonnycin,

4'/V-(1 ,4-dideoxy-4-amino-D-fructos-1 -yl)-4'-amino-4'-deoxyparomomycin, 4'/V-(5-annino-2,6-anhydro-1 ,5-dideoxy-L-gu/o-heptit-1 -yl)-4'-amino-4'-deoxy- paromomycin,

4'S-(1 -deoxy-beta-D-fructos-1 -yl)-4'-thioparomonnycin,

4'S-(1 ,4-dideoxy-4-amino-D-fructos-1 -yl)-4'-thioparomonnycin,

4'S-(5-amino-2,6-anhydro-1 .S-dideoxy-L-gu/o-heptit-l -ylJ^'-thioparomonnycin, 4'-(4-Amino-4-deoxy-alfa-D-glucopyranosylthio)-4'-deoxyparomomycin and 4'-(4-Amino-4-deoxy-beta-D-glucopyranosylthio)-4'-deoxyparonnonnycin.

21 . One or more compounds according to any one of claims 1 to 20 for the

treatment and/or prevention of a microbial infection, preferably a bacterial or protozoal infection, more preferably a bacterial infeciton, malaria, trypanosomiasis or leishmaniasis.

22. Pharmaceutical composition, comprising as active substance one or more

compounds according to any one of claims 1 to 20 or pharmaceuticclly acceptable derivatives or prodrugs thereof, optionally combined with

conventional excipients and/or carriers.

23. Method of treating and/or protecting patients having or being prone to develop a microbial, preferably bacterial or protozoal infection, the method comprising the administration of a therapeutically effective amount of a compound according to any one of claims 1 to 20 or an effective amount of the pharmaceutical composition according to claim 22.

Description:
New Aminoglycoside Antibiotics Targeting Bacterial

16S Ribosomal RNA lacking Ototoxicity

Field of the invention

The present invention relates to paromamine-/neamine-based compounds according to formula I or II having selective antimicrobial activity directed at ribosomal 16S RNA and lacking or having substantially reduced ototoxicity. Furthermore, the invention is directed to the use of said compounds for preparing a medicament, pharmaceutical preparations, and methods for preparing said compounds.

Background of the invention

Aminoglycoside antibiotics (AGAs) are clinically important drugs effective against a broad range of microorganisms. The clinical use of AGAs is restricted by toxicity (irreversible ototoxicity and reversible nephrotoxicity) and by the resistance of pathogens to AGAs. Common to 2-deoxystreptamine derived AGAs is a pseudodisaccha- ride core of the neamine type. It is composed of 2-deoxystreptamine (ring II) glyco- sidically linked to an aminodeoxyglucopyranose (ring I). Additional glycosyl moieties are attached to the hydroxy groups of the 2-deoxystreptamine moiety to give rise to a variety of compounds, categorized as 4,5- or 4,6-substituted deoxystreptamine- derived amino lycosides, such as paromomycin (1 a) and kanamycin A (1 b).

1a : Paromomycin 1 b : Kanamycin A : R = OH

1 c : Kanamycin B : R = NH 2

AGAs affect the fidelity of protein synthesis through binding to specific sites of the ribosomal RNA (rRNA). In spite of decades of use of ribosomal drugs, the structural features governing selectivity, i.e. the discrimination between prokaryotic and eukaryotic ribosomes, and the toxicity of these compounds are still not fully under- stood. Genetic studies (Hobbie et al., Antimicrob. Agents Chemother. 2006, 50, 1489; Hobbie et al., C. Antimicrob. Agents Chemother. 2005, 49, 51 12; Boettger et al., EMBO reports 2001 , 2, 318) and crystal structures of AGAs complexed with ribosomal subunits (Carter et al. Nature 2000, 407, 340; Francois et al. Nucleic Acids Res 2005, 33, 5677) have contributed to understanding the interactions of AGAs with the rRNA target.

Apparently the aminodeoxyglucopyranosyl ring I of 2-deoxystreptamine-dehved AGAs binds to the rRNA in the same way regardless of whether the 2-deoxystrep- tamine is 4,5- or 4,6-disubstituted. According to the crystal structures of several AGAs, ring I intercalates into the bulge formed by A1408, A1492 and A1493, and the base pair C1409-G1491 . Ring I stacks upon G1491 and forms a pseudo base pair with A1408 characterized by H-bonds from C(6')-OH to N(1 ) of A1408, and from C(5')-OH to N(6) of A1408. Additionally, ring I shows two non-specific interactions with the phosphate groups of the two flipped-out adenines 1492 and 1493: C(3')-OH forms an hydrogen bond with O2P of A1492, and C(4')-OH forms a hydrogen bond with O2P of A1493.

Neamine-based derivatives are currently under investigation for reducing bacterial aminoglyoside resistance and for use as anti-HIV agents.

U.S. patent application 2006/021 1634 A1 teaches the use of neamine-based compounds for inhibiting aminoglycoside-6 ' -N-acetyltransferases capable of reversing or inhibiting bacterial resistance to aminoglycoside antibiotics. These compounds are characterized by large substituents on the 6 ' position such as Coenzyme A. They are not suggested for use as antibiotics.

WO 2005/060573 teaches compositions for modulating the activity of a nucleic acid molecule comprising a peptide nucleic acid moiety conjugated to a neamine moiety. The document does not disclose antibiotic activity for these compositions.

Feng et al. (Angew. Chem. Int. Ed. 2005, 44, 6859-6862) discloses the regio- and chemoselective 6 ' -N-derivatisation of neamine-based aminoglycosides with coenzyme A resulting in bisubstrate inhibitors as probes for studying aminoglycoside 6 ' -N-acetyltransferases (AAC(6 ' )inhibitors). The same authors (Feng et al., J. Med. Chem 2006,4,5273-5281 ) describe second generation AAC(6 ' ) inhibitors based on neamine having long polypeptidic substituents in the 6 ' position.

Riguet et al. (Tetrahedron 60, 2004: 8053-8064) teach a route for preparing neamine-based derivatives with heterocyclic substituents bound by linker units for targeting HIV1 TAR RNA. Later the same authors teach (Bioorganic & Medicinal Chemistry Letters 15 (2005) 4651 -4655) neamine-based dimers and trimers for targeting HIV-1 TAR RNA.

A major drawback to the use of aminoglycosides has been their ototoxicity, i.e., their ability to cause irreversible hearing damage, affecting approximately 20% of patients in brief courses of treatment. This ototoxicity is linked to the destruction of the sensory cells of the inner ear, and has consistently been associated with both natural and semi-synthetic aminoglycosides. Aminoglycoside ototoxicity occurs both in a sporadic dose-dependent manner in the general population and in an aggravated form in genetically susceptible individuals, the latter linked to mutations in mitochondrial rRNA, in particular transition mutation A1555G in the A-site of the mitoribosomal small subunit.

The mechanisms involved in aminoglycoside ototoxicity are still a matter of debate, but compelling evidence now suggests a causal involvement of reactive oxygen species (ROS). The origin of ROS generation, however, remains unresolved and both non-enzymatic and enzymatic mechanisms have been suggested. Recent evidence implies mitochondrial protein synthesis as a key element in aminoglycoside ototoxicity, as experimental evidence for both aminoglycoside-induced dysfunction of the mitochondrial ribosome and A1555G-linked mitochondrial hypersusceptibility to aminoglycoside antibiotics was provided. Given this link, the hypothesis can be put forward that aminoglycoside ototoxicity is associated with the compound's antimito- ribosomal activity. Defective mitochondrial function reportedly elicits ROS and the antimitoribosomal activity of aminoglycosides may result in ROS generation and/or impairment to withstand oxidative stress.

WO 2008/092690 A1 , a previous patent application by the instant inventors describes paromamine-based antibiotic compounds having selective antimicrobial activity directed at ribosomal 16S RNA, which have reduced or no side effects over known paromamine-based compounds for antibiotic use.

Apramycin is a structurally unique aminoglycoside commonly used in veterinary medicine and effective against a wide range of Gram-positive and Gram-negative bacteria.

The object underlying the present invention is to provide novel and improved antimicrobial compounds that are not modified by common microbial resistance determinants and that target microbial, in particular bacterial 16S ribosomal RNA, i.e. the compounds do not target at all or target to a substantially less degree eukaryotic cytosolic and/or mitochiondrial ribosomes. In particular, it is the objective to provide antibiotics essentially lacking or having substantially reduced ototoxicity and/or other antibiotic-related side effects.

Description of the invention

It was surprisingly found that aminoglycoside paro- and neam-compounds selectively target microbial 16 S RNA and lack or have substantially reduced ototoxicity if polar substituents, preferably heterocyclic rings, more preferably hexose and/or pentose moieties are chosen for specific positions.

In a first aspect the resent invention relates to compounds of formula (I):

or formula (II):

wherein:

X denotes -0-, -S- or CH 2 , preferably -0-;

Y denotes -0-, -S-, -CH 2 -, -NH- or -NR 1 -, preferably -0-;

R 1 and R 1 denote in each case independently of one another hydrogen, linear or branched, substituted or non-substituted alkyl, alkenyl, alkynyl or alkylidene, or alternatively R 1 and R 1 together form part of a heterocyclic ring, preferably selected from the group consisting of aziridin, azetidin, pyrrolidin, piperidin, piperazin, morpholin;

(i) Z denotes -0-, -NH-, -S-, substituted or non-substituted -CH 2 - or a direct bond to R 2 , and

R 2 denotes a substituted or non-substituted heterocyclic ring directly or indirectly linked to Z, and

R 3 Z 1 denotes hydrogen, amino, aminoalkyl or hydroxyl;

or YR 1 and ZR 2 together form a substituted or non-substituted cycloalkyi or heterocyclic ring linked directly or indirectly to a heterocyclic ring, and

R 3 Z 1 denotes hydrogen, amino, aminoalkyl or hydroxyl; or

(ii) Z 1 denotes -0-, -NH-, -S-, substituted or non-substituted -CH 2 - or a direct bond to R 3 ,

R 3 denotes a substituted or non-substituted heterocyclic ring directly or indirectly linked to Z 1 , and

R 2 Z denotes hydrogen, amino, aminoalkyl or hydroxyl;

(iii) R 7 denotes a substituted or non-substituted, directly or indirectly linked

heterocyclic ring, and R 3 denotes hydrogen, amino, aminoalkyl or hydroxyl;

R 4 denotes in each case, independently of one another, hydrogen, amino, aminoalkyl or hydroxyl;

R 5 denotes hydrogen, a mono-, oligo- or polysaccharide, preferably a mono-, di- or trisaccharide, more preferably a mono- or disaccharide, most preferably a disac- charide, especially preferred a 2,6-diamino-2,6-dideoxy-p-L-idopyranosyl-(1 - 3)-p-D- ribofuranosyl moiety, a 3-amino-3-deoxy-a-D-glucopyranosyl moiety or a β-D-ribo- furanosyl moiety;

R 6 denotes hydrogen or glycosyl residues;

R 8 denotes hydrogen, halogen, linear or branched, substituted or non-substituted alkyl, preferably hydrogen or CH 3 ;

R 11 or R 12 denote in each case, independently of one another, hydrogen, linear or branched, substituted or non-substituted alkyl or acyl, preferably linear or branched, substituted or non-substituted acyl;

and their diastereoisomers or enantiomers in the form of their bases or salts of physiologically compatible acids.

In the context of the present invention it is understood that antecedent terms such as linear or branched, substituted or non-substituted indicate that each one of the subsequent terms is to be interpreted as being modified by said antecedent term. For example, the scope of the term "linear or branched, substituted or non-substituted alkyl, alkenyl, alkynyl, alkylidene, carbocycle" encompasses linear or branched, substituted or non-substituted alkyl; linear or branched, substituted or non-substituted alkenyl; linear or branched, substituted or non-substituted alkynyl; linear or branched, substituted or non-substituted alkylidene; and linear or branched, substituted or non- substituted carbocycle. For example, the term "C 2 -C 12 alkenyl, alkynyl, or alkylidene" indicates the group of compounds having 2 to 12 carbons and alkenyl, alkynyl, or alkylidene functionality.

The compounds of the present invention are stable and resistant to bacterial degradation. Some preferred embodiments of the compounds are more resistant against bacterial determinants than others.

In a preferred embodiment of the present invention substituents R 1 and R 1 of the above compounds I and II denote independently of one another hydrogen, linear or branched, substituted or non-substituted CrC 6 alkyl, C 3 -C 6 alkenyl, C3-C7 cycloalkyl, C 3 - C 6 heterocyclic, C 3 -C 6 heteroaryl, C 6 aryl, preferably aralkyl, more preferably C 6 aryl C C 6 alkyl.

In a further preferred embodiment R 8 denotes halogen, linear or branched, substituted or non-substituted CrC 8 , preferably CrC 6 , more preferably C C 4 alkyl, most preferably H or CH 3 .

In a more preferred embodiment of the compounds of the invention YR 1 denotes a substituted or non-substituted, primary or secondary amine, alcohol or aminoalcohol, preferably selected from the group consisting of -NH-(CH 2 )iH, -NH-0-(CH 2 )iH, -NH- (CH 2 )rOH, -NH-0-(CH 2 )-(CH 2 )i-OH, wherein i is 0 to 6, preferably 0, 1 or 2, with the proviso that for -NH-(CH 2 )rOH i is not 1 and for -NH-O-(CH 2 )-(CH 2 )i-OH i is not 0. The proviso excludes unstable compounds from the list.

When any of R 3 Z 1 , R 2 Z, R 3 and R 4 denote aminoalkyl, it is further preferred that the alkyl component thereof is Ci t0 6, preferably Ci t0 3 alkyl.

It was surprisingly found that unlike most aminoglycoside antibiotics such as genta- micin, tobramycin and kanamycin the potent aminoglycoside apramycin does not elicit aminoglycoside-induced ototoxicity due to hair cell damage as demonstrated in an established in vivo guinea pig model of chronic ototoxicity (see examples). In contrast to the before-mentioned typical aminoglycoside antibiotics, apramycin affects mitohybrid ribosomes significantly less. This effect can be transferred to other antibiotic aminoglycoside compounds, when substitutents R 2 or R 3 in compounds of formula I or substi- tuent R 7 in compounds of formula II of the present invention denote a substituted or non-substituted heterocyclic ring.

In a preferred embodiment compounds of the invention are those, wherein R 2 , R 3 or R 7 denotes a substituted or non-substituted, saturated or unsaturated 3 to 8, preferably 4 to 7, more preferably 5 or 6-membered heterocyclic ring linked directly or indirectly via a Linker L to Z or Z 1 , wherein the heterocyclic ring has one or two hetero- atoms selected independently from N, O, and S. For R 3 the heterocyclic ring can be directly or indirectly linked to Z 1 . For R 2 the heterocyclic ring can be directly or indirectly linked to Z. A suitable linker is preferably selected from the group consisting of (a) -(CH 2 )i- for i = 1 to 5, preferably 1 to 3, more preferably 1 or 2; (b) -(CH 2 )i-NH- for i = 0 to 5, preferably 0 to 3; (c) -(CH 2 )i-NR 13 - for i = 0 to 5, preferably 0 to 3, wherein R 13 is a linear or branched, unsubstituted or substituted alkyl, preferably a linear or branched, unsubstituted or substituted Ci-6 alkyl, preferably substituted by - OH, -CH 3 , or -CH 2 CH 2 OH; (d) -(CH 2 )i-S(0)j for j = 0 to 2 and i = 0 to 3; and (e) - (CH 2 )i-O- for i= 0 to 5, preferably 0 to 3.

In a more preferred embodiment the invention relates to compounds of the invention, wherein R 2 , R 3 or R 7 denotes a hexose or pentose moiety, preferably furanosyl- or pyranosyl moiety, more preferably a glycosyl moiety selected from D or L, alpha or beta, gluco, ido, alio, manno, galacto, talo, altro, or gu/o-configurated hexopyranosyl, or D or L, alpha or beta, arabino, xylo, ribo, or /yxo-configu rated pentopyranosyl or pentofura- nosyl residues, wherein all C-substituents are OH or alternatively one or two OH groups are substituted by H, NH 2 , NHCH 3 , NHCH 2 CH 3 , NH-cyclopropyl, NHCH 2 CH 2 OH, N(CH 3 ) 2 groups, preferably by NH 2 groups, and more preferably with one NH 2 group being at po- sition 4 of pyranosyl or at position 5 of furanosyl moieties and also alternatively one or two OH groups are substituted by halogen, preferably chlorine, bromine, fluorine or iodine, more preferably a fluorine.

In a very preferred embodiment R 2 , R 3 or R 7 denote alpha-D-4-amino-4-desoxy- glucopyranosyl.

In another preferred embodiment the invention relates to compounds of the invention, wherein ZR 2 or Z 1 R 3 denotes a moiety selected from the group consisting of - O-CH 2 -Glycosyl, -CH 2 -O-Glycosyl, O-Glycosyl, -CH 2 -Glycosyl and -S-glycosyl.

In another preferred embodiment the invention relates to compounds of the invention, wherein ZR 2 or Z 1 R 3 denotes a -CH 2 -NH 2 -glycosyl, wherein the glycosyl moiety is selected from D or L, alfa or beta ribo, arabino, xylo or /yxo-configurated 1 - hexulopyranosyl derivatives (so-called Amadori products), wherein C-substituents are all OH or alternatively one or two OH groups are substituted by NH 2 , NHCH 3 , NHCH 2 CH 3 , NH-cyclopropyl, NHCH 2 CH 2 OH, or N(CH 3 ) 2 groups, preferably substituted by NH 2 groups, and more preferably one OH being substituted with NH 2 group at position 4.

For the compounds of the invention it is also preferred that R 2 , R 3 or R 7 denote a glycosyl derivative without substitutents at positions 2 and 3 or 3 and 4, and optionally one additional bond between C2 and C3 or between C3 and C4, respectively.

It is further preferred that R 2 , R 3 or R 7 denote a glycosyl derivative of formula (III) or (IV)

wherein the hashed line indicates an (R) or (S) configuration; each of Q 1 , Q 2 , Q 3 , Q 4 , Q 5 and Q 6 are selected independently of one another from the group consisting of -OH, -NH 2 , -NHMe, -NHEt or NMe 2 ; J 1 denotes H, -CH 2 OH, -CH 2 NH 2 , - CH 2 NHMe, -CH 2 NHEt, CH 2 N(CH 3 ) 2 , CHNH-cyclopropyl, or CH 3 ; J 2 denotes H or - CH 2 OH; L is a linker, preferably selected from the group consisting of (a) -(CH 2 )i- for i = 1 to 5, preferably 1 to 3, more preferably 1 or 2; (b) -(CH 2 )i-NH- for i = 0 to 5, preferably 0 to 3; (c) -(CH 2 )i-NR 13 - for i = 0 to 5, preferably 0 to 3, wherein R 13 is a linear or branched, unsubstituted or substituted alkyl, preferably a linear or branched, unsubstituted or substituted Ci-6 alkyl, preferably substi- tuted by -OH, -CH 3 , or -CH 2 CH 2 OH; (d) -(CH 2 )i-S(0)j for j = 0 to 2 and i = 0 to 3; and (e) -(CH 2 )i-O- for i= 0 to 5, preferably 0 to 3.

Furthermore, it is preferred that Y and Z in formulas (I) and (II) are oxygen, preferably X, Y and Z are oxygen.

In another preferred embodiment the compounds of the invention are those, wherein YR 1 and ZR 2 together form a substituted or non-substituted (hetero)cycloalkyl ring, more preferably YR 1 and ZR 2 together form a 6-membered 4 ' ,6 ' -(hetero)cycloalkyl or substituted 4 ' ,6 ' -(hetero)cycloalkyl ring, preferably an alkyi substituted 4 ' , 6 ' - (hetero)cycloalkyl ring, wherein the alkyi component is preferably a C1-C6 alkyi.

For compounds of the invention it is more preferred that R 1 or R 8 comprises, preferably is, a substituted or non-substituted (C-1-C5 alkyl)aryl group and R 2 denotes a hexose or pentose moiety, preferably furanosyl- or pyranosyl moiety, more preferably a glycosyl moiety selected from D or L, alpha or beta, gluco, ido, alio, manno, galacto, talo, altro or gulo- configurated hexopyranosyl, or D or L, alpha or beta, arabino, xylo, ribo or /yxo-configurated pentopyranosyl or pentofuranosyl residues, wherein all C-substituents are OH or alternatively one or two OH groups are substituted by NH 2 , NHCH 3 , NHCH 2 - CH 3 , NH-cyclopropyl, NHCH 2 CH 2 OH or N(CH 3 ) 2 groups, preferably by NH 2 groups, and more preferably with one NH 2 group being at position 4 of pyranosyl or at position 5 of furanosyl derivatives.

Also preferred are compounds, wherein R 3 is hydroxyl and/or R 4 is amino.

For substituent R 5 it is preferred that R 5 is selected from the group consisting of mono- or oligosaccharide, preferably a mono-, di- or trisaccharide, more preferably a mono- or disaccharide, most preferably a disaccharide, especially preferred a 2,6- diamino-2,6-dideoxy-p-L-idopyranosyl-(1→-3)-p-D-hbofuranos yl moiety, a 3-amino-3- deoxy-a-D-glucopyranosyl moiety or a β-D-ribofuranosyl moiety.

In a more preferred embodiment of the compounds of the invention R 5 denotes hydrogen if R 6 denotes a glycosyl, preferably a β-D-ribofuranosyl residue or R 6 denotes hydrogen if R 5 denotes a glycosyl residue, preferably a β-D-ribofuranosyl residue.

For compounds of the invention described by formula II it is preferred that R 8 denotes hydrogen, chlorine, bromine, fluorine, iodine, a linear or branched, preferably linear, substituted or non-substituted CrC 8 alkyi, preferably a substituted linear C 1 -C 3 alkyi, more preferably an aryl-substituted C 1 -C 3 alkyi, most preferably an aryl-substituted ethyl group.

For substituent R 7 it is preferred that it comprises a halogen, preferably a chlorine, bromine, fluorine or iodine, more preferably a fluorine. In the following a list of preferred and specific but non-limiting compounds of the invention is provided: 4'-(2-Amino-2-deoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy - paromomycin; 4'-(3-Amino-3-deoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy -paromo- mycin; 4'-(4-Amino-4-deoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy -paromomycin; 4'- (6-Amino-6-deoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-pa romomycin; 4'-(2,3- Diamino-2,3-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy -paromomycin; 4'-(2,4- Diamino-2,4-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy -paromomycin; 4'-(2,6- Diamino-2,6-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy -paromomycin; 4'-(3,4- Diamino-3,4-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy -paromomycin; 4'-(3,6- Diamino-3,6-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy -paromomycin; 4'-(4,6- Diamino-4,6-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy -paromomycin; 4'-(2- Amino-2,3-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-p aromomycin; 4'-(2- Amino-2,4-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-p aromomycin; 4'-(2- Amino-2,6-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-p aromomycin; 4'-(3- Amino-2,3-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-p aromomycin; 4'-(3- Amino-3,4-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-p aromomycin; 4'-(3- Amino-3,6-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-p aromomycin; 4'-(4- Amino-2,4-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-p aromomycin; 4'-(4- Amino-3,4-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-p aromo-mycin; 4'-(4- Amino-4,6-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-p aromomycin; 4'-(6- Amino-2,6-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-p aromomycin; 4'-(6- Amino-3,6-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-p aromomycin; 4'-(6- Amino-4,6-dideoxy-alfa-D-glucopyranosyloxymethyl)-4'-deoxy-p aromomycin; 4'-(2- Amino-2-deoxy-beta-D-glucopyranosyloxymethyl)-4'-deoxy-parom omycin; 4'-(3-Amino-3- deoxy-beta-D-glucopyranosyloxymethyl)-4'-deoxy-paromomycin; 4'-(4-Amino-4-deoxy- beta-D-glucopyranosyloxymethyl)-4'-deoxy-paromomycin; 4'-(6-Amino-6-deoxy-beta-D- glucopyranosyloxymethyl)-4'-deoxy-paromomycin; 4'-(2,3-Diamino-2,3-dideoxy-beta-D- glucopyranosyloxymethyl)-4'-deoxy-paromomycin; 4'-(2,4-Diamino-2,4-dideoxy-beta-D- glucopyranosyloxymethyl)-4'-deoxy-paromomycin; 4'-(2,6-Diamino-2,6-dideoxy-beta-D- glucopyranosyloxymethyl)-4'-deoxy-paromomycin; 4'-(3,4-Diamino-3,4-dideoxy-beta-D- glucopyranosyloxymethyl)-4'-deoxy-paromomycin; 4'-(3,6-Diamino-3,6-dideoxy-beta-D- glucopyranosyloxymethyl)-4'-deoxy-paromomycin; 4'-(4,6-Diamino-4,6-dideoxy-beta-D- glucopyranosyloxymethyl)-4'-deoxy-paromomycin; 4'-(2-Amino-2,3-dideoxy-beta-D- glucopyranosyloxymethyl)-4'-deoxy-paromomycin; 4'-(2-Amino-2,4-dideoxy-beta-D- glucopyranosyloxymethyl)-4'-deoxy-paromomycin; 4'-(2-Amino-2,6-dideoxy-beta-D- glucopyranosyloxymethyl)-4'-deoxy-paromomycin; 4'-(3-Amino-2,3-dideoxy-beta-D- glucopyranosyloxymethyl)-4'-deoxy-paromomycin; 4'-(3-Amino-3,4-dideoxy-beta-D- glucopyranosyloxymethyl)-4'-deoxy-paromomycin; 4'-(3-Amino-3,6-dideoxy-beta-D- glucopyranosyloxymethyl)-4'-deoxy-paromomycin; 4'-(4-Amino-2,4-dideoxy-beta-D- glucopyranosyloxymethyl)-4'-deoxy-paromomycin; 4'-(4-Amino-3,4-dideoxy-beta-D- glucopyranosyloxymethyl)-4'-deoxy-paromomycin; 4'-(4-Amino-4,6-dideoxy-beta-D- glucopyranosyloxymethyl)-4'-deoxy-paromomycin; 4'-(6-Amino-2,6-dideoxy-alfa-D- glucopyranosyloxymethyl)-4'-deoxy-paromomycin; 4'-(6-Amino-3,6-dideoxy-alfa-D- glucopyranosyloxymethyl)-4'-deoxy-paromomycin; 4'-(6-Amino-4,6-dideoxy-alfa-D- glucopyranosyloxymethyl)-4'-deoxy-paromomycin; 4'-0-(5-Amino-2,6-anhydro-1 ,5- deoxy-D-g/ycero-D-gi//o-heptit-1 -yl)-paromomycin; 4'-0-(4-Amino-2,6-anhydro-1 ,4- deoxy-D-g/ycero-D-gi//o-heptit-1 -yl)-paromomycin; 4'-0-(5-Amino-2,6-anhydro-1 ,5- deoxy-D-g/ycero-D-/ ' c o-heptit-1 -yl)-paromomycin; 4'-0-(4-Amino-2,6-anhydro-4-deoxy-D- g/ycero-D-/ ' c o-heptit-1 -yl)-paromomycin; 4',6'-0-[(R)-(1 (R)-4-amino-1 ,6-anhydro-4-deoxy- glucit-1 -yl)methylene]-paromomycin; 4',6'-0-[(R)-(1 (R)-3-amino-1 ,6-anhydro-3-deoxy- glucit-1 -yl)methylene]-paromomycin; 4W-(1 -deoxy-beta-D-fructos-1 -yl)-4'-amino-4'- deoxyparomomycin; 4W-(1 ,4-dideoxy-4-amino-D-fructos-1 -yl)-4'-amino-4'-deoxyparo- momycin; 4'/V-(5-amino-2,6-anhydro-1 ,5-dideoxy-L-gt//o-heptit-1 -yl)-4'-amino-4'-deoxy- paromomycin; 4'S-(1 -deoxy-beta-D-fructos-1 -yl)-4'-thioparomomycin; 4'S-(1 ,4-dideoxy-4- amino-D-fructos-1 -yl)-4'-thioparomomycin; 4'S-(5-amino-2,6-anhydro-1 ,5-dideoxy-L- gu/o-heptit-1 -yl)-4'-thioparomomycin; 4'-(4-Amino-4-deoxy-alfa-D-glucopyranosylthio)-4'- deoxyparomomycin and 4'-(4-Amino-4-deoxy-beta-D-glucopyranosylthio)-4'-deoxyparo- momycin.

In all compounds disclosed herein, in the event that the nomenclature conflicts with the structure, it shall be understood that the compound is defined by the structure.

The invention includes all compounds described herein containing one or more asymmetric carbon atoms that may occur as racemates and racemic mixtures, single enantiomers, diastereoisomeric mixtures and individual diastereoisomers. All such isomeric forms of these compounds are expressly included in the present invention. Each stereogenic carbon may be in the R or S configuration or a combination of configurations. It is understood that the stereogenic structure of the paromamine core of the compounds of the invention is fixed as shown in formulas I and II.

Some of the compounds of the general formulas (I) and (II) disclosed herein can exist in more than one tautomeric form. The present invention includes all such tautomers. All terms as used herein shall be understood by their ordinary meaning as known in the art.

The term "heteroatom" as used herein shall be understood to mean atoms other than carbon and hydrogen such as and preferably O, N, S and P.

The terms alkyl, alkenyl, alkynyl, alkylidene, etc. shall be understood as encompassing linear as well as branched forms of carbon-containing chains where structurally possible. In these carbon chains one or more carbon atoms can be optionally replaced by heteroatoms, preferably by O, S or N. If N is not substituted it is NH. The heteroatoms may replace either terminal or internal carbon atoms within a linear or branched carbon chain. Such groups can be substituted as herein described by groups such as oxo to result in definitions such as but not limited to alkoxycarbonyl, acryl, amido and thioxo.

The term "carbocycle" shall be understood to mean an aliphatic hydrocarbon radical containing from 3 to 20, preferably from 3 to 12 carbon atoms, more preferably 5 or 6 carbon atoms. Carbocycles include hydrocarbon rings containing from 3 to 10 carbon atoms. These carbocycles may be either aromatic or non-aromatic systems. The non-aromatic ring systems may be mono or polyunsaturated. Preferred carbocycles include but are not limited to cyclopropyl, cyclobutyl, cyclopentyl, cyclopentenyl, cyclo- hexyl, cyclohexenyl, cycloheptanyl, cycloheptenyl, phenyl, indanyl, indenyl, benzocyclo- butanyl, dihydronaphthyl, tetrahydronaphthyl, naphthyl, decahydronaphthyl,

benzocycloheptanyl, and benzocycloheptenyl. Certain terms for cycloalkyl such as cyclobutanyl and cyclobutyl shall be used interchangeably.

The term "cycloalkyl" shall be understood to mean aliphatic hydrocarbon- containing rings having from 3 to 12 carbon atoms. These non-aromatic ring systems may be mono- or polyunsaturated, i.e. the term encompasses cycloalkenyl and cyclo- alkynyl. The cycloalkyl may comprise heteroatoms, preferably O, S or N, and be substituted or non-substituted. Preferred and non-limiting cycloalkyls include cyclopropyl, cyclobutyl, cyclopentyl, cyclopentenyl, cyclohexyl, cyclohexenyl, cycloheptanyl, cycloheptenyl, benzocyclobutanyl, benzocycloheptanyl und benzocycloheptenyl.

The term "heterocyclic" refers to a stable non-aromatic, preferably 3 to 20 mem- bered, more preferably 3 to 12 membered, most preferably 5 or 6 membered, monocyclic or multicyclic, preferably 8 to 12 membered bicyclic, heteroatom-containing cyclic radical, that may be either saturated or unsaturated. Each heterocycle consists of carbon atoms and one or more, preferably 1 to 4 heteroatoms chosen from nitrogen, oxygen and sulphur. The heterocyclic residue may be bound to the remaining structure of the complete molecule by any atom of the cycle, which results in a stable structure. Exemplary heterocycles include but are not limited to pyrrolidinyl, pyrrolinyl, morpholinyl, thio- morpholinyl, thiomorpholinyl sulfoxide, thiomorpholinyl sulfone, dioxalanyl, piperidinyl, piperazinyl, tetrahydrofuranyl, 1 -oxo-A4-thiomorpholinyl, 13-oxa-1 1 -aza-tricyclo[7.3.1.0- 2,7]tridecy-2,4,6-triene, tetrahydropyranyl, 2-oxo-2H-pyranyl, tetrahydrofuranyl, 1 ,3-di- oxolanone, 1 ,3-dioxanone, 1 ,4-dioxanyl, 8-oxa-3-aza-bicyclo[3.2.1]octanyl, 2-oxa-5-aza- bicyclo[2.2.1]heptanyl, 2-thia-5-aza-bicyclo[2.2.1]heptanyl, piperidinonyl, tetrahydro-pyri- midonyl, pentamethylene sulphide, pentamethylene sulfoxide, pentamethylene sulfone, tetramethylene sulphide, tetramethylene sulfoxide and tetramethylene sulfone.

The term "aryl" as used herein shall be understood to mean an aromatic carbo- cycle or heteroaryl as defined herein. Each aryl or heteroaryl unless otherwise specified includes its partially or fully hydrogenated derivative. For example, quinolinyl may include decahydroquinolinyl and tetrahydroquinolinyl; naphthyl may include its hydrogenated derivatives such as tetrahydronaphthyl. Other partially or fully hydrogenated derivatives of the aryl and heteroaryl compounds described herein will be apparent to one of ordinary skill in the art. Naturally, the term encompasses aralkyl and alkylaryl, both of which are preferred embodiments for practicing the compounds of the present invention. For example, the term aryl encompasses phenyl, indanyl, indenyl, dihydronaphthyl, tetrahydronaphthyl, naphthyl and decahydronaphthyl.

The term "heteroaryl" shall be understood to mean an aromatic C3-C 20 , preferably 5 to 8 membered monoxyclic or preferably 8 - 12 membered bicyclic ring containing 1 to 4 heteroatoms such as N, O and S. Exemplary heteroaryls comprise aziridinyl, thienyl, furanyl, isoxazolyl, oxazolyl, thiazolyl, thiadiazolyl, tetrazolyl, pyrazolyl, pyrrolyl, imida- zolyl, pyridinyl, pyrimidinyl, pyrazinyl, pyridazinyl, pyranyl, quinoxalinyl, indolyl, benzimi- dazolyl, benzoxazolyl, benzothiazolyl, benzothienyl, quinolinyl, quinazolinyl, naphthyri- dinyl, indazolyl, triazolyl, pyrazolo[3,4-i ]pyrimidinyl, purinyl, pyrrolo[2,3-j ]pyridinyl, pyra- zole[3,4-i ]pyridinyl, tubercidinyl, oxazo[4,5-i ]pyridinyl and imidazo[4,5-i ]pyridinyl.

Terms which are analogues of the above cyclic moieties such as aryloxy or heteroaryl amine shall be understood to mean an aryl, heteroaryl, heterocycle as defined above attached to its respective group.

As used herein, the terms "nitrogen" and "sulphur" include any oxidized form of nitrogen and sulphur and the quaternized form of any basic nitrogen as long as the resulting compound is chemically stable. For example, for an -S-C 1 -6 alkyl radical shall be understood to include -S(O)-Ci -6 alkyl and -S(O) 2 -Ci- 6 alkyl.

The term "oligosaccharide" is intended to indicate 1 to 10, preferably 1 to 5, more preferably 1 to 3 linked saccharides.

The compounds of the invention are only those which are contemplated to be 'chemically stable' as will be appreciated by those skilled in the art. For example, compounds having a 'dangling valency' or a 'carbanion' are not compounds contemplated by the inventive disclosed herein.

The above described compounds have demonstrated a strong and antimicrobial, in particular antibacterial, 16 S RNA specific activity making them particularly useful for preparing medicaments lacking toxicity due to the essential lack of activity in eukaryotic cells, i.e. no interaction with eukaryotic cytosolic and/or mitochondrial RNA. In addition, compounds of the present invention will affect human cytosolic and/or mitochondrial ribosomes significantly less than conventional aminoglycoside antibiotics such as gentamicin, tobramycin and kanmycin. Without wishing to be bound by theory, it is assumed that the high selectivity for bacterial ribosomes is due to the polar substitutents R2, R3 or R7 in the compounds of formulas I and II, which seem to function similarly to the corresponding glycosyl substituent in apramycin. The structural analysis for apramycin-ribosome interaction supports this working hypothesis.

Because of the above described highly selective activity another aspect of the present invention relates to the use of one or more compounds of the invention for preparing a medicament.

In a preferred embodiment one or more compounds of the present invention are used for preparing a medicament for the treatment and/or prevention of a microbial, preferably a protozoal or bacterial, infection.

In a further preferred embodiment the invention relates to the use of one or more compounds according to the invention for preparing a medicament for the treatment and/or prevention of a microbial, preferably protozoal or bacterial infection, more preferably a bacterial infection, trypanosomiasis, leishmaniasis or malaria.

A further aspect of the present invention concerns pharmaceutical

compositions, comprising as active substance one or more compounds of the present invention or pharmaceuticclly acceptable derivatives or prodrugs thereof, optionally combined with conventional excipients and/or carriers.

The invention includes pharmaceutically acceptable derivatives of compounds of formulae (I) and (II). A "pharmaceutically acceptable derivative" refers to any pharmaceutically acceptable salt or ester or any other compound which, upon administration to a patient, is capable of providing (directly or indirectly) a compound of the invention, or a pharmacologically active metabolite or pharmacologically active residue thereof. A pharmacologically active metabolite shall be understood to mean any compound of the invention capable of being metabolized enzymatically or chemically. This includes, for example, hydroxylated or oxidized derivative compounds of the formula (I) and (II). Preferred embodiments relate to pharmaceutically acceptable derivatives of compounds of formulas (I) and (II) that are hydrates.

Pharmaceutically acceptable salts include those derived from pharmaceutically acceptable inorganic and organic acids and bases. Examples of suitable acids include hydrochloric, hydrobromic, sulphuric, nitric, perchloric, fumaric, maleic, phosphoric, glycolic, lactic, salicylic, succinic, toluene-p-sulfuric, tartaric, acetic, citric, methane- sulfonic, formic, benzoic, malonic, naphthalene-2-sulfuric and benzenesulfonic acids. Other acids, such as oxalic acid, while not themselves pharmaceutically acceptable, may be employed in the preparation of salts useful as intermediates in obtaining the compounds and their pharmaceutically acceptable acid addition salts. Salts derived from appropriate bases include alkali metal (e.g., sodium), alkaline earth metal (e.g. magnesium), ammonium and N-(CrC 4 alkyl) 4 + salts.

In addition, the scope of the invention also encompasses prodrugs of compounds of the formulas (I) and (II). Prodrugs include those compounds that, upon simple chemical transformation, are modified to produce compounds of the invention. Simple chemical transformations include hydrolysis, oxidation and reduction. Specifically, when a prodrug is administered to a patient, the prodrug may be transformed into a compound disclosed hereinabove, thereby imparting the desired pharmacological effect.

The compounds of the invention have demonstrated a selective inhibition of the bacterial ribosome. These drugs do not affect the eukaryotic ribosome because they do not target eukaryotic mitochondrial or cytosolic 16S ribosomal RNA as demonstrated in tests with genetically engineered ribosomes carrying eukaryotic 16 S RNA nucleotide positions.

Hence, in a further aspect the present invention is directed to the use of one or more compounds according to the invention for preparing a medicament. Preferably, the compounds of the invention are used for preparing a medicament for the treatment and/or prevention of a bacterial infection, trypanosomiasis or leishmaniasis.

In the above respect the present invention also relates to a pharmaceutical composition, comprising as active substance one or more compounds according to the invention or pharmaceuticclly acceptable derivatives or prodrugs thereof, optionally combined with conventional excipients and/or carriers.

For therapeutic or prophylactic use the compounds of the invention may be administered in any conventional dosage form in any conventional manner. Routes of administration include, but are not limited to, intravenously, intramuscularly, subcuta- neously, intrasynovially, by infusion, sublingually, transdermally, orally, topically, or by inhalation. The preferred modes of administration are oral and intravenous.

The compounds may be administered alone or in combination with adjuvants that enhance stability of the inhibitors, facilitate administration of pharmaceutical compositions containing them in certain embodiments, provide increased dissolution or dispersion, increase inhibitory activity, provide adjunct therapy, and the like, including other active ingredients. Advantageously such combination therapies utilize lower dosages of the conventional therapeutics, thus avoiding possible toxicity and adverse side effects incurred when those agents are used as monotherapies. The above described compounds may be physically combined with the conventional therapeutics or other adjuvants into a single pharmaceutical composition. Reference is this regard may be made to Cappola et al.: U.S. patent application no. 09/902,822, PCT/US 01/21860 und US provisional application no. 60/313,527, each incorporated by reference herein in their entirety. Advantageously, the compounds may then be administered together in a single dosage form. In some embodiments, the pharmaceutical compositions comprising such combinations of compounds contain at least about 5 %, but more preferably at least about 20 %, of a compound of formula (2) or (3) (w/w) or a combination thereof. The optimum percentage (w/w) of a compound of the invention may vary and is within the purview of those skilled in the art. Alternatively, the compounds may be administered separately (either serially or in parallel). Separate dosing allows for greater flexibility in the dosing regime.

As mentioned above, dosage forms of the compounds described herein include pharmaceutically acceptable carriers and adjuvants known to those of ordinary skill in the art. These carriers and adjuvants include, for example, ion exchangers, alumina, aluminium stearate, lecithin, serum proteins, buffer substances, water, salts or electrolytes and cellulose-based substances. Preferred dosage forms include, tablet, capsule, caplet, liquid, solution, suspension, emulsion, lozenges, syrup, reconstitutable powder, granule, suppository and transdermal patch. Methods for preparing such dosage forms are known (see, for example, H. C. Ansel and N. G. Popovish, Pharmaceutical Dosage Forms and Drug Delivery Systems, 5 th ed., Lea and Febiger (1990)). Dosage levels and requirements are well-recognized in the art and may be selected by those of ordinary skill in the art from available methods and techniques suitable for a particular patient. In some embodiments, dosage levels range from about 1 - 100 mg/dose for a 70 kg patient. Although one dose per day may be sufficient, up to 5 doses per day may be given. For oral doses, up to 2000 mg/day may be required. Reference in this regard may also be made to US provisional application no. 60/339,249. As the skilled artisan will appreciate, lower or higher doses may be required depending on particular factors. For instance, specific doses and treatment regimens will depend on factors such as the patient's general health profile, the severity and course of the patient's disorder or disposition thereto, and the judgment of the treating physician.

For example, the compounds of the present invention can be administered the same way as paromomycin and other paromamine compounds. They may be administered orally or parenterally.

Preferably, the compounds of the invention are administered as sulfate salts. In the case of intestinal amoebiasis the oral dosage for both adults and children may be 5 to 70, preferably 15 to 50, more preferably 25 to 35 mg compound of the invention per kg body weight daily, administered in three doses with meals for five to ten days. In the case of hepathic coma, the oral daily dosage is 4 g in divided doses given at regular intervals for 5 to 6 days.

Compounds of the invention may be formulated into capsules the same way paromomycin is formulated (e.g. Humatin ® , Parke-Davis). Each capsule may contain 100 to 500, preferably 150 to 300, more preferably 200 to 250 mg of a compound of the invention. For example, nonmedicinal ingredients in capsules for the compounds of the present invention are - capsule shell: D&C yellow No. 10, FD&C blue No. 1 , FD&C red No. 3, FD&C yellow No. 6, gelatin and titanium dioxide. Bottles of 100. (see also Martindale: the complete drug reference, 34 th Edition, 2005, Pharmaceutical Press, p 612.)

It is emphasized that compounds of the present invention may be administered in higher dosages than paromomycin or other unspecific antibiotics because the compounds of the invention are selective for microbial, in particular bacterial, ribosomes and spare eukaryotic ribosomes, thus lacking serious side effects.

In the following the subject-matter of the invention will be described in more detail referring to specific embodiments which are not intended to be construed as limiting to the scope of the invention.

Figures

Fig. 1 illustrates the crystal structure of apramycin in complex with 30S

(a) Decoding site of 30S Thermus thermophilus subunit in complex with apramycin (E. coli numbering used throughout). Ribosomal protein S12 is indicated. The unbiased mFo-DFc difference electron density map is displayed at 3.0σ. (b) The interactions between apramycin and 16S rRNA nucleotides (distances are given in Angstrom). Ring I, II and III represent 2-deoxystreptamine, bicyclic ring and ring III of apramycin. The hydrogen bonds are represented by dashed lines, with the distance length stated. Fig.2 shows the results of aminoglycoside-induced misreading as dose-response curves of aminoglycoside-induced misincorporation of amino acids using 245 near-cognate CGC mutant F-luc mRNA as template. Shown is luciferase activity upon translation of mutant template relative to wild-type F-luc mRNA (mean ±SD; n = 3).

Left part:

(a) Mitochondrial wild-type hybrid (Mit13) ribosomes;

(b) Mitochondrial A1555G mutant hybrid ribosomes. Apramycin (filled circle), gentamicin (open triangle), tobramycin (open rhombus) and kanamycin (open square).

Right part:

(c) M. smegmatis bacterial ribosomes;

(d) E. coli bacterial ribosomes. Apramycin (filled circle), aprosamine (dash, solid line), neamine (cross, broken line) was used as control.

Fig 3 illustrates the drug-induced loss of hair cells in cochlear explants and loss of auditory function in vivo

(a) Hair cells in the basal part of the mouse organ of Corti explants were stained for actin with rhodamine-phalloidin after 20 hr incubation. Panel a) control without drugs, panel b) 0.2 mM apramycin, panel c) 0.2 mM gentamicin. Panels a) and b) show essentially normal morphology with orderly arranged three rows of outer hair cells (OHC) and one row of inner hair cells (IHC). In panel c) loss of OHC is essentially complete while some IHC remain (arrowheads). Scale bar indicates 50 μιη.

(b) Dose-response relationship of drug-induced hair cell loss in cochlear explants. Hair cell loss was quantified along the entire length of the explant and plotted against drug concentration. Circles and solid line: gentamicin; squares and dotted line: apramycin. Data points represent means + sem, n = 3 to 12 per data point.

(c) Explants of the organ of Corti (panel a: control) were incubated for 16 h with 0.2 mM gentamicin (panel b) or 2 mM apramycin (panel c) and reacted with antibody to 3- nitrotyrosine. Nuclei were visualized with Hoechst 33342 myosin Vila antibody was used to outline hair cells.

(d) Effect of chronic aminoglycoside treatment in-vivo on auditory brain stem response.

"Threshold shift" is the difference in auditory threshold before and three weeks after treatment. Circles and solid line: gentamicin; squares and dotted line: apramycin. Data points represent means + sem, n = 3 to 1 1 per data point (except for 160mg gentamicin with only 1 surviving animal). Note that the threshold shift is given in dB, which corresponds to a logarithmic scale, i.e. every 10 dB indicates a 1 -log10 difference in energy. Fig.4 is a secondary-structure comparison of decoding-site rRNA sequences in the small ribosomal subunit. (a) Decoding region of 16S rRNA helix 44 in wild-type ribosomes of M. smegmatis; rRNA nucleotides are numbered according to the bacterial nomenclature, i.e., to homologous E. coli 16S rRNA positions, (b) Homologous 18S rRNA sequence in human ribosomes; rRNA residues are numbered according to the human cytoplasmic ribosome nomenclature, (c) Homologous 12S rRNA sequence in human mitochondrial ribosomes; rRNA residues are numbered according to the mitochondrial nomenclature, (d) Mitochondrial 12S rRNA sequence with mutation A1555G conferring hypersuscepti- bility to aminoglycoside antibiotics indicated, (e-f) Decoding site rRNA of human-bacterial hybrid ribosomes. The transplanted helix is boxed. The aminoglycoside binding pocket (indicated in (a)) is composed mainly of nucleotides of the A-site loop, in particular homologous E. coli positions G1405-C1496, U1406-U1495, C1407-G1494, A1408, A1492, A1493, C1409-G149110-12.

Fig. 5 illustrates the aminoglycoside-induced inhibition of protein synthesis measured as luciferase activity in cell-free translation assays of firefly luciferase mRNA. Dose- response curves of (a) bacterial ribosomes, (b) cytosolic hybrid ribosomes, (c) mitochondrial wild-type and (d) mitochondrial A1555G mutant hybrid ribosomes. Apramycin (filled circle), gentamicin (open triangle), tobramycin (black open rhombus) and kanamycin (open square). Corresponding IC 5 o values are given in Table 1.

Fig. 6 shows the chemical structures of common aminoglycoside antibiotics.

Fig. 7 Apramycin activity on bacterial ribosomes in comparison to aprosamine; neamine was used as control, (a), (b): E. coli ribosomes; (c), (d): M. smegmatis ribosomes. (a), (c): Translation inhibition as measured by firefly enzymatic activity upon translation of F- luc mRNA WT; (b), (d): Misreading induction as measured by firefly enzymatic activity upon translation of F-luc mRNA 245 CGC mutant. Apramycin (filled circle), aprosamine (dash, solid line), neamine (cross, broken line).

Fig. 8 shows cytocochleograms for the quantitative evaluation of hair cell loss. Surface preparations (as shown in Fig. 3 for murine explants) of guinea pig cochleae were quantitatively evaluated by counting the presence or absence of hair cells along the entire length of the cochlea. Following treatment of guinea pigs with 140 mg gentami- cin/kg body weight (top), outer hair cells (OHC) in the apex of the cochlea are still well preserved but loss of cells steeply increases apicalwards with a total loss in the upper 50% of the cochlea. Inner hair cells (IHC) are better maintained but show scattered loss towards the base. In contrast, following treatment with 217 mg apramycin/kg body weight (bottom), only minimal loss of cells is observed. Representative examples of treatment with gentamicin and apramycin are shown.

Fig. 9 illustrates a modelled structural drug-target interaction for 4 ' ,6 ' -0-alpha-D4- amino-4-desoxy-a-D-glucopyranosylparomomycin (Fig. 9c) and 4 ' -alpha-D4-amino-4- desoxy-a-D-glucopyranosylparomomyin (Fig. 9d) in complex with 30S. Modelling was based on crystal structures available (apramycin - see Fig. 1 ; 4',6'-0-benzylidene acetals and 4-0-benzyl ethers of paromomycin, unpublished data).

Tables

Table 1 Aminoglycoside-induced inhibition of protein synthesis (IC 50 μΜ)

A site rRNA

Mitochondrial

(mt) mt A1555G Cytosolic

Aminoglycoside Bacterial hybrid hybrid hybrid

Apramycin 0.08 ± 0.02 1 15.6 ± 27.8 47.5 ± 10.7 89.4 ± 21.2 Gentamicin 0.02 ± 0.01 1 1.1 ± 1.6 0.69 ± 0.12 40.4 ± 10.4 Tobramycin 0.03 ± 0.01 32.6 ± 2.1 1.07 ± 0.19 58.5 ± 1 1.8 Kanamycin 0.04 ± 0.02 31.1 ± 14.3 1.12 ± 0.16 91.2 ± 12.3

IC 50 values represent the drug concentrations in μΜ required to inhibit in-vitro synthesis of functional firefly luciferase to 50% (triplicates and standard deviation).

Table 2 Site-directed mutagenesis of the A site and aminoglycoside

susceptibility

MIC (Mg/ml)

Apramycin Gentamicin Tobramycin Kanamycin wild-type 1 -2 1 1 2-4

A1408G >1024 >1024 1024 >1024

G1491A 256 2 2 8

G1491 U >1024 32 64 64

G1491C >1024 16 16 32

Suppl. Table 1 Activity of apramycin in comparison to available aminoglycosides against clinical isolates of E. coli, P. aeruginosa and methicillin resistant S. aureus (MRSA)

MIC (Mg/ml)

Strain Apramycin Gentamicin Tobramycin Kanamycin

AG055 E. coli 8 16 2 4-8

AG056 E. coli 8-16 2 2 4-8

AG058 E. coli 8-16 2-4 2 8

AG003 E. coli 8-16 128-256 8 16

AG059 E. coli 8 32-64 32-64 >256

AG060 E. coli 8 128 16 >256

AG061 E. coli 16 256 16-32 256

AG062 E. coli 8-16 128-256 128-256 128-256

AG063 E. coli 8 >256 >256 >256

AG064 E. coli 8 128 64-128 64-128

AG065 E. coli 8 64-128 64 64

AG066 E. coli 8-16 128-256 128 4-8

AG067 E. coli 16 128-256 128-256 >256

AG068 E. coli 8-16 64-128 32-64 >256

AG077 P. 8 1 -2 1 128 aeruginosa

AG083 P. 16 4-8 1 -2 256 aeruginosa

AG084 P. 4 32 32 >256 aeruginosa

AG087 P. 16 4-8 2 128-256 aeruginosa

AG041 MRSA 8 0.5 0.5-1 2-4

AG040 MRSA 8 0.5 >256 128-256

AG044 MRSA 16 16 8 64

AG045 MRSA 8-16 16 8 64

AG053 MRSA 8 64 16-32 256

AG042 MRSA 8 32-64 >256 256

AG046 MRSA 8-16 >256 128-256 >256 AG047 MRSA 8-16 >256 >256 >256

AG048 MRSA 8-16 >256 >256 >512

AG050 MRSA 4-8 128 32-64 >256

AG051 MRSA 8 128 32-64 >256

AG052 MRSA 8 16-32 8-16 >256

Suppl. Table 2 Mutant A sites and drug susceptibility tested in cell free

translation assays (luciferase synthesis, IC 5 o μΜ) 3

A site Apramycin Gentamicin Tobramycin Kanamycin wild-type 0.08 ± 0.02 0.02 ± 0.01 0.03 ± 0.01 0.04 ± 0.02

A1408G 257.8 ± 72.9 121.7 ± 63.6 1 13.7 ± 47.3 103.1 ± 28.3

G1491A 9.96 ± 2.40 0.16 ± 0.02 0.25 ± 0.01 0.18 ± 0.04

G1491 C 61.6 ± 12.4 1.35 ± 0.02 3.04 ± 0.03 1.61 ± 0.21

a IC 50 values represent the drug concentrations in μΜ required to inhibit in-vitro

synthesis of functional firefly luciferase to 50% (triplicates and standard deviation).

Examples

Materials and Methods

Construction of mutant strains

The single rRNA allelic rpsL+ M. smegmatis ArrnB (SZ380) was obtained by unmarked deletion mutagenesis and used for all genetic constructions (Hobbie et al., Biochimie 88, 1033-1043 (2006). Genetic manipulations of the single chromosomal rRNA operon was done as described previously (Pfister et al., J. Mol. Biol. 346, 467-475 (2005)). In brief, PCR mutagenesis was used to generate mutant rDNAs, which were then cloned into an integration-proficient plasmid and transformed into M. smegmatis ArrnB. Selective plating and RecA-mediated homologous recombination were used for gene replacement. Successful gene replacement was controlled by sequence analysis.

Bacterial strains

Clinical isolates of Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus were obtained from the Diagnostic Department, Institute of Medical Microbiology, University Zurich.

Isolation and purification of ribosomes. Ribosomes were purified from bacterial cell pellets as described previously (Bruellet al., Biochemistry 47, 8828-8839 (2008)). In brief, ribosome particles were isolated by successive centrifugations and fractionated by sucrose gradient (10-40%) centrifugation. The 70S ribosome-enriched fraction was pelleted, resuspended in association buffer, incubated for 30 min at 4°C, dispensed into aliquots, and stored at - 80°C following shock freezing in liquid nitrogen. Ribosome concentrations of 70S were determined by absorption measurements on the basis of 23 pmol ribosomes per A260 unit.

Cell-free luciferase translation assays

Purified 70S hybrid ribosomes were used in translation reactions of luciferase mRNA. Firefly and renilla luciferase mRNAs were produced using T7 RNA polymerase (Fermentas) in-vitro on templates of modified plasmids pGL4.14 (firefly luciferase) and pGL4.75 (renilla luciferase) (both Promega). In these plasmids the mammalian promoter driving transcription of luciferases was replaced by the T7 bacteriophage promoter. A typical translation reaction with a total volume of 30 μΙ_ contained 0.25 μΜ 70S ribosomes, 4 μg firefly luciferase (F-luc) mRNA, 0.4 μg Renilla luciferase (R-luc) mRNA, 40% (vol/vol) of M. smegmatis S100 extract, 200 μΜ amino acid mixture, 24 units of RiboLock (Fermentas), 0.4 mg/ml of total E. coli tRNA, and energy was supplied by addition of 12 μΙ_ of commercial S30 Premix without amino acids (Promega). In addition to hybrid ribosomes rabbit reticulocyte lysate (Promega) was used for in-vitro translation of F-luc and R-luc mRNAs. A standard 30 μΙ reaction contained 20 μΙ reticulocyte lysate, 4 μg F-luc and 0.4 μμg R-luc mRNAs, 200 μΜ amino acid mixture, and 24 units RiboLock (Fermentas). Following addition of serially diluted aminoglycosides, the reaction mixture was incubated at 37°C for 35 min and stopped on ice. Thirty microliter samples of the reaction mixture were assayed for F-luc and R-luc luciferase activities using the Dual-Luciferase Reporter Assay System (Promega). Luminescence was measured using a luminometer (Bio-Tek Instruments; FLx800). The R-luc activity was used as an internal standard. Misreading was assessed in a gain of function assay as described (Salas- Marco, J., and D. M. Bedwell, J. Mol. Biol. 348, 801 -815 (2005)). Arg245 (CGC near- cognate and AGA non-cognate codon) was introduced into the firefly luciferase protein to replace residue His245 (CAC codon). Arg245 F-luc mRNA and wt F-luc mRNA were used in in-vitro translation reactions, in addition R-luc mRNA was used as internal control. Misreading was quantified by calculating mutant firefly/renilla luciferase activity as compared to wild-type firefly/renilla luciferase activity. Antibiotics. Gentamicin, kanamycin, tobramycin, and apramycin were obtained from Sigma. Aprosamine was synthesized using standard carbohydrate chemistry and checked by NMR.

Minimal inhibitory concentrations

Minimal inhibitory concentrations (MIC) were determined by broth microdilution assays as described recently (Pfister et al., J. Mol. Biol. 346, 467-475 (2005). Microtiter plates were incubated overnight for E. coli, P. aeruginosa and S. aureus, and 72 hrs for M. smegmatis.

Crystal structure analysis

Thermus thermophilus 30S ribosomes were purified and crystallised as described previously (Wimberly et al., Nature 407, 327-339 (2000). Crystals were soaked in the cryoprotectant solution (100 mM MES-KOH pH6.5, 200 mM KCI, 75 mM NH4CI, 15 mM MgCI2 and 26% MPD) that contains 100 μΜ of apramycin for 4 days before flash-frozen. Crystals were pre-screened and data set was collected at Swiss Light Source (SLS). Data were integrated and scaled using XDS45. A starting model consisting of the empty 30S ribosome34 (without anticodon-stem loop (ASL), mRNA and ions) was used for initial refinement and phase calculation using CNS46. The ASL and mRNA were then fitted into the unbiased difference map (mFo-DFc map) and the model was subjected to another round of refinement. Finally, five apramycin ligands were placed manually into an unbiased difference map (mFo-DFc map) using COOT47 which was refined to the resolution of 3.5 A. One apramycin molecule was bound specifically to the helix 44 at the decoding center. Another four secondary binding sites of apramycin were found at the platform and body of 16S rRNA, likely in a unspecific manner, due to high concentration of ligand soaking. The final refinement in CNS had Rwork/Rfree of 19.4%/23.5%.

Cochlear explants

Drugs were screened for toxicity to hair cells in cochlear explants from mice of post-natal day 339. The dissected tissue was placed on a collagen-coated incubation dish in 1 mL of serum-free Basal Medium Eagle plus serum-free supplement (Invitrogen, Carlsbad, CA, USA), 1 % bovine serum albumin, 2 mM glutamine, and 5 mg/mL glucose. The explants were incubated (37oC, 5% CO2) for 4 h, and an additional 1 mL of culture medium was added to submerse the explants. After 24 h the medium was exchanged for new medium containing the drugs and incubated for 20 h. Cultures were fixed overnight in 4% paraformaldehyde at 4oC, then permeabilized for 30 min with 3% Triton X-100 in PBS, washed three times with PBS and blocked with 10% goat serum for 30 min at room temperature. Following incubation at room temperature for 40 min with rhodamine- phalloidin (Molecular Probes), hair cell presence was determined by light microscopy of the phalloidin-stained stereociliary bundles and circumferential F-actin rings on the cuticular plate. Alternatively, the fixed cultures were reacted with a mouse monoclonal antibody to 3-nitrotyrosine (Enzo Life Sciences, Plymouth Meeting, PA; dilution 1 :1000) or a rabbit polycloncal antibody to myosin Vila (Proteus Biosciences, Ramona, CA;

dilution 1 :200) for 24 h at 4°C. They were coupled, respectively, with secondary antibodies (dilution 1 :200) Alexa Fluor 488 (goat anti-mouse, green) or Alexa Fluor 546 (goat anti-rabbit, red) for 2 h at room temperature (Molecular Probes, Eugene, OR). Staining for nuclei with Hoechst 33342 (1 :1000) was for 45 min at room temperature. In vivo ototoxicity

Pigmented male guinea pigs of initially about 200 g (Elm Hill Laboratories) had free access to water and food and were acclimated for one week prior to experiments. Drugs were administered once daily subcutaneously for 16 days at dosages indicated in the figure legends; saline injections served as controls. Auditory function was measured as auditory brainstem response (ABR). Each animal had its threshold determined prior to the study, and at three weeks post drug treatment. Animals were anesthetized with an intraperitoneal injection of 40 mg ketamine and 10 mg xylazine/kg body weight and ABR measurements were performed at 12 kHz as described previously (Lautermann et al., Hear. Res. 86, 15-24 (1995).

Example 1 - Ribosomal specificity of aminoglycoside antibiotics

To study drug specificity cell-free translation assays were used on a range of genetically engineered hybrid ribosomes (see Fig. 4). In these hybrid ribosomes a central 34-nucleotide part of bacterial 16S rRNA helix 44 is replaced with various human homologs resulting in rRNA decoding A sites corresponding to those in cytosolic and mitochondrial (wild-type, A1555G mutant) ribosomes. These hybrid ribosomes have been established as a valid strategy to study the ribosomal specificity of aminoglycoside antibiotics Hobbie et al., Proc. Natl. Acad. Sci. U.S.A. 105, 3244-3249 (2008), Hobbie et al., Nucleic Acids Res. 35, 6086-6093 (2007). Dose-response curves of aminoglycoside- induced inhibition of luciferase synthesis were analyzed to define the IC 50 values of individual aminoglycosides (Table 1 and Fig. 5). As comparators the injectable 4,6- disubstituted 2-deoxystreptamines were used for treatment of systemic infections in clinical medicine, i.e., gentamicin, tobramycin, and kanamycin (for chemical structures see Fig. 6). Apramycin, gentamicin, tobramycin, and kanamycin are similarly active towards bacterial ribosomes (IC 50 0.02-0.08 μΜ) and show comparable activity for eukaryotic cytosolic ribosomes (IC 50 cytosolic hybrids 40.4-91.2 μΜ). In contrast and in comparison to gentamicin, tobramycin, and kanamycin, apramycin affects mitohybrid ribosomes significantly less. While this is observed already with mitohybrid ribosomes carrying the wild-type mitochondrial A site (IC 50 apramycin 1 15.6 μΜ versus 1 1.1 -32.6 μΜ for the 4,6-disubstituted aminoglycolsides), this 4-10-fold difference becomes 50-fold with mitohybrid ribosomes carrying the A1555G mutant mitochondrial A site (IC 50 apramycin 47.5 μΜ versus 0.69-1.12 μΜ for the 4,6-disubstituted aminoglycosides).

Example 2 - Structural analysis of apramycin-ribosome Interaction

Crystals of the 30S subunit were prepared as described previously (Wimberly et al., Nature 407, 327-339 (2000)). Crystals were soaked with apramycin and analysed by X-ray diffraction. Diffraction data to 3.5 Angstrom resolution were used to solve the structure (Fig. 1 ). The hydrogen bonding pattern and position of the apramycin 2-deoxy- streptamine moiety (ring I) is similar to those of the 2-deoxystreptamine ring of 4,6- disubstituted aminoglycosides, with hydrogen bonds between apramycin N3 and N7 of G1494 and apramycin N1 and 04 of U1495. The bicyclic ring II of apramycin stacks upon the guanine base of the C1409-G1491 base pair, with the ring oxygen and the 6' hydroxyl forming hydrogen bonds to N6 and N1 of A1408, to result in a pseudo base pair interaction. Ring III is positioned in the minor groove of the 1409-1491 base pair with an orientation orthogonal to the plane of the base pair interaction. Modelling 4 ' ,6 ' -0-alpha- D4-amino-4-desoxy-a-D-glucopyranosylparomomycin (Fig. 9c) and 4 ' -alpha-D4-amino-4- desoxy-a-D-glucopyranosylparomomyin (Fig. 9d) (derivatives of paromomycin) in the h44 binding pocket on the basis of available crystal structures of apramycin (see Fig. 1 ), 4',6'-0-benzylidine acetals and 4'-0-benzyl ethers of paromomycin (data not shown) reveals that a glycosyl residue at R 2 or R 7 (see formula I and II) adopts a structural interaction with the ribosome similar to that of apramycin's ring III (Fig. 9).

Example 3 - Mutagenesis studies

The basis of any differences in specificity between apramycin and the other aminoglycosides most likely relates to structural differences. The bicyclic ring II of apramycin stacks less well onto G1491 , compared to the more flexible monocyclic ring I in 4,6-disubstituted 2-deoxystreptamines, and the 6' hydroxyl group interacting by hydrogen bonding with N1 of A1408, is axial versus an equatorial hydroxyl group in the disubstituted 2-deoxystreptamines. Altogether, this should restrain apramycins' flexibility, suggesting that its binding may be more sensitive to mutations of G1491. Compared to mutational alterations of residue 1491 , a 1408 A→G mutation would result in replacing the hydrogen bond between the ring oxygen of the bicyclic ring II and N6 of adenine by a repulsive interaction with the 06 of guanine. The effects of mutations in A1408 and G1491 were tested by experimentally studying drug susceptibility of recombinant microorganisms with the A-site modified by site-directed mutagenesis (Table 2). An A1408G conferred high-level resistance, as did any mutational alteration of residue G1491.

Example 4 - Aminoglycoside-induced misreading

Drug-induced misreading in mitohybrid ribosomes was assessed in a dual- luciferase (Grentzmann et al., RNA 4, 479-486 (1998)) gain-of-function assay. Mutation at aa 245 (wild-type CAC histidine) in the active site of firefly luciferase results in loss of enzymatic activity, with enzymatic function being restored by misreading.

Aminoglycoside-induced misreading is codon-restricted, with the near-cognate CGC codon being used as test codon and the non-cognate AGA codon as negative control (Salas-Marco, J., and D. M. Bedwell, J. Mol. Biol. 348, 801 -815 (2005), Kramer et al., RNA 16, 1797-1808 (2010). Wild-type renilla luciferase activity served as internal standard to monitor translation activity. In contrast to the comparator aminoglycosides, apramycin shows very little, if any, misreading on both wild-type mitohybrid and mutant A1555G mitohybrid ribosomes (see Fig. 2). Lack of misreading induction by apramycin is also observed in bacterial ribosomes (see Figs. 2 and 7). The data on the structure and function of apramycin ribosome interaction invite the question of how apramycin avoids misreading induction. Compared to the 30S apramycin crystal structure which was fitted in the presence of a cognate tRNA/anticodon stem loop positioned in the A-site, a bacterial A-site oligonucleotide apramycin complex suggests a hydrogen bond interaction between ring III 2" OH and the ribose moiety of A1492 (Han et al., Angew. Chem. Int. Ed. Engl. 44, 2694-2700 (2005)). This could possibly interfere with the switch of residue A1492 to adopt a fully flipped-out conformation as is associated with aminoglycoside-induced misreading (Carter et al., Nature 407, 340-348 (2000). This hypothesis, based on the available bacterial structures, predicts that in contrast to apramycin, aprosamine - which is identical to apramycin except that it lacks ring III - should readily induce misreading on bacterial ribosomes. To test the hypothesis aprosamine was synthesized following published procedures and assessed misreading induction on bacterial ribosomes. In contrast to apramycin, aprosamine readily induced misreading (see Figs. 2 and 7).

Example 5 - ln-vitro and in-vivo toxicity studies

In organ cultures of the early postnatal mouse, treatment with gentamicin caused the typical ototoxic pattern of hair cell loss, a preferential loss of outer hair cells in a base-to-apex gradient that is characteristic of aminoglycoside damage to the cochlea in both human and experimental animals. The dose-response curve shows that 50% of all hair cells and 100% of hair cells in the base of the cochlea were destroyed at 0.2 mM gentamicin, and complete elimination of outer hair cells was observed at 0.5 mM. In contrast, apramycin at a dose of 0.2 mM does not adversely affect cells even in the base, the most vulnerable region. At 2 mM, apramycin begins to affect basal hair cells but does not yet cause a significant overall hair cell loss (Fig. 3a, b). 3-Nitrotyrosine, indicative of peroxynitrite formation, was determined as a marker for oxidative stress. It was absent from control incubations (Fig. 3c, panel a) but appeared by 16 h in the basal regions of explants damaged by 0.2 mM gentamicin (fig.3c, panel b) or 2 mM apramycin (Fig. 3c, panel c). There was no immunoreactivity to nitrotyrosine with 0.2 mM apramycin or in the undamaged regions of the explants treated with 2 mM apramycin (not shown). Morphological assessment of hair cells and measurements of auditory evoked brain stem response (ABR) were used to evaluate drug actions in the guinea pig in-vivo.

Gentamicin ototoxicity rises very steeply from essentially no effect on auditory thresholds at 120 mg/kg to complete deafness at 160 mg/kg (Fig. 3d). In contrast, apramycin ototoxicity progresses more gradually and even at a concentration of 430 mg

apramycin/kg cochlear function was partly retained. Pathology in cochlear surface preparations was consistent with the functional results obtained from the ABR

measurements. Treatment with 140 mg gentamicin/kg resulted in a base-to-apex gradient of hair cell loss with a complete destruction of hair cells in the basal half of the cochlea. Following treatment with 217 mg apramycin/kg only scattered hair cell loss was observed (Fig. 8).

Example 6 - Antibacterial activity

The antimicrobial activity of apramycin was assessed by determining minimal inhibitory concentration (MIC) values various clinical isolates. Apramycin shows good activity against aminoglycoside resistant clinical isolates of E. coli, Pseudomonas aeruginosa, and Staphylococcus aureus, including methicillin resistant S. aureus (MRSA) (see Suppl. Table 1 ).

Discussion of the Examples

Apramycin is structurally unique among the aminoglycosides in that it contains a bicyclic sugar moiety and a monosubstituted 2-deoxystreptamine ring. When compared to the clinically used 4,6-disubstituted 2-deoxystreptamines gentamicin, tobramycin, and kanamycin, apramycin shows high affinity for bacterial ribosomes and comparable selectivity for eukaryotic cytosolic ribosomes. In contrast to the former drugs, however, apramycin affects the mitohybrid ribosomes significantly less. Most significantly, apramycin does not show much of a preferential activity for the A1555G mutant as compared to the wild-type mitochondrial hybrid ribosomes, as it is typical for 4,6- and 4,5-aminoglycosides (Hobbie et al., Proc. Natl. Acad. Sci. U.S.A. 105, 3244-3249 (2008), Hobbie et al., Proc. Natl. Acad. Sci. U. S. A. 105, 20888-20893 (2008). Apramycin's unique profile of drug-ribosome interaction separates it from available 4,5- and 4,6- disubstituted aminoglycosides. Together with gentamicin, tobramycin, and kanamycin, apramycin shares low-level efficacy towards A1408G mutants. In contrast to the former aminoglycosides and unique to apramycin is the sensitivity to any alteration of residue G1491. This pattern of ribosomal drug susceptibility was corroborated in cell-free translation assays (see Suppl. Table 2). As aminoglycoside selectivity rests upon single nucleotide differences in the A-site (G1408, A1491 in eukaryotic cytosolic ribosomes; C1491 in eukaryotic mitoribosomes, see Fig. 4), these findings provide an adequate explanation for the increased selectivity of apramycin, as compared to the disubstituted 2-deoxystreptamine aminoglycosides. Aminoglycosides are known to affect translational fidelity of ribosomes by inducing misreading of the genetic code (Davies, J., L. Gorini, and B. D. Davis, Mol. Pharmacol. 1 , 93-106 (1965)) and aminoglycoside-induced mitochondrial mistranslation has been suggested as a key element in aminoglycoside ototoxicity. In contrast to the 4,6-disubstituted 2-deoxystreptamines apramycin does not show significant misreading on mitochondrial wild-type and A1555G mutant hybrid ribosomes. The unique structure of the apramycin-h44 complex, with ring III positioned in the minor groove of the 1409-1491 base pair, suggests a possible hypothesis for the low misreading-inducing capacity of apramycin, as compared to the disubstituted 2- deoxystreptamines. Ring III has an orientation orthogonal to the plane of the 1409-1491 base pair which should possibly allow the formation of direct hydrogen bonds between the highly flexible A1492 and ring III. Indeed, such a hydrogen bond interaction between ring III 2" OH and the ribose moiety of A1492 is suggested by the bacterial

oligonucleotide structure (see Han et al. Angew. Chem. Int. Ed. Engl. 45, 3310-3314 (2006)). In contrast to the disubstituted 2-deoxystreptamines which displace

A1491/A1493 directly into a position where they make contact with the minor groove of the codon-anticodon helix, and thereby induce accommodation of near-cognate tRNA (i.e. misreading), apramycin could be able to partially stabilize a flipped out A1492 in an intermediate position. As a result, apramycin inhibits translocation but does not induce misreading. This hypothesis was tested experimenttally, and demonstrated that, in contrast to apramycin and as predicted by the hypothesis, aprosamine (= apramycin without ring III) readily induced misreading on bacterial ribosomes.

Animal models, such as the guinea pig, accurately reflect human ototoxicity and have extensively been used to elucidate mechanisms and prevention of drug damage. Furthermore, short-term cultures of murine organ of Corti explants have proven useful in efficient screening for ototoxic potential in-vitro (Zhen, J. L, and L. Gao, Eur. J.

Neurosci. 8, 1897-1905 (1996), Chen, F.-Q., J. Schacht, and S.-H. , J. Neurochem. 108, 1226-1236 (2009). Both approaches were used in the current study to compare the toxicity of apramycin to that of gentamicin, a well characterized and commonly used aminoglycoside. In the organotypic cultures, the appearance of nitrotyrosine becomes evident at antibiotic levels that begin to cause hair cell loss regardless of their absolute concentration. This correlation with ototoxicity supports the notion that generation of ROS is an integral part of the mechanisms that lead to cell death. The lesser toxicity of apramycin observed in short-term cultures of Corti explants is clearly borne out in the pathology and pathophysiology caused in-vivo. Consistent with the functional results obtained from ABR measurements in-vivo treatment with apramycin resulted in little hair cell loss as revealed in a dose-by-dose comparison to gentamicin. Guinea pigs treated with gentamicin also showed signs of general toxicity. At a dose of 140 mg/kg gentamicin 8/8 animals had significant lower weight gain as compared to the saline-treated controls, and at a dose of 160 mg/kg 2/3 animals died during the experiments. In contrast, all animals treated with apramycin remained healthy during the complete course of the experiment and even at a dose of 430 mg/kg no drug-related death was observed. Renal necropsy and analysis of blood urea nitrogen and creatinine likewise did not reveal any nephrotoxic side effects of apramycin. It should also be noted that the concentrations of drugs used in animal models exceed those in clinical medicine by an order of magnitude so as to obtain relatively high and reliable ABR threshold shifts. Gentamicin has a clinical incidence of ototoxicity of 10 to >20% in treatment of acute infections, the much lesser toxicity of apramycin should provide a significant safety margin and considerably fewer side effects.

Taken together, the structural, biochemical, and toxicology studies leading to the present invention have revealed properties of apramycin, i.e. the dissociation of antibacterial and antimitoribosomal activity, that can be exploited and transferred for providing new and better aminoglycoside antibiotics for the treatment of human infectious diseases.