1
|
Alberto-Silva AS, Hemmer S, Bock HA, Alves da Silva L, Scott KR, Kastner N, Bhatt M, Niello M, Jäntsch K, Kudlacek O, Bossi E, Stockner T, Meyer MR, McCorvy JD, Brandt SD, Kavanagh P, Sitte HH. Bioisosteric analogs of MDMA with improved pharmacological profile. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.08.588083. [PMID: 38645142 PMCID: PMC11030374 DOI: 10.1101/2024.04.08.588083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
3,4-Methylenedioxymethamphetamine (MDMA, ' ecstasy' ) is re-emerging in clinical settings as a candidate for the treatment of specific psychiatric disorders (e.g. post-traumatic stress disorder) in combination with psychotherapy. MDMA is a psychoactive drug, typically regarded as an empathogen or entactogen, which leads to transporter-mediated monoamine release. Despite its therapeutic potential, MDMA can induce dose-, individual-, and context-dependent untoward effects outside safe settings. In this study, we investigated whether three new methylenedioxy bioisosteres of MDMA improve its off-target profile. In vitro methods included radiotracer assays, transporter electrophysiology, bioluminescence resonance energy transfer and fluorescence-based assays, pooled human liver microsome/S9 fraction incubation with isozyme mapping, and liquid chromatography coupled to high-resolution mass spectrometry. In silico methods included molecular docking. Compared with MDMA, all three MDMA bioisosteres (ODMA, TDMA, and SeDMA) showed similar pharmacological activity at human serotonin and dopamine transporters (hSERT and hDAT, respectively) but decreased activity at 5-HT 2A/2B/2C receptors. Regarding their hepatic metabolism, they differed from MDMA, with N -demethylation being the only metabolic route shared, and without forming phase II metabolites. Additional screening for their interaction with human organic cation transporters (hOCTs) and plasma membrane transporter (hPMAT) revealed a weaker interaction of the MDMA analogs with hOCT1, hOCT2, and hPMAT. Our findings suggest that these new MDMA analogs might constitute appealing therapeutic alternatives to MDMA, sparing the primary pharmacological activity at hSERT and hDAT, but displaying a reduced activity at 5-HT 2A/2B/2C receptors and reduced hepatic metabolism. Whether these MDMA bioisosteres may pose lower risk alternatives to the clinically re-emerging MDMA warrants further studies.
Collapse
|
2
|
A Greener Technique for Microwave-Assisted O-Silylation and Silyl Ether Deprotection of Uridine and Other Substrates. CHEMISTRY 2022. [DOI: 10.3390/chemistry4040112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A single clean, good-yielding, environment-friendly microwave-assisted procedure for O-silylation of uridine with tert-butyldimethylsilyl chloride (TBDMSCl), 1,8-Diazabicyclo(5.4.0)undec-7-ene (DBU) and potassium nitrate as catalyst under solvent-free conditions is reported. Subsequent silyl ether deprotection is accomplished with a reusable acidic resin via microwave irradiation. Both the silylation and desilylation protocols have been applied to a panel of alcohols of pharmaceutical interest.
Collapse
|
3
|
Synthesis and Biological Evaluation of 1,3-Dideazapurine-Like 7-Amino-5-Hydroxymethyl-Benzimidazole Ribonucleoside Analogues as Aminoacyl-tRNA Synthetase Inhibitors. Molecules 2020; 25:molecules25204751. [PMID: 33081246 PMCID: PMC7587597 DOI: 10.3390/molecules25204751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 12/03/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) have become viable targets for the development of antimicrobial agents due to their crucial role in protein translation. A series of six amino acids were coupled to the purine-like 7-amino-5-hydroxymethylbenzimidazole nucleoside analogue following an optimized synthetic pathway. These compounds were designed as aaRS inhibitors and can be considered as 1,3-dideazaadenine analogues carrying a 2-hydroxymethyl substituent. Despite our intentions to obtain N1-glycosylated 4-aminobenzimidazole congeners, resembling the natural purine nucleosides glycosylated at the N9-position, we obtained the N3-glycosylated benzimidazole derivatives as the major products, resembling the respective purine N7-glycosylated nucleosides. A series of X-ray crystal structures of class I and II aaRSs in complex with newly synthesized compounds revealed interesting interactions of these “base-flipped” analogues with their targets. While the exocyclic amine of the flipped base mimics the reciprocal interaction of the N3-purine atom of aminoacyl-sulfamoyl adenosine (aaSA) congeners, the hydroxymethyl substituent of the flipped base apparently loses part of the standard interactions of the adenine N1 and the N6-amine as seen with aaSA analogues. Upon the evaluation of the inhibitory potency of the newly obtained analogues, nanomolar inhibitory activities were noted for the leucine and isoleucine analogues targeting class I aaRS enzymes, while rather weak inhibitory activity against the corresponding class II aaRSs was observed. This class bias could be further explained by detailed structural analysis.
Collapse
|
4
|
Salah SB, Necibi F, Goumont R, Boubaker T. Electrophilicities of 4‐Nitrobenzochalcogenadiazoles. ChemistrySelect 2020. [DOI: 10.1002/slct.202001928] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Saida Ben Salah
- Laboratoire C.H.P.N.R Faculté des Sciences de Monastir Université de Monastir Avenue de l'Environnement 5019 Monastir Tunisia
| | - Feriel Necibi
- Laboratoire C.H.P.N.R Faculté des Sciences de Monastir Université de Monastir Avenue de l'Environnement 5019 Monastir Tunisia
| | - Régis Goumont
- Institut Lavoisier de Versailles UMR 8180 Université de Versailles 45, Avenue des Etats-Unis 78035 Versailles Cedex France
| | - Taoufik Boubaker
- Laboratoire C.H.P.N.R Faculté des Sciences de Monastir Université de Monastir Avenue de l'Environnement 5019 Monastir Tunisia
| |
Collapse
|
5
|
Salah SB, Zaier R, Ayachi S, Goumont R, Boubaker T. The N-alkylation of 4-nitrobenzochalcogenadiazoles: Synthesis and theoretical approach. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.06.091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
6
|
Synthesis and Biological Evaluation of Lipophilic Nucleoside Analogues as Inhibitors of Aminoacyl-tRNA Synthetases. Antibiotics (Basel) 2019; 8:antibiotics8040180. [PMID: 31600972 PMCID: PMC6963541 DOI: 10.3390/antibiotics8040180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/02/2019] [Accepted: 10/04/2019] [Indexed: 11/16/2022] Open
Abstract
Emerging antibiotic resistance in pathogenic bacteria and reduction of compounds in the existing antibiotics discovery pipeline is the most critical concern for healthcare professionals. A potential solution aims to explore new or existing targets/compounds. Inhibition of bacterial aminoacyl-tRNA synthetase (aaRSs) could be one such target for the development of antibiotics. The aaRSs are a group of enzymes that catalyze the transfer of an amino acid to their cognate tRNA and therefore play a pivotal role in translation. Thus, selective inhibition of these enzymes could be detrimental to microbes. The 5′-O-(N-(L-aminoacyl)) sulfamoyladenosines (aaSAs) are potent inhibitors of the respective aaRSs, however due to their polarity and charged nature they cannot cross the bacterial membranes. In this work, we increased the lipophilicity of these existing aaSAs in an effort to promote their penetration through the bacterial membrane. Two strategies were followed, either attaching a (permanent) alkyl moiety at the adenine ring via alkylation of the N6-position or introducing a lipophilic biodegradable prodrug moiety at the alpha-terminal amine, totaling eight new aaSA analogues. All synthesized compounds were evaluated in vitro using either a purified Escherichiacoli aaRS enzyme or in presence of total cellular extract obtained from E. coli. The prodrugs showed comparable inhibitory activity to the parent aaSA analogues, indicating metabolic activation in cellular extracts, but had little effect on bacteria. During evaluation of the N6-alkylated compounds against different microbes, the N6-octyl containing congener 6b showed minimum inhibitory concentration (MIC) of 12.5 µM against Sarcina lutea while the dodecyl analogue 6c displayed MIC of 6.25 µM against Candidaalbicans.
Collapse
|
7
|
|
8
|
Nautiyal M, De Graef S, Pang L, Gadakh B, Strelkov SV, Weeks SD, Van Aerschot A. Comparative analysis of pyrimidine substituted aminoacyl-sulfamoyl nucleosides as potential inhibitors targeting class I aminoacyl-tRNA synthetases. Eur J Med Chem 2019; 173:154-166. [PMID: 30995568 DOI: 10.1016/j.ejmech.2019.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/01/2019] [Accepted: 04/01/2019] [Indexed: 12/27/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) catalyse the ATP-dependent coupling of an amino acid to its cognate tRNA. Being vital for protein translation aaRSs are considered a promising target for the development of novel antimicrobial agents. 5'-O-(N-aminoacyl)-sulfamoyl adenosine (aaSA) is a non-hydrolysable analogue of the aaRS reaction intermediate that has been shown to be a potent inhibitor of this enzyme family but is prone to chemical instability and enzymatic modification. In an attempt to improve the molecular properties of this scaffold we synthesized a series of base substituted aaSA analogues comprising cytosine, uracil and N3-methyluracil targeting leucyl-, tyrosyl- and isoleucyl-tRNA synthetases. In in vitro assays seven out of the nine inhibitors demonstrated Kiapp values in the low nanomolar range. To complement the biochemical studies, X-ray crystallographic structures of Neisseria gonorrhoeae leucyl-tRNA synthetase and Escherichia coli tyrosyl-tRNA synthetase in complex with the newly synthesized compounds were determined. These highlighted a subtle interplay between the base moiety and the target enzyme in defining relative inhibitory activity. Encouraged by this data we investigated if the pyrimidine congeners could escape a natural resistance mechanism, involving acetylation of the amine of the aminoacyl group by the bacterial N-acetyltransferases RimL and YhhY. With RimL the pyrimidine congeners were less susceptible to inactivation compared to the equivalent aaSA, whereas with YhhY the converse was true. Combined the various insights resulting from this study will pave the way for the further rational design of aaRS inhibitors.
Collapse
Affiliation(s)
- Manesh Nautiyal
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 Box 1041, B-3000, Leuven, Belgium
| | - Steff De Graef
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 Box 822, B-3000, Leuven, Belgium
| | - Luping Pang
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 Box 1041, B-3000, Leuven, Belgium; Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 Box 822, B-3000, Leuven, Belgium
| | - Bharat Gadakh
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 Box 1041, B-3000, Leuven, Belgium
| | - Sergei V Strelkov
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 Box 822, B-3000, Leuven, Belgium
| | - Stephen D Weeks
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 Box 822, B-3000, Leuven, Belgium
| | - Arthur Van Aerschot
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 Box 1041, B-3000, Leuven, Belgium.
| |
Collapse
|
9
|
New organotin(IV) chlorides derived from N-(2-hydroxyphenyl)aryloxy sulfamates. Synthesis, characterization and DSC investigation. J CHEM SCI 2019. [DOI: 10.1007/s12039-018-1586-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
10
|
Francklyn CS, Mullen P. Progress and challenges in aminoacyl-tRNA synthetase-based therapeutics. J Biol Chem 2019; 294:5365-5385. [PMID: 30670594 DOI: 10.1074/jbc.rev118.002956] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) are universal enzymes that catalyze the attachment of amino acids to the 3' ends of their cognate tRNAs. The resulting aminoacylated tRNAs are escorted to the ribosome where they enter protein synthesis. By specifically matching amino acids to defined anticodon sequences in tRNAs, ARSs are essential to the physical interpretation of the genetic code. In addition to their canonical role in protein synthesis, ARSs are also involved in RNA splicing, transcriptional regulation, translation, and other aspects of cellular homeostasis. Likewise, aminoacylated tRNAs serve as amino acid donors for biosynthetic processes distinct from protein synthesis, including lipid modification and antibiotic biosynthesis. Thanks to the wealth of details on ARS structures and functions and the growing appreciation of their additional roles regulating cellular homeostasis, opportunities for the development of clinically useful ARS inhibitors are emerging to manage microbial and parasite infections. Exploitation of these opportunities has been stimulated by the discovery of new inhibitor frameworks, the use of semi-synthetic approaches combining chemistry and genome engineering, and more powerful techniques for identifying leads from the screening of large chemical libraries. Here, we review the inhibition of ARSs by small molecules, including the various families of natural products, as well as inhibitors developed by either rational design or high-throughput screening as antibiotics and anti-parasitic therapeutics.
Collapse
Affiliation(s)
- Christopher S Francklyn
- From the Department of Biochemistry, College of Medicine, University of Vermont, Burlington, Vermont 05405
| | - Patrick Mullen
- From the Department of Biochemistry, College of Medicine, University of Vermont, Burlington, Vermont 05405
| |
Collapse
|
11
|
Atdjian C, Iannazzo L, Braud E, Ethève-Quelquejeu M. Synthesis of SAM-Adenosine Conjugates for the Study of m 6
A-RNA Methyltransferases. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800798] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Colette Atdjian
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques; Team “Chemistry of RNAs, nucleosides, peptides and heterocycles”; Université Paris Descartes; UMR 8601; 75005 Paris France
| | - Laura Iannazzo
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques; Team “Chemistry of RNAs, nucleosides, peptides and heterocycles”; Université Paris Descartes; UMR 8601; 75005 Paris France
| | - Emmanuelle Braud
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques; Team “Chemistry of RNAs, nucleosides, peptides and heterocycles”; Université Paris Descartes; UMR 8601; 75005 Paris France
| | - Mélanie Ethève-Quelquejeu
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques; Team “Chemistry of RNAs, nucleosides, peptides and heterocycles”; Université Paris Descartes; UMR 8601; 75005 Paris France
| |
Collapse
|
12
|
Zhang B, De Graef S, Nautiyal M, Pang L, Gadakh B, Froeyen M, Van Mellaert L, Strelkov SV, Weeks SD, Van Aerschot A. Family-wide analysis of aminoacyl-sulfamoyl-3-deazaadenosine analogues as inhibitors of aminoacyl-tRNA synthetases. Eur J Med Chem 2018; 148:384-396. [PMID: 29477072 DOI: 10.1016/j.ejmech.2018.02.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/05/2018] [Accepted: 02/06/2018] [Indexed: 11/16/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are enzymes that precisely attach an amino acid to its cognate tRNA. This process, which is essential for protein translation, is considered a viable target for the development of novel antimicrobial agents, provided species selective inhibitors can be identified. Aminoacyl-sulfamoyl adenosines (aaSAs) are potent orthologue specific aaRS inhibitors that demonstrate nanomolar affinities in vitro but have limited uptake. Following up on our previous work on substitution of the base moiety, we evaluated the effect of the N3-position of the adenine by synthesizing the corresponding 3-deazaadenosine analogues (aaS3DAs). A typical organism has 20 different aaRS, which can be split into two distinct structural classes. We therefore coupled six different amino acids, equally targeting the two enzyme classes, via the sulfamate bridge to 3-deazaadenosine. Upon evaluation of the inhibitory potency of the obtained analogues, a clear class bias was noticed, with loss of activity for the aaS3DA analogues targeting class II enzymes when compared to the equivalent aaSA. Evaluation of the available crystallographic structures point to the presence of a conserved water molecule which could have importance for base recognition within class II enzymes, a property that can be explored in future drug design efforts.
Collapse
Affiliation(s)
- Baole Zhang
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 Box 1041, B-3000 Leuven, Belgium
| | - Steff De Graef
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 Box 822, B-3000 Leuven, Belgium
| | - Manesh Nautiyal
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 Box 1041, B-3000 Leuven, Belgium
| | - Luping Pang
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 Box 1041, B-3000 Leuven, Belgium; Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 Box 822, B-3000 Leuven, Belgium
| | - Bharat Gadakh
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 Box 1041, B-3000 Leuven, Belgium
| | - Matheus Froeyen
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 Box 1041, B-3000 Leuven, Belgium
| | - Lieve Van Mellaert
- Laboratory Molecular Bacteriology, Rega Institute for Medical Research, KU Leuven, Herestraat 49 Box 1037, B-3000 Leuven, Belgium
| | - Sergei V Strelkov
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 Box 822, B-3000 Leuven, Belgium
| | - Stephen D Weeks
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 Box 822, B-3000 Leuven, Belgium
| | - Arthur Van Aerschot
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 Box 1041, B-3000 Leuven, Belgium.
| |
Collapse
|
13
|
Fujii H, Shimada N, Ohtawa M, Karaki F, Koshizuka M, Hayashida K, Kamimura M, Makino K, Nagamitsu T, Nagase H. Deprotection of silyl ethers by using SO3H silica gel: Application to sugar, nucleoside, and alkaloid derivatives. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.07.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
14
|
Serebryakova M, Tsibulskaya D, Mokina O, Kulikovsky A, Nautiyal M, Van Aerschot A, Severinov K, Dubiley S. A Trojan-Horse Peptide-Carboxymethyl-Cytidine Antibiotic from Bacillus amyloliquefaciens. J Am Chem Soc 2016; 138:15690-15698. [PMID: 27934031 PMCID: PMC5152938 DOI: 10.1021/jacs.6b09853] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Microcin
C and related antibiotics are Trojan-horse peptide-adenylates.
The peptide part is responsible for facilitated transport inside the
sensitive cell, where it gets processed to release a toxic warhead—a
nonhydrolyzable aspartyl-adenylate, which inhibits aspartyl-tRNA synthetase.
Adenylation of peptide precursors is carried out by MccB THIF-type
NAD/FAD adenylyltransferases. Here, we describe a novel microcin C-like
compound from Bacillus amyloliquefaciens. The B. amyloliquefaciens MccB demonstrates an unprecedented
ability to attach a terminal cytidine monophosphate to cognate precursor
peptide in cellular and cell free systems. The cytosine moiety undergoes
an additional modification—carboxymethylation—that is
carried out by the C-terminal domain of MccB and the MccS enzyme that
produces carboxy-SAM, which serves as a donor of the carboxymethyl
group. We show that microcin C-like compounds carrying terminal cytosines
are biologically active and target aspartyl-tRNA synthetase, and that
the carboxymethyl group prevents resistance that can occur due to
modification of the warhead. The results expand the repertoire of
known enzymatic modifications of peptides that can be used to obtain
new biological activities while avoiding or limiting bacterial resistance.
Collapse
Affiliation(s)
- Marina Serebryakova
- Institute of Gene Biology, Russian Academy of Science , 34/5 Vavilov str., 119334 Moscow, Russia.,A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Leninskie Gory 1, Bldg. 40, Moscow 119991, Russia
| | - Darya Tsibulskaya
- Institute of Gene Biology, Russian Academy of Science , 34/5 Vavilov str., 119334 Moscow, Russia
| | - Olga Mokina
- Institute of Gene Biology, Russian Academy of Science , 34/5 Vavilov str., 119334 Moscow, Russia.,Skolkovo Institute of Science and Technology , 3 Nobel str., 143026 Moscow, Russia
| | - Alexey Kulikovsky
- Institute of Gene Biology, Russian Academy of Science , 34/5 Vavilov str., 119334 Moscow, Russia.,Skolkovo Institute of Science and Technology , 3 Nobel str., 143026 Moscow, Russia
| | - Manesh Nautiyal
- KU Leuven , O&N Rega, Medicinal Chemistry, Herestraat 49 10, B-3000 Leuven, Belgium
| | - Arthur Van Aerschot
- KU Leuven , O&N Rega, Medicinal Chemistry, Herestraat 49 10, B-3000 Leuven, Belgium
| | - Konstantin Severinov
- Institute of Gene Biology, Russian Academy of Science , 34/5 Vavilov str., 119334 Moscow, Russia.,Skolkovo Institute of Science and Technology , 3 Nobel str., 143026 Moscow, Russia.,Waksman Institute for Microbiology , 190 Frelinghuysen Road, Piscataway, New Jersey 08854-8020, United States
| | - Svetlana Dubiley
- Institute of Gene Biology, Russian Academy of Science , 34/5 Vavilov str., 119334 Moscow, Russia.,Skolkovo Institute of Science and Technology , 3 Nobel str., 143026 Moscow, Russia
| |
Collapse
|
15
|
Serpi M, Ferrari V, Pertusati F. Nucleoside Derived Antibiotics to Fight Microbial Drug Resistance: New Utilities for an Established Class of Drugs? J Med Chem 2016; 59:10343-10382. [PMID: 27607900 DOI: 10.1021/acs.jmedchem.6b00325] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Novel antibiotics are urgently needed to combat the rise of infections due to drug-resistant microorganisms. Numerous natural nucleosides and their synthetically modified analogues have been reported to have moderate to good antibiotic activity against different bacterial and fungal strains. Nucleoside-based compounds target several crucial processes of bacterial and fungal cells such as nucleoside metabolism and cell wall, nucleic acid, and protein biosynthesis. Nucleoside analogues have also been shown to target many other bacterial and fungal cellular processes although these are not well characterized and may therefore represent opportunities to discover new drugs with unique mechanisms of action. In this Perspective, we demonstrate that nucleoside analogues, cornerstones of anticancer and antiviral treatments, also have great potential to be repurposed as antibiotics so that an old drug can learn new tricks.
Collapse
Affiliation(s)
- Michaela Serpi
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University , Redwood Building, King Edward VII Avenue, CF10 3NB Cardiff, United Kingdom
| | - Valentina Ferrari
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University , Redwood Building, King Edward VII Avenue, CF10 3NB Cardiff, United Kingdom
| | - Fabrizio Pertusati
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University , Redwood Building, King Edward VII Avenue, CF10 3NB Cardiff, United Kingdom
| |
Collapse
|
16
|
Ebejer JP, Charlton MH, Finn PW. Are the physicochemical properties of antibacterial compounds really different from other drugs? J Cheminform 2016; 8:30. [PMID: 27274770 PMCID: PMC4891840 DOI: 10.1186/s13321-016-0143-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 05/25/2016] [Indexed: 01/12/2023] Open
Abstract
Background It is now widely recognized that there is an urgent need for new antibacterial drugs, with novel mechanisms of action, to combat the rise of multi-drug resistant bacteria. However, few new compounds are reaching the market. Antibacterial drug discovery projects often succeed in identifying potent molecules in biochemical assays but have been beset by difficulties in obtaining antibacterial activity. A commonly held view, based on analysis of marketed antibacterial compounds, is that antibacterial drugs possess very different physicochemical properties to other drugs, and that this profile is required for antibacterial activity. Results We have re-examined this issue by performing a cheminformatics analysis of the literature data available in the ChEMBL database. The physicochemical properties of compounds with a recorded activity in an antibacterial assay were calculated and compared to two other datasets extracted from ChEMBL, marketed antibacterials and drugs marketed for other therapeutic indications. The chemical class of the compounds and Gram-negative/Gram-positive profile were also investigated. This analysis shows that compounds with antibacterial activity have physicochemical property profiles very similar to other drug classes. Conclusions The observation that many current antibacterial drugs lie in regions of physicochemical property space far from conventional small molecule therapeutics is correct. However, the inference that a compound must lie in one of these “outlier” regions in order to possess antibacterial activity is not supported by our analysis. Electronic supplementary material The online version of this article (doi:10.1186/s13321-016-0143-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jean-Paul Ebejer
- InhibOx Limited, Oxford Centre for Innovation, New Road, Oxford, OX1 1BY UK ; Centre for Molecular Medicine and Biobanking, University of Malta, Msida, MSD 2080 Malta
| | - Michael H Charlton
- InhibOx Limited, Oxford Centre for Innovation, New Road, Oxford, OX1 1BY UK
| | - Paul W Finn
- InhibOx Limited, Oxford Centre for Innovation, New Road, Oxford, OX1 1BY UK ; University of Buckingham, Hunter Street, Buckingham, MK18 1EG UK
| |
Collapse
|