1
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Kaur J, Sharma A, Mundlia P, Sood V, Pandey A, Singh G, Barnwal RP. RNA-Small-Molecule Interaction: Challenging the "Undruggable" Tag. J Med Chem 2024. [PMID: 38498010 DOI: 10.1021/acs.jmedchem.3c01354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
RNA targeting, specifically with small molecules, is a relatively new and rapidly emerging avenue with the promise to expand the target space in the drug discovery field. From being "disregarded" as an "undruggable" messenger molecule to FDA approval of an RNA-targeting small-molecule drug Risdiplam, a radical change in perspective toward RNA has been observed in the past decade. RNAs serve important regulatory functions beyond canonical protein synthesis, and their dysregulation has been reported in many diseases. A deeper understanding of RNA biology reveals that RNA molecules can adopt a variety of structures, carrying defined binding pockets that can accommodate small-molecule drugs. Due to its functional diversity and structural complexity, RNA can be perceived as a prospective target for therapeutic intervention. This perspective highlights the proof of concept of RNA-small-molecule interactions, exemplified by targeting of various transcripts with functional modulators. The advent of RNA-oriented knowledge would help expedite drug discovery.
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Affiliation(s)
- Jaskirat Kaur
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Akanksha Sharma
- Department of Biophysics, Panjab University, Chandigarh 160014, India
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014, India
| | - Poonam Mundlia
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Vikas Sood
- Department of Biochemistry, Jamia Hamdard, New Delhi 110062, India
| | - Ankur Pandey
- Department of Chemistry, Panjab University, Chandigarh 160014, India
| | - Gurpal Singh
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014, India
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2
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Zhang J, Lair C, Roubert C, Amaning K, Barrio MB, Benedetti Y, Cui Z, Xing Z, Li X, Franzblau SG, Baurin N, Bordon-Pallier F, Cantalloube C, Sans S, Silve S, Blanc I, Fraisse L, Rak A, Jenner LB, Yusupova G, Yusupov M, Zhang J, Kaneko T, Yang TJ, Fotouhi N, Nuermberger E, Tyagi S, Betoudji F, Upton A, Sacchettini JC, Lagrange S. Discovery of natural-product-derived sequanamycins as potent oral anti-tuberculosis agents. Cell 2023; 186:1013-1025.e24. [PMID: 36827973 PMCID: PMC9994261 DOI: 10.1016/j.cell.2023.01.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 08/03/2022] [Accepted: 01/27/2023] [Indexed: 02/25/2023]
Abstract
The emergence of drug-resistant tuberculosis has created an urgent need for new anti-tubercular agents. Here, we report the discovery of a series of macrolides called sequanamycins with outstanding in vitro and in vivo activity against Mycobacterium tuberculosis (Mtb). Sequanamycins are bacterial ribosome inhibitors that interact with the ribosome in a similar manner to classic macrolides like erythromycin and clarithromycin, but with binding characteristics that allow them to overcome the inherent macrolide resistance of Mtb. Structures of the ribosome with bound inhibitors were used to optimize sequanamycin to produce the advanced lead compound SEQ-9. SEQ-9 was efficacious in mouse models of acute and chronic TB as a single agent, and it demonstrated bactericidal activity in a murine TB infection model in combination with other TB drugs. These results support further investigation of this series as TB clinical candidates, with the potential for use in new regimens against drug-susceptible and drug-resistant TB.
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Affiliation(s)
- Jidong Zhang
- Sanofi R&D, Integrated Drug Discovery, CRVA, 94403 Vitry-sur-Seine, France
| | - Christine Lair
- Evotec ID (LYON) SAS, Lyon, France; Sanofi R&D, Infectious Diseases TSU, 31036 Toulouse, France
| | - Christine Roubert
- Evotec ID (LYON) SAS, Lyon, France; Sanofi R&D, Infectious Diseases TSU, 31036 Toulouse, France
| | - Kwame Amaning
- Sanofi R&D, Integrated Drug Discovery, CRVA, 94403 Vitry-sur-Seine, France
| | | | - Yannick Benedetti
- Sanofi R&D, Integrated Drug Discovery, CRVA, 94403 Vitry-sur-Seine, France
| | - Zhicheng Cui
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Zhongliang Xing
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Xiaojun Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Scott G Franzblau
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Nicolas Baurin
- Sanofi R&D, Integrated Drug Discovery, CRVA, 94403 Vitry-sur-Seine, France
| | | | | | - Stephanie Sans
- Evotec ID (LYON) SAS, Lyon, France; Sanofi R&D, Infectious Diseases TSU, 31036 Toulouse, France
| | - Sandra Silve
- Evotec ID (LYON) SAS, Lyon, France; Sanofi R&D, Infectious Diseases TSU, 31036 Toulouse, France
| | - Isabelle Blanc
- Evotec ID (LYON) SAS, Lyon, France; Sanofi R&D, Infectious Diseases TSU, 31036 Toulouse, France
| | - Laurent Fraisse
- Evotec ID (LYON) SAS, Lyon, France; Sanofi R&D, Infectious Diseases TSU, 31036 Toulouse, France
| | - Alexey Rak
- Sanofi R&D, Integrated Drug Discovery, CRVA, 94403 Vitry-sur-Seine, France
| | | | | | | | - Junjie Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Takushi Kaneko
- Global Alliance for TB Drug Development, New York, NY, USA
| | - T J Yang
- Global Alliance for TB Drug Development, New York, NY, USA
| | - Nader Fotouhi
- Global Alliance for TB Drug Development, New York, NY, USA
| | - Eric Nuermberger
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sandeep Tyagi
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fabrice Betoudji
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anna Upton
- Evotec ID (LYON) SAS, Lyon, France; Global Alliance for TB Drug Development, New York, NY, USA
| | - James C Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA.
| | - Sophie Lagrange
- Evotec ID (LYON) SAS, Lyon, France; Sanofi R&D, Infectious Diseases TSU, 31036 Toulouse, France
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3
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WCK 4873 (INN: Nafithromycin): Structure-Activity relationship (SAR) identifying a novel lactone ketolide with activity against Streptococcus pneumoniae (SPN) and Streptococcus pyogenes (SPY). RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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4
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Liu XP, Lv W, Zhao F, Ding J, Zhang JR, Xue F, Zhang JZ, Liu LY, Cushman M, Li Y, Liang JH. Design and synthesis of novel macrolones bridged with linkers from 11,12-positions of macrolides. Bioorg Med Chem Lett 2022; 68:128761. [PMID: 35483593 DOI: 10.1016/j.bmcl.2022.128761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 04/11/2022] [Accepted: 04/21/2022] [Indexed: 11/02/2022]
Abstract
Resistance to telithromycin and off-target effects associated with the metabolic instability present serious and challenging problems for the development of novel macrolides. Herein, studies of hybrids of macrolides and quinolones (termed macrolones) bridged with linkers from 11,12-cyclic carbamate of macrolides revealed different structure-activity relationships from the previously reported macrolones bridged with linkers derived from 6-, 9- and 4''-positions of macrolides. The optimized macrolone 34 g with a longer and rigid sidechain than telithromycin had improved metabolic stability compared to telithromycin (t1/2: 110 vs 32 min), whose future has been heavily clouded by metabolic issues. Moreover, 34 g was 38-fold more potent than telithromycin against A2058/2059-mutated Mycoplasma pneumoniae (8 vs 315 μM), which may be attributed to a novel mode of action between the carboxylic acid of quinolone moiety and the bacterial ribosome. This work increases the prospect for discovery of novel and safe antibacterial agents to combat serious human infectious diseases.
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Affiliation(s)
- Xie-Peng Liu
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China
| | - Wei Lv
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47907, United States
| | - Fei Zhao
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China
| | - Jing Ding
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China
| | - Jue-Ru Zhang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China
| | - Feng Xue
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing 100034, China
| | - Jian-Zhong Zhang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China
| | - Li-Yong Liu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China
| | - Mark Cushman
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47907, United States
| | - Yun Li
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing 100034, China.
| | - Jian-Hua Liang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China; Yangtze Delta Region Academy of Beijing Institute of Technology, Jiaxing 314019, China.
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5
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Synthesis and biological evaluation of antibacterial activity of novel clarithromycin derivatives incorporating 1,2,3-triazole moieties at the 4''- and 11-OH positions. Bioorg Chem 2022; 127:106020. [PMID: 35841669 DOI: 10.1016/j.bioorg.2022.106020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/20/2022] [Accepted: 07/07/2022] [Indexed: 11/22/2022]
Abstract
Bacterial infection is still one of the diseases that threaten human health, and bacterial drug resistance is widespread worldwide. As a result, their eradication now largely relies on antibacterial drug discovery. Here, we reveal a novel approach to the development of 14-membered macrolide antibiotics by describing the design, synthesis, and evaluation of novel clarithromycin derivatives incorporating 1,2,3-triazole moieties at the 4''- and 11-OH positions. Using chemical synthesis, 35 clarithromycin derivatives were prepared, and their antibacterial properties were profiled. We found that compounds 8e-8h, 8l-8o, 8v, and 19d were as potent as azithromycin against Enterococcus faecalis ATCC29212. Furthermore, compounds 8c, 8d, 8n, and 8o showed slightly improved antibacterial activity (2-fold) against Acinetobacter baumannii ATCC19606 when compared with azithromycin and clarithromycin. In addition, compounds 8e, 8f, 8h, 8l, and 8v exhibited excellent antibacterial activity against Staphylococcus aureus ATCC43300, Staphylococcus aureus PR, and Streptococcus pneumoniae ER-2. These compounds were generally 64- to 128-fold more active than azithromycin, and 32- to 128-fold more active than clarithromycin. The results of molecular docking indicated that compound 8f may bind to the nucleotide residue A752 through hydrogen-bonding, hydrophobic, electrostatic, or π-π stacking interactions. The predicted ClogP data suggested that higher values of ClogP (>6.65) enhanced the antibacterial activity of compounds such as 8e, 8f, 8h, 8l, and 8v. The determination of the minimum bactericidal concentration showed that most of the tested compounds were bacteriostatic agents. From this study of bactericidal kinetics, we can conclude that compound 8f had a concentration- and time-dependent effect on the proliferation of Staphylococcus aureus ATCC43300. Finally, the results of the cytotoxicity assay showed that compound 8f exhibited no toxicity at the effective antibacterial concentration.
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6
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Kumura K, Umemura E, Hirai Y, Ajito K. Discovery of Novel Lincomycin Derivatives Effective against Resistant Streptococcus pneumoniae and Streptococcus pyogenes Possessing ErmB Gene. J SYN ORG CHEM JPN 2022. [DOI: 10.5059/yukigoseikyokaishi.80.676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ko Kumura
- Pharmaceutical Research Center, Meiji Seika Pharma Co., Ltd
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7
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Daher SS, Lee M, Jin X, Teijaro CN, Barnett PR, Freundlich JS, Andrade RB. Alternative approaches utilizing click chemistry to develop next-generation analogs of solithromycin. Eur J Med Chem 2022; 233:114213. [PMID: 35240514 PMCID: PMC9009214 DOI: 10.1016/j.ejmech.2022.114213] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/10/2022] [Accepted: 02/18/2022] [Indexed: 11/03/2022]
Abstract
The marked rise in bacterial drug resistance has created an urgent need for novel antibacterials belonging to new drug classes and ideally possessing new mechanisms of action. The superior biological activity of solithromycin against streptococci and other bacteria causative of community-acquired pneumonia pathogens, compared to telithromycin and other macrolides encouraged us to extensively explore this class of antibiotics. We, thus, present the design and synthesis of a novel series of solithromycin analogs. Three main strategies were pursued in structure-activity relationship studies covering the N-11 side chain and the desosamine motif, which are both chief elements for establishing strong interactions with the bacterial ribosome as the molecular target. Minimal inhibitory concentration assays were determined to assess the in vitro potency of the various analogs in relation to solithromycin. Two analogs exhibited improved activity compared to solithromycin against resistant strains, which can be assessed in further pre-clinical studies.
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Affiliation(s)
- Samer S Daher
- Department of Chemistry, Temple University, Philadelphia, PA, 19122, USA.
| | - Miseon Lee
- Department of Chemistry, Temple University, Philadelphia, PA, 19122, USA
| | - Xiao Jin
- Department of Chemistry, Temple University, Philadelphia, PA, 19122, USA
| | | | - Pamela R Barnett
- Department of Pharmacology, Physiology, Neuroscience, Rutgers University - New Jersey Medical School, Newark, NJ, 07103, USA
| | - Joel S Freundlich
- Department of Pharmacology, Physiology, Neuroscience, Rutgers University - New Jersey Medical School, Newark, NJ, 07103, USA; Department of Medicine, Rutgers University - New Jersey Medical School, Newark, NJ, 07103, USA
| | - Rodrigo B Andrade
- Department of Chemistry, Temple University, Philadelphia, PA, 19122, USA
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8
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Qin Y, Song D, Teng Y, Liu X, Zhang P, Zhang N, Zhang N, Chen W, Ma S. Design, synthesis and structure-activity relationships of novel N11-, C12- and C13-substituted 15-membered homo-aza-clarithromycin derivatives against various resistant bacteria. Bioorg Chem 2021; 113:104992. [PMID: 34051415 DOI: 10.1016/j.bioorg.2021.104992] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/12/2021] [Accepted: 05/11/2021] [Indexed: 12/01/2022]
Abstract
Bacterial infections are still the main significant problem of public health in the world, and their elimination will greatly rely on the discovery of antibacterial drugs. In the processes of our searching for novel macrolide derivatives with excellent activity against sensitive and resistant bacteria, three series of novel N11-, C12- and C13-substituted 15-membered homo-aza-clarithromycin derivatives were designed and synthesized as Series A, B and C by creatively opening the lactone ring of clarithromycin (CAM), introducing various 4-substituted phenyl-1H-1,2,3-triazole side chains at the N11, C12 or C13 position of CAM and macrolactonization. The results from their in vitro antibacterial activity demonstrated that compounds 20c, 20d and 20f displayed not only the most potent activity against S. aureus ATCC25923 with the MIC values of 0.5, 0.5 and 0.5 µg/mL, but also greatly improved activity against B. subtilis ATCC9372 with the MIC values of less than or equal to 0.25, 0.25 and 0.25 µg/mL, respectively. In particular, compound 11g exhibited the strongest antibacterial effectiveness against all the tested resistant bacterial strains and had well balanced activity with the MIC values of 4-8 µg/mL. Further study on minimum bactericidal concentration and kinetics confirmed that compound 11g possessed a bacteriostatic effect on bacterial proliferation. Moreover, the results of molecular docking revealed an potential additional binding force between compound 11g and U790 in addition to the normal binding force of macrolide skeleton, which may explain why this compound performed the most potent activity against resistant bacteria. The results of cytotoxic assay indicated that compounds 20c, 20d and 20f were non-toxic to human breast cancer MCF-7 cells at its effective antibacterial concentration.
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Affiliation(s)
- Yinhui Qin
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan 250012, PR China
| | - Di Song
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan 250012, PR China
| | - Yuetai Teng
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan 250012, PR China
| | - Xingbang Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan 250012, PR China
| | - Panpan Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan 250012, PR China
| | - Nan Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan 250012, PR China
| | - Na Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan 250012, PR China
| | - Weijin Chen
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan 250012, PR China
| | - Shutao Ma
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan 250012, PR China.
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9
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Context-specific action of macrolide antibiotics on the eukaryotic ribosome. Nat Commun 2021; 12:2803. [PMID: 33990576 PMCID: PMC8121947 DOI: 10.1038/s41467-021-23068-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/14/2021] [Indexed: 01/09/2023] Open
Abstract
Macrolide antibiotics bind in the nascent peptide exit tunnel of the bacterial ribosome and prevent polymerization of specific amino acid sequences, selectively inhibiting translation of a subset of proteins. Because preventing translation of individual proteins could be beneficial for the treatment of human diseases, we asked whether macrolides, if bound to the eukaryotic ribosome, would retain their context- and protein-specific action. By introducing a single mutation in rRNA, we rendered yeast Saccharomyces cerevisiae cells sensitive to macrolides. Cryo-EM structural analysis showed that the macrolide telithromycin binds in the tunnel of the engineered eukaryotic ribosome. Genome-wide analysis of cellular translation and biochemical studies demonstrated that the drug inhibits eukaryotic translation by preferentially stalling ribosomes at distinct sequence motifs. Context-specific action markedly depends on the macrolide structure. Eliminating macrolide-arrest motifs from a protein renders its translation macrolide-tolerant. Our data illuminate the prospects of adapting macrolides for protein-selective translation inhibition in eukaryotic cells.
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10
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Qin Y, Ma S. Recent Advances in the Development of Macrolide Antibiotics as Antimicrobial Agents. Mini Rev Med Chem 2020; 20:601-625. [PMID: 31868146 DOI: 10.2174/1389557520666191223160942] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/28/2018] [Accepted: 08/15/2019] [Indexed: 11/22/2022]
Abstract
The chemical modification of natural products has been a major method in the discovery and synthesis of new macrolide antibiotics (MA) to treat a variety of infectious diseases. However, a lot of MA obtained in the above methods are no longer effective, because the bacteria quickly develop their resistance to these new macrolides, which has become a great threat to successful treatment of infectious diseases, such as infections of the respiratory system and urinary system. In this paper, total synthetic methods for MA that include erythromycin A (ERY), azithromycin (AZM), the clinical candidate solithromycin (CEM-101), as well as 14-membered and 15-membered azaketolides have been systematically reviewed on the basis of the literature reported previously. The total synthetic methods we describe here helps to accelerate the discovery of newer MA to deal with the serious problem of bacterial resistance.
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Affiliation(s)
- Yinhui Qin
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Shutao Ma
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, China
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11
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Yu AM, Choi YH, Tu MJ. RNA Drugs and RNA Targets for Small Molecules: Principles, Progress, and Challenges. Pharmacol Rev 2020; 72:862-898. [PMID: 32929000 PMCID: PMC7495341 DOI: 10.1124/pr.120.019554] [Citation(s) in RCA: 198] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
RNA-based therapies, including RNA molecules as drugs and RNA-targeted small molecules, offer unique opportunities to expand the range of therapeutic targets. Various forms of RNAs may be used to selectively act on proteins, transcripts, and genes that cannot be targeted by conventional small molecules or proteins. Although development of RNA drugs faces unparalleled challenges, many strategies have been developed to improve RNA metabolic stability and intracellular delivery. A number of RNA drugs have been approved for medical use, including aptamers (e.g., pegaptanib) that mechanistically act on protein target and small interfering RNAs (e.g., patisiran and givosiran) and antisense oligonucleotides (e.g., inotersen and golodirsen) that directly interfere with RNA targets. Furthermore, guide RNAs are essential components of novel gene editing modalities, and mRNA therapeutics are under development for protein replacement therapy or vaccination, including those against unprecedented severe acute respiratory syndrome coronavirus pandemic. Moreover, functional RNAs or RNA motifs are highly structured to form binding pockets or clefts that are accessible by small molecules. Many natural, semisynthetic, or synthetic antibiotics (e.g., aminoglycosides, tetracyclines, macrolides, oxazolidinones, and phenicols) can directly bind to ribosomal RNAs to achieve the inhibition of bacterial infections. Therefore, there is growing interest in developing RNA-targeted small-molecule drugs amenable to oral administration, and some (e.g., risdiplam and branaplam) have entered clinical trials. Here, we review the pharmacology of novel RNA drugs and RNA-targeted small-molecule medications, with a focus on recent progresses and strategies. Challenges in the development of novel druggable RNA entities and identification of viable RNA targets and selective small-molecule binders are discussed. SIGNIFICANCE STATEMENT: With the understanding of RNA functions and critical roles in diseases, as well as the development of RNA-related technologies, there is growing interest in developing novel RNA-based therapeutics. This comprehensive review presents pharmacology of both RNA drugs and RNA-targeted small-molecule medications, focusing on novel mechanisms of action, the most recent progress, and existing challenges.
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MESH Headings
- Aptamers, Nucleotide/pharmacology
- Aptamers, Nucleotide/therapeutic use
- Betacoronavirus
- COVID-19
- Chemistry Techniques, Analytical/methods
- Chemistry Techniques, Analytical/standards
- Clustered Regularly Interspaced Short Palindromic Repeats
- Coronavirus Infections/drug therapy
- Drug Delivery Systems/methods
- Drug Development/organization & administration
- Drug Discovery
- Humans
- MicroRNAs/pharmacology
- MicroRNAs/therapeutic use
- Oligonucleotides, Antisense/pharmacology
- Oligonucleotides, Antisense/therapeutic use
- Pandemics
- Pneumonia, Viral/drug therapy
- RNA/adverse effects
- RNA/drug effects
- RNA/pharmacology
- RNA, Antisense/pharmacology
- RNA, Antisense/therapeutic use
- RNA, Messenger/drug effects
- RNA, Messenger/pharmacology
- RNA, Ribosomal/drug effects
- RNA, Ribosomal/pharmacology
- RNA, Small Interfering/pharmacology
- RNA, Small Interfering/therapeutic use
- RNA, Viral/drug effects
- Ribonucleases/metabolism
- Riboswitch/drug effects
- SARS-CoV-2
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Affiliation(s)
- Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, California (A.-M.Y., Y.H.C., M.-J.T.) and College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang-si, Gyonggi-do, Republic of Korea (Y.H.C.)
| | - Young Hee Choi
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, California (A.-M.Y., Y.H.C., M.-J.T.) and College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang-si, Gyonggi-do, Republic of Korea (Y.H.C.)
| | - Mei-Juan Tu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, California (A.-M.Y., Y.H.C., M.-J.T.) and College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang-si, Gyonggi-do, Republic of Korea (Y.H.C.)
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12
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Antibiotic Resistance by Enzymatic Modification of Antibiotic Targets. Trends Mol Med 2020; 26:768-782. [PMID: 32493628 DOI: 10.1016/j.molmed.2020.05.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 11/21/2022]
Abstract
Antibiotic resistance remains a significant threat to modern medicine. Modification of the antibiotic target is a resistance strategy that is increasingly prevalent among pathogens. Examples include resistance to glycopeptide and polymyxin antibiotics that occurs via chemical modification of their molecular targets in the cell envelope. Similarly, many ribosome-targeting antibiotics are impaired by methylation of the rRNA. In these cases, the antibiotic target is subjected to enzymatic modification rather than genetic mutation, and in many instances the resistance enzymes are readily mobilized among pathogens. Understanding the enzymes responsible for these modifications is crucial to combat resistance. Here, we review our current understanding of enzymatic modification of antibiotic targets as well as discuss efforts to combat these resistance mechanisms.
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A long-distance rRNA base pair impacts the ability of macrolide antibiotics to kill bacteria. Proc Natl Acad Sci U S A 2020; 117:1971-1975. [PMID: 31932436 PMCID: PMC6995004 DOI: 10.1073/pnas.1918948117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The bactericidal activity of macrolide antibiotics correlates with the presence of an extended alkyl-aryl side chain, which accounts for their slow departure rate from the ribosome. Here, we found that the base pair between 23S ribosomal RNA (rRNA) nucleotides 752 and 2609 located in the macrolide binding site is important for the ribosome functionality and for establishing the unique interactions with the extended side chain of macrolide antibiotics. Disruption of the 752-2609 base pair accelerates the departure of extended macrolides from the ribosome and reduces their cidality. Our results demonstrate that not only the chemical features of the antibiotic, but also the structure of the target site contribute to the ability of the inhibitor to kill bacteria. While most of the ribosome-targeting antibiotics are bacteriostatic, some members of the macrolide class demonstrate considerable bactericidal activity. We previously showed that an extended alkyl-aryl side chain is the key structural element determining the macrolides’ slow dissociation from the ribosome and likely accounts for the antibiotics’ cidality. In the nontranslating Escherichia coli ribosome, the extended side chain of macrolides interacts with 23S ribosomal RNA (rRNA) nucleotides A752 and U2609, that were proposed to form a base pair. However, the existence of this base pair in the translating ribosome, its possible functional role, and its impact on the binding and cidality of the antibiotic remain unknown. By engineering E. coli cells carrying individual and compensatory mutations at the 752 and 2609 rRNA positions, we show that integrity of the base pair helps to modulate the ribosomal response to regulatory nascent peptides, determines the slow dissociation rate of the extended macrolides from the ribosome, and increases their bactericidal effect. Our findings demonstrate that the ability of antibiotics to kill bacterial cells relies not only on the chemical nature of the inhibitor, but also on structural features of the target.
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A novel series of 11-O-carbamoyl-3-O-descladinosyl clarithromycin derivatives bearing 1,2,3-triazole group: Design, synthesis and antibacterial evaluation. Bioorg Med Chem Lett 2020; 30:126850. [DOI: 10.1016/j.bmcl.2019.126850] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/30/2019] [Accepted: 11/20/2019] [Indexed: 11/20/2022]
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Fernandes P, Pereira D, Watkins PB, Bertrand D. Differentiating the Pharmacodynamics and Toxicology of Macrolide and Ketolide Antibiotics. J Med Chem 2019; 63:6462-6473. [PMID: 31644280 DOI: 10.1021/acs.jmedchem.9b01159] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This is a review of the macrolide and ketolide field focusing on differentiating the pharmacodynamics and especially the toxicology of the macrolides and ketolides. We emphasize the diversity in pharmacodynamics and toxicity of the macrolides and ketolides, resulting from even small structural changes, which makes it important to consider the various different compounds separately, not necessarily as a class. The ketolide, telithromycin, was developed because of rising bacterial macrolide resistance but was withdrawn postapproval after visual disturbances, syncope, myasthenia gravis, and hepatotoxicity were noted. These diverse adverse effects could be attributed to inhibition of nicotinic acetylcholine receptors. Solithromycin, a later generation ketolide, was effective in treating bacterial pneumonia, but it was not approved by the U.S. Food and Drug Administration owing, in part, to its structural similarity to telithromycin. This Miniperspective describes that structurally similar macrolides/ketolides have clearly mechanistically distinct effects. Understanding these effects could help in developing and securing regulatory approval of a new macrolide/ketolide that is active against macrolide-resistant pathogenic bacteria.
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Affiliation(s)
| | - David Pereira
- Ponce De Leon Health, Fernandina Beach, Florida 32034, United States
| | - Paul B Watkins
- Schools of Pharmacy, Medicine and Public Health, Institute for Drug Safety Sciences, University of North Carolina, Chapel Hill, North Carolina 27514, United States
| | - Daniel Bertrand
- HiQScreen SÃrl, 6, Route de Compois, Vesenaz, 1222 Geneva, Switzerland
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16
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Janas A, Przybylski P. 14- and 15-membered lactone macrolides and their analogues and hybrids: structure, molecular mechanism of action and biological activity. Eur J Med Chem 2019; 182:111662. [DOI: 10.1016/j.ejmech.2019.111662] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/12/2019] [Accepted: 08/29/2019] [Indexed: 11/15/2022]
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17
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Design, synthesis and antibacterial evaluation of novel 15-membered 11a-azahomoclarithromycin derivatives with the 1, 2, 3-triazole side chain. Eur J Med Chem 2019; 180:321-339. [DOI: 10.1016/j.ejmech.2019.07.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/17/2019] [Accepted: 07/07/2019] [Indexed: 11/23/2022]
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18
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Liu X, Wang J, Chen M, Che R, Ding W, Yu F, Zhou Y, Cui W, Xiaoxu X, God'spower BO, Li Y. Comparative proteomic analysis reveals drug resistance of Staphylococcus xylosus ATCC700404 under tylosin stress. BMC Vet Res 2019; 15:224. [PMID: 31266490 PMCID: PMC6604186 DOI: 10.1186/s12917-019-1959-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 06/13/2019] [Indexed: 12/13/2022] Open
Abstract
Background As a kind of opportunist pathogen, Staphylococcus xylosus (S. xylosus) can cause mastitis. Antibiotics are widely used for treating infected animals and tylosin is a member of such group. Thus, the continuous use of antibiotics in dairy livestock enterprise will go a long way in increasing tylosin resistance. However, the mechanism of tylosin-resistant S. xylosus is not clear. Here, isobaric tag for relative and absolute quantitation (iTRAQ)-based quantitative proteomics methods was used to find resistance-related proteins. Results We compared the differential expression of S. xylosus in response to tylosin stress by iTRAQ. A total of 155 proteins (59 up-regulated, 96 down-regulated) with the fold-change of >1.2 or <0.8 (p value ≤0.05) were observed between the S. xylosus treated with 1/2 MIC (0.25 μg/mL) tylosin and the untreated S. xylosus. Bioinformatic analysis revealed that these proteins play important roles in stress-response and transcription. Then, in order to verify the relationship between the above changed proteins and mechanism of tylosin-resistant S. xylosus, we induced the tylosin-resistant S. xylosus, and performed quantitative PCR analysis to verify the changes in the transcription proteins and the stress-response proteins in tylosin-resistant S. xylosus at the mRNA level. The data displayed that ribosomal protein L23 (rplw), thioredoxin(trxA) and Aldehyde dehydrogenase A(aldA-1) are up-regulated in the tylosin-resistant S. xylosus, compared with the tylosin-sensitive strains. Conclusion Our findings demonstrate the important of stress-response and transcription in the tylosin resistance of S. xylosus and provide an insight into the prevention of this resistance, which would aid in finding new medicines . Electronic supplementary material The online version of this article (10.1186/s12917-019-1959-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xin Liu
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Jinpeng Wang
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Mo Chen
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Ruixiang Che
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Wenya Ding
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Fei Yu
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Yonghui Zhou
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Wenqiang Cui
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Xing Xiaoxu
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Bello-Onaghise God'spower
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
| | - Yanhua Li
- College of Veterinary Medicine, Northeast Agricultural University, 600 Road Changjiang, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China.
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19
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Vázquez-Laslop N, Mankin AS. How Macrolide Antibiotics Work. Trends Biochem Sci 2018; 43:668-684. [PMID: 30054232 PMCID: PMC6108949 DOI: 10.1016/j.tibs.2018.06.011] [Citation(s) in RCA: 177] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/17/2018] [Accepted: 06/29/2018] [Indexed: 01/24/2023]
Abstract
Macrolide antibiotics inhibit protein synthesis by targeting the bacterial ribosome. They bind at the nascent peptide exit tunnel and partially occlude it. Thus, macrolides have been viewed as 'tunnel plugs' that stop the synthesis of every protein. More recent evidence, however, demonstrates that macrolides selectively inhibit the translation of a subset of cellular proteins, and that their action crucially depends on the nascent protein sequence and on the antibiotic structure. Therefore, macrolides emerge as modulators of translation rather than as global inhibitors of protein synthesis. The context-specific action of macrolides is the basis for regulating the expression of resistance genes. Understanding the details of the mechanism of macrolide action may inform rational design of new drugs and unveil important principles of translation regulation.
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Affiliation(s)
- Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.
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20
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Golkar T, Zieliński M, Berghuis AM. Look and Outlook on Enzyme-Mediated Macrolide Resistance. Front Microbiol 2018; 9:1942. [PMID: 30177927 PMCID: PMC6109786 DOI: 10.3389/fmicb.2018.01942] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 07/31/2018] [Indexed: 01/14/2023] Open
Abstract
Since their discovery in the early 1950s, macrolide antibiotics have been used in both agriculture and medicine. Specifically, macrolides such as erythromycin and azithromycin have found use as substitutes for β-lactam antibiotics in patients with penicillin allergies. Given the extensive use of this class of antibiotics it is no surprise that resistance has spread among pathogenic bacteria. In these bacteria different mechanisms of resistance have been observed. Frequently observed are alterations in the target of macrolides, i.e., the ribosome, as well as upregulation of efflux pumps. However, drug modification is also increasingly observed. Two classes of enzymes have been implicated in macrolide detoxification: macrolide phosphotransferases and macrolide esterases. In this review, we present a comprehensive overview on what is known about macrolide resistance with an emphasis on the macrolide phosphotransferase and esterase enzymes. Furthermore, we explore how this information can assist in addressing resistance to macrolide antibiotics.
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Affiliation(s)
- Tolou Golkar
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Michał Zieliński
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Albert M Berghuis
- Department of Biochemistry, McGill University, Montreal, QC, Canada.,Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
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21
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Dinos GP. The macrolide antibiotic renaissance. Br J Pharmacol 2017; 174:2967-2983. [PMID: 28664582 DOI: 10.1111/bph.13936] [Citation(s) in RCA: 217] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/29/2017] [Accepted: 06/20/2017] [Indexed: 12/19/2022] Open
Abstract
Macrolides represent a large family of protein synthesis inhibitors of great clinical interest due to their applicability to human medicine. Macrolides are composed of a macrocyclic lactone of different ring sizes, to which one or more deoxy-sugar or amino sugar residues are attached. Macrolides act as antibiotics by binding to bacterial 50S ribosomal subunit and interfering with protein synthesis. The high affinity of macrolides for bacterial ribosomes, together with the highly conserved structure of ribosomes across virtually all of the bacterial species, is consistent with their broad-spectrum activity. Since the discovery of the progenitor macrolide, erythromycin, in 1950, many derivatives have been synthesised, leading to compounds with better bioavailability and acid stability and improved pharmacokinetics. These efforts led to the second generation of macrolides, including well-known members such as azithromycin and clarithromycin. Subsequently, in order to address increasing antibiotic resistance, a third generation of macrolides displaying improved activity against many macrolide resistant strains was developed. However, these improvements were accompanied with serious side effects, leading to disappointment and causing many researchers to stop working on macrolide derivatives, assuming that this procedure had reached the end. In contrast, a recent published breakthrough introduced a new chemical platform for synthesis and discovery of a wide range of diverse macrolide antibiotics. This chemical synthesis revolution, in combination with reduction in the side effects, namely, 'Ketek effects', has led to a macrolide renaissance, increasing the hope for novel and safe therapeutic agents to combat serious human infectious diseases.
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Affiliation(s)
- George P Dinos
- Department of Biochemistry, School of Medicine, University of Patras, Patras, Greece
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22
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Affiliation(s)
- Donna Matzov
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel;, ,
| | - Anat Bashan
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel;, ,
| | - Ada Yonath
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel;, ,
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23
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Nature nurtures the design of new semi-synthetic macrolide antibiotics. J Antibiot (Tokyo) 2016; 70:527-533. [PMID: 27899792 PMCID: PMC5509991 DOI: 10.1038/ja.2016.137] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 10/13/2016] [Accepted: 10/16/2016] [Indexed: 12/26/2022]
Abstract
Erythromycin and its analogs are used to treat respiratory tract and other infections. The broad use of these antibiotics during the last 5 decades has led to resistance that can range from 20% to over 70% in certain parts of the world. Efforts to find macrolides that were active against macrolide-resistant strains led to the development of erythromycin analogs with alkyl-aryl side chains that mimicked the sugar side chain of 16-membered macrolides, such as tylosin. Further modifications were made to improve the potency of these molecules by removal of the cladinose sugar to obtain a smaller molecule, a modification that was learned from an older macrolide, pikromycin. A keto group was introduced after removal of the cladinose sugar to make the new ketolide subclass. Only one ketolide, telithromycin, received marketing authorization but because of severe adverse events, it is no longer widely used. Failure to identify the structure-relationship responsible for this clinical toxicity led to discontinuation of many ketolides that were in development. One that did complete clinical development, cethromycin, did not meet clinical efficacy criteria and therefore did not receive marketing approval. Work on developing new macrolides was re-initiated after showing that inhibition of nicotinic acetylcholine receptors by the imidazolyl-pyridine moiety on the side chain of telithromycin was likely responsible for the severe adverse events. Solithromycin is a fourth-generation macrolide that has a fluorine at the 2-position, and an alkyl-aryl side chain that is different from telithromycin. Solithromycin interacts at three sites on the bacterial ribosome, has activity against strains resistant to older macrolides (including telithromycin), and is mostly bactericidal. Pharmaceutical scientists involved in the development of macrolide antibiotics have learned from the teachings of Professor Satoshi Omura and progress in this field was not possible without his endeavors.
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24
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Auerbach-Nevo T, Baram D, Bashan A, Belousoff M, Breiner E, Davidovich C, Cimicata G, Eyal Z, Halfon Y, Krupkin M, Matzov D, Metz M, Rufayda M, Peretz M, Pick O, Pyetan E, Rozenberg H, Shalev-Benami M, Wekselman I, Zarivach R, Zimmerman E, Assis N, Bloch J, Israeli H, Kalaora R, Lim L, Sade-Falk O, Shapira T, Taha-Salaime L, Tang H, Yonath A. Ribosomal Antibiotics: Contemporary Challenges. Antibiotics (Basel) 2016; 5:antibiotics5030024. [PMID: 27367739 PMCID: PMC5039520 DOI: 10.3390/antibiotics5030024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/07/2016] [Accepted: 06/20/2016] [Indexed: 11/30/2022] Open
Abstract
Most ribosomal antibiotics obstruct distinct ribosomal functions. In selected cases, in addition to paralyzing vital ribosomal tasks, some ribosomal antibiotics are involved in cellular regulation. Owing to the global rapid increase in the appearance of multi-drug resistance in pathogenic bacterial strains, and to the extremely slow progress in developing new antibiotics worldwide, it seems that, in addition to the traditional attempts at improving current antibiotics and the intensive screening for additional natural compounds, this field should undergo substantial conceptual revision. Here, we highlight several contemporary issues, including challenging the common preference of broad-range antibiotics; the marginal attention to alterations in the microbiome population resulting from antibiotics usage, and the insufficient awareness of ecological and environmental aspects of antibiotics usage. We also highlight recent advances in the identification of species-specific structural motifs that may be exploited for the design and the creation of novel, environmental friendly, degradable, antibiotic types, with a better distinction between pathogens and useful bacterial species in the microbiome. Thus, these studies are leading towards the design of “pathogen-specific antibiotics,” in contrast to the current preference of broad range antibiotics, partially because it requires significant efforts in speeding up the discovery of the unique species motifs as well as the clinical pathogen identification.
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Affiliation(s)
- Tamar Auerbach-Nevo
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - David Baram
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Anat Bashan
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Matthew Belousoff
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Elinor Breiner
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Chen Davidovich
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Giuseppe Cimicata
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Zohar Eyal
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Yehuda Halfon
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Miri Krupkin
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Donna Matzov
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Markus Metz
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Mruwat Rufayda
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Moshe Peretz
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Ophir Pick
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Erez Pyetan
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Haim Rozenberg
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Moran Shalev-Benami
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Itai Wekselman
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Raz Zarivach
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Ella Zimmerman
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Nofar Assis
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Joel Bloch
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Hadar Israeli
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Rinat Kalaora
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Lisha Lim
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Ofir Sade-Falk
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Tal Shapira
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Leena Taha-Salaime
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Hua Tang
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
| | - Ada Yonath
- Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.
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25
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Chellat MF, Raguž L, Riedl R. Targeting Antibiotic Resistance. Angew Chem Int Ed Engl 2016; 55:6600-26. [PMID: 27000559 PMCID: PMC5071768 DOI: 10.1002/anie.201506818] [Citation(s) in RCA: 296] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 10/10/2015] [Indexed: 12/11/2022]
Abstract
Finding strategies against the development of antibiotic resistance is a major global challenge for the life sciences community and for public health. The past decades have seen a dramatic worldwide increase in human-pathogenic bacteria that are resistant to one or multiple antibiotics. More and more infections caused by resistant microorganisms fail to respond to conventional treatment, and in some cases, even last-resort antibiotics have lost their power. In addition, industry pipelines for the development of novel antibiotics have run dry over the past decades. A recent world health day by the World Health Organization titled "Combat drug resistance: no action today means no cure tomorrow" triggered an increase in research activity, and several promising strategies have been developed to restore treatment options against infections by resistant bacterial pathogens.
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Affiliation(s)
- Mathieu F Chellat
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Luka Raguž
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Rainer Riedl
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland.
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26
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Seiple IB, Zhang Z, Jakubec P, Langlois-Mercier A, Wright PM, Hog DT, Yabu K, Allu SR, Fukuzaki T, Carlsen PN, Kitamura Y, Zhou X, Condakes ML, Szczypiński FT, Green WD, Myers AG. A platform for the discovery of new macrolide antibiotics. Nature 2016; 533:338-45. [PMID: 27193679 PMCID: PMC6526944 DOI: 10.1038/nature17967] [Citation(s) in RCA: 214] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 03/23/2016] [Indexed: 12/13/2022]
Abstract
The chemical modification of structurally complex fermentation products, a process known as semisynthesis, has been an important tool in the discovery and manufacture of antibiotics for the treatment of various infectious diseases. However, many of the therapeutics obtained in this way are no longer effective, because bacterial resistance to these compounds has developed. Here we present a practical, fully synthetic route to macrolide antibiotics by the convergent assembly of simple chemical building blocks, enabling the synthesis of diverse structures not accessible by traditional semisynthetic approaches. More than 300 new macrolide antibiotic candidates, as well as the clinical candidate solithromycin, have been synthesized using our convergent approach. Evaluation of these compounds against a panel of pathogenic bacteria revealed that the majority of these structures had antibiotic activity, some efficacious against strains resistant to macrolides in current use. The chemistry we describe here provides a platform for the discovery of new macrolide antibiotics and may also serve as the basis for their manufacture.
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Affiliation(s)
- Ian B Seiple
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Ziyang Zhang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Pavol Jakubec
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Audrey Langlois-Mercier
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Peter M Wright
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Daniel T Hog
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Kazuo Yabu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Senkara Rao Allu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Takehiro Fukuzaki
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Peter N Carlsen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Yoshiaki Kitamura
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Xiang Zhou
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Matthew L Condakes
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Filip T Szczypiński
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - William D Green
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Andrew G Myers
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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27
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Affiliation(s)
- Mathieu F. Chellat
- Institut für Chemie und Biotechnologie, FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Luka Raguž
- Institut für Chemie und Biotechnologie, FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Rainer Riedl
- Institut für Chemie und Biotechnologie, FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
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28
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Wakiyama Y, Kumura K, Umemura E, Ueda K, Masaki S, Kumura M, Fushimi H, Ajito K. Synthesis and structure–activity relationships of novel lincomycin derivatives. Part 1. Newly generated antibacterial activities against Gram-positive bacteria with erm gene by C-7 modification. J Antibiot (Tokyo) 2015; 69:368-80. [DOI: 10.1038/ja.2015.119] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 09/15/2015] [Accepted: 10/29/2015] [Indexed: 11/09/2022]
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29
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Eyal Z, Matzov D, Krupkin M, Wekselman I, Paukner S, Zimmerman E, Rozenberg H, Bashan A, Yonath A. Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus. Proc Natl Acad Sci U S A 2015; 112:E5805-14. [PMID: 26464510 PMCID: PMC4629319 DOI: 10.1073/pnas.1517952112] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The emergence of bacterial multidrug resistance to antibiotics threatens to cause regression to the preantibiotic era. Here we present the crystal structure of the large ribosomal subunit from Staphylococcus aureus, a versatile Gram-positive aggressive pathogen, and its complexes with the known antibiotics linezolid and telithromycin, as well as with a new, highly potent pleuromutilin derivative, BC-3205. These crystal structures shed light on specific structural motifs of the S. aureus ribosome and the binding modes of the aforementioned antibiotics. Moreover, by analyzing the ribosome structure and comparing it with those of nonpathogenic bacterial models, we identified some unique internal and peripheral structural motifs that may be potential candidates for improving known antibiotics and for use in the design of selective antibiotic drugs against S. aureus.
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Affiliation(s)
- Zohar Eyal
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Donna Matzov
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Miri Krupkin
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Itai Wekselman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Ella Zimmerman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Haim Rozenberg
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anat Bashan
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ada Yonath
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
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30
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Washington AZ, Tapadar S, George A, Oyelere AK. Exploiting translational stalling peptides in an effort to extend azithromycin interaction within the prokaryotic ribosome nascent peptide exit tunnel. Bioorg Med Chem 2015; 23:5198-209. [PMID: 26037612 DOI: 10.1016/j.bmc.2015.04.078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 04/18/2015] [Accepted: 04/29/2015] [Indexed: 10/23/2022]
Abstract
The ribosome is the primary protein synthesis machine in the cell and is a target for treatment of a variety of diseases including bacterial infection and cancer. The ribosomal peptide exit tunnel, the route of egress for the nascent peptide, is an inviting site for drug design. Toward a rational engagement of the nascent peptide components for the design of small molecule inhibitors of ribosome function, we designed and disclosed herein a set of N-10 indole functionalized azithromycin analogs. The indole moiety of these compounds is designed to mimic the translation stalling interaction of SecM W155 side-chain with the prokaryotic (Escherichia coli) ribosome A751 residue. Many of these N-10 functionalized compounds have enhanced translation inhibition activities against E. coli ribosome relative to azithromycin while a subset inhibited the growth of representative susceptible bacteria strains to about the same extent as azithromycin. Moreover, the inclusion of bovine serum in the bacterial growth media enhanced the anti-bacterial potency of the N-10 functionalized azithromycin analogs by as high as 10-fold.
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Affiliation(s)
- Arren Z Washington
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
| | - Subhasish Tapadar
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
| | - Alex George
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
| | - Adegboyega K Oyelere
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA; Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.
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31
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The design of novel classes of macrolides for neutrophil-dominated inflammatory diseases. Future Med Chem 2015; 6:657-74. [PMID: 24895894 DOI: 10.4155/fmc.14.14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Neutrophil-dominated inflammatory diseases, like chronic obstructive pulmonary disease, cystic fibrosis, bronchiectasis, bronchiolitis obliteras syndrome and non-eosinophilic asthma, present a significant medical problem lacking adequate therapy. Macrolide antibiotics have been reported to be effective in the treatment of the aforementioned diseases, for reasons unrelated to their antibacterial action. This has resulted in research activities aimed at gaining a better understanding of the immunomodulatory actions of macrolides and the synthesis of various novel anti-inflammatory macrolides without antimicrobial activity. Despite the difficult chemistry and lack of an extensive knowledge for their mechanism of action, several interesting molecules from this class, including potential clinical candidates, are on the horizon.
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32
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Washington AZ, Benicewicz DB, Canzoneri JC, Fagan CE, Mwakwari SC, Maehigashi T, Dunham CM, Oyelere AK. Macrolide-peptide conjugates as probes of the path of travel of the nascent peptides through the ribosome. ACS Chem Biol 2014; 9:2621-31. [PMID: 25198768 PMCID: PMC4245169 DOI: 10.1021/cb5003224] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Despite
decades of research on the bacterial ribosome, the ribosomal
exit tunnel is still poorly understood. Although it has been suggested
that the exit tunnel is simply a convenient route of egress for the
nascent chain, specific protein sequences serve to slow the rate of
translation, suggesting some degree of interaction between the nascent
peptide chain and the exit tunnel. To understand how the ribosome
interacts with nascent peptide sequences, we synthesized and characterized
a novel class of probe molecules. These peptide–macrolide (or
“peptolide”) conjugates were designed to present unique
peptide sequences to the exit tunnel. Biochemical and X-ray structural
analyses of the interactions between these probes and the ribosome
reveal interesting insights about the exit tunnel. Using translation
inhibition and RNA structure probing assays, we find the exit tunnel
has a relaxed preference for the directionality (N → C or C
→ N orientation) of the nascent peptides. Moreover, the X-ray
crystal structure of one peptolide derived from a positively charged,
reverse Nuclear Localization Sequence peptide, bound to the 70S bacterial
ribosome, reveals that the macrolide ring of the peptolide binds in
the same position as other macrolides. However, the peptide tail folds
over the macrolide ring, oriented toward the peptidyl transferase
center and interacting in a novel manner with 23S rRNA residue C2442
and His69 of ribosomal protein L4. These data suggest that these peptolides
are viable probes for interrogating nascent peptide–exit tunnel
interaction.
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Affiliation(s)
- Arren Z. Washington
- School
of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering
and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Derek B. Benicewicz
- School
of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering
and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Joshua C. Canzoneri
- School
of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering
and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Crystal E. Fagan
- Department
of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Sandra C. Mwakwari
- School
of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering
and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Tatsuya Maehigashi
- Department
of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Christine M. Dunham
- Department
of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Adegboyega K. Oyelere
- School
of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering
and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
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33
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Abstract
The ribosome is one of the main antibiotic targets in the bacterial cell. Crystal structures of naturally produced antibiotics and their semi-synthetic derivatives bound to ribosomal particles have provided unparalleled insight into their mechanisms of action, and they are also facilitating the design of more effective antibiotics for targeting multidrug-resistant bacteria. In this Review, I discuss the recent structural insights into the mechanism of action of ribosome-targeting antibiotics and the molecular mechanisms of bacterial resistance, in addition to the approaches that are being pursued for the production of improved drugs that inhibit bacterial protein synthesis.
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Abstract
Telithromycin (Ketek), Aventis Pharma), a ketolide, belongs to a new class of antibiotics that was developed for the treatment of upper and lower respiratory tract infections. The prevalence of penicillin and macrolide resistance among respiratory pathogens is increasing in the USA. Telithromycin is highly active against beta-lactam, macrolide and fluoroquinolone reduced-susceptibility pathogens. Its efficacy has been shown to be equal or superior to comparator agents in numerous studies. It has a broad in vitro spectrum versus usual respiratory pathogens and oral once-daily dosing that increases patient compliance. Telithromycin penetrates rapidly into neutrophils in bronchopulmonary tissue, with peak levels obtained in 1 to 2 h. Results of clinical trials show clinical-esponse rates similar to comparator agents. The most frequent adverse events involve the gastrointestinal system, with mild to moderate diarrhea and nausea. A low rate of discontinuation was observed in the studies. Telithromycin is an effective first-line treatment for mild to moderate respiratory infections in adults.
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Affiliation(s)
- Karen M Spiers
- Division of Infectious Diseases, William Beaumont Hospital, Royal Oak, MI 48073, USA.
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35
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Synthesis and antibacterial activity of a series of novel 9-O-acetyl- 4′-substituted 16-membered macrolides derived from josamycin. Bioorg Med Chem Lett 2014; 24:480-4. [DOI: 10.1016/j.bmcl.2013.12.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 11/25/2013] [Accepted: 12/10/2013] [Indexed: 11/19/2022]
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36
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Ajito K, Miura T, Furuuchi T, Tamura A. Sixteen-Membered Macrolides: Chemical Modifications and Future Applications. HETEROCYCLES 2014. [DOI: 10.3987/rev-13-785] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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37
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Insights into the mode of action of novel fluoroketolides, potent inhibitors of bacterial protein synthesis. Antimicrob Agents Chemother 2013; 58:472-80. [PMID: 24189263 DOI: 10.1128/aac.01994-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ketolides, the third generation of expanded-spectrum macrolides, have in the last years become a successful weapon in the endless war against macrolide-resistant pathogens. Ketolides are semisynthetic derivatives of the naturally produced macrolide erythromycin, displaying not only improved activity against some erythromycin-resistant strains but also increased bactericidal activity as well as inhibitory effects at lower drug concentrations. In this study, we present a series of novel ketolides carrying alkyl-aryl side chains at the C-6 position of the lactone ring and, additionally, one or two fluorine atoms attached either directly to the lactone ring at the C-2 position or indirectly via the C-13 position. According to our genetic and biochemical studies, these novel ketolides occupy the known macrolide binding site at the entrance of the ribosomal tunnel and exhibit lower MIC values against wild-type or mutant strains than erythromycin. In most cases, the ketolides display activities comparable to or better than the clinically used ketolide telithromycin. Chemical protection experiments using Escherichia coli ribosomes bearing U2609C or U754A mutations in 23S rRNA suggest that the alkyl-aryl side chain establishes an interaction with the U2609-A752 base pair, analogous to that observed with telithromycin but unlike the interactions formed by cethromycin. These findings reemphasize the versatility of the alkyl-aryl side chains with respect to species specificity, which will be important for future design of improved antimicrobial agents.
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38
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Zimmerman E, Bashan A, Yonath A. Antibiotics at the Ribosomal Exit Tunnel-Selected Structural Aspects. Antibiotics (Basel) 2013. [DOI: 10.1002/9783527659685.ch22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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39
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Design, synthesis and biological evaluation of azithromycin glycosyl derivatives as potential antibacterial agents. Bioorg Med Chem Lett 2013; 23:5057-60. [DOI: 10.1016/j.bmcl.2013.07.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 07/15/2013] [Accepted: 07/17/2013] [Indexed: 11/22/2022]
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40
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On the use of the antibiotic chloramphenicol to target polypeptide chain mimics to the ribosomal exit tunnel. Biochimie 2013; 95:1765-72. [PMID: 23770443 DOI: 10.1016/j.biochi.2013.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 06/04/2013] [Indexed: 11/23/2022]
Abstract
The ribosomal exit tunnel had recently become the centre of many functional and structural studies. Accumulated evidence indicates that the tunnel is not simply a passive conduit for the nascent chain, but a rather functionally important compartment where nascent peptide sequences can interact with the ribosome to signal translation to slow down or even stop. To explore further this interaction, we have synthesized short peptides attached to the amino group of a chloramphenicol (CAM) base, such that when bound to the ribosome these compounds mimic a nascent peptidyl-tRNA chain bound to the A-site of the peptidyltransferase center (PTC). Here we show that these CAM-peptides interact with the PTC of the ribosome while their effectiveness can be modulated by the sequence of the peptide, suggesting a direct interaction of the peptide with the ribosomal tunnel. Indeed, chemical footprinting in the presence of CAM-P2, one of the tested CAM-peptides, reveals protection of 23S rRNA nucleotides located deep within the tunnel, indicating a potential interaction with specific components of the ribosomal tunnel. Collectively, our findings suggest that the CAM-based peptide derivatives will be useful tools for targeting polypeptide chain mimics to the ribosomal tunnel, allowing their conformation and interaction with the ribosomal tunnel to be explored using further biochemical and structural methods.
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41
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Small MC, Lopes P, Andrade RB, MacKerell AD. Impact of ribosomal modification on the binding of the antibiotic telithromycin using a combined grand canonical monte carlo/molecular dynamics simulation approach. PLoS Comput Biol 2013; 9:e1003113. [PMID: 23785274 PMCID: PMC3681621 DOI: 10.1371/journal.pcbi.1003113] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 05/07/2013] [Indexed: 02/05/2023] Open
Abstract
Resistance to macrolide antibiotics is conferred by mutation of A2058 to G or methylation by Erm methyltransferases of the exocyclic N6 of A2058 (E. coli numbering) that forms the macrolide binding site in the 50S subunit of the ribosome. Ketolides such as telithromycin mitigate A2058G resistance yet remain susceptible to Erm-based resistance. Molecular details associated with macrolide resistance due to the A2058G mutation and methylation at N6 of A2058 by Erm methyltransferases were investigated using empirical force field-based simulations. To address the buried nature of the macrolide binding site, the number of waters within the pocket was allowed to fluctuate via the use of a Grand Canonical Monte Carlo (GCMC) methodology. The GCMC water insertion/deletion steps were alternated with Molecular Dynamics (MD) simulations to allow for relaxation of the entire system. From this GCMC/MD approach information on the interactions between telithromycin and the 50S ribosome was obtained. In the wild-type (WT) ribosome, the 2'-OH to A2058 N1 hydrogen bond samples short distances with a higher probability, while the effectiveness of telithromycin against the A2058G mutation is explained by a rearrangement of the hydrogen bonding pattern of the 2'-OH to 2058 that maintains the overall antibiotic-ribosome interactions. In both the WT and A2058G mutation there is significant flexibility in telithromycin's imidazole-pyridine side chain (ARM), indicating that entropic effects contribute to the binding affinity. Methylated ribosomes show lower sampling of short 2'-OH to 2058 distances and also demonstrate enhanced G2057-A2058 stacking leading to disrupted A752-U2609 Watson-Crick (WC) interactions as well as hydrogen bonding between telithromycin's ARM and U2609. This information will be of utility in the rational design of novel macrolide analogs with improved activity against methylated A2058 ribosomes.
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Affiliation(s)
- Meagan C. Small
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland, United States of America
| | - Pedro Lopes
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland, United States of America
| | - Rodrigo B. Andrade
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland, United States of America
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42
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Liang JH, Lv W, Li XL, An K, Cushman M, Wang H, Xu YC. Synthesis and antibacterial activity of 9-oxime ether non-ketolides, and novel binding mode of alkylides with bacterial rRNA. Bioorg Med Chem Lett 2013; 23:1387-93. [DOI: 10.1016/j.bmcl.2012.12.070] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 12/21/2012] [Accepted: 12/22/2012] [Indexed: 10/27/2022]
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43
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Magee TV, Han S, McCurdy SP, Nguyen TT, Granskog K, Marr ES, Maguire BA, Huband MD, Chen JM, Subashi TA, Shanmugasundaram V. Novel 3-O-carbamoyl erythromycin A derivatives (carbamolides) with activity against resistant staphylococcal and streptococcal isolates. Bioorg Med Chem Lett 2013; 23:1727-31. [PMID: 23414806 DOI: 10.1016/j.bmcl.2013.01.067] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 01/07/2013] [Accepted: 01/16/2013] [Indexed: 11/30/2022]
Abstract
A novel series of 3-O-carbamoyl erythromycin A derived analogs, labeled carbamolides, with activity versus resistant bacterial isolates of staphylococci (including macrolide and oxazolidinone resistant strains) and streptococci are reported. An (R)-2-aryl substituent on a pyrrolidine carbamate appeared to be critical for achieving potency against resistant strains. Crystal structures showed a distinct aromatic interaction between the (R)-2-aryl (3-pyridyl for 4d) substituent on the pyrrolidine and G2484 (G2505, Escherichia coli) of the Deinococcus radiodurans 50S ribosome (3.2Å resolution).
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Affiliation(s)
- Thomas V Magee
- Pfizer Cardiovascular, Metabolic, and Endocrine Diseases (CVMED) Chemistry, 620 Memorial Dr, Cambridge, MA 02139, USA.
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44
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Liang JH, An K, Lv W, Cushman M, Wang H, Xu YC. Synthesis, antibacterial activity and docking of 14-membered 9-O-(3-arylalkyl) oxime 11,12-cyclic carbonate ketolides. Eur J Med Chem 2013. [DOI: 10.1016/j.ejmech.2012.10.054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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45
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Synthesis and antibacterial activity of 6-O-(heteroaryl-isoxazolyl)propynyl 2-fluoro ketolides. Bioorg Med Chem Lett 2012; 22:5739-43. [DOI: 10.1016/j.bmcl.2012.06.092] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 06/16/2012] [Accepted: 06/18/2012] [Indexed: 10/28/2022]
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46
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Kostopoulou ON, Petropoulos AD, Dinos GP, Choli-Papadopoulou T, Kalpaxis DL. Investigating the entire course of telithromycin binding to Escherichia coli ribosomes. Nucleic Acids Res 2012; 40:5078-87. [PMID: 22362747 PMCID: PMC3367204 DOI: 10.1093/nar/gks174] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Applying kinetics and footprinting analysis, we show that telithromycin, a ketolide antibiotic, binds to Escherichia coli ribosomes in a two-step process. During the first, rapidly equilibrated step, telithromycin binds to a low-affinity site (KT = 500 nM), in which the lactone ring is positioned at the upper portion of the peptide exit tunnel, while the alkyl–aryl side chain of the drug inserts a groove formed by nucleotides A789 and U790 of 23S rRNA. During the second step, telithromycin shifts slowly to a high-affinity site (KT* = 8.33 nM), in which the lactone ring remains essentially at the same position, while the side chain interacts with the base pair U2609:A752 and the extended loop of protein L22. Consistently, mutations perturbing either the base pair U2609:A752 or the L22-loop hinder shifting of telithromycin to the final position, without affecting the initial step of binding. In contrast, mutation Lys63Glu in protein L4 placed on the opposite side of the tunnel, exerts only a minor effect on telithromycin binding. Polyamines disfavor both sequential steps of binding. Our data correlate well with recent crystallographic data and rationalize the changes in the accessibility of ribosomes to telithromycin in response to ribosomal mutations and ionic changes.
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Affiliation(s)
- Ourania N Kostopoulou
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
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47
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Kannan K, Mankin AS. Macrolide antibiotics in the ribosome exit tunnel: species-specific binding and action. Ann N Y Acad Sci 2012; 1241:33-47. [PMID: 22191525 DOI: 10.1111/j.1749-6632.2011.06315.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Macrolide antibiotics bind in the nascent peptide exit tunnel of the ribosome and inhibit protein synthesis. The majority of information on the principles of binding and action of these antibiotics comes from studies that employed model organisms. However, there is a growing understanding that the binding of macrolides to their target, as well as the mode of inhibition of translation, can be strongly influenced by variations in ribosome structure between bacterial species. Awareness of the existence of species-specific differences in drug action and appreciation of the extent of these differences can stimulate future work on developing better macrolide drugs. In this review, representative cases illustrating the organism-specific binding and action of macrolide antibiotics, as well as species-specific mechanisms of resistance are analyzed.
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Affiliation(s)
- Krishna Kannan
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 60607, USA
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48
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Abstract
The peptidyltransferase center of the large ribosomal subunit is responsible for catalyzing peptide bonds. This active site is the target of a variety of diverse antibiotics, many of which are used clinically. The past decade has seen a plethora of structures of antibiotics in complex with the large ribosomal subunit, providing unprecedented insight into the mechanism of action of these inhibitors. Ten distinct antibiotics (chloramphenicol, clindamycin, linezolid, tiamulin, sparsomycin, and five macrolides) have been crystallized in complex with four distinct ribosomal species, three bacterial, and one archaeal. This review aims to compare these structures in order to provide insight into the conserved and species-specific modes of interaction for particular members of each class of antibiotics. Coupled with the wealth of biochemical data, a picture is emerging defining the specific functional states of the ribosome that antibiotics preferentially target. Such mechanistic insight into antibiotic inhibition will be important for the development of the next generation of antimicrobial agents.
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49
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Synthesis and activity of new macrolones: Conjugates between 6(7)-(2′-aminoethyl)-amino-1-cyclopropyl-3-carboxylic acid (2′-hydroxyethyl) amides and 4″-propenoyl-azithromycin. Bioorg Med Chem 2011; 19:7270-80. [DOI: 10.1016/j.bmc.2011.07.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 07/06/2011] [Accepted: 07/08/2011] [Indexed: 11/21/2022]
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50
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Chancey ST, Zhou X, Zähner D, Stephens DS. Induction of efflux-mediated macrolide resistance in Streptococcus pneumoniae. Antimicrob Agents Chemother 2011; 55:3413-22. [PMID: 21537010 PMCID: PMC3122420 DOI: 10.1128/aac.00060-11] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2011] [Accepted: 04/25/2011] [Indexed: 01/17/2023] Open
Abstract
The antimicrobial efflux system encoded by the operon mef(E)-mel on the mobile genetic element MEGA in Streptococcus pneumoniae and other Gram-positive bacteria is inducible by macrolide antibiotics and antimicrobial peptides. Induction may affect the clinical response to the use of macrolides. We developed mef(E) reporter constructs and a disk diffusion induction and resistance assay to determine the kinetics and basis of mef(E)-mel induction. Induction occurred rapidly, with a >15-fold increase in transcription within 1 h of exposure to subinhibitory concentrations of erythromycin. A spectrum of environmental conditions, including competence and nonmacrolide antibiotics with distinct cellular targets, did not induce mef(E). Using 16 different structurally defined macrolides, induction was correlated with the amino sugar attached to C-5 of the macrolide lactone ring, not with the size (e.g., 14-, 15- or 16-member) of the ring or with the presence of the neutral sugar cladinose at C-3. Macrolides with a monosaccharide attached to C-5, known to block exit of the nascent peptide from the ribosome after the incorporation of up to eight amino acids, induced mef(E) expression. Macrolides with a C-5 disaccharide, which extends the macrolide into the ribosomal exit tunnel, disrupting peptidyl transferase activity, did not induce it. The induction of mef(E) did not require macrolide efflux, but the affinity of macrolides for the ribosome determined the availability for efflux and pneumococcal susceptibility. The induction of mef(E)-mel expression by inducing macrolides appears to be based on specific interactions of the macrolide C-5 saccharide with the ribosome that alleviate transcriptional attenuation of mef(E)-mel.
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Affiliation(s)
- Scott T. Chancey
- Division of Infectious Diseases, Department of Medicine
- Department of Veterans Affairs Medical Center, Atlanta, Georgia 30033
| | - Xiaoliu Zhou
- Division of Infectious Diseases, Department of Medicine
- Department of Veterans Affairs Medical Center, Atlanta, Georgia 30033
| | - Dorothea Zähner
- Division of Infectious Diseases, Department of Medicine
- Department of Veterans Affairs Medical Center, Atlanta, Georgia 30033
| | - David S. Stephens
- Division of Infectious Diseases, Department of Medicine
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322
- Department of Veterans Affairs Medical Center, Atlanta, Georgia 30033
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