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Riveros II, Yildirim I. Prediction of 3D RNA Structures from Sequence Using Energy Landscapes of RNA Dimers: Application to RNA Tetraloops. J Chem Theory Comput 2024; 20:4363-4376. [PMID: 38728627 DOI: 10.1021/acs.jctc.4c00189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
Access to the three-dimensional structure of RNA enables an ability to gain a more profound understanding of its biological mechanisms, as well as the ability to design RNA-targeting drugs, which can take advantage of the unique chemical environment imposed by a folded RNA structure. Due to the dynamic and structurally complex properties of RNA, both experimental and traditional computational methods have difficulty in determining RNA's 3D structure. Herein, we introduce TAPERSS (Theoretical Analyses, Prediction, and Evaluation of RNA Structures from Sequence), a physics-based fragment assembly method for predicting 3D RNA structures from sequence. Using a fragment library created using discrete path sampling calculations of RNA dinucleoside monophosphates, TAPERSS can sample the physics-based energy landscapes of any RNA sequence with relatively low computational complexity. We have benchmarked TAPERSS on 21 RNA tetraloops, using a combinatorial algorithm as a proof-of-concept. We show that TAPERSS was successfully able to predict the apo-state structures of all 21 RNA hairpins, with 16 of those structures also having low predicted energies as well. We demonstrate that TAPERSS performs most accurately on GNRA-like tetraloops with mostly stacked loop-nucleotides, while having limited success with more dynamic UNCG and CUYG tetraloops, most likely due to the influence of the RNA force field used to create the fragment library. Moreover, we show that TAPERSS can successfully predict the majority of the experimental non-apo states, highlighting its potential in anticipating biologically significant yet unobserved states. This holds great promise for future applications in drug design and related studies. With discussed improvements and implementation of more efficient sampling algorithms, we believe TAPERSS may serve as a useful tool for a physics-based conformational sampling of large RNA structures.
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Affiliation(s)
- Ivan Isaac Riveros
- Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, Florida 33458, United States
| | - Ilyas Yildirim
- Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, Florida 33458, United States
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2
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Boshoff HIM, Young K, Ahn YM, Yadav VD, Crowley BM, Yang L, Su J, Oh S, Arora K, Andrews J, Manikkam M, Sutphin M, Smith AJ, Weiner DM, Piazza MK, Fleegle JD, Gomez F, Dayao EK, Prideaux B, Zimmerman M, Kaya F, Sarathy J, Tan VY, Via LE, Tschirret-Guth R, Lenaerts AJ, Robertson GT, Dartois V, Olsen DB, Barry CE. Mtb-Selective 5-Aminomethyl Oxazolidinone Prodrugs: Robust Potency and Potential Liabilities. ACS Infect Dis 2024; 10:1679-1695. [PMID: 38581700 DOI: 10.1021/acsinfecdis.4c00025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2024]
Abstract
Linezolid is a drug with proven human antitubercular activity whose use is limited to highly drug-resistant patients because of its toxicity. This toxicity is related to its mechanism of action─linezolid inhibits protein synthesis in both bacteria and eukaryotic mitochondria. A highly selective and potent series of oxazolidinones, bearing a 5-aminomethyl moiety (in place of the typical 5-acetamidomethyl moiety of linezolid), was identified. Linezolid-resistant mutants were cross-resistant to these molecules but not vice versa. Resistance to the 5-aminomethyl molecules mapped to an N-acetyl transferase (Rv0133) and these mutants remained fully linezolid susceptible. Purified Rv0133 was shown to catalyze the transformation of the 5-aminomethyl oxazolidinones to their corresponding N-acetylated metabolites, and this transformation was also observed in live cells of Mycobacterium tuberculosis. Mammalian mitochondria, which lack an appropriate N-acetyltransferase to activate these prodrugs, were not susceptible to inhibition with the 5-aminomethyl analogues. Several compounds that were more potent than linezolid were taken into C3HeB/FeJ mice and were shown to be highly efficacious, and one of these (9) was additionally taken into marmosets and found to be highly active. Penetration of these 5-aminomethyl oxazolidinone prodrugs into caseum was excellent. Unfortunately, these compounds were rapidly converted into the corresponding 5-alcohols by mammalian metabolism which retained antimycobacterial activity but resulted in substantial mitotoxicity.
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Affiliation(s)
- Helena I M Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Katherine Young
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Yong-Mo Ahn
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Veena D Yadav
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institutes of Health, Bethesda, Maryland 20892, United States
| | | | - Lihu Yang
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Jing Su
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Sangmi Oh
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Kriti Arora
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Jenna Andrews
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Michelle Manikkam
- Tuberculosis Imaging Program, Division of Intramural Research, National Insititute of Allergy and Infectious Disease, National Insititutes of Health, Bethesda, Maryland 20892, United States
| | - Michelle Sutphin
- Tuberculosis Imaging Program, Division of Intramural Research, National Insititute of Allergy and Infectious Disease, National Insititutes of Health, Bethesda, Maryland 20892, United States
| | - Anthony J Smith
- Mycobacterial Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Ft Collins, Colorado 80521, United States
| | - Danielle M Weiner
- Tuberculosis Imaging Program, Division of Intramural Research, National Insititute of Allergy and Infectious Disease, National Insititutes of Health, Bethesda, Maryland 20892, United States
| | - Michaela K Piazza
- Tuberculosis Imaging Program, Division of Intramural Research, National Insititute of Allergy and Infectious Disease, National Insititutes of Health, Bethesda, Maryland 20892, United States
| | - Joel D Fleegle
- Tuberculosis Imaging Program, Division of Intramural Research, National Insititute of Allergy and Infectious Disease, National Insititutes of Health, Bethesda, Maryland 20892, United States
| | - Felipe Gomez
- Tuberculosis Imaging Program, Division of Intramural Research, National Insititute of Allergy and Infectious Disease, National Insititutes of Health, Bethesda, Maryland 20892, United States
| | - Emmannual K Dayao
- Tuberculosis Imaging Program, Division of Intramural Research, National Insititute of Allergy and Infectious Disease, National Insititutes of Health, Bethesda, Maryland 20892, United States
| | - Brendan Prideaux
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Matthew Zimmerman
- Hackensack Meridian Health Center for Discovery & Innovation, Nutley, New Jersey 07110, United States
| | - Firat Kaya
- Hackensack Meridian Health Center for Discovery & Innovation, Nutley, New Jersey 07110, United States
| | - Jansy Sarathy
- Hackensack Meridian Health Center for Discovery & Innovation, Nutley, New Jersey 07110, United States
| | - Vee Yang Tan
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Laura E Via
- Tuberculosis Imaging Program, Division of Intramural Research, National Insititute of Allergy and Infectious Disease, National Insititutes of Health, Bethesda, Maryland 20892, United States
| | | | - Anne J Lenaerts
- Mycobacterial Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Ft Collins, Colorado 80521, United States
| | - Gregory T Robertson
- Mycobacterial Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Ft Collins, Colorado 80521, United States
| | - Véronique Dartois
- Mycobacterial Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Ft Collins, Colorado 80521, United States
| | - David B Olsen
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Clifton E Barry
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institutes of Health, Bethesda, Maryland 20892, United States
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3
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Zou F, Cui Z, Lou S, Ou Y, Zhu C, Shu C, Chen J, Zhao R, Wu Z, Wang L, Chen Z, Chen H, Lan Y. Adverse drug events associated with linezolid administration: a real-world pharmacovigilance study from 2004 to 2023 using the FAERS database. Front Pharmacol 2024; 15:1338902. [PMID: 38434706 PMCID: PMC10904462 DOI: 10.3389/fphar.2024.1338902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/31/2024] [Indexed: 03/05/2024] Open
Abstract
Introduction: Linezolid is an oxazolidinone antibiotic that is active against drug-resistant Gram-positive bacteria and multidrug-resistant Mycobacterium tuberculosis. Real-world studies on the safety of linezolid in large populations are lacking. This study aimed to determine the adverse events associated with linezolid in real-world settings by analyzing data from the US Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS). Methods: We retrospectively extracted reports on adverse drug events (ADEs) from the FAERS database from the first quarter of 2004 to that of 2023. By using disproportionality analysis including reporting odds ratio (ROR), proportional reporting ratio (PRR), Bayesian Confidence Propagation Neural Network (BCPNN), along with the multi-item gamma Poisson shrinker (MGPS), we evaluated whether there was a significant association between linezolid and ADE. The time to onset of ADE was further analyzed in the general population and within each age, weight, reporting population, and weight subgroups. Results: A total of 11,176 reports of linezolid as the "primary suspected" drug and 263 significant adverse events of linezolid were identified, including some common adverse events such as thrombocytopenia (n = 1,139, ROR 21.98), anaemia (n = 704, ROR 7.39), and unexpected signals that were not listed on the drug label such as rhabdomyolysis (n = 90, ROR 4.33), and electrocardiogram QT prolonged (n = 73, ROR 4.07). Linezolid-induced adverse reactions involved 27 System Organ Class (SOC). Gender differences existed in ADE signals related to linezolid. The median onset time of all ADEs was 6 days, and most ADEs (n = 3,778) occurred within the first month of linezolid use but some may continue to occur even after a year of treatment (n = 46). Conclusion: This study reports the time to onset of adverse effects in detail at the levels of SOC and specific preferred term (PT). The results of our study provide valuable insights for optimizing the use of linezolid and reducing potential side effects, expected to facilitate the safe use of linezolid in clinical settings.
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Affiliation(s)
- Fan Zou
- Department of Tuberculosis, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Zhiwei Cui
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Siyu Lou
- Department of Tuberculosis, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Yingyong Ou
- Department of Tuberculosis, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Chengyu Zhu
- Department of Tuberculosis, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Chengjie Shu
- Department of Tuberculosis, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Junyou Chen
- Department of Tuberculosis, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Ruizhen Zhao
- Department of Tuberculosis, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Zhu Wu
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Li Wang
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Zhenyong Chen
- Department of Tuberculosis, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Huayu Chen
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yuanbo Lan
- Department of Tuberculosis, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
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4
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Grandini GS, Morgon NH, de Souza AR. Theoretical study of the interaction between the antibiotic linezolid and the active site of the 50S ribosomal subunit of the bacterium Haloarcula marismortui. Chirality 2024; 36:e23629. [PMID: 37961817 DOI: 10.1002/chir.23629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/04/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023]
Abstract
First antibiotic in the oxazolidinone class, linezolid fights gram-positive multiresistant bacteria by inhibiting protein synthesis through its interaction with the 50S subunit of the functional bacterial ribosome. For its antimicrobial action, it is necessary that its chiral carbon located in the oxazolidinone ring is in the S-conformation. Computational calculation at time-dependent density functional theory methodology, ultraviolet-visible (UV-Vis), and electronic circular dichroism spectra was obtained for noncomplexed and complexed forms of linezolid to verify the possible chirality of nitrogen atom in the acetamide group of the molecule. The molecular system has two chiral centers. So, there are now four possible configurations: RR, RS, SR, and SS. For a better understanding of the system, the electronic spectra at the PBE0/6-311++G(3df,2p) level of theory were obtained. The complexed form was obtained from the crystallographic data of the ribosome, containing the S-linezolid molecular system. The computational results obtained for the electronic properties are in good agreement with the experimental crystallographic data and available theoretical results.
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Affiliation(s)
| | - Nelson Henrique Morgon
- Institute of Chemistry, Department of Physical Chemistry, University of Campinas, Campinas, Brazil
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5
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Liu P, Jiang Y, Jiao L, Luo Y, Wang X, Yang T. Strategies for the Discovery of Oxazolidinone Antibacterial Agents: Development and Future Perspectives. J Med Chem 2023; 66:13860-13873. [PMID: 37807849 DOI: 10.1021/acs.jmedchem.3c01040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Oxazolidinones represent a significant class of synthetic bacterial protein synthesis inhibitors that are primarily effective against Gram-positive bacteria. The commercial success of linezolid, the first FDA-approved oxazolidinone antibiotic, has motivated researchers to develop more potent oxazolidinones by employing various drug development strategies to fight against antimicrobial resistance, some of which have shown promising results. Thus, this Perspective aims to discuss the strategies employed in constructing oxazolidinone-based antibacterial agents and summarize recent advances in discovering oxazolidinone antibiotics to provide valuable insights for potentially developing next-generation oxazolidinone antibacterial agents or other pharmaceuticals.
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Affiliation(s)
- Pingxian Liu
- Center of Infectious Diseases and Laboratory of Human Diseases and Immunotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yunhan Jiang
- Center of Infectious Diseases and Laboratory of Human Diseases and Immunotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- Department of Cardiovascular Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
- Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ling Jiao
- Center of Infectious Diseases and Laboratory of Human Diseases and Immunotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Youfu Luo
- State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiaodong Wang
- Department of Breast Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tao Yang
- Center of Infectious Diseases and Laboratory of Human Diseases and Immunotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
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6
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Pitcher NJ, Feder A, Bolden N, Zirbes CF, Pamatmat AJ, Boyken L, Hill JJ, Bartels AR, Thurman AL, Reeb VC, Porterfield HS, Moustafa AM, Planet PJ, Fischer AJ. Parallel evolution of linezolid-resistant Staphylococcus aureus in patients with cystic fibrosis. Microbiol Spectr 2023; 11:e0208423. [PMID: 37724867 PMCID: PMC10581212 DOI: 10.1128/spectrum.02084-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/10/2023] [Indexed: 09/21/2023] Open
Abstract
Linezolid is an antibiotic used to treat serious Staphylococcus aureus infections. Resistance to linezolid is considered rare but could emerge with repeated dosing. We recently reported widespread prescription of linezolid for a cohort of patients with cystic fibrosis (CF). The goals of this study were to determine the incidence of linezolid-resistant methicillin-resistant Staphylococcus aureus (MRSA) in CF and identify molecular mechanisms for linezolid resistance. We identified patients who cultured S. aureus resistant to linezolid with minimum inhibitory concentration (MIC) >4 at the University of Iowa CF Center between 2008 and 2018. We obtained isolates from these patients and retested susceptibility to linezolid using broth microdilution. We used whole genome sequencing to perform phylogenetic analysis of linezolid-resistant isolates and examine sequences for mutations or accessory genes that confer linezolid resistance. Between 2008 and 2018, 111 patients received linezolid, and 4 of these patients cultured linezolid-resistant S. aureus. We sequenced 11 resistant and 21 susceptible isolates from these 4 subjects. Phylogenetic analysis indicated that linezolid resistance developed in ST5 or ST105 backgrounds. Three individuals had linezolid-resistant S. aureus with a G2576T mutation in 23S rRNA. One of these subjects additionally had a mutS- mutL- hypermutating S. aureus that produced five resistant isolates with multiple ribosomal subunit mutations. In one subject, the genetic basis for linezolid resistance was unclear. We conclude that linezolid resistant S. aureus can occur through multiple genetic mechanisms in patients with repeated exposure to this antibiotic. IMPORTANCE Patients with cystic fibrosis have persistent lung infections with Staphylococcus aureus that require extensive antibiotic treatments. Linezolid, an antibiotic given by oral or intravenous route, is prescribed repeatedly for patients whose lung disease has progressed. After treatment with linezolid, S. aureus strains can evolve antibiotic resistance through multiple genetic mechanisms. In addition to a common mutation in the 23S ribosomal RNA known to confer linezolid resistance, S. aureus strains can evolve novel resistance based on a combination of mutations affecting the bacterial ribosome. This combination of mutations was observed in a strain that exhibited hypermutation owing to the loss of the DNA repair genes mutS and mutL. In this cohort of patients with cystic fibrosis, linezolid resistance was transient, possibly due to the growth disadvantage of resistant strains. However, ongoing chronic exposure to linezolid may create optimal conditions for the future emergence of resistance to this critical antibiotic.
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Affiliation(s)
- Nicholas J. Pitcher
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Andries Feder
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Nicholas Bolden
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Christian F. Zirbes
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Anthony J. Pamatmat
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Linda Boyken
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, lowa, USA
| | - Jared J. Hill
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Alyssa R. Bartels
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Andrew L. Thurman
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, lowa, USA
| | - Valerie C. Reeb
- State Hygienic Laboratory at the University of Iowa, Coralville, lowa, USA
| | | | - Ahmed M. Moustafa
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Paul J. Planet
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | - Anthony J. Fischer
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
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7
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Paredes-Amaya CC, Ulloa MT, García-Angulo VA. Fierce poison to others: the phenomenon of bacterial dependence on antibiotics. J Biomed Sci 2023; 30:67. [PMID: 37574554 PMCID: PMC10424368 DOI: 10.1186/s12929-023-00963-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/07/2023] [Indexed: 08/15/2023] Open
Abstract
Beyond the development of resistance, the effects of antibiotics on bacteria and microbial communities are complex and far from exhaustively studied. In the context of the current global antimicrobial resistance crisis, understanding the adaptive and physiological responses of bacteria to antimicrobials is of paramount importance along with the development of new therapies. Bacterial dependence on antibiotics is a phenomenon in which antimicrobials instead of eliminating the pathogens actually provide a boost for their growth. This trait comprises an extreme example of the complexities of responses elicited by microorganisms to these drugs. This compelling evolutionary trait was readily described along with the first wave of antibiotics use and dependence to various antimicrobials has been reported. Nevertheless, current molecular characterizations have been focused on dependence on vancomycin, linezolid and colistin, three critically important antibiotics frequently used as last resource therapy for multi resistant pathogens. Outstanding advances have been made in understanding the molecular basis for the dependence to vancomycin, including specific mutations involved. Regarding linezolid and colistin, the general physiological components affected by the dependence, namely ribosomes and membrane function respectively, have been established. Nonetheless the implications of antibiotic dependence in clinically relevant features, such as virulence, epidemics, relationship with development of resistance, diagnostics and therapy effectiveness require clarification. This review presents a brief introduction of the phenomenon of bacterial dependence to antibiotics and a summary on early and current research concerning the basis for this trait. Furthermore, the available information on the effect of dependence in key clinical aspects is discussed. The studies performed so far underline the need to fully disclose the biological and clinical significance of this trait in pathogens to successfully assess its role in resistance and to design adjusted therapies.
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Affiliation(s)
- Claudia C Paredes-Amaya
- Microbiology Department, Escuela de Ciencias Básicas, Facultad de Salud, Universidad del Valle, Cali, Colombia
| | - María Teresa Ulloa
- Microbiology and Micology Program, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Independencia 1027, Independencia, RM, Santiago, Chile
- Vertebral I+D+i - Corporation for Assistance for Burned Children (Coaniquem), Santiago, Chile
| | - Víctor Antonio García-Angulo
- Microbiology and Micology Program, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Independencia 1027, Independencia, RM, Santiago, Chile.
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8
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Seely SM, Parajuli NP, De Tarafder A, Ge X, Sanyal S, Gagnon MG. Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome. Nat Commun 2023; 14:4666. [PMID: 37537169 PMCID: PMC10400623 DOI: 10.1038/s41467-023-40416-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 07/26/2023] [Indexed: 08/05/2023] Open
Abstract
Aminoglycosides are a class of antibiotics that bind to ribosomal RNA and exert pleiotropic effects on ribosome function. Amikacin, the semisynthetic derivative of kanamycin, is commonly used for treating severe infections with multidrug-resistant, aerobic Gram-negative bacteria. Amikacin carries the 4-amino-2-hydroxy butyrate (AHB) moiety at the N1 amino group of the central 2-deoxystreptamine (2-DOS) ring, which may confer amikacin a unique ribosome inhibition profile. Here we use in vitro fast kinetics combined with X-ray crystallography and cryo-EM to dissect the mechanisms of ribosome inhibition by amikacin and the parent compound, kanamycin. Amikacin interferes with tRNA translocation, release factor-mediated peptidyl-tRNA hydrolysis, and ribosome recycling, traits attributed to the additional interactions amikacin makes with the decoding center. The binding site in the large ribosomal subunit proximal to the 3'-end of tRNA in the peptidyl (P) site lays the groundwork for rational design of amikacin derivatives with improved antibacterial properties.
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Affiliation(s)
- Savannah M Seely
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Narayan P Parajuli
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden
| | - Arindam De Tarafder
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden
| | - Xueliang Ge
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden.
| | - Matthieu G Gagnon
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, 77555, USA.
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, 77555, USA.
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9
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Chen CW, Leimer N, Syroegin EA, Dunand C, Bulman ZP, Lewis K, Polikanov YS, Svetlov MS. Structural insights into the mechanism of overcoming Erm-mediated resistance by macrolides acting together with hygromycin-A. Nat Commun 2023; 14:4196. [PMID: 37452045 PMCID: PMC10349075 DOI: 10.1038/s41467-023-39653-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023] Open
Abstract
The ever-growing rise of antibiotic resistance among bacterial pathogens is one of the top healthcare threats today. Although combination antibiotic therapies represent a potential approach to more efficiently combat infections caused by susceptible and drug-resistant bacteria, only a few known drug pairs exhibit synergy/cooperativity in killing bacteria. Here, we discover that well-known ribosomal antibiotics, hygromycin A (HygA) and macrolides, which target peptidyl transferase center and peptide exit tunnel, respectively, can act cooperatively against susceptible and drug-resistant bacteria. Remarkably, HygA slows down macrolide dissociation from the ribosome by 60-fold and enhances the otherwise weak antimicrobial activity of the newest-generation macrolide drugs known as ketolides against macrolide-resistant bacteria. By determining a set of high-resolution X-ray crystal structures of drug-sensitive wild-type and macrolide-resistant Erm-methylated 70S ribosomes in complex with three HygA-macrolide pairs, we provide a structural rationale for the binding cooperativity of these drugs and also uncover the molecular mechanism of overcoming Erm-type resistance by macrolides acting together with hygromycin A. Altogether our structural, biochemical, and microbiological findings lay the foundation for the subsequent development of synergistic antibiotic tandems with improved bactericidal properties against drug-resistant pathogens, including those expressing erm genes.
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Affiliation(s)
- Chih-Wei Chen
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Nadja Leimer
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Egor A Syroegin
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Clémence Dunand
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Zackery P Bulman
- Department of Pharmacy Practice, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Kim Lewis
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Yury S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA.
| | - Maxim S Svetlov
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA.
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10
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Gan WC, Ng HF, Ngeow YF. Mechanisms of Linezolid Resistance in Mycobacteria. Pharmaceuticals (Basel) 2023; 16:784. [PMID: 37375732 DOI: 10.3390/ph16060784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/05/2023] [Accepted: 05/13/2023] [Indexed: 06/29/2023] Open
Abstract
Mycobacteria form some of the most notorious and difficult-to-treat bacterial pathogens. As a group, they are intrinsically resistant to many commonly used antibiotics, such as tetracyclines and beta-lactams. In addition to intrinsic resistances, acquired multidrug resistance has also been observed and documented in Mycobacterium tuberculosis (MTB), Mycobacterium leprae and non-tuberculous mycobacteria (NTM). To combat multidrug resistant infections by these pathogens, innovative antimicrobials and treatment regimens are required. In this regard, linezolid, an oxazolidinone introduced for clinical use just two decades ago, was added to the therapeutic armamentarium for drug-resistant mycobacteria. It exhibits antibacterial activity by binding to the 50S ribosomal subunit and inhibiting protein synthesis. Unfortunately, linezolid resistance has now been documented in MTB and NTM, in many parts of the world. Most linezolid-resistant mycobacterial strains show mutations in the ribosome or related genes, such as in the rplC, rrl and tsnR genes. Non-ribosomal mechanisms appear to be rare. One such mechanism was associated with a mutation in fadD32, which encodes a protein that plays an important role in mycolic acid synthesis. Mycobacterial efflux proteins have also been implicated in linezolid resistance. This review summarises current knowledge of genetic determinants of linezolid resistance in mycobacteria, with the aim of contributing information that could facilitate the discovery of new therapeutic approaches to overcome, delay or avoid further developments of drug resistance among these important pathogens.
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Affiliation(s)
- Wei Chong Gan
- Dr. Wu Lien-Teh Centre for Research in Communicable Diseases, M. Kandiah Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Jalan Sungai Long, Bandar Sungai Long, Kajang 43000, Selangor, Malaysia
| | - Hien Fuh Ng
- Dr. Wu Lien-Teh Centre for Research in Communicable Diseases, M. Kandiah Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Jalan Sungai Long, Bandar Sungai Long, Kajang 43000, Selangor, Malaysia
| | - Yun Fong Ngeow
- Dr. Wu Lien-Teh Centre for Research in Communicable Diseases, M. Kandiah Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Jalan Sungai Long, Bandar Sungai Long, Kajang 43000, Selangor, Malaysia
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11
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Wang X, Jin B, Han Y, Wang T, Sheng Z, Tao Y, Yang H. Optimization and Antibacterial Evaluation of Novel 3-(5-Fluoropyridine-3-yl)-2-oxazolidinone Derivatives Containing a Pyrimidine Substituted Piperazine. Molecules 2023; 28:molecules28114267. [PMID: 37298744 DOI: 10.3390/molecules28114267] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/09/2023] [Accepted: 05/16/2023] [Indexed: 06/12/2023] Open
Abstract
In this study, a series of novel 3-(5-fluoropyridine-3-yl)-2-oxazolidinone derivatives were designed and synthesized based on compounds previously reported, and their antibacterial activity was investigated. Then their antibacterial activity was investigated for the first time. Preliminary screening results showed that all these compounds exhibited antibacterial activity against gram-positive bacteria, including 7 drug-sensitive strains and 4 drug-resistant strains, among which compound 7j exhibited an 8-fold stronger inhibitory effect than linezolid, with a minimum inhibitory concentration (MIC) value of 0.25 µg/mL. Further molecular docking studies predicted the possible binding mode between active compound 7j and the target. Interestingly, these compounds could not only hamper the formation of biofilms, but also have better safety, as confirmed by cytotoxicity experiments. All these results indicate that these 3-(5-fluoropyridine-3-yl)-2-oxazolidinone derivatives have the potential to be developed into novel candidates for the treatment of gram-positive bacterial infections.
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Affiliation(s)
- Xin Wang
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Bo Jin
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Yutong Han
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Tong Wang
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Zunlai Sheng
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin 150030, China
| | - Ye Tao
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin 150030, China
| | - Hongliang Yang
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin 150030, China
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12
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Obana N, Takada H, Crowe-McAuliffe C, Iwamoto M, Egorov AA, Wu KJY, Chiba S, Murina V, Paternoga H, Tresco BIC, Nomura N, Myers AG, Atkinson G, Wilson DN, Hauryliuk V. Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR. Nucleic Acids Res 2023; 51:4536-4554. [PMID: 36951104 PMCID: PMC10201436 DOI: 10.1093/nar/gkad193] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/17/2023] [Accepted: 03/06/2023] [Indexed: 03/24/2023] Open
Abstract
Genome-encoded antibiotic resistance (ARE) ATP-binding cassette (ABC) proteins of the F subfamily (ARE-ABCFs) mediate intrinsic resistance in diverse Gram-positive bacteria. The diversity of chromosomally-encoded ARE-ABCFs is far from being fully experimentally explored. Here we characterise phylogenetically diverse genome-encoded ABCFs from Actinomycetia (Ard1 from Streptomyces capreolus, producer of the nucleoside antibiotic A201A), Bacilli (VmlR2 from soil bacterium Neobacillus vireti) and Clostridia (CplR from Clostridium perfringens, Clostridium sporogenes and Clostridioides difficile). We demonstrate that Ard1 is a narrow spectrum ARE-ABCF that specifically mediates self-resistance against nucleoside antibiotics. The single-particle cryo-EM structure of a VmlR2-ribosome complex allows us to rationalise the resistance spectrum of this ARE-ABCF that is equipped with an unusually long antibiotic resistance determinant (ARD) subdomain. We show that CplR contributes to intrinsic pleuromutilin, lincosamide and streptogramin A resistance in Clostridioides, and demonstrate that C. difficile CplR (CDIF630_02847) synergises with the transposon-encoded 23S ribosomal RNA methyltransferase Erm to grant high levels of antibiotic resistance to the C. difficile 630 clinical isolate. Finally, assisted by uORF4u, our novel tool for detection of upstream open reading frames, we dissect the translational attenuation mechanism that controls the induction of cplR expression upon an antibiotic challenge.
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Affiliation(s)
- Nozomu Obana
- Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba, Japan
| | - Hiraku Takada
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Caillan Crowe-McAuliffe
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Mizuki Iwamoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Artyom A Egorov
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Kelvin J Y Wu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Shinobu Chiba
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan
- Institute for Protein Dynamics, Kyoto Sangyo University, Japan
| | | | - Helge Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Ben I C Tresco
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Nobuhiko Nomura
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Andrew G Myers
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Gemma C Atkinson
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Vasili Hauryliuk
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- University of Tartu, Institute of Technology, Tartu, Estonia
- Science for Life Laboratory, Lund, Sweden
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13
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Pitcher NJ, Feder A, Bolden N, Zirbes CF, Pamatmat AJ, Boyken L, Hill JJ, Thurman AL, Reeb VC, Porterfield HS, Moustafa AM, Planet PJ, Fischer AJ. Parallel Evolution of Linezolid Resistant Staphylococcus aureus in Patients with Cystic Fibrosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.539145. [PMID: 37205485 PMCID: PMC10187253 DOI: 10.1101/2023.05.02.539145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Background Linezolid is an antibiotic used to treat serious Staphylococcus aureus infections. Resistance to linezolid is considered rare but could emerge with repeated dosing. We recently reported widespread prescription of linezolid for a cohort of patients with cystic fibrosis (CF). Objectives The goals of this study were to determine the incidence of linezolid resistance in CF and identify molecular mechanisms for linezolid resistance. Methods We identified patients with S. aureus resistant to linezolid (MIC > 4) at the University of Iowa CF Center between 2008 and 2018. We obtained isolates from these patients and retested susceptibility to linezolid using broth microdilution. We used whole genome sequencing to perform phylogenetic analysis of linezolid resistant isolates and examine sequences for mutations or accessory genes that confer linezolid resistance. Main Results Between 2008 and 2018, 111 patients received linezolid and 4 of these patients cultured linezolid resistant S. aureus . We sequenced 11 resistant and 21 susceptible isolates from these 4 subjects. Phylogenetic analysis indicated that linezolid resistance developed in ST5 or ST105 backgrounds. Three individuals had linezolid resistant S. aureus with a G2576T mutation in 23S rRNA. One of these subjects additionally had a mutS - mutL - hypermutating S. aureus that produced 5 resistant isolates with multiple ribosomal subunit mutations. In one subject, the genetic basis for linezolid resistance was unclear. Conclusions Linezolid resistance evolved in 4 of 111 patients in this study. Linezolid resistance occurred by multiple genetic mechanisms. All resistant strains developed in ST5 or ST105 MRSA backgrounds. Key Point Linezolid resistance arises through multiple genetic mechanisms and could be facilitated by mutator phenotypes. Linezolid resistance was transient, possibly due to growth disadvantage.
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Affiliation(s)
- Nicholas J. Pitcher
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Andries Feder
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Nicholas Bolden
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Christian F. Zirbes
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Anthony J. Pamatmat
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Linda Boyken
- Pathology. University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Jared J. Hill
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Andrew L. Thurman
- Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Valérie C. Reeb
- State Hygienic Laboratory at the University of Iowa, Coralville, IA 52241
| | - Harry S. Porterfield
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Ahmed M. Moustafa
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Paul J. Planet
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Comparative Genomics, American Museum of Natural History, New York, NY 10024
| | - Anthony J. Fischer
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242
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14
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Jeremia L, Deprez BE, Dey D, Conn GL, Wuest WM. Ribosome-targeting antibiotics and resistance via ribosomal RNA methylation. RSC Med Chem 2023; 14:624-643. [PMID: 37122541 PMCID: PMC10131624 DOI: 10.1039/d2md00459c] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/17/2023] [Indexed: 03/05/2023] Open
Abstract
The rise of multidrug-resistant bacterial infections is a cause of global concern. There is an urgent need to both revitalize antibacterial agents that are ineffective due to resistance while concurrently developing new antibiotics with novel targets and mechanisms of action. Pathogen associated resistance-conferring ribosomal RNA (rRNA) methyltransferases are a growing threat that, as a group, collectively render a total of seven clinically-relevant ribosome-targeting antibiotic classes ineffective. Increasing frequency of identification and their growing prevalence relative to other resistance mechanisms suggests that these resistance determinants are rapidly spreading among human pathogens and could contribute significantly to the increased likelihood of a post-antibiotic era. Herein, with a view toward stimulating future studies to counter the effects of these rRNA methyltransferases, we summarize their prevalence, the fitness cost(s) to bacteria of their acquisition and expression, and current efforts toward targeting clinically relevant enzymes of this class.
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Affiliation(s)
- Learnmore Jeremia
- Department of Chemistry, Emory University 1515 Dickey Dr. Atlanta GA 30322 USA
| | - Benjamin E Deprez
- Department of Chemistry, Emory University 1515 Dickey Dr. Atlanta GA 30322 USA
| | - Debayan Dey
- Department of Biochemistry, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
| | - William M Wuest
- Department of Chemistry, Emory University 1515 Dickey Dr. Atlanta GA 30322 USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
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15
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Baran A, Kwiatkowska A, Potocki L. Antibiotics and Bacterial Resistance-A Short Story of an Endless Arms Race. Int J Mol Sci 2023; 24:ijms24065777. [PMID: 36982857 PMCID: PMC10056106 DOI: 10.3390/ijms24065777] [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: 01/31/2023] [Revised: 03/10/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Despite the undisputed development of medicine, antibiotics still serve as first-choice drugs for patients with infectious disorders. The widespread use of antibiotics results from a wide spectrum of their actions encompassing mechanisms responsible for: the inhibition of bacterial cell wall biosynthesis, the disruption of cell membrane integrity, the suppression of nucleic acids and/or proteins synthesis, as well as disturbances of metabolic processes. However, the widespread availability of antibiotics, accompanied by their overprescription, acts as a double-edged sword, since the overuse and/or misuse of antibiotics leads to a growing number of multidrug-resistant microbes. This, in turn, has recently emerged as a global public health challenge facing both clinicians and their patients. In addition to intrinsic resistance, bacteria can acquire resistance to particular antimicrobial agents through the transfer of genetic material conferring resistance. Amongst the most common bacterial resistance strategies are: drug target site changes, increased cell wall permeability to antibiotics, antibiotic inactivation, and efflux pumps. A better understanding of the interplay between the mechanisms of antibiotic actions and bacterial defense strategies against particular antimicrobial agents is crucial for developing new drugs or drug combinations. Herein, we provide a brief overview of the current nanomedicine-based strategies that aim to improve the efficacy of antibiotics.
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Affiliation(s)
- Aleksandra Baran
- Department of Biotechnology, College of Natural Sciences, University of Rzeszów, Pigonia 1, 35-310 Rzeszow, Poland
| | - Aleksandra Kwiatkowska
- Institute of Physical Culture Studies, College of Medical Sciences, University of Rzeszów, ul. Towarnickiego 3, 35-959 Rzeszów, Poland
| | - Leszek Potocki
- Department of Biotechnology, College of Natural Sciences, University of Rzeszów, Pigonia 1, 35-310 Rzeszow, Poland
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16
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Comparative Assessment of Docking Programs for Docking and Virtual Screening of Ribosomal Oxazolidinone Antibacterial Agents. Antibiotics (Basel) 2023; 12:antibiotics12030463. [PMID: 36978331 PMCID: PMC10044086 DOI: 10.3390/antibiotics12030463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Oxazolidinones are a broad-spectrum class of synthetic antibiotics that bind to the 50S ribosomal subunit of Gram-positive and Gram-negative bacteria. Many crystal structures of the ribosomes with oxazolidinone ligands have been reported in the literature, facilitating structure-based design using methods such as molecular docking. It would be of great interest to know in advance how well docking methods can reproduce the correct ligand binding modes and rank these correctly. We examined the performance of five molecular docking programs (AutoDock 4, AutoDock Vina, DOCK 6, rDock, and RLDock) for their ability to model ribosomal–ligand interactions with oxazolidinones. Eleven ribosomal crystal structures with oxazolidinones as the ligands were docked. The accuracy was evaluated by calculating the docked complexes’ root-mean-square deviation (RMSD) and the program’s internal scoring function. The rankings for each program based on the median RMSD between the native and predicted were DOCK 6 > AD4 > Vina > RDOCK >> RLDOCK. Results demonstrate that the top-performing program, DOCK 6, could accurately replicate the ligand binding in only four of the eleven ribosomes due to the poor electron density of said ribosomal structures. In this study, we have further benchmarked the performance of the DOCK 6 docking algorithm and scoring in improving virtual screening (VS) enrichment using the dataset of 285 oxazolidinone derivatives against oxazolidinone binding sites in the S. aureus ribosome. However, there was no clear trend between the structure and activity of the oxazolidinones in VS. Overall, the docking performance indicates that the RNA pocket’s high flexibility does not allow for accurate docking prediction, highlighting the need to validate VS. protocols for ligand-RNA before future use. Later, we developed a re-scoring method incorporating absolute docking scores and molecular descriptors, and the results indicate that the descriptors greatly improve the correlation of docking scores and pMIC values. Morgan fingerprint analysis was also used, suggesting that DOCK 6 underpredicted molecules with tail modifications with acetamide, n-methylacetamide, or n-ethylacetamide and over-predicted molecule derivatives with methylamino bits. Alternatively, a ligand-based approach similar to a field template was taken, indicating that each derivative’s tail groups have strong positive and negative electrostatic potential contributing to microbial activity. These results indicate that one should perform VS. campaigns of ribosomal antibiotics with care and that more comprehensive strategies, including molecular dynamics simulations and relative free energy calculations, might be necessary in conjunction with VS. and docking.
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17
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Recent advances in oxazolidinones as antituberculosis agents. Future Med Chem 2022; 14:1149-1165. [PMID: 35866418 DOI: 10.4155/fmc-2022-0079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Tuberculosis (TB) is an infectious and fatal disease caused by Mycobacterium tuberculosis (Mtb) and remains a serious public health threat; therefore, the development of new antitubercular agents is a priority for the World Health Organization's End TB strategy and the United Nations' Sustainable Development Goals to eradicate TB. Oxazolidinones are a class of synthetic antibacterial agents with a distinct mode of action developed for the treatment of Gram-positive bacterial infections. Many oxazolidinones exhibit good activity against Mtb, and some are currently in clinical trials for multidrug-resistant TB and extensively drug-resistant TB therapy. In this review, the mechanism of action, activity and toxicity of oxazolidinones and recent progress in the research and development of oxazolidinones as anti-TB agents are summarized.
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18
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Jin B, Wang T, Chen JY, Liu XQ, Zhang YX, Zhang XY, Sheng ZL, Yang HL. Synthesis and Biological Evaluation of 3-(Pyridine-3-yl)-2-Oxazolidinone Derivatives as Antibacterial Agents. Front Chem 2022; 10:949813. [PMID: 35923260 PMCID: PMC9339906 DOI: 10.3389/fchem.2022.949813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/13/2022] [Indexed: 11/16/2022] Open
Abstract
In this research, a series of 3-(pyridine-3-yl)-2-oxazolidinone derivatives was designed, synthesized, and evaluated for in vitro antibacterial activity, which included bacteriostatic, morphological, kinetic studies, and molecular docking. The results demonstrated that compounds 21b, 21d, 21e and 21f exhibited strong antibacterial activity similar to that of linezolid toward five Gram-positive bacteria. After observing the effect of the drug on the morphology and growth dynamics of the bacteria, the possible modes of action were predicted by molecular docking. Furthermore, the antibiofilm activity and the potential drug resistance assay was proceeded. These compounds exhibited universal antibiofilm activity and compound 21d showed significant concentration-dependent inhibition of biofilm formation. Compound 21d also showed a stable effect on S. pneumoniae (ATCC 49619) with less drug resistance growth for 15 days, which is much longer than that of linezolid. Overall, these results can be used to guide further exploration of novel antimicrobial agents.
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Affiliation(s)
- Bo Jin
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Tong Wang
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Jia-yi Chen
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Xiao-qing Liu
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Yi-xin Zhang
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Xiu-ying Zhang
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Zun-lai Sheng
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Hong-Liang Yang
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
- *Correspondence: Hong-Liang Yang,
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19
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Syroegin EA, Aleksandrova EV, Polikanov YS. Structural basis for the inability of chloramphenicol to inhibit peptide bond formation in the presence of A-site glycine. Nucleic Acids Res 2022; 50:7669-7679. [PMID: 35766409 PMCID: PMC9303264 DOI: 10.1093/nar/gkac548] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/08/2022] [Accepted: 06/28/2022] [Indexed: 12/11/2022] Open
Abstract
Ribosome serves as a universal molecular machine capable of synthesis of all the proteins in a cell. Small-molecule inhibitors, such as ribosome-targeting antibiotics, can compromise the catalytic versatility of the ribosome in a context-dependent fashion, preventing transpeptidation only between particular combinations of substrates. Classic peptidyl transferase center inhibitor chloramphenicol (CHL) fails to inhibit transpeptidation reaction when the incoming A site acceptor substrate is glycine, and the molecular basis for this phenomenon is unknown. Here, we present a set of high-resolution X-ray crystal structures that explain why CHL is unable to inhibit peptide bond formation between the incoming glycyl-tRNA and a nascent peptide that otherwise is conducive to the drug action. Our structures reveal that fully accommodated glycine residue can co-exist in the A site with the ribosome-bound CHL. Moreover, binding of CHL to a ribosome complex carrying glycyl-tRNA does not affect the positions of the reacting substrates, leaving the peptide bond formation reaction unperturbed. These data exemplify how small-molecule inhibitors can reshape the A-site amino acid binding pocket rendering it permissive only for specific amino acid residues and rejective for the other substrates extending our detailed understanding of the modes of action of ribosomal antibiotics.
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Affiliation(s)
- Egor A Syroegin
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Elena V Aleksandrova
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Yury S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.,Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.,Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
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20
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Recent Developments in Methicillin-Resistant Staphylococcus aureus (MRSA) Treatment: A Review. Antibiotics (Basel) 2022; 11:antibiotics11050606. [PMID: 35625250 PMCID: PMC9137690 DOI: 10.3390/antibiotics11050606] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 02/28/2022] [Accepted: 03/23/2022] [Indexed: 11/28/2022] Open
Abstract
Staphylococcus aureus (S. aureus) is a Gram-positive bacterium that may cause life-threatening diseases and some minor infections in living organisms. However, it shows notorious effects when it becomes resistant to antibiotics. Strain variants of bacteria, viruses, fungi, and parasites that have become resistant to existing multiple antimicrobials are termed as superbugs. Methicillin is a semisynthetic antibiotic drug that was used to inhibit staphylococci pathogens. The S. aureus resistant to methicillin is known as methicillin-resistant Staphylococcus aureus (MRSA), which became a superbug due to its defiant activity against the antibiotics and medications most commonly used to treat major and minor infections. Successful MRSA infection management involves rapid identification of the infected site, culture and susceptibility tests, evidence-based treatment, and appropriate preventive protocols. This review describes the clinical management of MRSA pathogenesis, recent developments in rapid diagnosis, and antimicrobial treatment choices for MRSA.
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21
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Ndukwe ARN, Wiedbrauk S, Boase NRB, Fairfull-Smith KE. Strategies to improve the potency of oxazolidinones towards bacterial biofilms. Chem Asian J 2022; 17:e202200201. [PMID: 35352479 PMCID: PMC9321984 DOI: 10.1002/asia.202200201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/28/2022] [Indexed: 11/29/2022]
Abstract
Biofilms are part of the natural lifecycle of bacteria and are known to cause chronic infections that are difficult to treat. Most antibiotics are developed and tested against bacteria in the planktonic state and are ineffective against bacterial biofilms. The oxazolidinones, including the last resort drug linezolid, are one of the main classes of synthetic antibiotics progressed to clinical use in the last 50 years. They have a unique mechanism of action and only develop low levels of resistance in the clinical setting. With the aim of providing insight into strategies to design more potent antibiotic compounds with activity against bacterial biofilms, we review the biofilm activity of clinically approved oxazolidinones and report on structural modifications to oxazolidinones and their delivery systems which lead to enhanced anti‐biofilm activity.
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Affiliation(s)
- Audrey R N Ndukwe
- Queensland University of Technology - QUT: Queensland University of Technology, Faculty of Science, AUSTRALIA
| | - Sandra Wiedbrauk
- Queensland University of Technology - QUT: Queensland University of Technology, Faculty of Science, AUSTRALIA
| | - Nathan R B Boase
- Queensland University of Technology - QUT: Queensland University of Technology, Faculty of Science, AUSTRALIA
| | - Kathryn E Fairfull-Smith
- Queensland University of Technology Faculty of Science, Centre for Materials Science, 2 George St, 4001, Brisbane, AUSTRALIA
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22
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Syroegin EA, Flemmich L, Klepacki D, Vazquez-Laslop N, Micura R, Polikanov YS. Structural basis for the context-specific action of the classic peptidyl transferase inhibitor chloramphenicol. Nat Struct Mol Biol 2022; 29:152-161. [DOI: 10.1038/s41594-022-00720-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 12/23/2021] [Indexed: 02/06/2023]
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23
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Tsai K, Stojković V, Lee DJ, Young ID, Szal T, Klepacki D, Vázquez-Laslop N, Mankin AS, Fraser JS, Fujimori DG. Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics. Nat Struct Mol Biol 2022; 29:162-171. [DOI: 10.1038/s41594-022-00723-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 01/05/2022] [Indexed: 01/02/2023]
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24
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Itoh Y, Singh V, Khawaja A, Naschberger A, Nguyen MD, Rorbach J, Amunts A. Structure of the mitoribosomal small subunit with streptomycin reveals Fe-S clusters and physiological molecules. eLife 2022; 11:77460. [PMID: 36480258 PMCID: PMC9731571 DOI: 10.7554/elife.77460] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 10/27/2022] [Indexed: 12/13/2022] Open
Abstract
The mitoribosome regulates cellular energy production, and its dysfunction is associated with aging. Inhibition of the mitoribosome can be caused by off-target binding of antimicrobial drugs and was shown to be coupled with a bilateral decreased visual acuity. Previously, we reported mitochondria-specific protein aspects of the mitoribosome, and in this article we present a 2.4-Å resolution structure of the small subunit in a complex with the anti-tuberculosis drug streptomycin that reveals roles of non-protein components. We found iron-sulfur clusters that are coordinated by different mitoribosomal proteins, nicotinamide adenine dinucleotide (NAD) associated with rRNA insertion, and posttranslational modifications. This is the first evidence of inter-protein coordination of iron-sulfur, and the finding of iron-sulfur clusters and NAD as fundamental building blocks of the mitoribosome directly links to mitochondrial disease and aging. We also report details of streptomycin interactions, suggesting that the mitoribosome-bound streptomycin is likely to be in hydrated gem-diol form and can be subjected to other modifications by the cellular milieu. The presented approach of adding antibiotics to cultured cells can be used to define their native structures in a bound form under more physiological conditions, and since streptomycin is a widely used drug for treatment, the newly resolved features can serve as determinants for targeting.
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Affiliation(s)
- Yuzuru Itoh
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
| | - Vivek Singh
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
| | - Anas Khawaja
- Department of Medical Biochemistry and Biophysics, Karolinska InstituteStockholmSweden,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska InstitutetStockholmSweden
| | - Andreas Naschberger
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
| | - Minh Duc Nguyen
- Department of Medical Biochemistry and Biophysics, Karolinska InstituteStockholmSweden,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska InstitutetStockholmSweden
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Karolinska InstituteStockholmSweden,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska InstitutetStockholmSweden
| | - Alexey Amunts
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
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25
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Qi Y, Ding X, Wang K, Yan P, Guo X, Ma S, Xiao M, Sun P, Liu S, Hou Y, Zhao Y. Design, synthesis, and antibacterial evaluation of a novel series of biaryloxazolidinone derivatives against Gram-positive bacteria. NEW J CHEM 2022. [DOI: 10.1039/d2nj00479h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of new biaryloxazolidinone derivatives has been designed and synthesized using the combination principle and blocking metabolic site to improve their antibacterial activity and stability.
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Affiliation(s)
- Yinliang Qi
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning, 110016, China
| | - Xiudong Ding
- Department of Clinical Laboratory, The Eighth Medical Center of PLA General Hospital, Beijing 100091, China
| | - Kun Wang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning, 110016, China
| | - Pingzhen Yan
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning, 110016, China
| | - Xinxin Guo
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning, 110016, China
| | - Shiwei Ma
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning, 110016, China
| | - Mingfei Xiao
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning, 110016, China
| | - Pengrui Sun
- Department of Clinical Laboratory, The Eighth Medical Center of PLA General Hospital, Beijing 100091, China
| | - Siyu Liu
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning, 110016, China
| | - Yunlei Hou
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning, 110016, China
| | - Yanfang Zhao
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning, 110016, China
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26
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Wang L, Zhang Y, Liu S, Huang N, Zeng W, Xu W, Zhou T, Shen M. Comparison of Anti-Microbic and Anti-Biofilm Activity Among Tedizolid and Radezolid Against Linezolid-Resistant Enterococcus faecalis Isolates. Infect Drug Resist 2021; 14:4619-4627. [PMID: 34764658 PMCID: PMC8577528 DOI: 10.2147/idr.s331345] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 10/13/2021] [Indexed: 12/24/2022] Open
Abstract
Background The emergence and spread of linezolid-resistant Enterococcus faecalis (E. faecalis) have emerged as a serious threat to human health globally. Therefore, this study aims to compare the anti-microbic as well as the anti-biofilm activity of linezolid, tedizolid, and radezolid against linezolid-resistant E. faecalis. Methods A total of 2128 E. faecalis isolates were assessed from the First Affiliated Hospital of Wenzhou Medical University from 2011 to 2019. Antibiotic sensitivity was evaluated using the micro broth dilution method. Oxazolidinone-resistant chromosomal and plasmid-borne genes such as cfr, cfr(A), cfr(B), cfr(C), cfr(D), optrA, and poxtA were detected by PCR and then sequenced to detect the presence of mutations in the domain V of the 23S rRNA and the ribosomal proteins L3, L4, and L22. Conjugation experiments were conducted using the broth method. The inhibition and eradication of biofilm were evaluated through crystal violet staining, whereas the efflux pump activities were detected by agar dilution. Results Out of 2128 isolated E. faecalis, 71 (3.34%) were linezolid-resistant isolates in which the MICs of tedizolid and radezolid ranged from 1 to 4 μg/mL and 0.5–1 μg/mL, respectively. The MIC50/MIC90 of tedizolid and radezolid were 4 and 8-fold lower than the linezolid, respectively. Out of 71 resistant isolates, 57 (80.28%) carried optrA, 1 (1.41%) carried cfr, 4 (5.63%) carried optrA and cfr, and 6 (8.45%) carried optrA and cfr(D), with no mutations of 23S rRNA gene and ribosomal proteins L3, L4, and L22. Besides, the transfer rate of the optrA, cfr, and cfr(D) was 17.91%, 0% and 0%, respectively. Radezolid showed more effectiveness in eradicating biofilm (8 × MIC). However, tedizolid was more effective than radezolid and linezolid in inhibiting the biofilm formation (1/4 MIC, 1/8MIC, and 1/16MIC). Additionally, in combination with CCCP, the MICs of radezolid in all linezolid-resistant isolates decreased ≥4-fold. Conclusion Radezolid showed greater antimicrobial activity than tedizolid and linezolid against linezolid-resistant E. faecalis. However, both tedizolid and radezolid showed differential activity on biofilm inhibition, eradication, and efflux pump compared to linezolid. Thus, our study might bring important clinical value in the application of these drugs for resistant pathogenic strains.
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Affiliation(s)
- Lingbo Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Ying Zhang
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Shixing Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Na Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Weiliang Zeng
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Wenya Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Tieli Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Mo Shen
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
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27
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Rekand IH, Brenk R. DrugPred_RNA-A Tool for Structure-Based Druggability Predictions for RNA Binding Sites. J Chem Inf Model 2021; 61:4068-4081. [PMID: 34286972 PMCID: PMC8389535 DOI: 10.1021/acs.jcim.1c00155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
![]()
RNA is an emerging
target for drug discovery. However, like for
proteins, not all RNA binding sites are equally suited to be addressed
with conventional drug-like ligands. To this end, we have developed
the structure-based druggability predictor DrugPred_RNA to identify
druggable RNA binding sites. Due to the paucity of annotated RNA binding
sites, the predictor was trained on protein pockets, albeit using
only descriptors that can be calculated for both RNA and protein binding
sites. DrugPred_RNA performed well in discriminating druggable from
less druggable binding sites for the protein set and delivered predictions
for selected RNA binding sites that agreed with manual assignment.
In addition, most drug-like ligands contained in an RNA test set were
found in pockets predicted to be druggable, further adding confidence
to the performance of DrugPred_RNA. The method is robust against conformational
and sequence changes in the binding sites and can contribute to direct
drug discovery efforts for RNA targets.
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Affiliation(s)
- Illimar Hugo Rekand
- Department of Biomedicine, University of Bergen, Jonas Lies Vei, 5020 Bergen, Norway
| | - Ruth Brenk
- Department of Biomedicine, University of Bergen, Jonas Lies Vei, 5020 Bergen, Norway
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28
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Zhao Q, Xin L, Liu Y, Liang C, Li J, Jian Y, Li H, Shi Z, Liu H, Cao W. Current Landscape and Future Perspective of Oxazolidinone Scaffolds Containing Antibacterial Drugs. J Med Chem 2021; 64:10557-10580. [PMID: 34260235 DOI: 10.1021/acs.jmedchem.1c00480] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The widespread use of antibiotics has made the problem of bacterial resistance increasingly serious, and the study of new drug-resistant bacteria has become the main direction of antibacterial drug research. Among antibiotics, the fully synthetic oxazolidinone antibacterial drugs linezolid and tedizolid have been successfully marketed and have achieved good clinical treatment effects. Oxazolidinone antibacterial drugs have good pharmacokinetic and pharmacodynamic characteristics and unique antibacterial mechanisms, and resistant bacteria are sensitive to them. This Perspective focuses on reviewing oxazolidinones based on the structural modification of linezolid and new potential oxazolidinone drugs in the past 10 years, mainly describing their structure, antibacterial activity, safety, druggability, and so on, and discusses their structure-activity relationships, providing insight into the reasonable design of safer and more potent oxazolidinone antibacterial drugs.
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Affiliation(s)
- Qianqian Zhao
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Liang Xin
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China.,Xi'an Xuri Shengchang Pharmaceutical Technology Co., Ltd., High-tech Zone, Xi'an 710075, P. R. China
| | - Yuzhi Liu
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Chengyuan Liang
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Jingyi Li
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Yanlin Jian
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Han Li
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Zhenfeng Shi
- Department of Urology Surgery Center, Xinjiang Uyghur People's Hospital, Urumqi 830002, P. R. China
| | - Hong Liu
- Zhuhai Jinan Selenium Source Nanotechnology Co., Ltd., Hengqin New Area, Zhuhai 519030, P. R. China
| | - Wenqiang Cao
- Zhuhai Jinan Selenium Source Nanotechnology Co., Ltd., Hengqin New Area, Zhuhai 519030, P. R. China
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29
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Oxazolidinone Antibiotics: Chemical, Biological and Analytical Aspects. Molecules 2021; 26:molecules26144280. [PMID: 34299555 PMCID: PMC8305375 DOI: 10.3390/molecules26144280] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/07/2021] [Accepted: 07/12/2021] [Indexed: 11/17/2022] Open
Abstract
This review covers the main aspects concerning the chemistry, the biological activity and the analytical determination of oxazolidinones, the only new class of synthetic antibiotics advanced in clinical use over the past 50 years. They are characterized by a chemical structure including the oxazolidone ring with the S configuration of substituent at C5, the acylaminomethyl group linked to C5 and the N-aryl substituent. The synthesis of oxazolidinones has gained increasing interest due to their unique mechanism of action that assures high antibiotic efficiency and low susceptibility to resistance mechanisms. Here, the main features of oxazolidinone antibiotics licensed or under development, such as Linezolid, Sutezolid, Eperezolid, Radezolid, Contezolid, Posizolid, Tedizolid, Delpazolid and TBI-223, are discussed. As they are protein synthesis inhibitors active against a wide spectrum of multidrug-resistant Gram-positive bacteria, their biological activity is carefully analyzed, together with the drug delivery systems recently developed to overcome the poor oxazolidinone water solubility. Finally, the most employed analytical techniques for oxazolidinone determination in different matrices, such as biological fluids, tissues, drugs and natural waters, are reviewed. Most are based on HPLC (High Performance Liquid Chromatography) coupled with UV-Vis or mass spectrometer detectors, but, to a lesser extent are also based on spectrofluorimetry or voltammetry.
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30
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Morgon NH, Grandini GS, Yoguim MI, Porto CM, Santana LC, Biswas S, de Souza AR. Potential activity of Linezolid against SARS-CoV-2 using electronic and molecular docking study. J Mol Model 2021; 27:222. [PMID: 34236527 PMCID: PMC8264178 DOI: 10.1007/s00894-021-04828-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/16/2021] [Indexed: 01/18/2023]
Abstract
The crescent evolution of a global pandemic COVID-19 and its respiratory syndrome (SARS-Cov-2) has been a constant concern (Ghosh 2021; Khan et al. 2021; Alazmi and Motwalli 2020; Vargas et al. 2020). The absence of a proven and effective medication has compelled all the scientific community to search for a new drug. The use of known drugs is a faster way to develop new therapies. Molecular docking is a powerful tool (Gao et al. J Mol Model 10: 44-54, 2004; Singh et al. J Mol Model 18: 39-51, 2012; Schulz-Gasch and Stahl J Mol Model 9:47-57, 2003) to study the interaction of potential drugs with SARS-CoV-2, Alsalme et al. (2020) and Sanders et al. (2020) spike protein as a consequence the main goal of this article is to present the result of the study of an interaction between (R and S)-Linezolid with receptor-binding domain (RBD) of SARS-Cov-2 spike protein complexed with human Angiostensin-converting enzyme 2 (ACE2) (6vW1 - from PDB). The Linezolid enantiomers were optimized at B3LYP/6-311++G(2d,p) level of theory. Molecular docking of the system (S)-Linezolid⋯RBD⋯ACE2 and (R)-Linezolid⋯RBD⋯ACE2 was performed, the analysis was made using LigPlot+ and NCIplot software packages, to understand the intermolecular interactions. The UV-Vis and ECD of the complexes - (R and S)-Linezolid⋯RBD⋯ACE2 were performed in two layers with DFT/6-311++G(3df,2p) and DFT/6-31G(d), respectively. The results showed that only the (S)-Linezolid had a stable interaction with - 8.05 kcal.mol- 1, whereas all the R-enantiomeric configurations had positive values of binding energy. The (S)-Linezolid had the same interactions as in the (S)-Linezolid ⋯ Haluarcula morismortui Ribosomal system, where it is well-known the fact that the latter has biological activity. A specific interaction on the fluorine ring justified an attenuation on the ECD signal, in comparison to isolated species. Therefore, some biological activity of (S)-Linezolid with SARS-CoV-2 RBD was expected, indicated by the modification of its ECD signal and justified by a similar interaction in the S-Linezolid⋯Haluarcula marismortui Ribosomal system.
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Affiliation(s)
- Nelson H Morgon
- Department of Physical Chemistry, Campinas State University, Institute of Chemistry, Campinas, São Paulo, 13083-970, Brazil.
| | - Giulia S Grandini
- School of Science, Department of Chemistry, São Paulo State University, Bauru, São Paulo, 17033-360, Brazil
| | - Maurício I Yoguim
- School of Science, Department of Chemistry, São Paulo State University, Bauru, São Paulo, 17033-360, Brazil
| | - Caio M Porto
- Department of Physical Chemistry, Campinas State University, Institute of Chemistry, Campinas, São Paulo, 13083-970, Brazil
| | - Lucas C Santana
- Department of Physical Chemistry, Campinas State University, Institute of Chemistry, Campinas, São Paulo, 13083-970, Brazil
| | - Srijit Biswas
- Department of Chemistry, University of Calcutta, 92, A.P.C. Road, Kolkata, 700009, India
| | - Aguinaldo R de Souza
- School of Science, Department of Chemistry, São Paulo State University, Bauru, São Paulo, 17033-360, Brazil
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31
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Wen S, Gao X, Zhao W, Huo F, Jiang G, Dong L, Zhao L, Wang F, Yu X, Huang H. Comparison of the in vitro activity of linezolid, tedizolid, sutezolid, and delpazolid against rapidly growing mycobacteria isolated in Beijing, China. Int J Infect Dis 2021; 109:253-260. [PMID: 34216736 DOI: 10.1016/j.ijid.2021.06.055] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/27/2021] [Accepted: 06/24/2021] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The natural resistance of rapidly growing mycobacteria (RGM) to multiple antibiotics renders the treatment of the infections caused less successful. The objective of this study was to evaluate the in vitro susceptibilities of four oxazolidinones against different RGM species. METHODS The microplate alamarBlue assay was performed to identify the minimum inhibitory concentrations (MICs) of four oxazolidinones - delpazolid, sutezolid, tedizolid, and linezolid - for 32 reference strains and 115 clinical strains of different RGM species. The MIC breakpoint concentration was defined as 16 μg/ml for linezolid. Next, the gene fragments associated with oxazolidinone resistance were amplified and sequenced, and mutations were defined in contrast with the sequences of the reference strains. RESULTS Tedizolid showed the strongest inhibitory activity against the Mycobacterium abscessus isolates. Delpazolid exhibited better antimicrobial activity against the Mycobacterium fortuitum isolates when compared to linezolid, with 4-fold lower MIC values. The protein alignment and structure-based analysis showed that there might be no correlation between oxazolidinone resistance and mutations in the rplC, rplD, and 23S rRNA genes in the tested RGM. CONCLUSIONS Tedizolid had the strongest inhibitory activity against M. abscessus in vitro, while delpazolid presented the best inhibitory activity against M. fortuitum. This provides important insights into the potential clinical application of oxazolidinones to treat RGM infections.
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Affiliation(s)
- Shu'an Wen
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Xiaopan Gao
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Weijie Zhao
- The Administration Office of Clinical Trial, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Fengmin Huo
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Guanglu Jiang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Lingling Dong
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Liping Zhao
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Fen Wang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Xia Yu
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing, China.
| | - Hairong Huang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing, China.
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32
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Pancu DF, Scurtu A, Macasoi IG, Marti D, Mioc M, Soica C, Coricovac D, Horhat D, Poenaru M, Dehelean C. Antibiotics: Conventional Therapy and Natural Compounds with Antibacterial Activity-A Pharmaco-Toxicological Screening. Antibiotics (Basel) 2021; 10:401. [PMID: 33917092 PMCID: PMC8067816 DOI: 10.3390/antibiotics10040401] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 12/11/2022] Open
Abstract
Antibiotics are considered as a cornerstone of modern medicine and their discovery offers the resolution to the infectious diseases problem. However, the excessive use of antibiotics worldwide has generated a critical public health issue and the bacterial resistance correlated with antibiotics inefficiency is still unsolved. Finding novel therapeutic approaches to overcome bacterial resistance is imperative, and natural compounds with antibacterial effects could be considered a promising option. The role played by antibiotics in tumorigenesis and their interrelation with the microbiota are still debatable and are far from being elucidated. Thus, the present manuscript offers a global perspective on antibiotics in terms of evolution from a historical perspective with an emphasis on the main classes of antibiotics and their adverse effects. It also highlights the connection between antibiotics and microbiota, focusing on the dual role played by antibiotics in tumorigenesis. In addition, using the natural compounds with antibacterial properties as potential alternatives for the classical antibiotic therapy is discussed.
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Affiliation(s)
- Daniel Florin Pancu
- Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 1, 300041 Timisoara, Romania; (D.F.P.); (D.H.); (M.P.)
| | - Alexandra Scurtu
- Faculty of Pharmacy, “Victor Babeș” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania; (A.S.); (M.M.); (C.S.); (D.C.); (C.D.)
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
| | - Ioana Gabriela Macasoi
- Faculty of Pharmacy, “Victor Babeș” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania; (A.S.); (M.M.); (C.S.); (D.C.); (C.D.)
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
| | - Daniela Marti
- Faculty of Medicine, Western University Vasile Goldis Arad, 94 Revolutiei Blvd., 310025 Arad, Romania
| | - Marius Mioc
- Faculty of Pharmacy, “Victor Babeș” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania; (A.S.); (M.M.); (C.S.); (D.C.); (C.D.)
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
| | - Codruta Soica
- Faculty of Pharmacy, “Victor Babeș” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania; (A.S.); (M.M.); (C.S.); (D.C.); (C.D.)
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
| | - Dorina Coricovac
- Faculty of Pharmacy, “Victor Babeș” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania; (A.S.); (M.M.); (C.S.); (D.C.); (C.D.)
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
| | - Delia Horhat
- Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 1, 300041 Timisoara, Romania; (D.F.P.); (D.H.); (M.P.)
| | - Marioara Poenaru
- Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 1, 300041 Timisoara, Romania; (D.F.P.); (D.H.); (M.P.)
| | - Cristina Dehelean
- Faculty of Pharmacy, “Victor Babeș” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania; (A.S.); (M.M.); (C.S.); (D.C.); (C.D.)
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
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Sharma A, De Rosa M, Singla N, Singh G, Barnwal RP, Pandey A. Tuberculosis: An Overview of the Immunogenic Response, Disease Progression, and Medicinal Chemistry Efforts in the Last Decade toward the Development of Potential Drugs for Extensively Drug-Resistant Tuberculosis Strains. J Med Chem 2021; 64:4359-4395. [PMID: 33826327 DOI: 10.1021/acs.jmedchem.0c01833] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Tuberculosis (TB) is a slow growing, potentially debilitating disease that has plagued humanity for centuries and has claimed numerous lives across the globe. Concerted efforts by researchers have culminated in the development of various strategies to combat this malady. This review aims to raise awareness of the rapidly increasing incidences of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis, highlighting the significant modifications that were introduced in the TB treatment regimen over the past decade. A description of the role of pathogen-host immune mechanisms together with strategies for prevention of the disease is discussed. The struggle to develop novel drug therapies has continued in an effort to reduce the treatment duration, improve patient compliance and outcomes, and circumvent TB resistance mechanisms. Herein, we give an overview of the extensive medicinal chemistry efforts made during the past decade toward the discovery of new chemotypes, which are potentially active against TB-resistant strains.
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Affiliation(s)
- Akanksha Sharma
- Department of Biophysics, Panjab University, Chandigarh 160014, India.,UIPS, Panjab University, Chandigarh 160014, India
| | - Maria De Rosa
- Drug Discovery Unit, Ri.MED Foundation, Palermo 90133, Italy
| | - Neha Singla
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Gurpal Singh
- UIPS, Panjab University, Chandigarh 160014, India
| | - Ravi P Barnwal
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Ankur Pandey
- Department of Chemistry, Panjab University, Chandigarh 160014, India
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Makarov GI, Reshetnikova RV. Investigation of radezolid interaction with non-canonical chloramphenicol binding site by molecular dynamics simulations. J Mol Graph Model 2021; 105:107902. [PMID: 33798835 DOI: 10.1016/j.jmgm.2021.107902] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 12/12/2022]
Abstract
Radezolid is a promising antibiotic of oxazolidinone family, which is able to overcome effect of some linezolid resistance mechanisms of bacterial ribosomes. The structure of the radezolid complex with ribosomes was never published but, by analogy with linezolid, it is considered to prevent the binding of aminoacyl-tRNA to the A-site of the ribosome large subunit. However, as with linezolid, it can be assumed that radezolid binds to the alternative binding site existing in the A,A/P,P-ribosome. In the present article we have investigated this issue by molecular dynamics simulations and proposed the structure of the radezolid complex with a E. coli ribosome, which is consistent with available data of biochemical investigations of radezolid action.
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Affiliation(s)
- G I Makarov
- South Ural State University, 454080, Chelyabinsk, Russia.
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35
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Shen T, Penewit K, Waalkes A, Xu L, Salipante SJ, Nath A, Werth BJ. Identification of a novel tedizolid resistance mutation in rpoB of MRSA after in vitro serial passage. J Antimicrob Chemother 2021; 76:292-296. [PMID: 33057715 DOI: 10.1093/jac/dkaa422] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/13/2020] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES Tedizolid is an oxazolidinone antimicrobial with activity against Gram-positive bacteria, including MRSA. Tedizolid resistance is uncommon and tedizolid's capacity to select for cross-resistance to other antimicrobials is incompletely understood. The objective of this study was to further explore the phenotypic and genetic basis of tedizolid resistance in MRSA. METHODS We selected for tedizolid resistance in an MRSA laboratory strain, N315, by serial passage until an isolate with an MIC ≥1 log2 dilution above the breakpoint for resistance (≥2 mg/L) was recovered. This isolate was subjected to WGS and susceptibility to a panel of related and unrelated antimicrobials was tested in order to determine cross-resistance. Homology modelling was performed to evaluate the potential impact of the mutation on target protein function. RESULTS After 10 days of serial passage we recovered a phenotypically stable mutant with a tedizolid MIC of 4 mg/L. WGS revealed only one single nucleotide variant (A1345G) in rpoB, corresponding to amino acid substitution D449N. MICs of linezolid, chloramphenicol, retapamulin and quinupristin/dalfopristin increased by ≥2 log2 dilutions, suggesting the emergence of the so-called 'PhLOPSa' resistance phenotype. Susceptibility to other drugs, including rifampicin, was largely unchanged. Homology models revealed that the mutated residue of RNA polymerase would be unlikely to directly affect oxazolidinone action. CONCLUSIONS To the best of our knowledge, this is the first time that an rpoB mutation has been implicated in resistance to PhLOPSa antimicrobials. The mechanism of resistance remains unclear, but is likely indirect, involving σ-factor binding or other alterations in transcriptional regulation.
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Affiliation(s)
- Tianwei Shen
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Kelsi Penewit
- Department of Laboratory Medicine, School of Medicine, University of Washington, Seattle, WA, USA
| | - Adam Waalkes
- Department of Laboratory Medicine, School of Medicine, University of Washington, Seattle, WA, USA
| | - Libin Xu
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Stephen J Salipante
- Department of Laboratory Medicine, School of Medicine, University of Washington, Seattle, WA, USA
| | - Abhinav Nath
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Brian J Werth
- Department of Pharmacy, School of Pharmacy, University of Washington, Seattle, WA, USA
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Selective toxicity of antibacterial agents-still a valid concept or do we miss chances and ignore risks? Infection 2020; 49:29-56. [PMID: 33367978 PMCID: PMC7851017 DOI: 10.1007/s15010-020-01536-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/04/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Selective toxicity antibacteribiotics is considered to be due to interactions with targets either being unique to bacteria or being characterized by a dichotomy between pro- and eukaryotic pathways with high affinities of agents to bacterial- rather than eukaryotic targets. However, the theory of selective toxicity oversimplifies the complex modes of action of antibiotics in pro- and eukaryotes. METHODS AND OBJECTIVE This review summarizes data describing multiple modes of action of antibiotics in eukaryotes. RESULTS Aminoglycosides, macrolides, oxazolidinones, chloramphenicol, clindamycin, tetracyclines, glycylcyclines, fluoroquinolones, rifampicin, bedaquillin, ß-lactams inhibited mitochondrial translation either due to binding to mitosomes, inhibition of mitochondrial RNA-polymerase-, topoisomerase 2ß-, ATP-synthesis, transporter activities. Oxazolidinones, tetracyclines, vancomycin, ß-lactams, bacitracin, isoniazid, nitroxoline inhibited matrix-metalloproteinases (MMP) due to chelation with zinc and calcium, whereas fluoroquinols fluoroquinolones and chloramphenicol chelated with these cations, too, but increased MMP activities. MMP-inhibition supported clinical efficacies of ß-lactams and daptomycin in skin-infections, and of macrolides, tetracyclines in respiratory-diseases. Chelation may have contributed to neuroprotection by ß-lactams and fluoroquinolones. Aminoglycosides, macrolides, chloramphenicol, oxazolidins oxazolidinones, tetracyclines caused read-through of premature stop codons. Several additional targets for antibiotics in human cells have been identified like interaction of fluoroquinolones with DNA damage repair in eukaryotes, or inhibition of mucin overproduction by oxazolidinones. CONCLUSION The effects of antibiotics on eukaryotes are due to identical mechanisms as their antibacterial activities because of structural and functional homologies of pro- and eukaryotic targets, so that the effects of antibiotics on mammals are integral parts of their overall mechanisms of action.
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Fostier CR, Monlezun L, Ousalem F, Singh S, Hunt JF, Boël G. ABC-F translation factors: from antibiotic resistance to immune response. FEBS Lett 2020; 595:675-706. [PMID: 33135152 DOI: 10.1002/1873-3468.13984] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 12/24/2022]
Abstract
Energy-dependent translational throttle A (EttA) from Escherichia coli is a paradigmatic ABC-F protein that controls the first step in polypeptide elongation on the ribosome according to the cellular energy status. Biochemical and structural studies have established that ABC-F proteins generally function as translation factors that modulate the conformation of the peptidyl transferase center upon binding to the ribosomal tRNA exit site. These factors, present in both prokaryotes and eukaryotes but not in archaea, use related molecular mechanisms to modulate protein synthesis for heterogenous purposes, ranging from antibiotic resistance and rescue of stalled ribosomes to modulation of the mammalian immune response. Here, we review the canonical studies characterizing the phylogeny, regulation, ribosome interactions, and mechanisms of action of the bacterial ABC-F proteins, and discuss the implications of these studies for the molecular function of eukaryotic ABC-F proteins, including the three human family members.
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Affiliation(s)
- Corentin R Fostier
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Laura Monlezun
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Farès Ousalem
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Shikha Singh
- Department of Biological Sciences, 702A Sherman Fairchild Center, Columbia University, New York, NY, USA
| | - John F Hunt
- Department of Biological Sciences, 702A Sherman Fairchild Center, Columbia University, New York, NY, USA
| | - Grégory Boël
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
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Abstract
The structural and regulatory elements in therapeutically relevant RNAs offer many opportunities for targeting by small molecules, yet fundamental understanding of what drives selectivity in small molecule:RNA recognition has been a recurrent challenge. In particular, RNAs tend to be more dynamic and offer less chemical functionality than proteins, and biologically active ligands must compete with the highly abundant and highly structured RNA of the ribosome. Indeed, the only small molecule drug targeting RNA other than the ribosome was just approved in August 2020, and our recent survey of the literature revealed fewer than 150 reported chemical probes that target non-ribosomal RNA in biological systems. This Feature outlines our efforts to improve small molecule targeting strategies and gain fundamental insights into small molecule:RNA recognition by analyzing patterns in both RNA-biased small molecule chemical space and RNA topological space privileged for differentiation. First, we synthesized libraries based on RNA binding scaffolds that allowed us to reveal general principles in small molecule:recognition and to ask precise chemical questions about drivers of affinity and selectivity. Elaboration of these scaffolds has led to recognition of medicinally relevant RNA targets, including viral and long noncoding RNA structures. More globally, we identified physicochemical, structural, and spatial properties of biologically active RNA ligands that are distinct from those of protein-targeted ligands, and we have provided the dataset and associated analytical tools as part of a publicly available online platform to facilitate RNA ligand discovery. At the same time, we used pattern recognition protocols to identify RNA topologies that can be differentially recognized by small molecules and have elaborated this technique to visualize conformational changes in RNA secondary structure. These fundamental insights into the drivers of RNA recognition in vitro have led to functional targeting of RNA structures in biological systems. We hope that these initial guiding principles, as well as the approaches and assays developed in their pursuit, will enable rapid progress toward the development of RNA-targeted chemical probes and ultimately new therapeutic approaches to a wide range of deadly human diseases.
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Affiliation(s)
- Amanda E Hargrove
- Department of Chemistry, Duke University, 124 Science Drive, Box 90346, Durham, NC 27708, USA.
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Cruz CD, Wrigstedt P, Moslova K, Iashin V, Mäkkylä H, Ghemtio L, Heikkinen S, Tammela P, Perea-Buceta JE. Installation of an aryl boronic acid function into the external section of N-aryl-oxazolidinones: Synthesis and antimicrobial evaluation. Eur J Med Chem 2020; 211:113002. [PMID: 33223262 DOI: 10.1016/j.ejmech.2020.113002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 10/23/2022]
Abstract
N-aryl-oxazolidinones is a prominent family of antimicrobials used for treating infections caused by clinically prevalent Gram-positive bacteria. Recently, boron-containing compounds have displayed intriguing potential in the antibiotic discovery setting. Herein, we report the unprecedented introduction of a boron-containing moiety such as an aryl boronic acid in the external region of the oxazolidinone structure via a chemoselective acyl coupling reaction. As a result, we accessed a series of analogues with a distal aryl boronic pharmacophore on the oxazolidinone scaffold. We identified that a peripheric linear conformation coupled with freedom of rotation and no further substitution on the external aryl boronic ring, an amido linkage with hydrogen bonding character, in addition to a para-relative disposition between boronic group and linker, are the optimal combination of structural features in this series for antimicrobial activity. In comparison to linezolid, the analogue comprising all those features, compound 20b, displayed levels of antimicrobial activity augmented by an eight-fold to a thirty-two-fold against a panel of Gram-positive strains, and a near one hundred-fold against Escherichia coli JW5503, a Gram-negative mutant strain with a defective efflux capability.
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Affiliation(s)
- Cristina D Cruz
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Finland
| | - Pauli Wrigstedt
- Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box 55, 00014, Finland
| | - Karina Moslova
- Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box 55, 00014, Finland
| | - Vladimir Iashin
- Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box 55, 00014, Finland
| | - Heidi Mäkkylä
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Finland
| | - Léo Ghemtio
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Finland
| | - Sami Heikkinen
- Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box 55, 00014, Finland
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Finland
| | - Jesus E Perea-Buceta
- Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box 55, 00014, Finland.
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Jiang J, Hou Y, Duan M, Wang B, Wu Y, Ding X, Zhao Y. Design, synthesis and antibacterial evaluation of novel oxazolidinone derivatives nitrogen-containing fused heterocyclic moiety. Bioorg Med Chem Lett 2020; 32:127660. [PMID: 33144245 DOI: 10.1016/j.bmcl.2020.127660] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/21/2020] [Accepted: 10/27/2020] [Indexed: 02/01/2023]
Abstract
A series of novel oxazolidinone derivatives with nitrogen-containing fused heterocyclic moiety were designed and synthesized in this article. Their antibacterial activities were measured against S. aureus, MRSA and MSSA by MIC assay. Most of them exhibited potent activity against Gram-positive pathogens comparable to Linezolid and Radezolid. Compound 3b, which exhibited significant antibacterial activity with MIC values ranging 0.5-1.0 μg/mL, might be a promising drug candidate for further investigation.
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Affiliation(s)
- Jia Jiang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Yunlei Hou
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Meibo Duan
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Baihang Wang
- Department of Clinical Laboratory, The 309th Hospital of Chinese People's Liberation Army, Beijing 100091, China
| | - Yachuang Wu
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Xiudong Ding
- Department of Clinical Laboratory, The 309th Hospital of Chinese People's Liberation Army, Beijing 100091, China.
| | - Yanfang Zhao
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China.
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Ding X, Wu Y, Tong A, Sun B, Zhao Y, Jiang Y. Evaluation of the Anti-Mycobacterial Activity of Newly Synthesized (S)-N-(3-(2-Fluoro-4'-(2-Amino-4-Thiazolyl)Biphenyl-4-Yl)-2-Oxo-1,3-Oxazolidie-5-Ylmethyl) Acetamide Derivative in Vitro and in Mycobacterium marinum-Infected Zebrafish. Jpn J Infect Dis 2020; 74:245-248. [PMID: 33132296 DOI: 10.7883/yoken.jjid.2020.307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Through our previous work, we have identified that novel oxazolidinone structures, the biaryloxazolidinone analogues containing a hydrazone moiety, act as promising antibacterial agents against gram-positive bacterial strains. Based on this active structure, in this study, we synthesized a series of novel oxazolidinones and determined their anti-mycobacterial activities in vitro and in Mycobacterium marinum-infected zebrafish. The in vitro anti-mycobacterial assay demonstrated that all of the synthesized compounds have potent efficacy against both H37Rv and clinical mycobacterial isolates. Among all the generated active agents, (S)-N-(3-(2-fluoro-4'-(2-amino-4-thiazolyl)biphenyl-4-yl)-2-oxo-1,3-oxazolidie-5-ylmethyl)acetamide (compound 7), whose in vitro MIC was 10-fold lower than that of linezolid, showed the strongest bactericidal effects, with ~2.2-log reduction of M. marinum load in zebrafish at 10 mg/kg dosage. Other novel oxazolidinones, compounds 9, 12, 16, and 21, exhibited reduction range of 1.1-1.8 log against M. marinum and displayed better efficacy than linezolid. Our results indicate that these identified compounds have the potential to be further developed as novel anti-mycobacterial agents.
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Affiliation(s)
- Xiudong Ding
- Department of clinical laboratory, the Eighth Medical Center of PLA General Hospital, China
| | - Yachuang Wu
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, China
| | - Aihua Tong
- Department of clinical laboratory, the Eighth Medical Center of PLA General Hospital, China
| | - Bin Sun
- Department of clinical laboratory, the Eighth Medical Center of PLA General Hospital, China
| | - Yanfang Zhao
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, China
| | - Ying Jiang
- Department of clinical laboratory, the Eighth Medical Center of PLA General Hospital, China
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Umumararungu T, Mukazayire MJ, Mpenda M, Mukanyangezi MF, Nkuranga JB, Mukiza J, Olawode EO. A review of recent advances in anti-tubercular drug development. Indian J Tuberc 2020; 67:539-559. [PMID: 33077057 DOI: 10.1016/j.ijtb.2020.07.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 03/24/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023]
Abstract
Tuberculosis is a global threat but in particular affects people from developing countries. It is thought that nearly a third of the population of the world live with its causative bacteria in a dormant form. Although tuberculosis is a curable disease, the chances of cure become slim as the disease becomes multidrug-resistant and the situation gets even worse as the disease becomes extensively drug-resistant. After approximately 5 decades without any new TB drug in the pipeline, there has been some good news in the recent years with the discovery of new drugs such as bedaquiline and delamanid as well as the discovery of new classes of anti-tubercular drugs. Some old drugs such as clofazimine, linezolid and many others which were not previously indicated for tuberculosis have been also repurposed for tuberculosis and they are performing well.
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Affiliation(s)
- Théoneste Umumararungu
- Department of Pharmacy, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Rwanda.
| | - Marie Jeanne Mukazayire
- Department of Pharmacy, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Rwanda
| | - Matabishi Mpenda
- Department of Pharmacy, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Rwanda
| | - Marie Françoise Mukanyangezi
- Department of Pharmacy, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Rwanda
| | - Jean Bosco Nkuranga
- Department of Chemistry, School of Science, College of Science and Technology, University of Rwanda, Rwanda
| | - Janvier Mukiza
- Department of Mathematical Science and Physical Education, School of Education, College of Education, University of Rwanda, Rwanda
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Novel Linezolid analogues with antiparasitic activity against Hymenolepis nana. Bioorg Chem 2020; 105:104359. [PMID: 33096310 DOI: 10.1016/j.bioorg.2020.104359] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/22/2020] [Accepted: 10/05/2020] [Indexed: 11/20/2022]
Abstract
The stereoselective synthesis and anti- Hymenolepis nana activity of six Linezolid-type compounds, obtained by chemical modification of l-Alanine, are reported in this work. The synthetic strategy was to prepare diasteromeric N,N-dibenzylamino oxazolidinones 1 and 2, and coupling with 4-(4-bromophenyl)morpholine (3) to obtain N,N-dibenzylamino Linezolid analogues 4 and 5. A hydrogenolysis reaction over 4 and 5 resulted in amino-free Linezolid analogues 6 and 7, which were acetylated to reach diasteromeric Linezolid analogues 8 and 9. The six Linezolid analogues 4-9 show in vitro antiparasitic activity against Hymenolepis nana cestode, but not against several bacterial strains. Interestingly, compounds 6, 7 and 9 exhibit high potency, having shorter paralysis and death times after exposure (6-10 and 18-21 min, respectively), shorter than those found with antihelmintic compound Praziquantel (20 and 30 min) at 20 mg/mL. In addition, a cytocompatibility assay of 6-9 with human cells (ARPE-19 cells) demonstrate a non-cytotoxic effect at 0.4 mM. These results show the pharmacological potential of the newly reported Linezolid-type analogues as antiparasitic agents against Hymenolepis nana.
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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: 179] [Impact Index Per Article: 44.8] [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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45
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Almeida LM, Gaca A, Bispo PM, Lebreton F, Saavedra JT, Silva RA, Basílio-Júnior ID, Zorzi FM, Filsner PH, Moreno AM, Gilmore MS. Coexistence of the Oxazolidinone Resistance-Associated Genes cfr and optrA in Enterococcus faecalis From a Healthy Piglet in Brazil. Front Public Health 2020; 8:518. [PMID: 33102417 PMCID: PMC7546817 DOI: 10.3389/fpubh.2020.00518] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 08/11/2020] [Indexed: 12/15/2022] Open
Abstract
Oxazolidinones are one of the most important antimicrobials potentially active against glycopeptide- and β-lactam-resistant Gram-positive pathogens. Linezolid—the first oxazolidinone to be approved for clinical use in 2000 by the US Food and Drug Administration—and the newer molecule in the class, tedizolid, inhibit protein synthesis by suppressing the formation of the 70S ribosomal complex in bacteria. Over the past two decades, transferable oxazolidinone resistance genes, in particular cfr and optrA, have been identified in Firmicutes isolated from healthcare-related infections, livestock, and the environment. Our goals in this study were to investigate the genetic contexts and the transferability of the cfr and optrA genes and examine genomic features, such as antimicrobial resistance genes, plasmid incompatibility types, and CRISPR-Cas defenses of a linezolid-resistant Enterococcus faecalis isolated in feces from a healthy pig during an antimicrobial surveillance program for animal production in Brazil. The cfr gene was found to be integrated into a transposon-like structure of 7,759 nt flanked by IS1216E and capable of excising and circularizing, distinguishing it from known genetic contexts for cfr in Enterococcus spp., while optrA was inserted into an Inc18 broad host-range plasmid of >58 kb. Conjugal transfer of cfr and optrA was shown by filter mating. The coexistence of cfr and optrA in an E. faecalis isolated from a healthy nursery pig highlights the need for monitoring the use of antibiotics in the Brazilian swine production system for controlling spread and proliferation of antibiotic resistance.
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Affiliation(s)
- Lara M Almeida
- Institute of Pharmaceutical Sciences, Federal University of Alagoas, Maceió, Brazil.,Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Anthony Gaca
- Department of Ophthalmology and Department of Microbiology, Harvard Medical School, Boston, MA, United States
| | - Paulo M Bispo
- Department of Ophthalmology and Department of Microbiology, Harvard Medical School, Boston, MA, United States
| | - François Lebreton
- Department of Ophthalmology and Department of Microbiology, Harvard Medical School, Boston, MA, United States
| | - Jose T Saavedra
- Department of Ophthalmology and Department of Microbiology, Harvard Medical School, Boston, MA, United States
| | - Rafael A Silva
- Institute of Pharmaceutical Sciences, Federal University of Alagoas, Maceió, Brazil
| | | | - Felipe M Zorzi
- School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Pedro H Filsner
- School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Andrea M Moreno
- School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Michael S Gilmore
- Department of Ophthalmology and Department of Microbiology, Harvard Medical School, Boston, MA, United States
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46
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Prolonged infusion of linezolid is associated with improved pharmacokinetic/pharmacodynamic (PK/PD) profiles in patients with external ventricular drains. Eur J Clin Pharmacol 2020; 77:79-86. [PMID: 32812063 DOI: 10.1007/s00228-020-02978-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/11/2020] [Indexed: 10/23/2022]
Abstract
OBJECTIVE We previously investigated the pharmacokinetic and pharmacodynamic (PK/PD) parameters of routine linezolid infusions (1 h) in patients with external ventricular drains (EVD). The aim of the study was to determine whether extended linezolid infusions (200 mg/h for 3 h) were more efficacious than short linezolid infusions (600 mg/h for 1 h). METHODS We collected cerebrospinal fluid (CSF) and plasma samples from 10 patients who received linezolid infusions after cerebral hemorrhage surgery with EVDs. Linezolid concentrations were measured by high-performance liquid chromatography (HPLC). A Monte Carlo simulation was used to measure the probability of target attainments (PTA) and the PK/PD indexes at four minimum inhibitory concentrations (MIC). RESULTS When the same dose (600 mg) was given as an extended infusion (3 h), linezolid reached its maximum concentrations in the plasma and CSF at 3.00 h and 4.40 h, respectively. The mean penetration of linezolid in CSF was 41.31%. Using the parameter of AUC0-24 h/MIC ≥ 100, the plasma PTA provided good coverage at > 90% when MIC was ≤ 1 μg/mL, while the values were 0 in CSF. Using the parameter %T (time) > MIC ≥ 85%, the PTA in both the plasma and CSF provided good coverage when MIC ≤ 2 μg/mL. Compared with routine infusions, prolonged infusion times (3 h) showed increased PTA of linezolid. CONCLUSIONS Prolonged infusion times increased the concentration of linezolid in the plasma, leading to improved therapeutic outcomes. However, this improvement did not exist in CSF. Lastly, the PK/PD indicator AUC/MIC ≥ 100 may be used to achieve improved outcomes in patients with critical infections.
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47
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Zhao H, Wang B, Fu L, Li G, Lu H, Liu Y, Sheng L, Li Y, Zhang B, Lu Y, Ma C, Huang H, Zhang D, Lu Y. Discovery of a Conformationally Constrained Oxazolidinone with Improved Safety and Efficacy Profiles for the Treatment of Multidrug-Resistant Tuberculosis. J Med Chem 2020; 63:9316-9339. [PMID: 32666789 DOI: 10.1021/acs.jmedchem.0c00500] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Tuberculosis (TB) remains a serious public health challenge, and the research and development of new anti-TB drugs is an essential component of the global strategy to eradicate TB. In this work, we discovered a conformationally constrained oxazolidinone 19c with improved anti-TB activity and safety profile through a focused lead optimization effort. Compound 19c displayed superior in vivo efficacy in a mouse TB infection model compared to linezolid and sutezolid. The druggability of compound 19c was demonstrated in a panel of assays including microsomal stability, cytotoxicity, cytochrome P450 enzyme inhibition, and pharmacokinetics in animals. Compound 19c demonstrated an excellent safety profile in a battery of safety assays, including mitochondrial protein synthesis, hERG K+, hCav1.2, and Nav1.5 channels, monoamine oxidase, and genotoxicity. In a 4 week repeated dose toxicology study in rats, 19c appeared to have less bone marrow suppression than linezolid, which has been a major liability of the oxazolidinone class.
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Affiliation(s)
- Hongyi Zhao
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Bin Wang
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, 97 Ma Chang Street, Beijing 101149, P. R. China
| | - Lei Fu
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, 97 Ma Chang Street, Beijing 101149, P. R. China
| | - Gang Li
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Haijia Lu
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Yuke Liu
- Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Li Sheng
- Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Yan Li
- Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Baoxi Zhang
- Beijing Key Laboratory of Polymorphic Drugs, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Yang Lu
- Beijing Key Laboratory of Polymorphic Drugs, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Chen Ma
- Beijing Key Laboratory of Polymorphic Drugs, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Haihong Huang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Dongfeng Zhang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Yu Lu
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, 97 Ma Chang Street, Beijing 101149, P. R. China
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48
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Hedgespeth BA, Tefft KM, Kendall AR. Reversible myelosuppression suspected to be secondary to linezolid in a cat with infected subcutaneous ureteral bypass systems. JFMS Open Rep 2020; 6:2055116920967226. [PMID: 33282333 PMCID: PMC7691925 DOI: 10.1177/2055116920967226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2020] [Indexed: 11/29/2022] Open
Abstract
CASE SUMMARY A 5-year-old castrated male domestic shorthair cat was presented for a multidrug-resistant Enterococcus faecium urinary tract infection within its bilateral subcutaneous ureteral bypass systems. After considerable consultation, the cat was treated with oral linezolid (10 mg/kg q12h) for two separate 2-week courses over 5 weeks. Over this time period, the cat became progressively neutropenic and thrombocytopenic, but was otherwise clinically stable. Upon cessation of the linezolid, the bicytopenia resolved within 12 days. RELEVANCE AND NOVEL INFORMATION The reversible myelosuppression in this case is suspected to be secondary to linezolid administration. While previously reported in people, this effect has not been reported at therapeutic doses in veterinary species. This report demonstrates the potential for adverse drug reaction development in cats treated with prolonged linezolid therapy and highlights the need for extreme caution when utilizing linezolid in patients with renal insufficiency. Linezolid is the only drug currently approved by the Food and Drug Administration to treat vancomycin-resistant enterococci infections in people; however, resistance to this antibiotic appears to be increasing. Multidrug-resistant organisms continue to be a real global public health threat in both human and veterinary medicine. Third-tier antibiotics should only be considered under extreme circumstances and after considerable consultation with a specialist. Please note that the authors of this manuscript followed American Veterinary Medical Association policies on stewardship and International Society for Companion Animal Infectious Diseases guidelines, and do not promote or encourage the use in daily practice.
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Affiliation(s)
- Barry A Hedgespeth
- Department of Clinical Sciences, North
Carolina State University, Raleigh, NC, USA
| | - Karen M Tefft
- Department of Clinical Sciences, North
Carolina State University, Raleigh, NC, USA
| | - Allison R Kendall
- Department of Clinical Sciences, North
Carolina State University, Raleigh, NC, USA
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49
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Zhuang Z, Wan D, Ding J, He S, Zhang Q, Wang X, Yuan Y, Lu Y, Z. Ding C, Lynch AS, M. Upton A, B. Cooper C, A. Denny W, Ma Z. Synergistic Activity of Nitroimidazole-Oxazolidinone Conjugates against Anaerobic Bacteria. Molecules 2020; 25:molecules25102431. [PMID: 32456032 PMCID: PMC7288012 DOI: 10.3390/molecules25102431] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/19/2020] [Accepted: 05/19/2020] [Indexed: 12/01/2022] Open
Abstract
The introductions of the bicyclic 4-nitroimidazole and the oxazolidinone classes of antimicrobial agents represented the most significant advancements in the infectious disease area during the past two decades. Pretomanid, a bicyclic 4-nitroimidazole, and linezolid, an oxazolidinone, are also part of a combination regimen approved recently by the US Food and Drug Administration for the treatment of pulmonary, extensively drug resistant (XDR), treatment-intolerant or nonresponsive multidrug-resistant (MDR) Mycobacterium tuberculosis (TB). To identify new antimicrobial agents with reduced propensity for the development of resistance, a series of dual-acting nitroimidazole-oxazolidinone conjugates were designed, synthesized and evaluated for their antimicrobial activity. Compounds in this conjugate series have shown synergistic activity against a panel of anaerobic bacteria, including those responsible for serious bacterial infections.
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Affiliation(s)
- Zhijun Zhuang
- TenNor Therapeutics Limited, 218 Xinghu Street, Building B2, Suite 711, Suzhou Industrial Park, Suzhou 215123, China; (Z.Z.); (D.W.); (J.D.); (S.H.); (Q.Z.); (X.W.); (Y.Y.)
| | - Dawei Wan
- TenNor Therapeutics Limited, 218 Xinghu Street, Building B2, Suite 711, Suzhou Industrial Park, Suzhou 215123, China; (Z.Z.); (D.W.); (J.D.); (S.H.); (Q.Z.); (X.W.); (Y.Y.)
| | - Jun Ding
- TenNor Therapeutics Limited, 218 Xinghu Street, Building B2, Suite 711, Suzhou Industrial Park, Suzhou 215123, China; (Z.Z.); (D.W.); (J.D.); (S.H.); (Q.Z.); (X.W.); (Y.Y.)
| | - Shijie He
- TenNor Therapeutics Limited, 218 Xinghu Street, Building B2, Suite 711, Suzhou Industrial Park, Suzhou 215123, China; (Z.Z.); (D.W.); (J.D.); (S.H.); (Q.Z.); (X.W.); (Y.Y.)
| | - Qian Zhang
- TenNor Therapeutics Limited, 218 Xinghu Street, Building B2, Suite 711, Suzhou Industrial Park, Suzhou 215123, China; (Z.Z.); (D.W.); (J.D.); (S.H.); (Q.Z.); (X.W.); (Y.Y.)
| | - Xiaomei Wang
- TenNor Therapeutics Limited, 218 Xinghu Street, Building B2, Suite 711, Suzhou Industrial Park, Suzhou 215123, China; (Z.Z.); (D.W.); (J.D.); (S.H.); (Q.Z.); (X.W.); (Y.Y.)
| | - Ying Yuan
- TenNor Therapeutics Limited, 218 Xinghu Street, Building B2, Suite 711, Suzhou Industrial Park, Suzhou 215123, China; (Z.Z.); (D.W.); (J.D.); (S.H.); (Q.Z.); (X.W.); (Y.Y.)
| | - Yu Lu
- Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, 97 Ma Chang Street, Beijing 101149, China;
| | - Charles Z. Ding
- WuXi AppTec. Co. Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China;
| | - Anthony Simon Lynch
- Janssen Research & Development LLC., 1400 McKean Road, Spring House, PA 18940, USA;
| | - Anna M. Upton
- Global Alliance for TB Drug Development, 40 Wall Street, New York, NY 10005, USA; (A.M.U.); (C.B.C.)
| | - Christopher B. Cooper
- Global Alliance for TB Drug Development, 40 Wall Street, New York, NY 10005, USA; (A.M.U.); (C.B.C.)
| | - William A. Denny
- Auckland Cancer Society Research Centre, School of Medical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand;
| | - Zhenkun Ma
- TenNor Therapeutics Limited, 218 Xinghu Street, Building B2, Suite 711, Suzhou Industrial Park, Suzhou 215123, China; (Z.Z.); (D.W.); (J.D.); (S.H.); (Q.Z.); (X.W.); (Y.Y.)
- Correspondence: ; Tel.: +86-512-8686-1980
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50
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García-Olaiz G, Alcántar-Zavala E, Ochoa-Terán A, Cabrera A, Muñiz-Salazar R, Montes-Ávila J, Salazar-Medina AJ, Alday E, Velazquez C, Medina-Franco JL, Laniado-Laborín R. Design, synthesis and evaluation of the antibacterial activity of new Linezolid dipeptide-type analogues. Bioorg Chem 2020; 95:103483. [DOI: 10.1016/j.bioorg.2019.103483] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/22/2019] [Accepted: 11/25/2019] [Indexed: 11/24/2022]
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