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Liang L, Liu Z, Chen J, Zha Q, Zhou Y, Li J, Hu Y, Chen X, Zhang T, Zhang N. Design and synthesis of Thieno[3, 2-b]pyridinone derivatives exhibiting potent activities against Mycobacterium tuberculosis in vivo by targeting Enoyl-ACP reductase. Eur J Med Chem 2024; 279:116806. [PMID: 39276583 DOI: 10.1016/j.ejmech.2024.116806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 08/18/2024] [Accepted: 08/27/2024] [Indexed: 09/17/2024]
Abstract
In this study, a series of novel thieno [3, 2-b]pyridinone derivatives were designed and synthesized using a scaffold hopping strategy. Six compounds showed potent anti-mycobacterial activity (minimum inhibitory concentration (MIC) ≤ 1 μg/mL) against Mycobacterium tuberculosis (Mtb) UAlRa. Compound 6c displayed good activity against Mtb UAlRv (MIC = 0.5-1 μg/mL). Compounds 6c and 6i also showed activity against Mtb UAlRa in macrophages and exhibited low cytotoxicity against LO-2 cells. The selected compounds displayed a narrow antibacterial spectrum, with no activity against representative Gram-positive, Gram-negative bacteria, as well as fungi. Furthermore, compound 6c demonstrated favorable oral pharmacokinetic properties with a T1/2 value of 47.99 h and exhibited good in vivo activity in an acute mouse model of tuberculosis (TB). The target of compound 6c was identified as a NADH-dependent enoyl-acyl carrier protein reductase (InhA) by genome sequencing of spontaneously compound 6c-resistant Mtb mutants, indicating that compound 6c may not require activation and can directly target InhA. In vitro antimicrobial assays against a recombinant M. smegmatis overexpressing the Mtb-InhA, along with InhA inhibition assays, confirmed that InhA is the target of thieno [3, 2-b]pyridinone derivatives. Overall, this study identified thieno [3, 2-b]pyridinone scaffold as a novel chemotype that is promising for the development of anti-TB agents.
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Affiliation(s)
- Lihong Liang
- Guangxi Key Laboratory of Drug Discovery and Optimization, School of Pharmacy, Guilin Medical University, Guilin, 541199, China
| | - Zhiyong Liu
- State Key Laboratory of Respiratory Disease, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China; Guangzhou National Laboratory, Guangzhou, 510005, China
| | - Jie Chen
- Jiaxing University Affiliated Hospital, The First Hospital of Jiaxing, Jiaxing, 314001, China
| | - Qin Zha
- Guangxi Key Laboratory of Drug Discovery and Optimization, School of Pharmacy, Guilin Medical University, Guilin, 541199, China
| | - Yihuan Zhou
- Guangxi Key Laboratory of Drug Discovery and Optimization, School of Pharmacy, Guilin Medical University, Guilin, 541199, China
| | - Jun Li
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, Shanghai Tech University, Shanghai, 201210, China
| | - Yangbo Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Xinwen Chen
- Guangzhou National Laboratory, Guangzhou, 510005, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China; Guangzhou National Laboratory, Guangzhou, 510005, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Niuniu Zhang
- Guangxi Key Laboratory of Drug Discovery and Optimization, School of Pharmacy, Guilin Medical University, Guilin, 541199, China.
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Mkhize B, Court R, Castel S, Joubert A, van der Merwe M, Maartens G, Conradie F, Wiesner L. Validation and application of an online extraction and liquid chromatography tandem mass spectrometry assay for the analysis of delamanid and its DM-6705 metabolite in human breast milk. J Pharm Biomed Anal 2024; 246:116225. [PMID: 38761519 DOI: 10.1016/j.jpba.2024.116225] [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] [Received: 03/12/2024] [Revised: 04/24/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
We developed and validated a bioanalytical assay to quantify delamanid and its key metabolite (DM-6705) in breast milk and aimed to quantify the secretion of these compounds in breast milk. Due to the hydrophobic nature of the analytes, special care was taken during sample preparation to prevent the formation of fatty deposits during protein precipitation. This was followed by online solid phase extraction and liquid chromatography with tandem mass spectrometry for detection. A Restek Viva BiPh C18 column (1.0 mm×50 mm, 5 µm) was used for extraction while chromatographic separation was performed using a Waters Xterra MS C18 (2.1 mm×100 mm, 5 μm) analytical column with an isocratic mobile phase consisting of acetonitrile, methanol, and 5 mM ammonium carbonate. The mass spectrometric detection of the analytes was performed using an AB Sciex 3200 mass spectrometer employing electrospray ionisation in the positive mode with multiple reaction motoring of the relevant precursor and product ions. Delamanid-d4 and OPC-14714 were used as internal standards. A quadratic (weighted 1/x concentration) regression was used to fit calibration curves for delamanid and DM-6705 over the concentration range of 10.0 - 1000 ng/mL. The intra- and inter-day validation accuracies of the quality control samples were between 92.1% and 98.3% for delamanid, and 97.0% and 102.8% for DM-6705. The percentage coefficient of variation (precision) was less than 7.8%. To our knowledge, this is the first report describing the concentrations of delamanid and DM-6705 in the breast milk of patients treated for rifampicin-resistant tuberculosis.
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Affiliation(s)
- Buyisile Mkhize
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Richard Court
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Sandra Castel
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Anton Joubert
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Marthinus van der Merwe
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Gary Maartens
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Francesca Conradie
- Department of Clinical Medicine, University of the Witwatersrand, South Africa
| | - Lubbe Wiesner
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa.
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Chengalroyen MD, Mehaffy C, Lucas M, Bauer N, Raphela ML, Oketade N, Warner DF, Lewinsohn DA, Lewinsohn DM, Dobos KM, Mizrahi V. Modulation of riboflavin biosynthesis and utilization in mycobacteria. Microbiol Spectr 2024; 12:e0320723. [PMID: 38916330 PMCID: PMC11302143 DOI: 10.1128/spectrum.03207-23] [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: 09/06/2023] [Accepted: 05/17/2024] [Indexed: 06/26/2024] Open
Abstract
Riboflavin (vitamin B2) is the precursor of the flavin coenzymes, FAD and FMN, which play a central role in cellular redox metabolism. While humans must obtain riboflavin from dietary sources, certain microbes, including Mycobacterium tuberculosis (Mtb), can biosynthesize riboflavin de novo. Riboflavin precursors have also been implicated in the activation of mucosal-associated invariant T (MAIT) cells which recognize metabolites derived from the riboflavin biosynthesis pathway complexed to the MHC-I-like molecule, MR1. To investigate the biosynthesis and function of riboflavin and its pathway intermediates in mycobacterial metabolism and physiology, we constructed conditional knockdowns (hypomorphs) in riboflavin biosynthesis and utilization genes in Mycobacterium smegmatis (Msm) and Mtb by inducible CRISPR interference. Using this comprehensive panel of hypomorphs, we analyzed the impact of gene silencing on viability, on the transcription of (other) riboflavin pathway genes, on the levels of the pathway proteins, and on riboflavin itself. Our results revealed that (i) despite lacking a canonical transporter, both Msm and Mtb assimilate exogenous riboflavin when supplied at high concentration; (ii) there is functional redundancy in lumazine synthase activity in Msm; (iii) silencing of ribA2 or ribF is profoundly bactericidal in Mtb; and (iv) in Msm, ribA2 silencing results in concomitant knockdown of other pathway genes coupled with RibA2 and riboflavin depletion and is also bactericidal. In addition to their use in genetic validation of potential drug targets for tuberculosis, this collection of hypomorphs provides a useful resource for future studies investigating the role of pathway intermediates in MAIT cell recognition of mycobacteria. IMPORTANCE The pathway for biosynthesis and utilization of riboflavin, precursor of the essential coenzymes, FMN and FAD, is of particular interest in the flavin-rich pathogen, Mycobacterium tuberculosis (Mtb), for two important reasons: (i) the pathway includes potential tuberculosis (TB) drug targets and (ii) intermediates from the riboflavin biosynthesis pathway provide ligands for mucosal-associated invariant T (MAIT) cells, which have been implicated in TB pathogenesis. However, the riboflavin pathway is poorly understood in mycobacteria, which lack canonical mechanisms to transport this vitamin and to regulate flavin coenzyme homeostasis. By conditionally disrupting each step of the pathway and assessing the impact on mycobacterial viability and on the levels of the pathway proteins as well as riboflavin, our work provides genetic validation of the riboflavin pathway as a target for TB drug discovery and offers a resource for further exploring the association between riboflavin biosynthesis, MAIT cell activation, and TB infection and disease.
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Affiliation(s)
- Melissa D. Chengalroyen
- Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Carolina Mehaffy
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Megan Lucas
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Niel Bauer
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Mabule L. Raphela
- Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Nurudeen Oketade
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Digby F. Warner
- Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Disease Research in Africa, University of Cape Town, Cape Town, South Africa
| | | | - David M. Lewinsohn
- Oregon Health and Science University, Portland, Oregon, USA
- Portland VA Medical Center, Portland, Oregon, USA
| | - Karen M. Dobos
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Valerie Mizrahi
- Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Disease Research in Africa, University of Cape Town, Cape Town, South Africa
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Paoli-Lombardo R, Primas N, Vanelle P. DprE1 and Ddn as promising therapeutic targets in the development of novel anti-tuberculosis nitroaromatic drugs. Eur J Med Chem 2024; 274:116559. [PMID: 38850856 DOI: 10.1016/j.ejmech.2024.116559] [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] [Received: 02/21/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 06/10/2024]
Abstract
Tuberculosis remains the second deadliest infectious disease in humans and a public health threat due to the emergence of multidrug-resistant (MDR-TB) and extensively drug-resistant (XDR-TB) strains. Therefore, it is urgent to identify new anti-tuberculosis treatments and novel therapeutic targets to prevent the emergence of resistance. In recent years, the study of anti-tuberculosis properties of nitroaromatic compounds has led to the identification of two novel biological targets, the deazaflavin (F420)-dependent nitroreductase Ddn and the decaprenylphosphoryl-β-d-ribose 2'-epimerase DprE1. This review aims to show why Ddn and DprE1 are promising therapeutic targets and highlight nitroaromatic compounds interest in developing new anti-tuberculosis treatments active against MDR-TB and XDR-TB. Despite renewed interest in the development of new anti-tuberculosis nitroaromatic compounds, pharmaceutical companies often exclude nitro-containing molecules from their drug discovery programs because of their toxic and mutagenic potential. This exclusion results in missed opportunities to identify new nitroaromatic compounds and promising therapeutic targets.
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Affiliation(s)
- Romain Paoli-Lombardo
- Aix Marseille Univ, CNRS, ICR UMR 7273, Laboratoire de Pharmaco-Chimie Radicalaire, 13385, Marseille, France; AP-HM, Service Central de la Qualité et de l'Information Pharmaceutiques, 13005, Marseille, France
| | - Nicolas Primas
- Aix Marseille Univ, CNRS, ICR UMR 7273, Laboratoire de Pharmaco-Chimie Radicalaire, 13385, Marseille, France; AP-HM, Service Central de la Qualité et de l'Information Pharmaceutiques, 13005, Marseille, France
| | - Patrice Vanelle
- Aix Marseille Univ, CNRS, ICR UMR 7273, Laboratoire de Pharmaco-Chimie Radicalaire, 13385, Marseille, France; AP-HM, Service Central de la Qualité et de l'Information Pharmaceutiques, 13005, Marseille, France.
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5
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Akbari Aghababa A, Nasiri MJ, Pakzad P, Mirsamadi ES. Delamanid and bedaquiline resistance patterns in Mycobacterium tuberculosis in Iran: A cross-sectional analysis. New Microbes New Infect 2024; 60-61:101437. [PMID: 38873345 PMCID: PMC11170162 DOI: 10.1016/j.nmni.2024.101437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 05/15/2024] [Accepted: 05/25/2024] [Indexed: 06/15/2024] Open
Abstract
Introduction The surge of multidrug-resistant TB (MDR-TB) in Iran poses a significant challenge to global healthcare. The introduction of delamanid (DLM) and bedaquiline (BDQ), two potent antimycobacterial drugs, marks a crucial advance. Nevertheless, as resistance in Mycobacterium tuberculosis is on the rise in Iran and resistance to these newer medications is emerging, investigations in this field are of utmost importance. Methods In this cross-sectional study, 38 MDR-TB strains were collected from five distinct regional TB laboratories in Iran. The clinical isolates were confirmed as M. tuberculosis using the phenotypic tests and IS6110-based PCR assay. Drug susceptibility testing (DST) for isoniazid, rifampicin, ethambutol, DLM, and BDQ was performed using WHO-approved methods. Sequencing was used to investigate genetic mutations in DLM (ddn, fgd1) and BDQ (Rv0678, atpE, pepQ) genes associated with resistance. Results Among the 38 collected MDR-TB isolates, 7 (18.5 %) exhibited resistance to DLM, while all remained susceptible to BDQ. Analysis of the sequencing data revealed that the ddn gene exhibited the highest number of mutations in DLM-resistant isolates, including 18 nonsynonymous mutations and 1 indel leading to frameshift mutations. A common mutation, Gly81Ser, was present in 4 of the DLM-resistant isolates (4/7; 57.1 %). A synonymous mutation, T960C, in the fgd1 gene was uniformly found in DLM-resistant samples. Notably, no significant mutations were observed in the atpE, Rv0678, or pepQ genes in any of the BDQ-susceptible isolates. Conclusions Our study underscores the emergence of DLM resistance in a subset of MDR-TB isolates in Iran, primarily associated with mutations in the ddn gene. This emphasizes the ongoing necessity for TB drug resistance surveillance and research. While BDQ remains efficacious, the emergence of DLM resistance is a concerning development, warranting further exploration into resistance mechanisms and the formulation of effective TB control strategies.
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Affiliation(s)
- AmirHossein Akbari Aghababa
- Department of Microbiology, Faculty of Biological Sciences, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Mohammad Javad Nasiri
- Department of Microbiology, Faculty of Biological Sciences, North Tehran Branch, Islamic Azad University, Tehran, Iran
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parviz Pakzad
- Department of Microbiology, Faculty of Biological Sciences, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Elnaz Sadat Mirsamadi
- Department of Microbiology, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
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6
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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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Rana HK, Singh AK, Kumar R, Pandey AK. Antitubercular drugs: possible role of natural products acting as antituberculosis medication in overcoming drug resistance and drug-induced hepatotoxicity. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:1251-1273. [PMID: 37665346 DOI: 10.1007/s00210-023-02679-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/16/2023] [Indexed: 09/05/2023]
Abstract
Mycobacterium tuberculosis (Mtb) is a pathogenic bacterium which causes tuberculosis (TB). TB control programmes are facing threats from drug resistance. Multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mtb strains need longer and more expensive treatment with many medications resulting in more adverse effects and decreased chances of treatment outcomes. The World Health Organization (WHO) has emphasised the development of not just new individual anti-TB drugs, but also novel medication regimens as an alternative treatment option for the drug-resistant Mtb strains. Many plants, as well as marine creatures (sponge; Haliclona sp.) and fungi, have been continuously used to treat TB in various traditional treatment systems around the world, providing an almost limitless supply of active components. Natural products, in addition to their anti-mycobacterial action, can be used as adjuvant therapy to increase the efficacy of conventional anti-mycobacterial medications, reduce their side effects, and reverse MDR Mtb strain due to Mycobacterium's genetic flexibility and environmental adaptation. Several natural compounds such as quercetin, ursolic acid, berberine, thymoquinone, curcumin, phloretin, and propolis have shown potential anti-mycobacterial efficacy and are still being explored in preclinical and clinical investigations for confirmation of their efficacy and safety as anti-TB medication. However, more high-level randomized clinical trials are desperately required. The current review provides an overview of drug-resistant TB along with the latest anti-TB medications, drug-induced hepatotoxicity and oxidative stress. Further, the role and mechanisms of action of first and second-line anti-TB drugs and new drugs have been highlighted. Finally, the role of natural compounds as anti-TB medication and hepatoprotectants have been described and their mechanisms discussed.
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Affiliation(s)
- Harvesh Kumar Rana
- Department of Biochemistry, University of Allahabad, Prayagraj (Allahabad), 211002, India
- Department of Zoology, Feroze Gandhi College, Raebareli, 229001, India
| | - Amit Kumar Singh
- Department of Biochemistry, University of Allahabad, Prayagraj (Allahabad), 211002, India
- Department of Botany, BMK Government. Girls College, Balod, Chhattisgarh, 491226, India
| | - Ramesh Kumar
- Department of Biochemistry, University of Allahabad, Prayagraj (Allahabad), 211002, India
- Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, 151401, India
| | - Abhay K Pandey
- Department of Biochemistry, University of Allahabad, Prayagraj (Allahabad), 211002, India.
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Negi A, Perveen S, Gupta R, Singh PP, Sharma R. Unraveling Dilemmas and Lacunae in the Escalating Drug Resistance of Mycobacterium tuberculosis to Bedaquiline, Delamanid, and Pretomanid. J Med Chem 2024; 67:2264-2286. [PMID: 38351709 DOI: 10.1021/acs.jmedchem.3c01892] [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: 02/23/2024]
Abstract
Delamanid, bedaquiline, and pretomanid have been recently added in the anti-tuberculosis (anti-TB) treatment regimens and have emerged as potential solutions for combating drug-resistant TB. These drugs have proven to be effective in treating drug-resistant TB when used in combination. However, concerns have been raised about the eventual loss of these drugs due to evolving resistance mechanisms and certain adverse effects such as prolonged QT period, gastrointestinal problems, hepatotoxicity, and renal disorders. This Perspective emphasizes the properties of these first-in-class drugs, including their mechanism of action, pharmacokinetics/pharmacodynamics profiles, clinical studies, adverse events, and underlying resistance mechanisms. A brief coverage of efforts toward the generation of best-in-class leads in each class is also provided. The ongoing clinical trials of new combinations of these drugs are discussed, thus providing a better insight into the use of these drugs while designing an effective treatment regimen for resistant TB cases.
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Affiliation(s)
- Anjali Negi
- Infectious Diseases Division, CSIR - Indian Institute of Integrative Medicine, Jammu-180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Summaya Perveen
- Infectious Diseases Division, CSIR - Indian Institute of Integrative Medicine, Jammu-180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Ria Gupta
- Natural Products and Medicinal Chemistry, CSIR - Indian Institute of Integrative Medicine, Jammu-180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Parvinder Pal Singh
- Natural Products and Medicinal Chemistry, CSIR - Indian Institute of Integrative Medicine, Jammu-180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Rashmi Sharma
- Infectious Diseases Division, CSIR - Indian Institute of Integrative Medicine, Jammu-180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
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9
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Brown TS, Tang L, Omar SV, Joseph L, Meintjes G, Maartens G, Wasserman S, Shah NS, Farhat MR, Gandhi NR, Ismail N, Brust JCM, Mathema B. Genotype-Phenotype Characterization of Serial Mycobacterium tuberculosis Isolates in Bedaquiline-Resistant Tuberculosis. Clin Infect Dis 2024; 78:269-276. [PMID: 37874928 DOI: 10.1093/cid/ciad596] [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: 06/23/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND Emerging resistance to bedaquiline (BDQ) threatens to undermine advances in the treatment of drug-resistant tuberculosis (DRTB). Characterizing serial Mycobacterium tuberculosis (Mtb) isolates collected during BDQ-based treatment can provide insights into the etiologies of BDQ resistance in this important group of DRTB patients. METHODS We measured mycobacteria growth indicator tube (MGIT)-based BDQ minimum inhibitory concentrations (MICs) of Mtb isolates collected from 195 individuals with no prior BDQ exposure who were receiving BDQ-based treatment for DRTB. We conducted whole-genome sequencing on serial Mtb isolates from all participants who had any isolate with a BDQ MIC >1 collected before or after starting treatment (95 total Mtb isolates from 24 participants). RESULTS Sixteen of 24 participants had BDQ-resistant TB (MGIT MIC ≥4 µg/mL) and 8 had BDQ-intermediate infections (MGIT MIC = 2 µg/mL). Participants with pre-existing resistance outnumbered those with resistance acquired during treatment, and 8 of 24 participants had polyclonal infections. BDQ resistance was observed across multiple Mtb strain types and involved a diverse catalog of mmpR5 (Rv0678) mutations, but no mutations in atpE or pepQ. Nine pairs of participants shared genetically similar isolates separated by <5 single nucleotide polymorphisms, concerning for potential transmitted BDQ resistance. CONCLUSIONS BDQ-resistant TB can arise via multiple, overlapping processes, including transmission of strains with pre-existing resistance. Capturing the within-host diversity of these infections could potentially improve clinical diagnosis, population-level surveillance, and molecular diagnostic test development.
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Affiliation(s)
- Tyler S Brown
- Section of Infectious Diseases, Boston University School of Medicine, Boston, Massachusetts, USA
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Linrui Tang
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Shaheed Vally Omar
- Centre for Tuberculosis, National Institute for Communicable Diseases, Johannesburg, South Africa
- Department of Molecular Medicine & Hematology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lavania Joseph
- Centre for Tuberculosis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Graeme Meintjes
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, and Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Gary Maartens
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, and Department of Medicine, University of Cape Town, Cape Town, South Africa
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Sean Wasserman
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, and Department of Medicine, University of Cape Town, Cape Town, South Africa
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - N Sarita Shah
- Departments of Epidemiology and Global Health and Medicine, Rollins School of Public Health and Emory School of Medicine, Atlanta, Georgia, USA
| | - Maha R Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Neel R Gandhi
- Departments of Epidemiology and Global Health and Medicine, Rollins School of Public Health and Emory School of Medicine, Atlanta, Georgia, USA
| | - Nazir Ismail
- Centre for Tuberculosis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - James C M Brust
- Department of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, USA
| | - Barun Mathema
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, New York, USA
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10
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Karabanovich G, Fabiánová V, Vocat A, Dušek J, Valášková L, Stolaříková J, Kitson RRA, Pávek P, Vávrová K, Djaout K, Mikušová K, Baulard AR, Cole ST, Korduláková J, Roh J. Both Nitro Groups Are Essential for High Antitubercular Activity of 3,5-Dinitrobenzylsulfanyl Tetrazoles and 1,3,4-Oxadiazoles through the Deazaflavin-Dependent Nitroreductase Activation Pathway. J Med Chem 2024; 67:81-109. [PMID: 38157261 PMCID: PMC10788908 DOI: 10.1021/acs.jmedchem.3c00925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 11/25/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024]
Abstract
3,5-Dinitrobenzylsulfanyl tetrazoles and 1,3,4-oxadiazoles, previously identified as having high in vitro activities against both replicating and nonreplicating mycobacteria and favorable cytotoxicity and genotoxicity profiles were investigated. First we demonstrated that these compounds act in a deazaflavin-dependent nitroreduction pathway and thus require a nitro group for their activity. Second, we confirmed the necessity of both nitro groups for antimycobacterial activity through extensive structure-activity relationship studies using 32 structural types of analogues, each in a five-membered series. Only the analogues with shifted nitro groups, namely, 2,5-dinitrobenzylsulfanyl oxadiazoles and tetrazoles, maintained high antimycobacterial activity but in this case mainly as a result of DprE1 inhibition. However, these analogues also showed increased toxicity to the mammalian cell line. Thus, both nitro groups in 3,5-dinitrobenzylsulfanyl-containing antimycobacterial agents remain essential for their high efficacy, and further efforts should be directed at finding ways to address the possible toxicity and solubility issues, for example, by targeted delivery.
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Affiliation(s)
- Galina Karabanovich
- Charles
University, Faculty of Pharmacy
in Hradec Králové, Akademika Heyrovského 1203, 50005 Hradec Králové, Czech Republic
| | - Viktória Fabiánová
- Faculty
of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Ilkovičova 6, Mlynská
dolina, 842 15 Bratislava, Slovakia
| | - Anthony Vocat
- Global
Health Institute, École Polytechnique
Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jan Dušek
- Charles
University, Faculty of Pharmacy
in Hradec Králové, Akademika Heyrovského 1203, 50005 Hradec Králové, Czech Republic
| | - Lenka Valášková
- Charles
University, Faculty of Pharmacy
in Hradec Králové, Akademika Heyrovského 1203, 50005 Hradec Králové, Czech Republic
| | - Jiřina Stolaříková
- Regional
Institute of Public Health, Department of
Bacteriology and Mycology, Partyzánské náměstí 7, 70200 Ostrava, Czech Republic
| | - Russell R. A. Kitson
- Charles
University, Faculty of Pharmacy
in Hradec Králové, Akademika Heyrovského 1203, 50005 Hradec Králové, Czech Republic
| | - Petr Pávek
- Charles
University, Faculty of Pharmacy
in Hradec Králové, Akademika Heyrovského 1203, 50005 Hradec Králové, Czech Republic
| | - Kateřina Vávrová
- Charles
University, Faculty of Pharmacy
in Hradec Králové, Akademika Heyrovského 1203, 50005 Hradec Králové, Czech Republic
| | - Kamel Djaout
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and
Immunity of Lille, F-59000 Lille, France
| | - Katarína Mikušová
- Faculty
of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Ilkovičova 6, Mlynská
dolina, 842 15 Bratislava, Slovakia
| | - Alain R. Baulard
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and
Immunity of Lille, F-59000 Lille, France
| | - Stewart T. Cole
- Global
Health Institute, École Polytechnique
Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jana Korduláková
- Faculty
of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Ilkovičova 6, Mlynská
dolina, 842 15 Bratislava, Slovakia
| | - Jaroslav Roh
- Charles
University, Faculty of Pharmacy
in Hradec Králové, Akademika Heyrovského 1203, 50005 Hradec Králové, Czech Republic
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11
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Peslalz P, Grieshober M, Kraus F, Bleisch A, Izzo F, Lichtenstein D, Hammer H, Vorbach A, Momoi K, Zanger UM, Brötz-Oesterhelt H, Braeuning A, Plietker B, Stenger S. Unnatural Endotype B PPAPs as Novel Compounds with Activity against Mycobacterium tuberculosis. J Med Chem 2023; 66:15073-15083. [PMID: 37822271 DOI: 10.1021/acs.jmedchem.3c01172] [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: 10/13/2023]
Abstract
Pre-SARS-CoV-2, tuberculosis was the leading cause of death by a single pathogen. Repetitive exposure of Mycobacterium tuberculosis(Mtb) supported the development of multidrug- and extensively drug-resistant strains, demanding novel drugs. Hyperforin, a natural type A polyprenylated polycyclic acylphloroglucinol from St. John's wort, exhibits antidepressant and antibacterial effects also against Mtb. Yet, Hyperforin's instability limits the utility in clinical practice. Here, we present photo- and bench-stable type B PPAPs with enhanced antimycobacterial efficacy. PPAP22 emerged as a lead compound, further improved as the sodium salt PPAP53, drastically enhancing solubility. PPAP53 inhibits the growth of virulent extracellular and intracellular Mtb without harming primary human macrophages. Importantly, PPAP53 is active against drug-resistant strains of Mtb. Furthermore, we analyzed the in vitro properties of PPAP53 in terms of CYP induction and the PXR interaction. Taken together, we introduce type PPAPs as a new class of antimycobacterial compounds, with remarkable antibacterial activity and favorable biophysical properties.
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Affiliation(s)
- Philipp Peslalz
- Chair of Organic Chemistry, Faculty of Chemistry and Food Chemistry, Technical University Dresden, Bergstr. 66, Dresden01069 ,Germany
| | - Mark Grieshober
- Institute for Medical Microbiology and Hygiene, University Hospital Ulm, Albert-Einstein-Allee 11, Ulm D-89081, Germany
| | - Frank Kraus
- Institut für Organische Chemie, Universität Stuttgart,Pfaffenwaldring 55, Stuttgart 70569, Germany
| | - Anton Bleisch
- Chair of Organic Chemistry, Faculty of Chemistry and Food Chemistry, Technical University Dresden, Bergstr. 66, Dresden01069 ,Germany
| | - Flavia Izzo
- Institut für Organische Chemie, Universität Stuttgart,Pfaffenwaldring 55, Stuttgart 70569, Germany
| | - Dajana Lichtenstein
- Department of Food Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, Berlin 10589, Germany
| | - Helen Hammer
- SIGNATOPE GmbH, Markwiesenstr. 55, Reutlingen 72770, Germany
| | - Andreas Vorbach
- Interfaculty Institute of Microbiology and Infection Medicine, Tübingen 72076, Germany
| | - Kyoko Momoi
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology Auerbachstr. 112, University of Tübingen, 70376 Stuttgart, Tübingen 72076, Germany
| | - Ulrich M Zanger
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology Auerbachstr. 112, University of Tübingen, 70376 Stuttgart, Tübingen 72076, Germany
| | - Heike Brötz-Oesterhelt
- Interfaculty Institute of Microbiology and Infection Medicine, Tübingen 72076, Germany
- German Center for Infection Research, Partner Site Tübingen, Tübingen 72076, Germany
| | - Albert Braeuning
- Department of Food Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, Berlin 10589, Germany
| | - Bernd Plietker
- Chair of Organic Chemistry, Faculty of Chemistry and Food Chemistry, Technical University Dresden, Bergstr. 66, Dresden01069 ,Germany
- Institut für Organische Chemie, Universität Stuttgart,Pfaffenwaldring 55, Stuttgart 70569, Germany
| | - Steffen Stenger
- Institute for Medical Microbiology and Hygiene, University Hospital Ulm, Albert-Einstein-Allee 11, Ulm D-89081, Germany
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12
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Mok S, Roycroft E, Flanagan PR, Wagener J, Fitzgibbon MM. Investigation of genomic mutations and their association with phenotypic resistance to new and repurposed drugs in Mycobacterium tuberculosis complex clinical isolates. J Antimicrob Chemother 2023; 78:2637-2644. [PMID: 37740935 PMCID: PMC10683940 DOI: 10.1093/jac/dkad252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/24/2023] [Indexed: 09/25/2023] Open
Abstract
BACKGROUND WGS has the potential to detect resistance-associated mutations and guide treatment of MDR TB. However, the knowledge base to confidently interpret mutations associated with the new and repurposed drugs is sparse, and phenotypic drug susceptibility testing is required to detect resistance. METHODS We screened 900 Mycobacterium tuberculosis complex genomes from Ireland, a low TB incidence country, for mutations in 13 candidate genes and assessed their association with phenotypic resistance to bedaquiline, clofazimine, linezolid, delamanid and pretomanid. RESULTS We identified a large diversity of mutations in the candidate genes of 195 clinical isolates, with very few isolates associated with phenotypic resistance to bedaquiline (n = 4), delamanid (n = 4) and pretomanid (n = 2). We identified bedaquiline resistance among two drug-susceptible TB isolates that harboured mutations in Rv0678. Bedaquiline resistance was also identified in two MDR-TB isolates harbouring Met146Thr in Rv0678, which dated back to 2007, prior to the introduction of bedaquiline. High-level delamanid resistance was observed in two isolates with deletions in ddn, which were also resistant to pretomanid. Delamanid resistance was detected in two further isolates that harboured mutations in fbiA, but did not show cross-resistance to pretomanid. All isolates were susceptible to linezolid and clofazimine, and no mutations found were associated with resistance. CONCLUSIONS More studies that correlate genotypic and phenotypic drug susceptibility data are needed to increase the knowledge base of mutations associated with resistance, in particular for pretomanid. Overall, this study contributes to the development of future mutation catalogues for M. tuberculosis complex isolates.
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Affiliation(s)
- Simone Mok
- Irish Mycobacteria Reference Laboratory, St James’s Hospital, Dublin, Ireland
- Department of Clinical Microbiology, School of Medicine, Trinity College Dublin, the University of Dublin, St James’s Hospital Campus, Dublin, Ireland
| | - Emma Roycroft
- Irish Mycobacteria Reference Laboratory, St James’s Hospital, Dublin, Ireland
- Department of Clinical Microbiology, School of Medicine, Trinity College Dublin, the University of Dublin, St James’s Hospital Campus, Dublin, Ireland
| | - Peter R Flanagan
- Irish Mycobacteria Reference Laboratory, St James’s Hospital, Dublin, Ireland
- Department of Clinical Microbiology, School of Medicine, Trinity College Dublin, the University of Dublin, St James’s Hospital Campus, Dublin, Ireland
| | - Johannes Wagener
- Irish Mycobacteria Reference Laboratory, St James’s Hospital, Dublin, Ireland
- Department of Clinical Microbiology, School of Medicine, Trinity College Dublin, the University of Dublin, St James’s Hospital Campus, Dublin, Ireland
| | - Margaret M Fitzgibbon
- Irish Mycobacteria Reference Laboratory, St James’s Hospital, Dublin, Ireland
- Department of Clinical Microbiology, School of Medicine, Trinity College Dublin, the University of Dublin, St James’s Hospital Campus, Dublin, Ireland
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13
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Koleske BN, Jacobs WR, Bishai WR. The Mycobacterium tuberculosis genome at 25 years: lessons and lingering questions. J Clin Invest 2023; 133:e173156. [PMID: 37781921 PMCID: PMC10541200 DOI: 10.1172/jci173156] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023] Open
Abstract
First achieved in 1998 by Cole et al., the complete genome sequence of Mycobacterium tuberculosis continues to provide an invaluable resource to understand tuberculosis (TB), the leading cause of global infectious disease mortality. At the 25-year anniversary of this accomplishment, we describe how insights gleaned from the M. tuberculosis genome have led to vital tools for TB research, epidemiology, and clinical practice. The increasing accessibility of whole-genome sequencing across research and clinical settings has improved our ability to predict antibacterial susceptibility, to track epidemics at the level of individual outbreaks and wider historical trends, to query the efficacy of the bacille Calmette-Guérin (BCG) vaccine, and to uncover targets for novel antitubercular therapeutics. Likewise, we discuss several recent efforts to extract further discoveries from this powerful resource.
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Affiliation(s)
- Benjamin N. Koleske
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - William R. Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - William R. Bishai
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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14
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Shahin AI, Zaraei SO, Alzuraiqi S, Abdulateef Z, Abbas NE, Al-Tel TH, El-Gamal MI. Evaluation of 2,3-dihydroimidazo[2,1- b]oxazole and imidazo[2,1- b]oxazole derivatives as chemotherapeutic agents. Future Med Chem 2023; 15:1885-1901. [PMID: 37814826 DOI: 10.4155/fmc-2023-0147] [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: 10/11/2023] Open
Abstract
Imidazo[2,1-b]oxazole and 2,3-dihydroimidazo[2,1-b]oxazole ring systems are commonly employed in therapeutically active molecules. In this article, the authors review the utilization of these core scaffolds as chemotherapeutic agents from 2018 to 2022. These scaffolds possess many important biological activities including antimicrobial and anticancer, among others. This review covers their biological activities and structure-activity relationships. One of the most important drugs in this class of compounds is the antitubercular agent delamanid. In this paper, the compounds structure-activity relationship and preclinical and clinical trial data are thoroughly presented.
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Affiliation(s)
- Afnan I Shahin
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Seyed-Omar Zaraei
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Shahed Alzuraiqi
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Zahaa Abdulateef
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Noora E Abbas
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Taleb H Al-Tel
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Mohammed I El-Gamal
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
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15
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Nguyen TVA, Nguyen QH, Nguyen TNT, Anthony RM, Vu DH, Alffenaar JWC. Pretomanid resistance: An update on emergence, mechanisms and relevance for clinical practice. Int J Antimicrob Agents 2023; 62:106953. [PMID: 37595848 DOI: 10.1016/j.ijantimicag.2023.106953] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/20/2023] [Accepted: 08/11/2023] [Indexed: 08/20/2023]
Abstract
Pretomanid (PA-824), a novel anti-tuberculosis (TB) nitroimidazoxazine, has been approved for multi-drug-resistant TB treatment for a few years. Pretomanid has been demonstrated to be highly active against Mycobacterium tuberculosis when combined with other anti-TB drugs. This review provides an update of the current knowledge on the modes of action, resistance mechanisms, emergence of drug resistance, and status of antimicrobial susceptibility testing for pretomanid and its relevance for clinical practice. Pretomanid resistance has been reported in in-vitro and animal models but not yet in clinical trials. Pretomanid-resistance-associated mutations have been reported in the fbiA, fbiB, fbiC, fbiD, ddn and fgd1 genes. However, understanding of in-vivo molecular resistance mechanisms remains limited, and complicates the development of accurate antimicrobial susceptibility testing methods for pretomanid. As such, no reference method for antimicrobial susceptibility testing of pretomanid has been established to guide clinical use. Further studies linking specific mutations, in-vitro susceptibility, drug exposure and resistance mechanisms to treatment failure with pretomanid should be prioritized.
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Affiliation(s)
- Thi Van Anh Nguyen
- LMI DRISA, University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Quang Huy Nguyen
- LMI DRISA, University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Tran Nam Tien Nguyen
- National Centre of Drug information and Adverse Drug Reaction Monitoring, Hanoi University of Pharmacy, Hanoi, Vietnam
| | - Richard M Anthony
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Dinh Hoa Vu
- National Centre of Drug information and Adverse Drug Reaction Monitoring, Hanoi University of Pharmacy, Hanoi, Vietnam
| | - Jan-Willem C Alffenaar
- School of Pharmacy, Faculty of Medicine and Health, University of Sydney, Sydney, Australia; Westmead Hospital, Sydney, Australia; Sydney Institute for Infectious Diseases, University of Sydney, Sydney, Australia.
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16
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Eke IE, Williams JT, Haiderer ER, Albrecht VJ, Murdoch HM, Abdalla BJ, Abramovitch RB. Discovery and characterization of antimycobacterial nitro-containing compounds with distinct mechanisms of action and in vivo efficacy. Antimicrob Agents Chemother 2023; 67:e0047423. [PMID: 37610224 PMCID: PMC10508139 DOI: 10.1128/aac.00474-23] [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: 04/11/2023] [Accepted: 06/30/2023] [Indexed: 08/24/2023] Open
Abstract
Nitro-containing compounds have emerged as important agents in the control of tuberculosis (TB). From a whole-cell high-throughput screen for Mycobacterium tuberculosis (Mtb) growth inhibitors, 10 nitro-containing compounds were prioritized for characterization and mechanism of action studies. HC2209, HC2210, and HC2211 are nitrofuran-based prodrugs that need the cofactor F420 machinery for activation. Unlike pretomanid which depends only on deazaflavin-dependent nitroreductase (Ddn), these nitrofurans depend on Ddn and possibly another F420-dependent reductase for activation. These nitrofurans also differ from pretomanid in their potent activity against Mycobacterium abscessus. Four dinitrobenzamides (HC2217, HC2226, HC2238, and HC2239) and a nitrofuran (HC2250) are proposed to be inhibitors of decaprenyl-phosphoryl-ribose 2'-epimerase 1 (DprE1), based on isolation of resistant mutations in dprE1. Unlike other DprE1 inhibitors, HC2250 was found to be potent against non-replicating persistent bacteria, suggesting additional targets. Two of the compounds, HC2233 and HC2234, were found to have potent, sterilizing activity against replicating and non-replicating Mtb in vitro, but a proposed mechanism of action could not be defined. In a pilot in vivo efficacy study, HC2210 was orally bioavailable and efficacious in reducing bacterial load by ~1 log in a chronic murine TB infection model.
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Affiliation(s)
- Ifeanyichukwu E. Eke
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - John T. Williams
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Elizabeth R. Haiderer
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Veronica J. Albrecht
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Heather M. Murdoch
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Bassel J. Abdalla
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Robert B. Abramovitch
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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17
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Chengalroyen MD, Mehaffy C, Lucas M, Bauer N, Raphela ML, Oketade N, Warner DF, Lewinsohn DA, Lewinsohn DM, Dobos KM, Mizrahi V. Modulation of riboflavin biosynthesis and utilization in mycobacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.555301. [PMID: 37693561 PMCID: PMC10491194 DOI: 10.1101/2023.08.30.555301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Riboflavin (vitamin B2) is the precursor of the flavin coenzymes, FAD and FMN, which play a central role in cellular redox metabolism. While humans must obtain riboflavin from dietary sources, certain microbes, including Mycobacterium tuberculosis (Mtb), can biosynthesize riboflavin de novo. Riboflavin precursors have also been implicated in the activation of mucosal-associated invariant T (MAIT) cells which recognize metabolites derived from the riboflavin biosynthesis pathway complexed to the MHC-I-like molecule, MR1. To investigate the biosynthesis and function of riboflavin and its pathway intermediates in mycobacterial metabolism, physiology and MAIT cell recognition, we constructed conditional knockdowns (hypomorphs) in riboflavin biosynthesis and utilization genes in Mycobacterium smegmatis (Msm) and Mtb by inducible CRISPR interference. Using this comprehensive panel of hypomorphs, we analyzed the impact of gene silencing on viability, on the transcription of (other) riboflavin pathway genes, on the levels of the pathway proteins and on riboflavin itself. Our results revealed that (i) despite lacking a canonical transporter, both Msm and Mtb assimilate exogenous riboflavin when supplied at high concentration; (ii) there is functional redundancy in lumazine synthase activity in Msm; (iii) silencing of ribA2 or ribF is profoundly bactericidal in Mtb; and (iv) in Msm, ribA2 silencing results in concomitant knockdown of other pathway genes coupled with RibA2 and riboflavin depletion and is also bactericidal. In addition to their use in genetic validation of potential drug targets for tuberculosis, this collection of hypomorphs provides a useful resource for investigating the role of pathway intermediates in MAIT cell recognition of mycobacteria.
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Affiliation(s)
- Melissa D. Chengalroyen
- Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, South Africa
| | - Carolina Mehaffy
- Department of Microbiology, Immunology and Pathology, Colorado State University, Colorado, USA
| | - Megan Lucas
- Department of Microbiology, Immunology and Pathology, Colorado State University, Colorado, USA
| | - Niel Bauer
- Department of Microbiology, Immunology and Pathology, Colorado State University, Colorado, USA
| | - Mabule L. Raphela
- Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, South Africa
| | - Nurudeen Oketade
- Department of Microbiology, Immunology and Pathology, Colorado State University, Colorado, USA
| | - Digby F. Warner
- Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, South Africa
- Wellcome Centre for Infectious Disease Research in Africa, University of Cape Town, South Africa
| | | | - David M. Lewinsohn
- Oregon Health and Science University, Oregon, USA
- Portland VA Medical Center, Oregon, USA
| | - Karen M. Dobos
- Department of Microbiology, Immunology and Pathology, Colorado State University, Colorado, USA
| | - Valerie Mizrahi
- Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, South Africa
- Wellcome Centre for Infectious Disease Research in Africa, University of Cape Town, South Africa
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18
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Abrahams KA, Batt SM, Gurcha SS, Veerapen N, Bashiri G, Besra GS. DprE2 is a molecular target of the anti-tubercular nitroimidazole compounds pretomanid and delamanid. Nat Commun 2023; 14:3828. [PMID: 37380634 DOI: 10.1038/s41467-023-39300-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 06/01/2023] [Indexed: 06/30/2023] Open
Abstract
Mycobacterium tuberculosis is one of the global leading causes of death due to a single infectious agent. Pretomanid and delamanid are new antitubercular agents that have progressed through the drug discovery pipeline. These compounds are bicyclic nitroimidazoles that act as pro-drugs, requiring activation by a mycobacterial enzyme; however, the precise mechanisms of action of the active metabolite(s) are unclear. Here, we identify a molecular target of activated pretomanid and delamanid: the DprE2 subunit of decaprenylphosphoribose-2'-epimerase, an enzyme required for the synthesis of cell wall arabinogalactan. We also provide evidence for an NAD-adduct as the active metabolite of pretomanid. Our results highlight DprE2 as a potential antimycobacterial target and provide a foundation for future exploration into the active metabolites and clinical development of pretomanid and delamanid.
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Affiliation(s)
- Katherine A Abrahams
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Sarah M Batt
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Sudagar S Gurcha
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Natacha Veerapen
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Ghader Bashiri
- Laboratory of Molecular and Microbial Biochemistry, School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland, 1010, New Zealand
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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19
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Katariya MM, Snee M, Tunnicliffe RB, Kavanagh ME, Boshoff HIM, Amadi CN, Levy CW, Munro AW, Abell C, Leys D, Coyne AG, McLean KJ. Structure Based Discovery of Inhibitors of CYP125 and CYP142 from Mycobacterium tuberculosis. Chemistry 2023; 29:e202203868. [PMID: 36912255 PMCID: PMC10205683 DOI: 10.1002/chem.202203868] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023]
Abstract
Mycobacterium tuberculosis (Mtb) was responsible for approximately 1.6 million deaths in 2021. With the emergence of extensive drug resistance, novel therapeutic agents are urgently needed, and continued drug discovery efforts required. Host-derived lipids such as cholesterol not only support Mtb growth, but are also suspected to function in immunomodulation, with links to persistence and immune evasion. Mtb cytochrome P450 (CYP) enzymes facilitate key steps in lipid catabolism and thus present potential targets for inhibition. Here we present a series of compounds based on an ethyl 5-(pyridin-4-yl)-1H-indole-2-carboxylate pharmacophore which bind strongly to both Mtb cholesterol oxidases CYP125 and CYP142. Using a structure-guided approach, combined with biophysical characterization, compounds with micromolar range in-cell activity against clinically relevant drug-resistant isolates were obtained. These will incite further development of much-needed additional treatment options and provide routes to probe the role of CYP125 and CYP142 in Mtb pathogenesis.
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Affiliation(s)
- Mona M. Katariya
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Matthew Snee
- Department of ChemistryManchester Institute of BiotechnologyUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Richard B. Tunnicliffe
- Department of ChemistryManchester Institute of BiotechnologyUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Madeline E. Kavanagh
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Department of ChemistryThe Skaggs Institute for Chemical BiologyThe Scripps Research InstituteLa JollaCA 92-37USA
| | - Helena I. M. Boshoff
- Tuberculosis Research SectionNational Institute of Allergy and Infectious DiseasesLaboratory of Clinical Immunology and MicrobiologyNational Institutes of HealthBethesdaMD 20892USA
| | - Cecilia N. Amadi
- Department of ChemistryManchester Institute of BiotechnologyUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Colin W. Levy
- Department of ChemistryManchester Institute of BiotechnologyUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Andrew W. Munro
- Department of ChemistryManchester Institute of BiotechnologyUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Chris Abell
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - David Leys
- Department of ChemistryManchester Institute of BiotechnologyUniversity of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Anthony G. Coyne
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Kirsty J. McLean
- Department of Biological and Geographical SciencesUniversity of HuddersfieldSchool of Applied SciencesQueensgateHuddersfieldHD1 3DHUK
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20
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Ismail N, Dippenaar A, Warren RM, Peters RPH, Omar SV. Emergence of Canonical and Noncanonical Genomic Variants following In Vitro Exposure of Clinical Mycobacterium tuberculosis Strains to Bedaquiline or Clofazimine. Antimicrob Agents Chemother 2023; 67:e0136822. [PMID: 36892309 PMCID: PMC10112258 DOI: 10.1128/aac.01368-22] [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: 10/10/2022] [Accepted: 02/09/2023] [Indexed: 03/10/2023] Open
Abstract
In Mycobacterium tuberculosis, bedaquiline and clofazimine resistance occurs primarily through Rv0678 variants, a gene encoding a repressor protein that regulates mmpS5/mmpL5 efflux pump gene expression. Despite the shared effect of both drugs on efflux, little else is known about other pathways affected. We hypothesized that in vitro generation of bedaquiline- or clofazimine-resistant mutants could provide insight into additional mechanisms of action. We performed whole-genome sequencing and determined phenotypic MICs for both drugs on progenitor and mutant progenies. Mutants were induced through serial passage on increasing concentrations of bedaquiline or clofazimine. Rv0678 variants were identified in both clofazimine- and bedaquiline-resistant mutants, with concurrent atpE SNPs occurring in the latter. Of concern was the acquisition of variants in the F420 biosynthesis pathway in clofazimine-resistant mutants obtained from either a fully susceptible (fbiD: del555GCT) or rifampicin mono-resistant (fbiA: 283delTG and T862C) progenitor. The acquisition of these variants possibly implicates a shared pathway between clofazimine and nitroimidazoles. Pathways associated with drug tolerance and persistence, F420 biosynthesis, glycerol uptake and metabolism, efflux, and NADH homeostasis appear to be affected following exposure to these drugs. Shared genes affected by both drugs include Rv0678, glpK, nuoG, and uvrD1. Genes with variants in the bedaquiline resistant mutants included atpE, fadE28, truA, mmpL5, glnH, and pks8, while clofazimine-resistant mutants displayed ppsD, fbiA, fbiD, mutT3, fadE18, Rv0988, and Rv2082 variants. These results show the importance of epistatic mechanisms as a means of responding to drug pressure and highlight the complexity of resistance acquisition in M. tuberculosis.
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Affiliation(s)
- N. Ismail
- SAMRC Centre for Tuberculosis Research/DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Prinshof, Gauteng, South Africa
| | - A. Dippenaar
- Global Health Institute, Department of Family Medicine and Population Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - R. M. Warren
- SAMRC Centre for Tuberculosis Research/DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - R. P. H. Peters
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Prinshof, Gauteng, South Africa
- Department of Medical Microbiology, School CAPHRI (Care and Public Health Research Institute), Maastricht University, Maastricht, The Netherlands
| | - S. V. Omar
- Department of Medical Microbiology, School CAPHRI (Care and Public Health Research Institute), Maastricht University, Maastricht, The Netherlands
- National Institute for Communicable Diseases/National Health Laboratory Service, Centre for Tuberculosis, National TB Reference Laboratory & WHO Supranational TB Reference Laboratory, Johannesburg, Gauteng, South Africa
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21
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Waller NJE, Cheung CY, Cook GM, McNeil MB. The evolution of antibiotic resistance is associated with collateral drug phenotypes in Mycobacterium tuberculosis. Nat Commun 2023; 14:1517. [PMID: 36934122 PMCID: PMC10024696 DOI: 10.1038/s41467-023-37184-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/06/2023] [Indexed: 03/20/2023] Open
Abstract
The increasing incidence of drug resistance in Mycobacterium tuberculosis has diminished the efficacy of almost all available antibiotics, complicating efforts to combat the spread of this global health burden. Alongside the development of new drugs, optimised drug combinations are needed to improve treatment success and prevent the further spread of antibiotic resistance. Typically, antibiotic resistance leads to reduced sensitivity, yet in some cases the evolution of drug resistance can lead to enhanced sensitivity to unrelated drugs. This phenomenon of collateral sensitivity is largely unexplored in M. tuberculosis but has the potential to identify alternative therapeutic strategies to combat drug-resistant strains that are unresponsive to current treatments. Here, by using drug susceptibility profiling, genomics and evolutionary studies we provide evidence for the existence of collateral drug sensitivities in an isogenic collection M. tuberculosis drug-resistant strains. Furthermore, in proof-of-concept studies, we demonstrate how collateral drug phenotypes can be exploited to select against and prevent the emergence of drug-resistant strains. This study highlights that the evolution of drug resistance in M. tuberculosis leads to collateral drug responses that can be exploited to design improved drug regimens.
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Affiliation(s)
- Natalie J E Waller
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Chen-Yi Cheung
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Matthew B McNeil
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.
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22
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Mundhe P, Kidwai S, Saini SM, Singh HR, Singh R, Chandrashekharappa S. Design, Synthesis, Characterization, and Anti-tubercular activity of Novel Ethyl-3-benzoyl-6, 8-difluoroindolizine-1-carboxylate Analogues: Molecular Target Identification and Molecular Docking Studies. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
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23
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Batt SM, Toth S, Rodriguez B, Abrahams KA, Veerapen N, Chiodarelli G, Cox LR, Moynihan PJ, Lelievre J, Fütterer K, Besra GS. Assay development and inhibition of the Mt-DprE2 essential reductase from Mycobacterium tuberculosis. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001288. [PMID: 36748627 PMCID: PMC9993113 DOI: 10.1099/mic.0.001288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
DprE2 is an essential enzyme in the synthesis of decaprenylphosphoryl-β-d-arabinofuranose (DPA) and subsequently arabinogalactan, and is a significant new drug target for M. tuberculosis. Two compounds from the GSK-177 box set, GSK301A and GSK032A, were identified through Mt-DprE2-target overexpression studies. The Mt-DprE1-DprE2 complex was co-purified and a new in vitro DprE2 assay developed, based on the oxidation of the reduced nicotinamide adenine dinucleotide cofactor of DprE2 (NADH/NADPH). The Mt-DprE1-DprE2 complex showed interesting kinetics in both the DprE1 resazurin-based assay, where Mt-DprE2 was found to enhance Mt-DprE1 activity and reduce substrate inhibition; and also in the DprE2 assay, which similarly exhibited substrate inhibition and a difference in kinetics of the two potential cofactors, NADH and NADPH. Although, no inhibition was observed in the DprE2 assay by the two GSK set compounds, spontaneous mutant generation indicated a possible explanation in the form of a pro-drug activation pathway, involving fgd1 and fbiC.
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Affiliation(s)
- Sarah M Batt
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Szilvi Toth
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Beatriz Rodriguez
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Madrid, Spain
| | - Katherine A Abrahams
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Natacha Veerapen
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | | | - Liam R Cox
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, UK
| | - Patrick J Moynihan
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Joel Lelievre
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Madrid, Spain
| | - Klaus Fütterer
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
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24
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Yan W, Zheng Y, Dou C, Zhang G, Arnaout T, Cheng W. The pathogenic mechanism of Mycobacterium tuberculosis: implication for new drug development. MOLECULAR BIOMEDICINE 2022; 3:48. [PMID: 36547804 PMCID: PMC9780415 DOI: 10.1186/s43556-022-00106-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is a tenacious pathogen that has latently infected one third of the world's population. However, conventional TB treatment regimens are no longer sufficient to tackle the growing threat of drug resistance, stimulating the development of innovative anti-tuberculosis agents, with special emphasis on new protein targets. The Mtb genome encodes ~4000 predicted proteins, among which many enzymes participate in various cellular metabolisms. For example, more than 200 proteins are involved in fatty acid biosynthesis, which assists in the construction of the cell envelope, and is closely related to the pathogenesis and resistance of mycobacteria. Here we review several essential enzymes responsible for fatty acid and nucleotide biosynthesis, cellular metabolism of lipids or amino acids, energy utilization, and metal uptake. These include InhA, MmpL3, MmaA4, PcaA, CmaA1, CmaA2, isocitrate lyases (ICLs), pantothenate synthase (PS), Lysine-ε amino transferase (LAT), LeuD, IdeR, KatG, Rv1098c, and PyrG. In addition, we summarize the role of the transcriptional regulator PhoP which may regulate the expression of more than 110 genes, and the essential biosynthesis enzyme glutamine synthetase (GlnA1). All these enzymes are either validated drug targets or promising target candidates, with drugs targeting ICLs and LAT expected to solve the problem of persistent TB infection. To better understand how anti-tuberculosis drugs act on these proteins, their structures and the structure-based drug/inhibitor designs are discussed. Overall, this investigation should provide guidance and support for current and future pharmaceutical development efforts against mycobacterial pathogenesis.
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Affiliation(s)
- Weizhu Yan
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Yanhui Zheng
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Chao Dou
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
| | - Guixiang Zhang
- grid.13291.380000 0001 0807 1581Division of Gastrointestinal Surgery, Department of General Surgery and Gastric Cancer center, West China Hospital, Sichuan University, No. 37. Guo Xue Xiang, Chengdu, 610041 China
| | - Toufic Arnaout
- Kappa Crystals Ltd., Dublin, Ireland ,MSD Dunboyne BioNX, Co. Meath, Ireland
| | - Wei Cheng
- grid.412901.f0000 0004 1770 1022Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041 China
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25
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Wu SH, Xiao YX, Hsiao HC, Jou R. Development and Assessment of a Novel Whole-Gene-Based Targeted Next-Generation Sequencing Assay for Detecting the Susceptibility of Mycobacterium tuberculosis to 14 Drugs. Microbiol Spectr 2022; 10:e0260522. [PMID: 36255328 PMCID: PMC9769975 DOI: 10.1128/spectrum.02605-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/23/2022] [Indexed: 01/07/2023] Open
Abstract
Targeted next-generation sequencing (tNGS) has emerged as an alternative method for detecting drug-resistant tuberculosis (DR-TB). To provide comprehensive drug susceptibility information and to address mutations missed by available commercial molecular diagnostics, we developed and evaluated a tNGS panel with 22 whole-gene targets using the Ion Torrent platform to predict drug resistance to 14 drugs, namely, rifampicin (RIF), isoniazid (INH), ethambutol (EMB), pyrazinamide (PZA), moxifloxacin (MFX), levofloxacin (LFX), amikacin (AMK), capreomycin (CM), kanamycin (KM), streptomycin (SM), bedaquiline (BDQ), clofazimine (CFZ), linezolid (LZD), and delamanid (DLM). We selected 50 and 35 Mycobacterium tuberculosis isolates with various DR profiles as the training set and the challenge set, respectively. Comparative variant analyses of the DR genes were performed using Sanger sequencing and whole-genome sequencing (WGS). Phenotypic drug susceptibility testing (pDST) results were used as gold standards. Regarding the limit of detection, the tNGS assay detected 2.9 to 3.8% minority variants in 4% mutant mixtures. The sensitivity and specificity of tNGS were 97.0% (95% confidence interval [CI] = 93.1 to 98.7%) and 99.1% (95% CI = 97.7 to 99.7%), respectively. The concordance of tNGS with pDST was 98.5% (95% CI = 97.2 to 99.2%), which was comparable to that of WGS (98.7%, 95% CI = 97.4 to 99.3%) and better than that of Sanger sequencing (96.9%, 95% CI = 95.3 to 98.0%). The agreement between tNGS and pDST was almost perfect for RIF, INH, EMB, MFX, LFX, AMK, CM, KM, SM, BDQ, and LZD (kappa value = 0.807 to 1.000) and substantial for PZA (kappa value = 0.791). Our customized novel whole-gene-based tNGS panel is highly consistent with pDST and WGS for comprehensive and accurate prediction of drug resistance in a strengthened and streamlined DR-TB laboratory program. IMPORTANCE We developed and validated a tNGS assay that was the first to target 22 whole genes instead of regions of drug resistance genes and comprehensively detected susceptibility to 14 anti-TB drugs, with great flexibility to include new or repurposed drugs. Notably, we demonstrated that our custom-designed Ion AmpliSeq TB research panel platform had high concordance with pDST and could significantly reduce turnaround time (by approximately 70%) to meet a clinically actionable time frame. Our tNGS assay is a promising DST solution for providing needed clinical information for precision medicine-guided therapies for DR-TB and allows the rollout of active pharmacovigilance.
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Affiliation(s)
- Sheng-Han Wu
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Yu-Xin Xiao
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Hseuh-Chien Hsiao
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Ruwen Jou
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
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26
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Spontaneous Mutational Patterns and Novel Mutations for Delamanid Resistance in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2022; 66:e0053122. [PMID: 36448833 PMCID: PMC9765178 DOI: 10.1128/aac.00531-22] [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: 12/03/2022] Open
Abstract
Delamanid (DLM) and pretomanid (PTM) are recent additions to the anti-tuberculosis (TB) drug armamentarium, and they offer more effective options for drug-resistant TB treatment. In particular, DLM is included in Group C, which is recommended for use in longer multidrug-resistant (MDR)-TB regimens. Previous studies have shown that resistance to DLM/PTM is caused by mutations in the ddn, fgd1, fbiA, fbiB, fbiC, and fbiD genes, which are related to the F420-dependent bioactivation pathway. Herein, we conduct in vitro selection of DLM-resistant strains using clinical Mycobacterium tuberculosis (MTB) isolates with various drug resistance profiles. The spontaneous resistance frequency of drug-susceptible (DS) MTB (1.14 × 10-6 to 1.04 × 10-4) to DLM was similar to that of H37Rv (8.88 × 10-6 to 9.96 × 10-6) but higher than those of multidrug-resistant MTB (2.03 × 10-7 to 3.18 × 10-6) and extensively drug-resistant (XDR) MTB (4.67 × 10-8 to 3.60 × 10-6). Of the 100 independently selected DLM-resistant MTB mutants, 65% harbored mutations in genes associated with either DLM prodrug activation (ddn, 39.73%; fgd1, 16.44%) or the F420 biosynthetic pathway (fbiA, 16.44%; fbiB, 5.48%; fbiC, 21.92%). Of the 45 mutations we identified, 38 were not previously reported. A structure analysis revealed that several point mutations affected the ligand binding or structural stability of enzymes related to DLM resistance, which would block the enzyme activity required for prodrug activation. Our results elucidate the in vitro spontaneous DLM-resistance patterns of different clinical strains, which could improve the understanding of the causes of DLM resistance in clinical strains and of the effects on drug resistance of different mutations in genes that are related to the DLM activation pathway.
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27
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Edwards BD, Field SK. The Struggle to End a Millennia-Long Pandemic: Novel Candidate and Repurposed Drugs for the Treatment of Tuberculosis. Drugs 2022; 82:1695-1715. [PMID: 36479687 PMCID: PMC9734533 DOI: 10.1007/s40265-022-01817-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2022] [Indexed: 12/12/2022]
Abstract
This article provides an encompassing review of the current pipeline of putative and developed treatments for tuberculosis, including multidrug-resistant strains. The review has organized each compound according to its site of activity. To provide context, mention of drugs within current recommended treatment regimens is made, thereafter followed by discussion on recently developed and upcoming molecules at established and novel targets. The review is designed to provide a clinically applicable understanding of the compounds that are deemed most currently relevant, including those already under clinical study and those that have shown promising pre-clinical results. An extensive review of the efficacy and safety data for key contemporary drugs already incorporated into treatment regimens, such as bedaquiline, pretomanid, and linezolid, is provided. The three levels of the bacterial cell wall (mycolic acid, arabinogalactan, and peptidoglycan layers) are highlighted and important compounds designed to target each layer are delineated. Amongst others, the highly optimistic and potent anti-mycobacterial activity of agents such as BTZ-043, PBTZ 169, and OPC-167832 are emphasized. The evolving spectrum of oxazolidinones, such as sutezolid, delpazolid, and TBI-223, all aiming to exceed the efficacy achieved with linezolid yet offer a safer alternative to the potential toxicity, are reviewed. New and exciting prospective agents with novel mechanisms of impact against TB, including 3-aminomethyl benzoxaboroles and telacebec, are underscored. We describe new diaryloquinolines in development, striving to build on the immense success of bedaquiline. Finally, we discuss some of these compounds that have shown encouraging additive or synergistic benefit when used in combination, providing some promise for the future in treating this ancient scourge.
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Affiliation(s)
- Brett D Edwards
- Division of Infectious Diseases and Tuberculosis Services, Alberta Health Services, Department of Medicine, Cumming School of Medicine, University of Calgary, Peter Lougheed Centre, 3500, 26 Avenue NE, Calgary, AB, T1Y6J4, Canada.
| | - Stephen K Field
- Division of Infectious Diseases and Tuberculosis Services, Alberta Health Services, Department of Medicine, Cumming School of Medicine, University of Calgary, Peter Lougheed Centre, 3500, 26 Avenue NE, Calgary, AB, T1Y6J4, Canada
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28
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Mokrousov I, Slavchev I, Solovieva N, Dogonadze M, Vyazovaya A, Valcheva V, Masharsky A, Belopolskaya O, Dimitrov S, Zhuravlev V, Portugal I, Perdigão J, Dobrikov GM. Molecular Insight into Mycobacterium tuberculosis Resistance to Nitrofuranyl Amides Gained through Metagenomics-like Analysis of Spontaneous Mutants. Pharmaceuticals (Basel) 2022; 15:ph15091136. [PMID: 36145357 PMCID: PMC9504009 DOI: 10.3390/ph15091136] [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: 08/12/2022] [Revised: 09/04/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
We performed synthesis of new nitrofuranyl amides and investigated their anti-TB activity and primary genetic response of mycobacteria through whole-genome sequencing (WGS) of spontaneous resistant mutants. The in vitro activity was assessed on reference strain Mycobacterium tuberculosis H37Rv. The most active compound 11 was used for in vitro selection of spontaneous resistant mutants. The same mutations in six genes were detected in bacterial cultures grown under increased concentrations of 11 (2×, 4×, 8× MIC). The mutant positions were presented as mixed wild type and mutant alleles while increasing the concentration of the compound led to the semi-proportional and significant increase in mutant alleles. The identified genes belong to different categories and pathways. Some of them were previously reported as mediating drug resistance or drug tolerance, and counteracting oxidative and nitrosative stress, in particular: Rv0224c, fbiC, iniA, and Rv1592c. Gene-set interaction analysis revealed a certain weak interaction for gene pairs Rv1592–Rv1639c and Rv1592–Rv0224c. To conclude, this study experimentally demonstrated a multifaceted primary genetic response of M. tuberculosis to the action of nitrofurans. All three 11-treated subcultures independently presented the same six SNPs, which suggests their non-random occurrence and likely causative relationship between compound action and possible resistance mechanism.
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Affiliation(s)
- Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, 197101 St. Petersburg, Russia
- Henan International Joint Laboratory of Children’s Infectious Diseases, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China
- Correspondence: (I.M.); (G.M.D.)
| | - Ivaylo Slavchev
- Institute of Organic Chemistry with Centre of Phytochemistry, Acad. G. Bonchev Street, bl. 9, 1113 Sofia, Bulgaria
| | - Natalia Solovieva
- St. Petersburg Research Institute of Phthisiopulmonology, 191036 St. Petersburg, Russia
| | - Marine Dogonadze
- St. Petersburg Research Institute of Phthisiopulmonology, 191036 St. Petersburg, Russia
| | - Anna Vyazovaya
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, 197101 St. Petersburg, Russia
| | - Violeta Valcheva
- The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Acad. G. Bonchev Street, bl. 26, 1113 Sofia, Bulgaria
| | - Aleksey Masharsky
- Resource Center “Bio-bank Center”, Research Park of St. Petersburg State University, 198504 St. Petersburg, Russia
| | - Olesya Belopolskaya
- Resource Center “Bio-bank Center”, Research Park of St. Petersburg State University, 198504 St. Petersburg, Russia
| | - Simeon Dimitrov
- The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Acad. G. Bonchev Street, bl. 26, 1113 Sofia, Bulgaria
| | - Viacheslav Zhuravlev
- St. Petersburg Research Institute of Phthisiopulmonology, 191036 St. Petersburg, Russia
| | - Isabel Portugal
- iMed.ULisboa–Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, 1649004 Lisbon, Portugal
| | - João Perdigão
- iMed.ULisboa–Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, 1649004 Lisbon, Portugal
| | - Georgi M. Dobrikov
- Institute of Organic Chemistry with Centre of Phytochemistry, Acad. G. Bonchev Street, bl. 9, 1113 Sofia, Bulgaria
- Correspondence: (I.M.); (G.M.D.)
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Volynets GP, Gudzera OI, Usenko MO, Gorbatiuk OB, Yarmoluk SM, Tukalo MA. Probing interactions of aminoacyl-adenylate with Mycobacterium tuberculosis methionyl-tRNA synthetase through in silico site-directed mutagenesis and free energy calculation. J Biomol Struct Dyn 2022:1-9. [PMID: 35930324 DOI: 10.1080/07391102.2022.2107574] [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: 10/16/2022]
Abstract
Methionyl-tRNA synthetase (MetRS) is an attractive molecular target for antibiotic discovery. Recently, we have developed several classes of small-molecular inhibitors of Mycobacterium tuberculosis MetRS possessing antibacterial activity. In this article, we performed in silico site-directed mutagenesis of aminoacyl-adenylate binding site of M. tuberculosis MetRS in order to identify crucial amino acid residues for substrate interaction. The umbrella sampling algorithm was used to calculate the binding free energy (ΔG) of these mutated forms with methionyl-adenylate analogue. According to the obtained results, the replacement of Glu24 and Leu293 by alanine leads to the most significant decrease in the binding free energy (ΔG) for adenylate analogue with methionyl-tRNA synthetase indicating increasing of the affinity, which in turn causes the loss of compounds inhibitory activity. Therefore, these amino acid residues can be proposed for further experimental site-directed mutagenesis to confirm binding mode of inhibitors and should be taken into account during chemical optimization to overcome resistance due to mutations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Galyna P Volynets
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, the NAS of Ukraine, Kyiv, Ukraine
| | - Olga I Gudzera
- Department of Protein Synthesis Enzymology, Institute of Molecular Biology and Genetics, the NAS of Ukraine, Kyiv, Ukraine
| | - Mariia O Usenko
- Department of Cell Regulatory Mechanisms, Institute of Molecular Biology and Genetics, the NAS of Ukraine, Kyiv, Ukraine
| | - Oksana B Gorbatiuk
- Department of Cell Regulatory Mechanisms, Institute of Molecular Biology and Genetics, the NAS of Ukraine, Kyiv, Ukraine
| | - Sergiy M Yarmoluk
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, the NAS of Ukraine, Kyiv, Ukraine
| | - Michael A Tukalo
- Department of Protein Synthesis Enzymology, Institute of Molecular Biology and Genetics, the NAS of Ukraine, Kyiv, Ukraine
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Identification of dual-targeted Mycobacterium tuberculosis aminoacyl-tRNA synthetase inhibitors using machine learning. Future Med Chem 2022; 14:1223-1237. [PMID: 35876255 DOI: 10.4155/fmc-2022-0085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background: The most serious challenge in the treatment of tuberculosis is the multidrug resistance of Mycobacterium tuberculosis to existing antibiotics. As a strategy to overcome resistance we used a multitarget drug design approach. The purpose of the work was to discover dual-targeted inhibitors of mycobacterial LeuRS and MetRS with machine learning. Methods: The artificial neural networks were built using module nnet from R 3.6.1. The inhibitory activity of compounds toward LeuRS and MetRS was investigated in aminoacylation assays. Results: Using a machine-learning approach, we identified dual-targeted inhibitors of LeuRS and MetRS among 2-(quinolin-2-ylsulfanyl)-acetamide derivatives. The most active compound inhibits MetRS and LeuRS with IC50 values of 33 μm and 23.9 μm, respectively. Conclusion: 2-(Quinolin-2-ylsulfanyl)-acetamide scaffold can be useful for further research.
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Tsui CKM, Sorrentino F, Narula G, Mendoza-Losana A, del Rio RG, Herrán EP, Lopez A, Bojang A, Zheng X, Remuiñán-Blanco MJ, Av-Gay Y. Hit Compounds and Associated Targets in Intracellular Mycobacterium tuberculosis. Molecules 2022; 27:molecules27144446. [PMID: 35889319 PMCID: PMC9324642 DOI: 10.3390/molecules27144446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/04/2022] [Accepted: 07/07/2022] [Indexed: 02/04/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis, is one of the most devastating infectious agents in the world. Chemical-genetic characterization through in vitro evolution combined with whole genome sequencing analysis was used identify novel drug targets and drug resistance genes in Mtb associated with its intracellular growth in human macrophages. We performed a genome analysis of 53 Mtb mutants resistant to 15 different hit compounds. We found nonsynonymous mutations/indels in 30 genes that may be associated with drug resistance acquisitions. Beyond confirming previously identified drug resistance mechanisms such as rpoB and lead targets reported in novel anti-tuberculosis drug screenings such as mmpL3, ethA, and mbtA, we have discovered several unrecognized candidate drug targets including prrB. The exploration of the Mtb chemical mutant genomes could help novel drug discovery and the structural biology of compounds and associated mechanisms of action relevant to tuberculosis treatment.
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Affiliation(s)
- Clement K. M. Tsui
- Department of Medicine and Microbiology and Immunology, Life Science Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (C.K.M.T.); (F.S.); (G.N.); (A.L.); (A.B.); (X.Z.)
- National Centre for Infectious Diseases, Tan Tock Seng Hospital, Singapore 308442, Singapore
| | - Flavia Sorrentino
- Department of Medicine and Microbiology and Immunology, Life Science Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (C.K.M.T.); (F.S.); (G.N.); (A.L.); (A.B.); (X.Z.)
- GSK, Global Health Medicines R&D, PTM, Tres Cantos, 28760 Madrid, Spain; (A.M.-L.); (R.G.d.R.); (E.P.H.); (M.J.R.-B.)
| | - Gagandeep Narula
- Department of Medicine and Microbiology and Immunology, Life Science Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (C.K.M.T.); (F.S.); (G.N.); (A.L.); (A.B.); (X.Z.)
| | - Alfonso Mendoza-Losana
- GSK, Global Health Medicines R&D, PTM, Tres Cantos, 28760 Madrid, Spain; (A.M.-L.); (R.G.d.R.); (E.P.H.); (M.J.R.-B.)
- Department of Bioengineering and Aerospace Engineering, Carlos III University of Madrid, 28040 Madrid, Spain
| | - Ruben Gonzalez del Rio
- GSK, Global Health Medicines R&D, PTM, Tres Cantos, 28760 Madrid, Spain; (A.M.-L.); (R.G.d.R.); (E.P.H.); (M.J.R.-B.)
| | - Esther Pérez Herrán
- GSK, Global Health Medicines R&D, PTM, Tres Cantos, 28760 Madrid, Spain; (A.M.-L.); (R.G.d.R.); (E.P.H.); (M.J.R.-B.)
| | - Abraham Lopez
- Department of Medicine and Microbiology and Immunology, Life Science Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (C.K.M.T.); (F.S.); (G.N.); (A.L.); (A.B.); (X.Z.)
- GSK, Global Health Medicines R&D, PTM, Tres Cantos, 28760 Madrid, Spain; (A.M.-L.); (R.G.d.R.); (E.P.H.); (M.J.R.-B.)
| | - Adama Bojang
- Department of Medicine and Microbiology and Immunology, Life Science Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (C.K.M.T.); (F.S.); (G.N.); (A.L.); (A.B.); (X.Z.)
| | - Xingji Zheng
- Department of Medicine and Microbiology and Immunology, Life Science Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (C.K.M.T.); (F.S.); (G.N.); (A.L.); (A.B.); (X.Z.)
| | - Modesto Jesus Remuiñán-Blanco
- GSK, Global Health Medicines R&D, PTM, Tres Cantos, 28760 Madrid, Spain; (A.M.-L.); (R.G.d.R.); (E.P.H.); (M.J.R.-B.)
| | - Yossef Av-Gay
- Department of Medicine and Microbiology and Immunology, Life Science Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (C.K.M.T.); (F.S.); (G.N.); (A.L.); (A.B.); (X.Z.)
- Correspondence: ; Tel.: +1-604-822-3432
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Luo W, Huang Z, Xu D, Yang M, Zhu Y, Shen L, Chen S, Tao X, Bin W, Hu Y, Franzblau SG, Jiang N, Wei Y, Wei X, Ding CZ. Discovery and preclinical evaluations of JBD0131, a novel nitrodihydro-imidazooxazole anti-tuberculosis agent. Bioorg Med Chem Lett 2022; 72:128871. [PMID: 35777718 DOI: 10.1016/j.bmcl.2022.128871] [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] [Received: 05/24/2022] [Revised: 06/08/2022] [Accepted: 06/25/2022] [Indexed: 11/18/2022]
Abstract
Multidrug-resistant pulmonary tuberculosis (MDR-TB) is a major health problem worldwide. The treatment for MDR-TB requires medications for a long duration (up to 20-24 months) with second-line drugs resulting in unfavorable outcomes. Nitroimidazoles are promising antimycobacterial agents known to inhibit both aerobic and anaerobic mycobacterial activity. Delamanid and pretomanid are two nitroimidazoles approved by the regulatory agencies for MDR-TB treatment. However, both agents possess unsatisfactory absorption and QTc prolongation. In our search for a safer nitroimidazole, we discovered JBD0131 (2). It exhibited excellent anti-mycobacterial activity against M. tuberculosis H37Rv in vitro and in vivo, improved PK and absorption, reduced QT prolongation potential of delamanid. JBD0131 is currently in clinical development in China for pulmonary tuberculosis (CTR20202308).
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Affiliation(s)
- Wei Luo
- WuXi AppTec, 666 Gaoxin Road, East Lake High-tech Development Zone, Wuhan 430075, China
| | - Zhigang Huang
- WuXi AppTec, 666 Gaoxin Road, East Lake High-tech Development Zone, Wuhan 430075, China
| | - Deming Xu
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Meng Yang
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Yusong Zhu
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Liang Shen
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Shuhui Chen
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Xin Tao
- Changzhou Yinsheng Pharmacy Co., Ltd., Weitang Chemical Industry Zone, Changzhou 213000, China
| | - Wang Bin
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Tuberculosis, and Thoracic Tumor Research Institute, Beijing, China
| | - Yinghu Hu
- WuXi AppTec, 666 Gaoxin Road, East Lake High-tech Development Zone, Wuhan 430075, China
| | - Scott G Franzblau
- Institute for Tuberculosis Research, College of Pharmacy, The University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, United States
| | - Ning Jiang
- Jumbo Drug Bank Co., Ltd., No.18, Section 2, Bio-city Middle Road, High-tech Zone, Chengdu, Sichuan 610000, China
| | - Yuquan Wei
- State Key Lab of Biotherapy, Sichuan University, No 17, The Third Renmin South Road, Chengdu, Sichuan 610041, China
| | - Xiawei Wei
- Jumbo Drug Bank Co., Ltd., No.18, Section 2, Bio-city Middle Road, High-tech Zone, Chengdu, Sichuan 610000, China.
| | - Charles Z Ding
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China.
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Li H, Yuan J, Duan S, Pang Y. Resistance and tolerance of Mycobacterium tuberculosis to antimicrobial agents-How M. tuberculosis can escape antibiotics. WIREs Mech Dis 2022; 14:e1573. [PMID: 35753313 DOI: 10.1002/wsbm.1573] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/22/2022] [Accepted: 05/30/2022] [Indexed: 12/13/2022]
Abstract
Tuberculosis (TB) poses a serious threat to public health worldwide since it was discovered. Until now, TB has been one of the top 10 causes of death from a single infectious disease globally. The treatment of active TB cases majorly relies on various anti-tuberculosis drugs. However, under the selection pressure by drugs, the continuous evolution of Mycobacterium tuberculosis (Mtb) facilitates the emergence of drug-resistant strains, further resulting in the accumulation of tubercle bacilli with multiple drug resistance, especially deadly multidrug-resistant TB and extensively drug-resistant TB. Researches on the mechanism of drug action and drug resistance of Mtb provide a new scheme for clinical management of TB patients, and prevention of drug resistance. In this review, we summarized the molecular mechanisms of drug resistance of existing anti-TB drugs to better understand the evolution of drug resistance of Mtb, which will provide more effective strategies against drug-resistant TB, and accelerate the achievement of the EndTB Strategy by 2035. This article is categorized under: Infectious Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Haoran Li
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Jinfeng Yuan
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Shujuan Duan
- School of Medical Technology, Guangdong Medical University, Dongguan, China
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
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Antitubercular, Cytotoxicity, and Computational Target Validation of Dihydroquinazolinone Derivatives. Antibiotics (Basel) 2022; 11:antibiotics11070831. [PMID: 35884084 PMCID: PMC9311641 DOI: 10.3390/antibiotics11070831] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 02/04/2023] Open
Abstract
A series of 2,3-dihydroquinazolin-4(1H)-one derivatives (3a–3m) was screened for in vitro whole-cell antitubercular activity against the tubercular strain H37Rv and multidrug-resistant (MDR) Mycobacterium tuberculosis (MTB) strains. Compounds 3l and 3m with di-substituted aryl moiety (halogens) attached to the 2-position of the scaffold showed a minimum inhibitory concentration (MIC) of 2 µg/mL against the MTB strain H37Rv. Compound 3k with an imidazole ring at the 2-position of the dihydroquinazolin-4(1H)-one also showed significant inhibitory action against both the susceptible strain H37Rv and MDR strains with MIC values of 4 and 16 µg/mL, respectively. The computational results revealed the mycobacterial pyridoxal-5′-phosphate (PLP)-dependent aminotransferase (BioA) enzyme as the potential target for the tested compounds. In vitro, ADMET calculations and cytotoxicity studies against the normal human dermal fibroblast cells indicated the safety and tolerability of the test compounds 3k–3m. Thus, compounds 3k–3m warrant further optimization to develop novel BioA inhibitors for the treatment of drug-sensitive H37Rv and drug-resistant MTB.
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Singh R, Shaheer M, Sobhia ME. Molecular dynamic assisted investigation on impact of mutations in deazaflavin dependent nitroreductase against pretomanid: a computational study. J Biomol Struct Dyn 2022:1-23. [PMID: 35574601 DOI: 10.1080/07391102.2022.2069156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In the past decade, TB drugs belonging to the nitroimidazole class, pretomanid and delamanid, have been authorised to treat MDR-TB and XDR-TB. With a novel inhibition mechanism and a reduction in the span of treatment, it is now being administered in various combinations. This approach is not the ultimate remedy since the target protein Deazaflavin dependent nitroreductase (Ddn) has a high mutation frequency, and already pretomanid resistant clinical isolates are reported in various studies. Ddn is essential for M.tuberculosis to emerge from hypoxia, and point mutations in critical residues confer resistance to Nitro-imidazoles. Among the pool of available mutants, we have selected seven mutants viz DdnL49P, DdnY65S, DdnS78Y, DdnK79Q, DdnW88R, DdnY133C, and DdnY136S, all of which exhibited resistance to pretomanid. To address this issue, through computational study primarily by MD simulation, we attempted to elucidate these point mutations' impact and investigate the resistance mechanism. Hence, the DdnWT and mutant (MT) complexes were subjected to all-atom molecular dynamics (MD) simulations for 100 ns. Interestingly, we observed the escalation of the distance between cofactor and ligand in some mutants, along with a significant change in ligand conformation relative to the DdnWT. Moreover, we confirmed that mutations rendered ligand instability and were ejected from the binding pocket as a result. In conclusion, the results obtained provide a new structural insight and vital clues for designing novel inhibitors to combat nitroimidazole resistanceCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ravi Singh
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Punjab, India
| | - Muhammed Shaheer
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Punjab, India
| | - M Elizabeth Sobhia
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Punjab, India
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Dohál M, Dvořáková V, Šperková M, Pinková M, Spitaleri A, Norman A, Cabibbe AM, Rasmussen EM, Porvazník I, Škereňová M, Solovič I, Cirillo DM, Mokrý J. Whole genome sequencing of multidrug-resistant Mycobacterium tuberculosis isolates collected in the Czech Republic, 2005-2020. Sci Rep 2022; 12:7149. [PMID: 35505072 PMCID: PMC9062869 DOI: 10.1038/s41598-022-11287-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/21/2022] [Indexed: 01/11/2023] Open
Abstract
The emergence and spread of resistant tuberculosis (TB) pose a threat to public health, so it is necessary to diagnose the drug-resistant forms in a clinically short time frame and closely monitor their transmission. In this study, we carried out a first whole genome sequencing (WGS)-based analysis of multidrug resistant (MDR) M. tuberculosis strains to explore the phylogenetic lineages diversity, drug resistance mechanisms, and ongoing transmission chains within the country. In total, 65 isolates phenotypically resistant to at least rifampicin and isoniazid collected in the Czech Republic in 2005-2020 were enrolled for further analysis. The agreement of the results obtained by WGS with phenotypic drug susceptibility testing (pDST) in the determination of resistance to isoniazid, rifampicin, pyrazinamide, streptomycin, second-line injectables and fluoroquinolones was more than 80%. Phylogenetic analysis of WGS data revealed that the majority of MDR M. tuberculosis isolates were the Beijing lineage 2.2.1 (n = 46/65; 70.8%), while the remaining strains belonged to Euro-American lineage. Cluster analysis with a predefined cut-off distance of less than 12 single nucleotide polymorphisms between isolates showed 19 isolates in 6 clusters (clustering rate 29.2%), located mainly in the region of the capital city of Prague. This study highlights the utility of WGS as a high-resolution approach in the diagnosis, characterization of resistance patterns, and molecular-epidemiological analysis of resistant TB in the country.
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Affiliation(s)
- Matúš Dohál
- Department of Pharmacology and Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University, Bratislava, Slovakia.
| | - Věra Dvořáková
- National Reference Laboratory for Mycobacteria, National Institute of Public Health, Praha, Czech Republic
| | - Miluše Šperková
- National Reference Laboratory for Mycobacteria, National Institute of Public Health, Praha, Czech Republic
| | - Martina Pinková
- National Reference Laboratory for Mycobacteria, National Institute of Public Health, Praha, Czech Republic
| | - Andrea Spitaleri
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Anders Norman
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | | | - Erik Michael Rasmussen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Igor Porvazník
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, Slovakia
- Faculty of Health, Catholic University, Ružomberok, Slovakia
| | - Mária Škereňová
- Department of Molecular Medicine and Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University, Bratislava, Slovakia
- Department of Clinical Biochemistry, Jessenius Faculty of Medicine in Martin, Comenius University, Bratislava, Slovakia
| | - Ivan Solovič
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, Slovakia
- Faculty of Health, Catholic University, Ružomberok, Slovakia
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Juraj Mokrý
- Department of Pharmacology and Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University, Bratislava, Slovakia
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Progress Report: Antimicrobial Drug Discovery in the Resistance Era. Pharmaceuticals (Basel) 2022; 15:ph15040413. [PMID: 35455410 PMCID: PMC9030565 DOI: 10.3390/ph15040413] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 02/05/2023] Open
Abstract
Antibiotic resistance continues to be a most serious threat to public health. This situation demands that the scientific community increase their efforts for the discovery of alternative strategies to circumvent the problems associated with conventional small molecule therapeutics. The Global Antimicrobial Resistance and Use Surveillance System (GLASS) Report (published in June 2021) discloses the rapidly increasing number of bacterial infections that are mainly caused by antimicrobial-resistant bacteria. These concerns have initiated various government agencies and other organizations to educate the public regarding the appropriate use of antibiotics. This review discusses a brief highlight on the timeline of antimicrobial drug discovery with a special emphasis on the historical development of antimicrobial resistance. In addition, new antimicrobial targets and approaches, recent developments in drug screening, design, and delivery were covered. This review also discusses the emergence and roles of various antibiotic adjuvants and combination therapies while shedding light on current challenges and future perspectives. Overall, the emergence of resistant microbial strains has challenged drug discovery but their efforts to develop alternative technologies such as nanomaterials seem to be promising for the future.
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Dookie N, Khan A, Padayatchi N, Naidoo K. Application of Next Generation Sequencing for Diagnosis and Clinical Management of Drug-Resistant Tuberculosis: Updates on Recent Developments in the Field. Front Microbiol 2022; 13:775030. [PMID: 35401475 PMCID: PMC8988194 DOI: 10.3389/fmicb.2022.775030] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 02/17/2022] [Indexed: 11/30/2022] Open
Abstract
The World Health Organization’s End TB Strategy prioritizes universal access to an early diagnosis and comprehensive drug susceptibility testing (DST) for all individuals with tuberculosis (TB) as a key component of integrated, patient-centered TB care. Next generation whole genome sequencing (WGS) and its associated technology has demonstrated exceptional potential for reliable and comprehensive resistance prediction for Mycobacterium tuberculosis isolates, allowing for accurate clinical decisions. This review presents a descriptive analysis of research describing the potential of WGS to accelerate delivery of individualized care, recent advances in sputum-based WGS technology and the role of targeted sequencing for resistance detection. We provide an update on recent research describing the mechanisms of resistance to new and repurposed drugs and the dynamics of mixed infections and its potential implication on TB diagnosis and treatment. Whilst the studies reviewed here have greatly improved our understanding of recent advances in this arena, it highlights significant challenges that remain. The wide-spread introduction of new drugs in the absence of standardized DST has led to rapid emergence of drug resistance. This review highlights apparent gaps in our knowledge of the mechanisms contributing to resistance for these new drugs and challenges that limit the clinical utility of next generation sequencing techniques. It is recommended that a combination of genotypic and phenotypic techniques is warranted to monitor treatment response, curb emerging resistance and further dissemination of drug resistance.
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Affiliation(s)
- Navisha Dookie
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- *Correspondence: Navisha Dookie,
| | - Azraa Khan
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
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Abstract
Given the low treatment success rates of drug-resistant tuberculosis (TB), novel TB drugs are urgently needed. The landscape of TB treatment has changed considerably over the last decade with the approval of three new compounds: bedaquiline, delamanid and pretomanid. Of these, delamanid and pretomanid belong to the same class of drugs, the nitroimidazoles. In order to close the knowledge gap on how delamanid and pretomanid compare with each other, we summarize the main findings from preclinical research on these two compounds. We discuss the compound identification, mechanism of action, drug resistance, in vitro activity, in vivo pharmacokinetic profiles, and preclinical in vivo activity and efficacy. Although delamanid and pretomanid share many similarities, several differences could be identified. One finding of particular interest is that certain Mycobacterium tuberculosis isolates have been described that are resistant to either delamanid or pretomanid, but with preserved susceptibility to the other compound. This might imply that delamanid and pretomanid could replace one another in certain regimens. Regarding bactericidal activity, based on in vitro and preclinical in vivo activity, delamanid has lower MICs and higher mycobacterial load reductions at lower drug concentrations and doses compared with pretomanid. However, when comparing in vivo preclinical bactericidal activity at dose levels equivalent to currently approved clinical doses based on drug exposure, this difference in activity between the two compounds fades. However, it is important to interpret these comparative results with caution knowing the variability inherent in preclinical in vitro and in vivo models.
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Affiliation(s)
- Saskia E. Mudde
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
- Corresponding author. E-mail:
| | | | - Anne Lenaerts
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Hannelore I. Bax
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Section of Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jurriaan E. M. De Steenwinkel
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
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40
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Pardeshi V, Lokhande T, Shelke A, Tuse T, Pawar B, Bonde C. A breakthrough in the treatment of multidrug-resistant tuberculosis: A novel and effective approach. EGYPTIAN JOURNAL OF CHEST DISEASES AND TUBERCULOSIS 2022. [DOI: 10.4103/ecdt.ecdt_24_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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41
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Black TA, Buchwald UK. The pipeline of new molecules and regimens against drug-resistant tuberculosis. J Clin Tuberc Other Mycobact Dis 2021; 25:100285. [PMID: 34816020 PMCID: PMC8593651 DOI: 10.1016/j.jctube.2021.100285] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The clinical development and regulatory approval of bedaquiline, delamanid and pretomanid over the last decade brought about significant progress in the management of drug-resistant tuberculosis, providing all-oral regimens with favorable safety profiles. The Nix-TB and ZeNix trials of a bedaquiline - pretomanid - linezolid regimen demonstrated for the first time that certain forms of drug-resistant tuberculosis can be cured in the majority of patients within 6 months. Ongoing Phase 3 studies containing these drugs may further advance optimized regimen compositions. Investigational drugs in clinical development that target clinically validated mechanisms, such as second generation oxazolidinones (sutezolid, delpazolid, TBI-223) and diarylquinolines (TBAJ-876 and TBAJ-587) promise improved potency and/or safety compared to the first-in-class drugs. Compounds with novel targets involved in diverse bacterial functions such as cell wall synthesis (DrpE1, MmpL3), electron transport, DNA synthesis (GyrB), cholesterol metabolism and transcriptional regulation of ethionamide bioactivation pathways have advanced to early clinical studies with the potential to enhance antibacterial activity when added to new or established anti-TB drug regimens. Clinical validation of preclinical in vitro and animal model predictions of new anti-TB regimens may further improve the translational value of these models to identify optimal anti-TB therapies.
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Affiliation(s)
- Todd A. Black
- Global Alliance for TB Drug Development, 40 Wall Street, 24th Floor, New York, NY 10005, USA
| | - Ulrike K. Buchwald
- Global Alliance for TB Drug Development, 40 Wall Street, 24th Floor, New York, NY 10005, USA
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42
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Furió V, Moreno-Molina M, Chiner-Oms Á, Villamayor LM, Torres-Puente M, Comas I. An evolutionary functional genomics approach identifies novel candidate regions involved in isoniazid resistance in Mycobacterium tuberculosis. Commun Biol 2021; 4:1322. [PMID: 34819627 PMCID: PMC8613195 DOI: 10.1038/s42003-021-02846-z] [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] [Received: 12/02/2020] [Accepted: 11/03/2021] [Indexed: 12/20/2022] Open
Abstract
Efforts to eradicate tuberculosis are hampered by the rise and spread of antibiotic resistance. Several large-scale projects have aimed to specifically link clinical mutations to resistance phenotypes, but they were limited in both their explanatory and predictive powers. Here, we combine functional genomics and phylogenetic associations using clinical strain genomes to decipher the architecture of isoniazid resistance and search for new resistance determinants. This approach has allowed us to confirm the main target route of the antibiotic, determine the clinical relevance of redox metabolism as an isoniazid resistance mechanism and identify novel candidate genes harboring resistance mutations in strains with previously unexplained isoniazid resistance. This approach can be useful for characterizing how the tuberculosis bacilli acquire resistance to new antibiotics and how to forestall them. Victoria Furió et al. apply functional genomics and evolutionary analyses to the study of antibiotic resistance in tuberculosis. Focusing on isoniazid resistance and using genomic data from clinical strains, they identify novel candidate genes with resistance mutations and further uncover the mechanisms underlying drug resistance.
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Affiliation(s)
- Victoria Furió
- Institute of Biomedicine of Valencia (IBV-CSIC), Valencia, 46020, Spain.
| | | | - Álvaro Chiner-Oms
- Institute of Biomedicine of Valencia (IBV-CSIC), Valencia, 46020, Spain
| | | | | | - Iñaki Comas
- Institute of Biomedicine of Valencia (IBV-CSIC), Valencia, 46020, Spain.,CIBER in Epidemiology and Public Health, Madrid, 28029, Spain
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43
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Comparative Efficacy of the Novel Diarylquinoline TBAJ-876 and Bedaquiline against a Resistant Rv0678 Mutant in a Mouse Model of Tuberculosis. Antimicrob Agents Chemother 2021; 65:e0141221. [PMID: 34570644 PMCID: PMC8597756 DOI: 10.1128/aac.01412-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Bedaquiline (BDQ, B) is the first-in-class diarylquinoline to be approved for treatment of tuberculosis (TB). Recent guidelines recommend its use in treatment of multidrug- and extensively drug-resistant tuberculosis (MDR/XDR-TB). The newly approved regimen combining BDQ with pretomanid and linezolid is the first 6-month oral regimen proven to be effective against MDR/XDR-TB. However, the emergence of BDQ resistance, primarily due to inactivating mutations in the Rv0678 gene encoding a repressor of the MmpS5-MmpL5 transporter, threatens to undermine the efficacy of new BDQ-containing regimens. Since the shift in MIC due to these mutations is relatively small (2–8×), safer, and more potent, diarylquinoline analogues may be more effective than BDQ. TBAJ-876, which is in phase 1 trials, has more potent in vitro activity and a superior pre-clinical safety profile than BDQ. Using a murine model of TB, we evaluated the dose-dependent activity of TBAJ-876 compared to BDQ against the wild-type H37Rv strain and an isogenic Rv0678 loss-of-function mutant. Although the mutation affected the MIC of both drugs, the MIC of TBAJ-876 against the mutant was 10-fold lower than that of BDQ. TBAJ-876 at doses ≥6.25 mg/kg had greater efficacy against both strains compared to BDQ at 25 mg/kg, when administered alone or in combination with pretomanid and linezolid. Likewise, no selective amplification of BDQ-resistant bacteria was observed at TBAJ-876 doses ≥6.25 mg/kg. These results indicate that replacing BDQ with TBAJ-876 may shorten the duration of TB treatment and be more effective in treating and preventing infections caused by Rv0678 mutants.
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44
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Khoshnood S, Taki E, Sadeghifard N, Kaviar VH, Haddadi MH, Farshadzadeh Z, Kouhsari E, Goudarzi M, Heidary M. Mechanism of Action, Resistance, Synergism, and Clinical Implications of Delamanid Against Multidrug-Resistant Mycobacterium tuberculosis. Front Microbiol 2021; 12:717045. [PMID: 34690963 PMCID: PMC8529252 DOI: 10.3389/fmicb.2021.717045] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/02/2021] [Indexed: 11/21/2022] Open
Abstract
Multidrug-resistant (MDR) isolates of Mycobacterium tuberculosis (MTB) remain a primary global threat to the end of tuberculosis (TB) era. Delamanid (DLM) is a nitro-dihydro-imidazooxazole derivative utilized to treat MDR-TB. DLM has distinct mechanism of action, inhibiting methoxy- and keto-mycolic acid (MA) synthesis through the F420 coenzyme mycobacteria system and generating nitrous oxide. While DLM resistance among MTB strains is uncommon, there are increasing reports in Asia and Europe, and such resistance will prolong the treatment courses of patients infected with MDR-TB. In this review, we address the antimycobacterial properties of DLM, report the global prevalence of DLM resistance, discuss the synergism of DLM with other anti-TB drugs, and evaluate the documented clinical trials to provide new insights into the clinical use of this antibiotic.
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Affiliation(s)
- Saeed Khoshnood
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Elahe Taki
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Nourkhoda Sadeghifard
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Vahab Hassan Kaviar
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | | | - Zahra Farshadzadeh
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ebrahim Kouhsari
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Mehdi Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohsen Heidary
- Department of Laboratory Sciences, School of Paramedical Sciences, Sabzevar University of Medical Sciences, Sabzevar, Iran
- Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran
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45
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Genetic diversity of candidate loci linked to Mycobacterium tuberculosis resistance to bedaquiline, delamanid and pretomanid. Sci Rep 2021; 11:19431. [PMID: 34593898 PMCID: PMC8484543 DOI: 10.1038/s41598-021-98862-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/16/2021] [Indexed: 02/08/2023] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis, is one of the deadliest infectious diseases worldwide. Multidrug and extensively drug-resistant strains are making disease control difficult, and exhausting treatment options. New anti-TB drugs bedaquiline (BDQ), delamanid (DLM) and pretomanid (PTM) have been approved for the treatment of multi-drug resistant TB, but there is increasing resistance to them. Nine genetic loci strongly linked to resistance have been identified (mmpR5, atpE, and pepQ for BDQ; ddn, fgd1, fbiA, fbiB, fbiC, and fbiD for DLM/PTM). Here we investigated the genetic diversity of these loci across >33,000 M. tuberculosis isolates. In addition, epistatic mutations in mmpL5-mmpS5 as well as variants in ndh, implicated for DLM/PTM resistance in M. smegmatis, were explored. Our analysis revealed 1,227 variants across the nine genes, with the majority (78%) present in isolates collected prior to the roll-out of BDQ and DLM/PTM. We identified phylogenetically-related mutations, which are unlikely to be resistance associated, but also high-impact variants such as frameshifts (e.g. in mmpR5, ddn) with likely functional effects, as well as non-synonymous mutations predominantly in MDR-/XDR-TB strains with predicted protein destabilising effects. Overall, our work provides a comprehensive mutational catalogue for BDQ and DLM/PTM associated genes, which will assist with establishing associations with phenotypic resistance; thereby, improving the understanding of the causative mechanisms of resistance for these drugs, leading to better treatment outcomes.
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46
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Grinter R, Greening C. Cofactor F420: an expanded view of its distribution, biosynthesis and roles in bacteria and archaea. FEMS Microbiol Rev 2021; 45:fuab021. [PMID: 33851978 PMCID: PMC8498797 DOI: 10.1093/femsre/fuab021] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/11/2021] [Indexed: 12/11/2022] Open
Abstract
Many bacteria and archaea produce the redox cofactor F420. F420 is structurally similar to the cofactors FAD and FMN but is catalytically more similar to NAD and NADP. These properties allow F420 to catalyze challenging redox reactions, including key steps in methanogenesis, antibiotic biosynthesis and xenobiotic biodegradation. In the last 5 years, there has been much progress in understanding its distribution, biosynthesis, role and applications. Whereas F420 was previously thought to be confined to Actinobacteria and Euryarchaeota, new evidence indicates it is synthesized across the bacterial and archaeal domains, as a result of extensive horizontal and vertical biosynthetic gene transfer. F420 was thought to be synthesized through one biosynthetic pathway; however, recent advances have revealed variants of this pathway and have resolved their key biosynthetic steps. In parallel, new F420-dependent biosynthetic and metabolic processes have been discovered. These advances have enabled the heterologous production of F420 and identified enantioselective F420H2-dependent reductases for biocatalysis. New research has also helped resolve how microorganisms use F420 to influence human and environmental health, providing opportunities for tuberculosis treatment and methane mitigation. A total of 50 years since its discovery, multiple paradigms associated with F420 have shifted, and new F420-dependent organisms and processes continue to be discovered.
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Affiliation(s)
- Rhys Grinter
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Chris Greening
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
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47
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Venugopala KN, Chandrashekharappa S, Deb PK, Tratrat C, Pillay M, Chopra D, Al-Shar'i NA, Hourani W, Dahabiyeh LA, Borah P, Nagdeve RD, Nayak SK, Padmashali B, Morsy MA, Aldhubiab BE, Attimarad M, Nair AB, Sreeharsha N, Haroun M, Shashikanth S, Mohanlall V, Mailavaram R. Anti-tubercular activity and molecular docking studies of indolizine derivatives targeting mycobacterial InhA enzyme. J Enzyme Inhib Med Chem 2021; 36:1472-1487. [PMID: 34210233 PMCID: PMC8259857 DOI: 10.1080/14756366.2021.1919889] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
A series of 1,2,3-trisubstituted indolizines (2a-2f, 3a-3d, and 4a-4c) were screened for in vitro whole-cell anti-tubercular activity against the susceptible H37Rv and multidrug-resistant (MDR) Mycobacterium tuberculosis (MTB) strains. Compounds 2b-2d, 3a-3d, and 4a-4c were active against the H37Rv-MTB strain with minimum inhibitory concentration (MIC) ranging from 4 to 32 µg/mL, whereas the indolizines 4a-4c, with ethyl ester group at the 4-position of the benzoyl ring also exhibited anti-MDR-MTB activity (MIC = 16-64 µg/mL). In silico docking study revealed the enoyl-acyl carrier protein reductase (InhA) and anthranilate phosphoribosyltransferase as potential molecular targets for the indolizines. The X-ray diffraction analysis of the compound 4b was also carried out. Further, a safety study (in silico and in vitro) demonstrated no toxicity for these compounds. Thus, the indolizines warrant further development and may represent a novel promising class of InhA inhibitors and multi-targeting agents to combat drug-sensitive and drug-resistant MTB strains.
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Affiliation(s)
- Katharigatta N Venugopala
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia.,Department of Biotechnology and Food Technology, Durban University of Technology, Durban, South Africa
| | | | - Pran Kishore Deb
- Faculty of Pharmacy, Department of Pharmaceutical Sciences, Philadelphia University, Amman, Jordan
| | - Christophe Tratrat
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Melendhran Pillay
- Department of Microbiology, National Health Laboratory Services, KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban, South Africa
| | - Deepak Chopra
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Nizar A Al-Shar'i
- Faculty of Pharmacy, Department of Medicinal Chemistry and Pharmacognosy, Jordan University of Science and Technology, Irbid, Jordan
| | - Wafa Hourani
- Faculty of Pharmacy, Department of Pharmaceutical Sciences, Philadelphia University, Amman, Jordan
| | - Lina A Dahabiyeh
- Department of Pharmaceutical Sciences, School of Pharmacy, The University of Jordan, Amman, Jordan
| | - Pobitra Borah
- Pratiksha Institute of Pharmaceutical Sciences, Guwahati, India
| | - Rahul D Nagdeve
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, India
| | - Susanta K Nayak
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, India
| | - Basavaraj Padmashali
- Department of Chemistry, School of Basic Science, Rani Channamma University, Belagavi, India
| | - Mohamed A Morsy
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia.,Faculty of Medicine, Department of Pharmacology, Minia University, El-Minia, Egypt
| | - Bandar E Aldhubiab
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Mahesh Attimarad
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Anroop B Nair
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Nagaraja Sreeharsha
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia.,Department of Pharmaceutics, Vidya Siri College of Pharmacy, Bangalore, India
| | - Michelyne Haroun
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Sheena Shashikanth
- Department of Studies in Organic Chemistry, University of Mysore, Mysore, India
| | - Viresh Mohanlall
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, South Africa
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48
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Stancil SL, Mirzayev F, Abdel-Rahman SM. Profiling Pretomanid as a Therapeutic Option for TB Infection: Evidence to Date. Drug Des Devel Ther 2021; 15:2815-2830. [PMID: 34234413 PMCID: PMC8253981 DOI: 10.2147/dddt.s281639] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/28/2021] [Indexed: 11/23/2022] Open
Abstract
Tuberculosis (TB) is the most deadly infectious disease globally. Although most individuals achieve a cure, a substantial portion develop multi-drug resistant TB which is exceedingly difficult to treat, and the number of effective agents is dwindling. Development of new anti-tubercular medications is imperative to combat existing drug resistance and accelerate global eradication of TB. Pretomanid (PA-824) represents one of the newest drug classes (ie, nitroimidazooxazines) approved in 2019 by the United States Food and Drug Administration as part of a multi-drug regimen (with bedaquiline and linezolid, BPaL) and recommended by the World Health Organization (WHO) to treat extensively-resistant (XR-TB) and multi-drug resistant tuberculosis (MDR-TB). Approval was granted through the FDA's Limited Population Pathway for Antibacterial and Antifungal Drugs, which accelerates approval for antimicrobial drugs used to treat life-threatening or serious infections in a limited population with unmet need. This review details the pharmacology, efficacy, and safety of this new agent and describes evidence to date for its role in the treatment of drug resistant TB including published, ongoing, and planned studies.
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Affiliation(s)
- Stephani L Stancil
- Division of Adolescent Medicine, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.,Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.,Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, MO, 64108, USA
| | | | - Susan M Abdel-Rahman
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.,Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, MO, 64108, USA
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49
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Kadura S, King N, Nakhoul M, Zhu H, Theron G, Köser CU, Farhat M. Systematic review of mutations associated with resistance to the new and repurposed Mycobacterium tuberculosis drugs bedaquiline, clofazimine, linezolid, delamanid and pretomanid. J Antimicrob Chemother 2021; 75:2031-2043. [PMID: 32361756 DOI: 10.1093/jac/dkaa136] [Citation(s) in RCA: 115] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 03/09/2020] [Accepted: 03/12/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Improved genetic understanding of Mycobacterium tuberculosis (MTB) resistance to novel and repurposed anti-tubercular agents can aid the development of rapid molecular diagnostics. METHODS Adhering to PRISMA guidelines, in March 2018, we performed a systematic review of studies implicating mutations in resistance through sequencing and phenotyping before and/or after spontaneous resistance evolution, as well as allelic exchange experiments. We focused on the novel drugs bedaquiline, delamanid, pretomanid and the repurposed drugs clofazimine and linezolid. A database of 1373 diverse control MTB whole genomes, isolated from patients not exposed to these drugs, was used to further assess genotype-phenotype associations. RESULTS Of 2112 papers, 54 met the inclusion criteria. These studies characterized 277 mutations in the genes atpE, mmpR, pepQ, Rv1979c, fgd1, fbiABC and ddn and their association with resistance to one or more of the five drugs. The most frequent mutations for bedaquiline, clofazimine, linezolid, delamanid and pretomanid resistance were atpE A63P, mmpR frameshifts at nucleotides 192-198, rplC C154R, ddn W88* and ddn S11*, respectively. Frameshifts in the mmpR homopolymer region nucleotides 192-198 were identified in 52/1373 (4%) of the control isolates without prior exposure to bedaquiline or clofazimine. Of isolates resistant to one or more of the five drugs, 59/519 (11%) lacked a mutation explaining phenotypic resistance. CONCLUSIONS This systematic review supports the use of molecular methods for linezolid resistance detection. Resistance mechanisms involving non-essential genes show a diversity of mutations that will challenge molecular diagnosis of bedaquiline and nitroimidazole resistance. Combined phenotypic and genotypic surveillance is needed for these drugs in the short term.
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Affiliation(s)
- Suha Kadura
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA.,Pulmonary and Critical Care Division, St. Elizabeth's Medical Center, 736 Cambridge Street, Boston, MA 02135, USA
| | - Nicholas King
- Yale University, Faculty of Arts and Sciences, 260 Whitney Ave, New Haven, CT 06511, USA.,Boston Healthcare for the Homeless Program, 780 Albany Street, Boston, MA 02118, USA
| | - Maria Nakhoul
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
| | - Hongya Zhu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Grant Theron
- NRF-DST Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Claudio U Köser
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, UK
| | - Maha Farhat
- Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA.,Pulmonary and Critical Care Division, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
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50
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Treatment of Multidrug-Resistant and Extensively Drug-Resistant Tuberculosis in Children: The Role of Bedaquiline and Delamanid. Microorganisms 2021; 9:microorganisms9051074. [PMID: 34067732 PMCID: PMC8156326 DOI: 10.3390/microorganisms9051074] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/03/2021] [Accepted: 05/10/2021] [Indexed: 12/19/2022] Open
Abstract
Multidrug-resistant (MDR) tuberculosis (TB) has been emerging at an alarming rate over the last few years. It has been estimated that about 3% of all pediatric TB is MDR, meaning about 30,000 cases each year. Although most children with MDR-TB can be successfully treated, up to five years ago effective treatment was associated with a high incidence of severe adverse effects and patients with extensively drug-resistant (XDR) TB had limited treatment options and no standard regimen. The main objective of this manuscript is to discuss our present knowledge of the management of MDR- and XDR-TB in children, focusing on the characteristics and available evidence on the use of two promising new drugs: bedaquiline and delamanid. PubMed was used to search for all of the studies published up to November 2020 using key words such as "bedaquiline" and "delamanid" and "children" and "multidrug-resistant tuberculosis" and "extensively drug-resistant tuberculosis". The search was limited to articles published in English and providing evidence-based data. Although data on pediatric population are limited and more studies are needed to confirm the efficacy and safety of bedaquiline and delamanid, their use in children with MDR-TB/XDR-TB appears to have good tolerability and efficacy. However, more evidence on these new anti-TB drugs is needed to better guide their use in children in order to design effective shorter regimens and reduce adverse effects, drug interactions, and therapeutic failure.
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