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Carnero Canales CS, Marquez Cazorla JI, Marquez Cazorla RM, Roque-Borda CA, Polinário G, Figueroa Banda RA, Sábio RM, Chorilli M, Santos HA, Pavan FR. Breaking barriers: The potential of nanosystems in antituberculosis therapy. Bioact Mater 2024; 39:106-134. [PMID: 38783925 PMCID: PMC11112550 DOI: 10.1016/j.bioactmat.2024.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/17/2024] [Accepted: 05/05/2024] [Indexed: 05/25/2024] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis, continues to pose a significant threat to global health. The resilience of TB is amplified by a myriad of physical, biological, and biopharmaceutical barriers that challenge conventional therapeutic approaches. This review navigates the intricate landscape of TB treatment, from the stealth of latent infections and the strength of granuloma formations to the daunting specters of drug resistance and altered gene expression. Amidst these challenges, traditional therapies often fail, contending with inconsistent bioavailability, prolonged treatment regimens, and socioeconomic burdens. Nanoscale Drug Delivery Systems (NDDSs) emerge as a promising beacon, ready to overcome these barriers, offering better drug targeting and improved patient adherence. Through a critical approach, we evaluate a spectrum of nanosystems and their efficacy against MTB both in vitro and in vivo. This review advocates for the intensification of research in NDDSs, heralding their potential to reshape the contours of global TB treatment strategies.
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Affiliation(s)
| | | | | | - Cesar Augusto Roque-Borda
- Tuberculosis Research Laboratory, School of Pharmaceutical Science, Sao Paulo State University (UNESP), Araraquara, 14800-903, Brazil
| | - Giulia Polinário
- Tuberculosis Research Laboratory, School of Pharmaceutical Science, Sao Paulo State University (UNESP), Araraquara, 14800-903, Brazil
| | | | - Rafael Miguel Sábio
- School of Pharmaceutical Science, Sao Paulo State University (UNESP), Araraquara, 14800-903, Brazil
- Department of Biomaterials and Biomedical Technology, University Medical Center Groningen (UMCG), University of Groningen, Groningen, 9713 AV, the Netherlands
| | - Marlus Chorilli
- School of Pharmaceutical Science, Sao Paulo State University (UNESP), Araraquara, 14800-903, Brazil
| | - Hélder A. Santos
- Department of Biomaterials and Biomedical Technology, University Medical Center Groningen (UMCG), University of Groningen, Groningen, 9713 AV, the Netherlands
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, FI-00014, Finland
| | - Fernando Rogério Pavan
- Tuberculosis Research Laboratory, School of Pharmaceutical Science, Sao Paulo State University (UNESP), Araraquara, 14800-903, Brazil
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2
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Niu H, Gu J, Zhang Y. Bacterial persisters: molecular mechanisms and therapeutic development. Signal Transduct Target Ther 2024; 9:174. [PMID: 39013893 PMCID: PMC11252167 DOI: 10.1038/s41392-024-01866-5] [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: 11/04/2023] [Revised: 05/06/2024] [Accepted: 05/13/2024] [Indexed: 07/18/2024] Open
Abstract
Persisters refer to genetically drug susceptible quiescent (non-growing or slow growing) bacteria that survive in stress environments such as antibiotic exposure, acidic and starvation conditions. These cells can regrow after stress removal and remain susceptible to the same stress. Persisters are underlying the problems of treating chronic and persistent infections and relapse infections after treatment, drug resistance development, and biofilm infections, and pose significant challenges for effective treatments. Understanding the characteristics and the exact mechanisms of persister formation, especially the key molecules that affect the formation and survival of the persisters is critical to more effective treatment of chronic and persistent infections. Currently, genes related to persister formation and survival are being discovered and confirmed, but the mechanisms by which bacteria form persisters are very complex, and there are still many unanswered questions. This article comprehensively summarizes the historical background of bacterial persisters, details their complex characteristics and their relationship with antibiotic tolerant and resistant bacteria, systematically elucidates the interplay between various bacterial biological processes and the formation of persister cells, as well as consolidates the diverse anti-persister compounds and treatments. We hope to provide theoretical background for in-depth research on mechanisms of persisters and suggest new ideas for choosing strategies for more effective treatment of persistent infections.
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Affiliation(s)
- Hongxia Niu
- School of Basic Medical Science and Key Laboratory of Blood-stasis-toxin Syndrome of Zhejiang Province, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
| | - Jiaying Gu
- School of Basic Medical Science and Key Laboratory of Blood-stasis-toxin Syndrome of Zhejiang Province, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
| | - Ying Zhang
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China.
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250022, Shandong, China.
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3
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Qian W, Ma N, Zeng X, Shi M, Wang M, Yang Z, Tsui SKW. Identification of novel single nucleotide variants in the drug resistance mechanism of Mycobacterium tuberculosis isolates by whole-genome analysis. BMC Genomics 2024; 25:478. [PMID: 38745294 PMCID: PMC11094924 DOI: 10.1186/s12864-024-10390-3] [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: 01/11/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Tuberculosis (TB) represents a major global health challenge. Drug resistance in Mycobacterium tuberculosis (MTB) poses a substantial obstacle to effective TB treatment. Identifying genomic mutations in MTB isolates holds promise for unraveling the underlying mechanisms of drug resistance in this bacterium. METHODS In this study, we investigated the roles of single nucleotide variants (SNVs) in MTB isolates resistant to four antibiotics (moxifloxacin, ofloxacin, amikacin, and capreomycin) through whole-genome analysis. We identified the drug-resistance-associated SNVs by comparing the genomes of MTB isolates with reference genomes using the MuMmer4 tool. RESULTS We observed a strikingly high proportion (94.2%) of MTB isolates resistant to ofloxacin, underscoring the current prevalence of drug resistance in MTB. An average of 3529 SNVs were detected in a single ofloxacin-resistant isolate, indicating a mutation rate of approximately 0.08% under the selective pressure of ofloxacin exposure. We identified a set of 60 SNVs associated with extensively drug-resistant tuberculosis (XDR-TB), among which 42 SNVs were non-synonymous mutations located in the coding regions of nine key genes (ctpI, desA3, mce1R, moeB1, ndhA, PE_PGRS4, PPE18, rpsA, secF). Protein structure modeling revealed that SNVs of three genes (PE_PGRS4, desA3, secF) are close to the critical catalytic active sites in the three-dimensional structure of the coding proteins. CONCLUSION This comprehensive study elucidates novel resistance mechanisms in MTB against antibiotics, paving the way for future design and development of anti-tuberculosis drugs.
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Affiliation(s)
- Weiye Qian
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Nan Ma
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Xi Zeng
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mai Shi
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Mingqiang Wang
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Zhiyuan Yang
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, 310018, China.
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China.
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4
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Perveen S, Kumari D, Singh K, Sharma R. Tuberculosis drug discovery: Progression and future interventions in the wake of emerging resistance. Eur J Med Chem 2022; 229:114066. [PMID: 34973508 DOI: 10.1016/j.ejmech.2021.114066] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/13/2021] [Accepted: 12/19/2021] [Indexed: 02/06/2023]
Abstract
The emergence of drug resistance continues to afflict TB control where drug resistant strains have become a global health concern. Contrary to drug-sensitive TB, the treatment of MDR/XDR-TB is more complicated requiring the administration of second-line drugs that are inefficient than the first line drugs and are associated with greater side effects. The emergence of drug resistant Mtb strains had coincided with an innovation void in the field of drug discovery of anti-mycobacterials. However, the approval of bedaquiline and delamanid recently for use in MDR/XDR-TB has given an impetus to the TB drug discovery. The review discusses the drug discovery efforts in the field of tuberculosis with a focus on the strategies adopted and challenges confronted by TB research community. Here, we discuss the diverse clinical candidates in the current TB drug discovery pipeline. There is an urgent need to combat the current TB menace through multidisciplinary approaches and strategies making use of the recent advances in understanding the molecular biology and pathogenesis of Mtb. The review highlights the recent advances in drug discovery, with the host directed therapeutics and nanoparticles-drug delivery coming up as important tools to fight tuberculosis in the future.
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Affiliation(s)
- Summaya Perveen
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Diksha Kumari
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Kuljit Singh
- Infectious Diseases Division, 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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Overcoming the Challenges of Pyrazinamide Susceptibility Testing in Clinical Mycobacterium tuberculosis Isolates. Antimicrob Agents Chemother 2021; 65:e0261720. [PMID: 33972244 DOI: 10.1128/aac.02617-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pyrazinamide (PZA) is one of the first-line agents used for the treatment of tuberculosis. However, current phenotypic PZA susceptibility testing in the Bactec MGIT 960 system is unreliable, and false resistance is well documented. Rapid identification of resistance-associated mutations can confirm the phenotypic result. This study aimed to investigate the use of genotypic methods in combination with phenotypic susceptibility testing for confirmation of PZA-resistant Mycobacterium tuberculosis isolates. Sanger sequencing and/or whole-genome sequencing were performed to detect mutations in pncA, rpsA, panD, and clpC1. Isolates were screened for heteroresistance, and PZA susceptibility testing was performed using the Bactec MGIT 960 system using a reduced inoculum to investigate false resistance. Overall, 40 phenotypically PZA-resistant isolates were identified. Of these, PZA resistance was confirmed in 22/40 (55%) isolates by detecting mutations in the pncA, rpsA, and panD genes. Of the 40 isolates, 16 (40%) were found to be susceptible using the reduced inoculum method (i.e., false resistance). No mutations were detected in two PZA-resistant isolates. False resistance was observed in isolates with MICs close to the critical concentration. In particular, East African Indian strains (lineage 1) appeared to have an elevated MIC that is close to the critical concentration. While this study illustrates the complexity and challenges associated with PZA susceptibility testing of M. tuberculosis, we conclude that a combination of genotypic and phenotypic drug susceptibility testing methods is required for accurate detection of PZA resistance.
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6
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Atypical Genetic Basis of Pyrazinamide Resistance in Monoresistant Mycobacterium tuberculosis. Antimicrob Agents Chemother 2021; 65:AAC.01916-20. [PMID: 33722890 PMCID: PMC8315952 DOI: 10.1128/aac.01916-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/02/2021] [Indexed: 02/07/2023] Open
Abstract
Pyrazinamide (PZA) is a widely used antitubercular chemotherapeutic. Typically, PZA resistance (PZA-R) emerges in Mycobacterium tuberculosis strains with existing resistance to isoniazid and rifampin (i.e., multidrug resistance [MDR]) and is conferred by loss-of-function pncA mutations that inhibit conversion to its active form, pyrazinoic acid (POA). PZA-R departing from this canonical scenario is poorly understood. Here, we genotyped pncA and purported alternative PZA-R genes (panD, rpsA, and clpC1) with long-read sequencing of 19 phenotypically PZA-monoresistant isolates collected in Sweden and compared their phylogenetic and genomic characteristics to a large set of MDR PZA-R (MDRPZA-R) isolates. We report the first association of ClpC1 mutations with PZA-R in clinical isolates, in the ClpC1 promoter (clpC1p−138) and the N terminus of ClpC1 (ClpC1Val63Ala). Mutations have emerged in both these regions under POA selection in vitro, and the N-terminal region of ClpC1 has been implicated further, through its POA-dependent efficacy in PanD proteolysis. ClpC1Val63Ala mutants spanned 4 Indo-Oceanic sublineages. Indo-Oceanic isolates invariably harbored ClpC1Val63Ala and were starkly overrepresented (odds ratio [OR] = 22.2, P < 0.00001) among PZA-monoresistant isolates (11/19) compared to MDRPZA-R isolates (5/80). The genetic basis of Indo-Oceanic isolates’ overrepresentation in PZA-monoresistant tuberculosis (TB) remains undetermined, but substantial circumstantial evidence suggests that ClpC1Val63Ala confers low-level PZA resistance. Our findings highlight ClpC1 as potentially clinically relevant for PZA-R and reinforce the importance of genetic background in the trajectory of resistance development.
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7
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Appetecchia F, Consalvi S, Scarpecci C, Biava M, Poce G. SAR Analysis of Small Molecules Interfering with Energy-Metabolism in Mycobacterium tuberculosis. Pharmaceuticals (Basel) 2020; 13:E227. [PMID: 32878317 PMCID: PMC7557483 DOI: 10.3390/ph13090227] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/28/2020] [Accepted: 08/28/2020] [Indexed: 12/13/2022] Open
Abstract
Tuberculosis remains the world's top infectious killer: it caused a total of 1.5 million deaths and 10 million people fell ill with TB in 2018. Thanks to TB diagnosis and treatment, mortality has been falling in recent years, with an estimated 58 million saved lives between 2000 and 2018. However, the emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mtb strains is a major concern that might reverse this progress. Therefore, the development of new drugs acting upon novel mechanisms of action is a high priority in the global health agenda. With the approval of bedaquiline, which targets mycobacterial energy production, and delamanid, which targets cell wall synthesis and energy production, the energy-metabolism in Mtb has received much attention in the last decade as a potential target to investigate and develop new antimycobacterial drugs. In this review, we describe potent anti-mycobacterial agents targeting the energy-metabolism at different steps with a special focus on structure-activity relationship (SAR) studies of the most advanced compound classes.
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Affiliation(s)
| | | | | | | | - Giovanna Poce
- Department of Chemistry and Technologies of Drug, Sapienza University of Rome, piazzale A. Moro 5, 00185 Rome, Italy; (F.A.); (S.C.); (C.S.); (M.B.)
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8
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Antimicrobial Susceptibility Pattern of Helicobacter heilmannii and Helicobacter ailurogastricus Isolates. Microorganisms 2020; 8:microorganisms8060957. [PMID: 32630563 PMCID: PMC7355750 DOI: 10.3390/microorganisms8060957] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/04/2020] [Accepted: 06/23/2020] [Indexed: 12/13/2022] Open
Abstract
A combined agar and broth dilution method followed by qPCR was used to determine the antimicrobial susceptibility of feline H. heilmannii and H. ailurogastricus isolates. All H. ailurogastricus isolates showed a monomodal distribution of MICs for all the antimicrobial agents tested. For H. heilmannii, a bimodal distribution was observed for azithromycin, enrofloxacin, spectinomycin, and lincomycin. Single nucleotide polymorphisms (SNPs) were found in 50S ribosomal proteins L2 and L3 of the H. heilmannii isolate not belonging to the WT population for azithromycin, and in 30S ribosomal proteins S1, S7, and S12 of the isolate not belonging to the WT population for spectinomycin. The antimicrobial resistance mechanism to enrofloxacin and lincomycin remains unknown (2 and 1 H. heilmannii isolate(s), resp.). Furthermore, H. heilmannii isolates showed higher MICs for neomycin compared to H. ailurogastricus isolates which may be related to the presence of SNPs in several 30S and 50S ribosomal protein encoding genes and ribosomal RNA methyltransferase genes. This study shows that acquired resistance to azithromycin, spectinomycin, enrofloxacin, and lincomycin occasionally occurs in feline H. heilmannii isolates. As pets may constitute a source of infection for humans, this should be kept in mind when dealing with a human patient infected with H. heilmannii.
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9
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Vallejos-Sánchez K, Lopez JM, Antiparra R, Toscano E, Saavedra H, Kirwan DE, Amzel LM, Gilman RH, Maruenda H, Sheen P, Zimic M. Mycobacterium tuberculosis ribosomal protein S1 (RpsA) and variants with truncated C-terminal end show absence of interaction with pyrazinoic acid. Sci Rep 2020; 10:8356. [PMID: 32433489 PMCID: PMC7239899 DOI: 10.1038/s41598-020-65173-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/29/2020] [Indexed: 01/31/2023] Open
Abstract
Pyrazinamide (PZA) is an antibiotic used in first- and second-line tuberculosis treatment regimens. Approximately 50% of multidrug-resistant tuberculosis and over 90% of extensively drug-resistant tuberculosis strains are also PZA resistant. Despite the key role played by PZA, its mechanisms of action are not yet fully understood. It has been postulated that pyrazinoic acid (POA), the hydrolyzed product of PZA, could inhibit trans-translation by binding to Ribosomal protein S1 (RpsA) and competing with tmRNA, the natural cofactor of RpsA. Subsequent data, however, indicate that these early findings resulted from experimental artifact. Hence, in this study we assess the capacity of POA to compete with tmRNA for RpsA. We evaluated RpsA wild type (WT), RpsA ∆A438, and RpsA ∆A438 variants with truncations towards the carboxy terminal end. Interactions were measured using Nuclear Magnetic Resonance spectroscopy (NMR), Isothermal Titration Calorimetry (ITC), Microscale Thermophoresis (MST), and Electrophoretic Mobility Shift Assay (EMSA). We found no measurable binding between POA and RpsA (WT or variants). This suggests that RpsA may not be involved in the mechanism of action of PZA in Mycobacterium tuberculosis, as previously thought. Interactions observed between tmRNA and RpsA WT, RpsA ∆A438, and each of the truncated variants of RpsA ∆A438, are reported.
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Affiliation(s)
- Katherine Vallejos-Sánchez
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía. Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Juan M Lopez
- Pontificia Universidad Católica del Perú, Departamento de Ciencias, Sección Química, Centro de Espectroscopía de Resonancia Magnética Nuclear (CERMN), Lima, Perú
| | - Ricardo Antiparra
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía. Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Emily Toscano
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía. Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Harry Saavedra
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD., USA
| | - Daniela E Kirwan
- Infection and Immunity Research Institute, St George's, University of London, London, England
| | - L M Amzel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD., USA
| | - R H Gilman
- International Health Department. Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Helena Maruenda
- Pontificia Universidad Católica del Perú, Departamento de Ciencias, Sección Química, Centro de Espectroscopía de Resonancia Magnética Nuclear (CERMN), Lima, Perú
| | - Patricia Sheen
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía. Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Mirko Zimic
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía. Universidad Peruana Cayetano Heredia, Lima, Perú.
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10
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Khan MT, Ali S, Zeb MT, Kaushik AC, Malik SI, Wei DQ. Gibbs Free Energy Calculation of Mutation in PncA and RpsA Associated With Pyrazinamide Resistance. Front Mol Biosci 2020; 7:52. [PMID: 32328498 PMCID: PMC7160322 DOI: 10.3389/fmolb.2020.00052] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/16/2020] [Indexed: 12/16/2022] Open
Abstract
A central approach for better understanding the forces involved in maintaining protein structures is to investigate the protein folding and thermodynamic properties. The effect of the folding process is often disturbed in mutated states. To explore the dynamic properties behind mutations, molecular dynamic (MD) simulations have been widely performed, especially in unveiling the mechanism of drug failure behind mutation. When comparing wild type (WT) and mutants (MTs), the structural changes along with solvation free energy (SFE), and Gibbs free energy (GFE) are calculated after the MD simulation, to measure the effect of mutations on protein structure. Pyrazinamide (PZA) is one of the first-line drugs, effective against latent Mycobacterium tuberculosis isolates, affecting the global TB control program 2030. Resistance to this drug emerges due to mutations in pncA and rpsA genes, encoding pyrazinamidase (PZase) and ribosomal protein S1 (RpsA) respectively. The question of how the GFE may be a measure of PZase and RpsA stabilities, has been addressed in the current review. The GFE and SFE of MTs have been compared with WT, which were already found to be PZA-resistant. WT structures attained a more stable state in comparison with MTs. The physiological effect of a mutation in PZase and RpsA may be due to the difference in energies. This difference between WT and MTs, depicted through GFE plots, might be useful in predicting the stability and PZA-resistance behind mutation. This study provides useful information for better management of drug resistance, to control the global TB problem.
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Affiliation(s)
- Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Sajid Ali
- Department of Microbiology, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
| | | | - Aman Chandra Kaushik
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Shaukat Iqbal Malik
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
- Peng Cheng Laboratory, Shenzhen, China
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11
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The molecular basis of pyrazinamide activity on Mycobacterium tuberculosis PanD. Nat Commun 2020; 11:339. [PMID: 31953389 PMCID: PMC6969166 DOI: 10.1038/s41467-019-14238-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/16/2019] [Indexed: 11/18/2022] Open
Abstract
Pyrazinamide has been a mainstay in the multidrug regimens used to treat tuberculosis. It is active against the persistent, non-replicating mycobacteria responsible for the protracted therapy required to cure tuberculosis. Pyrazinamide is a pro-drug that is converted into pyrazinoic acid (POA) by pyrazinamidase, however, the exact target of the drug has been difficult to determine. Here we show the enzyme PanD binds POA in its active site in a manner consistent with competitive inhibition. The active site is not directly accessible to the inhibitor, suggesting the protein must undergo a conformational change to bind the inhibitor. This is consistent with the slow binding kinetics we determined for POA. Drug-resistant mutations cluster near loops that lay on top of the active site. These resistant mutants show reduced affinity and residence time of POA consistent with a model where resistance occurs by destabilizing the closed conformation of the active site. The important tuberculosis drug pyrazinamide (PZA) is converted to its active form pyrazinoic acid (POA) in Mycobacterium tuberculosis (Mtb). Here the authors identify the pantothenate biosynthesis pathway enzyme aspartate decarboxylase (PanD) as the target of PZA and determine the POA bound Mtb PanD crystal structure.
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12
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Gopal P, Grüber G, Dartois V, Dick T. Pharmacological and Molecular Mechanisms Behind the Sterilizing Activity of Pyrazinamide. Trends Pharmacol Sci 2019; 40:930-940. [PMID: 31704175 PMCID: PMC6884696 DOI: 10.1016/j.tips.2019.10.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 11/20/2022]
Abstract
Inclusion of pyrazinamide (PZA) in the tuberculosis (TB) drug regimen during the 1970s enabled a reduction in treatment duration from 12 to 6 months. PZA has this remarkable effect in patients despite displaying poor potency against Mycobacterium tuberculosis (Mtb) in vitro. The pharmacological basis for the in vivo sterilizing activity of the drug has remained obscure and its bacterial target controversial. Recently it was shown that PZA penetrates necrotic caseous TB lung lesions and kills nongrowing, drug-tolerant bacilli. Furthermore, it was uncovered that PZA inhibits bacterial Coenzyme A biosynthesis. It may block this pathway by triggering degradation of its target, aspartate decarboxylase. The elucidation of the pharmacological and molecular mechanisms of PZA provides the basis for the rational discovery of the next-generation PZA with improved in vitro potency while maintaining attractive pharmacological properties.
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Affiliation(s)
- Pooja Gopal
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Republic of Singapore; Current address: MSD Translational Medicine Research Centre, Merck Research Laboratories, 8 Biomedical Grove, Singapore 138665, Republic of Singapore.
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Véronique Dartois
- Center for Discovery and Innovation, Hackensack Meridian Health, 340 Kingsland Street Building 102, Nutley, NJ 07110, USA; Department of Medical Sciences, Hackensack Meridian School of Medicine at Seton Hall University, 340 Kingsland Street, Nutley, NJ 07110, USA
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, 340 Kingsland Street Building 102, Nutley, NJ 07110, USA; Department of Medical Sciences, Hackensack Meridian School of Medicine at Seton Hall University, 340 Kingsland Street, Nutley, NJ 07110, USA; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Republic of Singapore
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13
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Asai M, Li Y, Khara JS, Robertson BD, Langford PR, Newton SM. Galleria mellonella: An Infection Model for Screening Compounds Against the Mycobacterium tuberculosis Complex. Front Microbiol 2019; 10:2630. [PMID: 31824448 PMCID: PMC6882372 DOI: 10.3389/fmicb.2019.02630] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 10/29/2019] [Indexed: 01/08/2023] Open
Abstract
Drug screening models have a vital role in the development of novel antimycobacterial agents which are urgently needed to tackle drug-resistant tuberculosis (TB). We recently established the larvae of the insect Galleria mellonella (greater wax moth) as a novel infection model for the Mycobacterium tuberculosis complex. Here we demonstrate its use as a rapid and reproducible screen to evaluate antimycobacterial drug efficacy using larvae infected with bioluminescent Mycobacterium bovis BCG lux. Treatment improved larval survival outcome and, with the exception of pyrazinamide, was associated with a significant reduction in in vivo mycobacterial bioluminescence over a 96 h period compared to the untreated controls. Isoniazid and rifampicin displayed the greatest in vivo efficacy and survival outcome. Thus G. mellonella, infected with bioluminescent mycobacteria, can rapidly determine in vivo drug efficacy, and has the potential to significantly reduce and/or replace the number of animals used in TB research.
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Affiliation(s)
- Masanori Asai
- Section of Paediatric Infectious Diseases, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Yanwen Li
- Department of Pharmacy, National University of Singapore, Singapore, Singapore
| | - Jasmeet Singh Khara
- Section of Paediatric Infectious Diseases, Department of Infectious Disease, Imperial College London, London, United Kingdom.,Department of Pharmacy, National University of Singapore, Singapore, Singapore
| | - Brian D Robertson
- MRC Centre for Molecular Bacteriology and Infection, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Paul R Langford
- Section of Paediatric Infectious Diseases, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Sandra M Newton
- Section of Paediatric Infectious Diseases, Department of Infectious Disease, Imperial College London, London, United Kingdom
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Mabhula A, Singh V. Drug-resistance in Mycobacterium tuberculosis: where we stand. MEDCHEMCOMM 2019; 10:1342-1360. [PMID: 31534654 PMCID: PMC6748343 DOI: 10.1039/c9md00057g] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/05/2019] [Indexed: 12/16/2022]
Abstract
Tuberculosis (TB), an infectious disease caused by the bacterium Mycobacterium tuberculosis (Mtb), has burdened vulnerable populations in modern day societies for decades. Recently, this global health threat has been heightened by the emergence and propagation of multi drug-resistant (MDR) and extensively drug-resistant (XDR) strains of Mtb that are resistant to current treatment regimens. The End-TB strategy, launched by the World Health Organization (WHO), aims to reduce TB-related deaths by 90%. This program encourages universal access to drug susceptibility testing, which is not widely available owing to the lack of laboratory capacity or resources in certain under-resourced areas. Clinical assays are further complicated by the slow growth of Mtb, resulting in the long turn-around time of tests which severely limits their application in guiding a patient's treatment regimen. This review provides a comprehensive overview of current TB treatments, mechanisms of resistance to anti-tubercular drugs and their diagnosis and the current pipeline of drugs targeting drug-resistant TB (DR-TB) with particular attention paid to ways in which drug-resistance is combated.
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Affiliation(s)
- Amanda Mabhula
- Department of Chemistry , University of Cape Town , Rondebosch 7701 , South Africa
- South African Medical Research Council Drug Discovery and Development Research Unit , Department of Chemistry and Institute of Infectious Disease and Molecular Medicine , University of Cape Town , Rondebosch 7701 , South Africa .
| | - Vinayak Singh
- South African Medical Research Council Drug Discovery and Development Research Unit , Department of Chemistry and Institute of Infectious Disease and Molecular Medicine , University of Cape Town , Rondebosch 7701 , South Africa .
- Drug Discovery and Development Centre (H3D) , Institute of Infectious Disease and Molecular Medicine , University of Cape Town , Rondebosch 7701 , South Africa
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Revised Interpretation of the Hain Lifescience GenoType MTBC To Differentiate Mycobacterium canettii and Members of the Mycobacterium tuberculosis Complex. Antimicrob Agents Chemother 2019; 63:AAC.00159-19. [PMID: 30962348 DOI: 10.1128/aac.00159-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/02/2019] [Indexed: 11/20/2022] Open
Abstract
Using 894 phylogenetically diverse genomes of the Mycobacterium tuberculosis complex (MTBC), we simulated in silico the ability of the Hain Lifescience GenoType MTBC assay to differentiate the causative agents of tuberculosis. Here, we propose a revised interpretation of this assay to reflect its strengths (e.g., it can distinguish some strains of Mycobacterium canettii and variants of Mycobacterium bovis that are not intrinsically resistant to pyrazinamide) and limitations (e.g., Mycobacterium orygis cannot be differentiated from Mycobacterium africanum).
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