1
|
Srivastava V, Navabharath M, Khan M, Samal M, Parveen R, Singh SV, Ahmad S. A comprehensive review on Phyto-MAP: A novel approach of drug discovery against Mycobacterium avium subspecies paratuberculosis using AYUSH heritage. JOURNAL OF ETHNOPHARMACOLOGY 2024; 333:118482. [PMID: 38908495 DOI: 10.1016/j.jep.2024.118482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/19/2024] [Accepted: 06/20/2024] [Indexed: 06/24/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Indian system of Traditional medicine, AYUSH (Ayurveda, Yoga, Unani, Siddha, and Homeopathy) has great potential with a History of Safe Use (HOSU) of thousands of medicinal plants included in pharmacopoeias. The multi-targeted approach of phytoconstituents present in different traditionally used medicinal plants makes them suitable candidates for research against various infective pathogens. MAP which is a dairy-borne pathogen is associated with the development of Johne's disease in ruminants and Crohn's disease like autoimmune disorders in human beings. There are no reliable treatment alternatives available against MAP, leaving surgical removal of intestines as the sole option. Hence, there exists an urgent need to search for leads against such infection. AIM OF THE STUDY The present review has been conducted to find out the ethnopharmacological evidence about the potential of phytoconstituents against Mycobacterium avium subspecies paratuberculosis (MAP), along with the proposal of a potential phyto-MAP mechanism for the very first time taking anti-inflammatory, immunomodulatory, and anti-microbial traditional claims into consideration. MATERIALS AND METHODS We have analyzed and reviewed different volumes of the two main traditional scriptures of India i.e. Ayurvedic Pharmacopoeia of India (API) and Unani Pharmacopoeia of India (UPI), respectively-for identification of potential anti-MAP plants based on their claims for related disorders. These plants were further investigated systematically for their scientific publications of the last 20 years (2002-2022) available through electronic databases including Google Scholar, Pubmed, and Scopus. The studies conducted in vitro, cell lines, and in vivo levels were taken into consideration along with the associated mechanisms of phytoconstituents. RESULTS A total of 70 potential medicinal plants have been identified. Based on the ethnopharmacology, a potential phyto-paratuberculosis (Phyto-paraTB) mechanism has been proposed and out of 70, seven potential anti-MAP plants have been identified to have a great future as anti-MAP. CONCLUSION A novel and scientifically viable plan has been proposed for addressing anti-MAP plants for stimulating research against MAP and related disorders using mass-trusted AYUSH medicine, which can be used as an alternative remedy in resistance cases otherwise can be advocated as an adjuvant with modern treatments for better management of the disease.
Collapse
Affiliation(s)
- Varsha Srivastava
- Centre of Excellence in Unani Medicine (Pharmacognosy and Pharmacology), Bioactive Natural Product Laboratory, Department of Pharmacognosy and Phytochemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, Delhi, India.
| | - Manthena Navabharath
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Mathura, Uttar Pradesh, India.
| | - Muzayyana Khan
- Centre of Excellence in Unani Medicine (Pharmacognosy and Pharmacology), Bioactive Natural Product Laboratory, Department of Pharmacognosy and Phytochemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, Delhi, India.
| | - Monalisha Samal
- Centre of Excellence in Unani Medicine (Pharmacognosy and Pharmacology), Bioactive Natural Product Laboratory, Department of Pharmacognosy and Phytochemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, Delhi, India.
| | - Rabea Parveen
- Department of Pharmaceutics, Jamia Hamdard, New Delhi, Delhi, India.
| | - Shoor Vir Singh
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Mathura, Uttar Pradesh, India.
| | - Sayeed Ahmad
- Centre of Excellence in Unani Medicine (Pharmacognosy and Pharmacology), Bioactive Natural Product Laboratory, Department of Pharmacognosy and Phytochemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, Delhi, India.
| |
Collapse
|
2
|
Kotimoole CN, Ramya VK, Kaur P, Reiling N, Shandil RK, Narayanan S, Flo TH, Prasad TSK. Discovery of Species-Specific Proteotypic Peptides To Establish a Spectral Library Platform for Identification of Nontuberculosis Mycobacteria from Mass Spectrometry-Based Proteomics. J Proteome Res 2024; 23:1102-1117. [PMID: 38358903 DOI: 10.1021/acs.jproteome.3c00850] [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: 02/17/2024]
Abstract
Nontuberculous mycobacteria are opportunistic bacteria pulmonary and extra-pulmonary infections in humans that closely resemble Mycobacterium tuberculosis. Although genome sequencing strategies helped determine NTMs, a common assay for the detection of coinfection by multiple NTMs with M. tuberculosis in the primary attempt of diagnosis is still elusive. Such a lack of efficiency leads to delayed therapy, an inappropriate choice of drugs, drug resistance, disease complications, morbidity, and mortality. Although a high-resolution LC-MS/MS-based multiprotein panel assay can be developed due to its specificity and sensitivity, it needs a library of species-specific peptides as a platform. Toward this, we performed an analysis of proteomes of 9 NTM species with more than 20 million peptide spectrum matches gathered from 26 proteome data sets. Our metaproteomic analyses determined 48,172 species-specific proteotypic peptides across 9 NTMs. Notably, M. smegmatis (26,008), M. abscessus (12,442), M. vaccae (6487), M. fortuitum (1623), M. avium subsp. paratuberculosis (844), M. avium subsp. hominissuis (580), and M. marinum (112) displayed >100 species-specific proteotypic peptides. Finally, these peptides and corresponding spectra have been compiled into a spectral library, FASTA, and JSON formats for future reference and validation in clinical cohorts by the biomedical community for further translation.
Collapse
Affiliation(s)
- Chinmaya Narayana Kotimoole
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Vadageri Krishnamurthy Ramya
- Foundation for Neglected Disease Research, 20A, KIADB Industrial Area, Veerapura Village, Doddaballapur, Bengaluru 561203, India
| | - Parvinder Kaur
- Foundation for Neglected Disease Research, 20A, KIADB Industrial Area, Veerapura Village, Doddaballapur, Bengaluru 561203, India
| | - Norbert Reiling
- Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Parkallee 22, D-23845 Borstel, Germany
- German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, 23845 Borstel, Germany
| | - Radha Krishan Shandil
- Foundation for Neglected Disease Research, 20A, KIADB Industrial Area, Veerapura Village, Doddaballapur, Bengaluru 561203, India
| | - Shridhar Narayanan
- Foundation for Neglected Disease Research, 20A, KIADB Industrial Area, Veerapura Village, Doddaballapur, Bengaluru 561203, India
| | - Trude Helen Flo
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Kunnskapssenteret, Øya 424.04.035, Norway
| | | |
Collapse
|
3
|
Joshi H, Kandari D, Maitra SS, Bhatnagar R, Banerjee N. Identification of genes associated with persistence in Mycobacterium smegmatis. Front Microbiol 2024; 15:1302883. [PMID: 38410395 PMCID: PMC10894938 DOI: 10.3389/fmicb.2024.1302883] [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: 09/27/2023] [Accepted: 01/22/2024] [Indexed: 02/28/2024] Open
Abstract
The prevalence of bacterial persisters is related to their phenotypic diversity and is responsible for the relapse of chronic infections. Tolerance to antibiotic therapy is the hallmark of bacterial persistence. In this study, we have screened a transposon library of Mycobacterium smegmatis mc2155 strain using antibiotic tolerance, survival in mouse macrophages, and biofilm-forming ability of the mutants. Out of 10 thousand clones screened, we selected ten mutants defective in all the three phenotypes. Six mutants showed significantly lower persister abundance under different stress conditions. Insertions in three genes belonging to the pathways of oxidative phosphorylation msmeg_3233 (cydA), biotin metabolism msmeg_3194 (bioB), and oxidative metabolism msmeg_0719, a flavoprotein monooxygenase, significantly reduced the number of live cells, suggesting their role in pathways promoting long-term survival. Another group that displayed a moderate reduction in CFU included a glycosyltransferase, msmeg_0392, a hydrogenase subunit, msmeg_2263 (hybC), and a DNA binding protein, msmeg_2211. The study has revealed potential candidates likely to facilitate the long-term survival of M. smegmatis. The findings offer new targets to develop antibiotics against persisters. Further, investigating the corresponding genes in M. tuberculosis may provide valuable leads in improving the treatment of chronic and persistent tuberculosis infections.
Collapse
Affiliation(s)
- Hemant Joshi
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Divya Kandari
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
- Divacc Research Laboratories Pvt. Ltd., incubated under Atal Incubation Centre, Jawaharlal Nehru University, New Delhi, India
| | - Subhrangsu Sundar Maitra
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Rakesh Bhatnagar
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Nirupama Banerjee
- Divacc Research Laboratories Pvt. Ltd., incubated under Atal Incubation Centre, Jawaharlal Nehru University, New Delhi, India
| |
Collapse
|
4
|
Xie W, Wang L, Luo D, Soni V, Rosenn EH, Wang Z. Mycobacterium smegmatis, a Promising Vaccine Vector for Preventing TB and Other Diseases: Vaccinomics Insights and Applications. Vaccines (Basel) 2023; 11:1302. [PMID: 37631870 PMCID: PMC10459588 DOI: 10.3390/vaccines11081302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/17/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Mycobacterium smegmatis (M.sm) is frequently used as an alternative model organism in Mycobacterium tuberculosis (M.tb) studies. While containing high sequence homology with M.tb, it is considered non-pathogenic in humans. As such it has been used to study M.tb and other infections in vivo and more recently been explored for potential therapeutic applications. A body of previous research has highlighted the potential of using genetically modified M.sm displaying rapid growth and unique immunostimulatory characteristics as an effective vaccine vector. Novel systems biology techniques can further serve to optimize these delivery constructs. In this article, we review recent advancements in vaccinomics tools that support the efficacy of a M.sm-based vaccine vector. Moreover, the integration of systems biology and molecular omics techniques in these pioneering studies heralds a potential accelerated pipeline for the development of next-generation recombinant vaccines against rapidly developing diseases.
Collapse
Affiliation(s)
- Weile Xie
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Longlong Wang
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dan Luo
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Vijay Soni
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Eric H. Rosenn
- School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Zhe Wang
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
5
|
Nayak T, Kakkar A, Singh RK, Jaiswal LK, Singh AK, Temple L, Gupta A. Isolation and characterization of a novel mycobacteriophage Kashi-VT1 infecting Mycobacterium species. Front Cell Infect Microbiol 2023; 13:1173894. [PMID: 37545854 PMCID: PMC10400892 DOI: 10.3389/fcimb.2023.1173894] [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: 02/28/2023] [Accepted: 06/19/2023] [Indexed: 08/08/2023] Open
Abstract
Mycobacteriophages are viruses that infect members of genus Mycobacterium. Because of the rise in antibiotic resistance in mycobacterial diseases such as tuberculosis, mycobacteriophages have received renewed attention as alternative therapeutic agents. Mycobacteriophages are highly diverse, and, on the basis of their genome sequences, they are grouped into 30 clusters and 10 singletons. In this article, we have described the isolation and characterization of a novel mycobacteriophage Kashi-VT1 (KVT1) infecting Mycobacterium >smegmatis mc2 155 (M. smegmatis) and Mycobacterium fortuitum isolated from Varanasi, India. KVT1 is a cluster K1 temperate phage that belongs to Siphoviridae family as visualized in transmission electron microscopy. The phage genome is 61,010 base pairs with 66.5% Guanine/Cytosine (GC) content, encoding 101 putative open reading frames. The KVT1 genome encodes an immunity repressor, a tyrosine integrase, and an excise protein, which are the characteristics of temperate phages. It also contains genes encoding holin, lysin A, and lysin B involved in host cell lysis. The one-step growth curve demonstrated that KVT1 has a latency time of 90 min and an average burst size of 101 phage particles per infected cell. It can withstand a temperature of up to 45°C and has a maximum viability between pH 8 and 9. Some mycobacteriophages from cluster K are known to infect the pathogenic Mycobacterium tuberculosis (M. tuberculosis); hence, KVT1 holds potential for the phage therapy against tuberculosis, and it can also be engineered to convert into an exclusively lytic phage.
Collapse
Affiliation(s)
- Tanmayee Nayak
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Anuja Kakkar
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Rakesh Kumar Singh
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Lav Kumar Jaiswal
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Anand Kumar Singh
- Interdisciplinary School of Life Sciences, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Louise Temple
- School of Integrated Sciences, James Madison University, Harrisonburg, VA, United States
| | - Ankush Gupta
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| |
Collapse
|
6
|
Simcox BS, Tomlinson BR, Shaw LN, Rohde KH. Mycobacterium abscessus DosRS two-component system controls a species-specific regulon required for adaptation to hypoxia. Front Cell Infect Microbiol 2023; 13:1144210. [PMID: 36968107 PMCID: PMC10034137 DOI: 10.3389/fcimb.2023.1144210] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 02/15/2023] [Indexed: 03/12/2023] Open
Abstract
Mycobacterium abscessus (Mab), an emerging opportunistic pathogen, predominantly infects individuals with underlying pulmonary diseases such as cystic fibrosis (CF). Current treatment outcomes for Mab infections are poor due to Mab's inherent antibiotic resistance and unique host interactions that promote phenotypic tolerance and hinder drug access. The hypoxic, mucus-laden airways in the CF lung and antimicrobial phagosome within macrophages represent hostile niches Mab must overcome via alterations in gene expression for survival. Regulatory mechanisms important for the adaptation and long-term persistence of Mab within the host are poorly understood, warranting further genetic and transcriptomics study of this emerging pathogen. DosRS Mab , a two-component signaling system (TCS), is one proposed mechanism utilized to subvert host defenses and counteract environmental stress such as hypoxia. The homologous TCS of Mycobacterium tuberculosis (Mtb), DosRS Mtb , is known to induce a ~50 gene regulon in response to hypoxia, carbon monoxide (CO) and nitric oxide (NO) in vitro and in vivo. Previously, a small DosR Mab regulon was predicted using bioinformatics based on DosR Mtb motifs however, the role and regulon of DosRS Mab in Mab pathogenesis have yet to be characterized in depth. To address this knowledge gap, our lab generated a Mab dosRS knockout strain (MabΔdosRS) to investigate differential gene expression, and phenotype in an in vitro hypoxia model of dormancy. qRT-PCR and lux reporter assays demonstrate Mab_dosR and 6 predicted downstream genes are induced in hypoxia. In addition, RNAseq revealed induction of a much larger hypoxia response comprised of >1000 genes, including 127 differentially expressed genes in a dosRS mutant strain. Deletion of DosRS Mab led to attenuated growth under low oxygen conditions, a shift in morphotype from smooth to rough, and down-regulation of 216 genes. This study provides the first look at the global transcriptomic response of Mab to low oxygen conditions encountered in the airways of CF patients and within macrophage phagosomes. Our data also demonstrate the importance of DosRS Mab for adaptation of Mab to hypoxia, highlighting a distinct regulon (compared to Mtb) that is significantly larger than previously described, including both genes conserved across mycobacteria as well as Mab-specific genes.
Collapse
Affiliation(s)
- Breven S. Simcox
- Division of Immunology and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
| | - Brooke R. Tomlinson
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL, United States
| | - Lindsey N. Shaw
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL, United States
| | - Kyle H. Rohde
- Division of Immunology and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
| |
Collapse
|
7
|
Abstract
The genus Mycobacterium contains several slow-growing human pathogens, including Mycobacterium tuberculosis, Mycobacterium leprae, and Mycobacterium avium. Mycobacterium smegmatis is a nonpathogenic and fast growing species within this genus. In 1990, a mutant of M. smegmatis, designated mc2155, that could be transformed with episomal plasmids was isolated, elevating M. smegmatis to model status as the ideal surrogate for mycobacterial research. Classical bacterial models, such as Escherichia coli, were inadequate for mycobacteria research because they have low genetic conservation, different physiology, and lack the novel envelope structure that distinguishes the Mycobacterium genus. By contrast, M. smegmatis encodes thousands of conserved mycobacterial gene orthologs and has the same cell architecture and physiology. Dissection and characterization of conserved genes, structures, and processes in genetically tractable M. smegmatis mc2155 have since provided previously unattainable insights on these same features in its slow-growing relatives. Notably, tuberculosis (TB) drugs, including the first-line drugs isoniazid and ethambutol, are active against M. smegmatis, but not against E. coli, allowing the identification of their physiological targets. Furthermore, Bedaquiline, the first new TB drug in 40 years, was discovered through an M. smegmatis screen. M. smegmatis has become a model bacterium, not only for M. tuberculosis, but for all other Mycobacterium species and related genera. With a repertoire of bioinformatic and physical resources, including the recently established Mycobacterial Systems Resource, M. smegmatis will continue to accelerate mycobacterial research and advance the field of microbiology.
Collapse
|
8
|
Gupta R, Rohde KH. Implementation of a mycobacterial CRISPRi platform in Mycobacterium abscessus and demonstration of the essentiality of ftsZ Mab. Tuberculosis (Edinb) 2023; 138:102292. [PMID: 36495774 DOI: 10.1016/j.tube.2022.102292] [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: 08/13/2022] [Revised: 11/22/2022] [Accepted: 11/27/2022] [Indexed: 12/04/2022]
Abstract
Mycobacterium abscessus (Mab) is a highly drug-resistant non-tuberculous mycobacterial species that causes debilitating TB-like pulmonary infections. The lack of genetic tools has hampered characterization of its extensive repertoire of virulence factors, antimicrobial resistance mechanisms, and drug targets. In this study, we evaluated the performance of a mycobacterial single plasmid CRISPRi-dCas9 system optimized for M. tuberculosis and M. smegmatis for inducible gene silencing in Mab. The efficacy of CRISPRi-mediated repression of two antibiotic resistance genes (blaMab, whiB7Mab) and two putative essential genes (ftsZMab,topAMab) was determined by measuring mRNA transcript levels and phenotypic outcomes. While our results support the utility of this mycobacterial CRISPRi dCas9Sth1 single-plasmid platform for inducible silencing of specific target genes in Mab, they also highlighted several caveats and nuances that may warrant species-specific optimization for Mab. We observed overall lower levels of gene repression in Mab including variable silencing of different target genes despite use of PAMs of similar predicted strength. In addition, leaky gene repression in the absence of inducer was noted for some genes but not others. Nonetheless, using CRISPRi we demonstrated the silencing of multiple target genes and validated ftsZMab as an essential gene and promising drug target for the first time.
Collapse
Affiliation(s)
- Rashmi Gupta
- Division of Immunity and Pathogenesis, College of Medicine, Burnett School of Biomedical Sciences, University of Central Florida, 6900 Lake Nona Blvd, FL, 32827, USA.
| | - Kyle H Rohde
- Division of Immunity and Pathogenesis, College of Medicine, Burnett School of Biomedical Sciences, University of Central Florida, 6900 Lake Nona Blvd, FL, 32827, USA.
| |
Collapse
|
9
|
Ang CW, Lee BM, Jackson CJ, Wang Y, Franzblau SG, Francisco AF, Kelly JM, Bernhardt PV, Tan L, West NP, Sykes ML, Hinton AO, Bolisetti R, Avery VM, Cooper MA, Blaskovich MA. Nitroimidazopyrazinones with Oral Activity against Tuberculosis and Chagas Disease in Mouse Models of Infection. J Med Chem 2022; 65:13125-13142. [DOI: 10.1021/acs.jmedchem.2c00972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chee Wei Ang
- Center for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
- School of Science, Monash University Malaysia, Subang Jaya, 47500 Selangor, Malaysia
| | - Brendon M. Lee
- Research School of Chemistry, Australian National University, Sullivans Creek Road, Acton ACT 2601, Australia
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, New York 10021, United States
| | - Colin J. Jackson
- Research School of Chemistry, Australian National University, Sullivans Creek Road, Acton ACT 2601, Australia
| | - Yuehong Wang
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Scott G. Franzblau
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Amanda F. Francisco
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - John M. Kelly
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Paul V. Bernhardt
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Lendl Tan
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Nicholas P. West
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Melissa L. Sykes
- Discovery Biology, Griffith Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, Queensland 4111, Australia
| | - Alexandra O. Hinton
- Center for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Raghu Bolisetti
- Center for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Vicky M. Avery
- Discovery Biology, Griffith Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, Queensland 4111, Australia
- School of Environment and Science, Griffith University, Nathan, Queensland 4111, Australia
| | - Matthew A. Cooper
- Center for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Mark A.T. Blaskovich
- Center for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| |
Collapse
|
10
|
Investigating the Antituberculosis Activity of Selected Commercial Essential Oils and Identification of Active Constituents Using a Biochemometrics Approach and In Silico Modeling. Antibiotics (Basel) 2022; 11:antibiotics11070948. [PMID: 35884202 PMCID: PMC9311982 DOI: 10.3390/antibiotics11070948] [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: 06/24/2022] [Revised: 07/08/2022] [Accepted: 07/10/2022] [Indexed: 02/04/2023] Open
Abstract
Tuberculosis (TB) is a disease caused by Mycobacterium tuberculosis which has become prevalent due to the emergence of resistant M. tuberculosis strains. The use of essential oils (EOs) as potential anti-infective agents to treat microbial infections, including TB, offers promise due to their long historical use and low adverse effects. The current study aimed to investigate the in vitro anti-TB activity of 85 commercial EOs, and identify compounds responsible for the activity, using a biochemometrics approach. A microdilution assay was used to determine the antimycobacterial activity of the EOs towards some non-pathogenic Mycobacterium strains. In parallel, an Alamar blue assay was used to investigate antimycobacterial activity towards the pathogenic M. tuberculosis strain. Chemical profiling of the EOs was performed using gas chromatography-mass spectrometry (GC-MS) analysis. Biochemometrics filtered out putative biomarkers using orthogonal projections to latent structures discriminant analysis (OPLS-DA). In silico modeling was performed to identify potential therapeutic targets of the active biomarkers. Broad-spectrum antimycobacterial activity was observed for Cinnamomum zeylanicum (bark) (MICs = 1.00, 0.50, 0.25 and 0.008 mg/mL) and Levisticum officinale (MICs = 0.50, 0.5, 0.5 and 0.004 mg/mL) towards M. smegmatis, M. fortuitum, M. gordonae and M. tuberculosis, respectively. Biochemometrics predicted cinnamaldehyde, thymol and eugenol as putative biomarkers. Molecular docking demonstrated that cinnamaldehyde could serve as a scaffold for developing a novel class of antimicrobial compounds by targeting FtsZ and PknB from M. tuberculosis.
Collapse
|
11
|
Anand P, Akhter Y. A review on enzyme complexes of electron transport chain from Mycobacterium tuberculosis as promising drug targets. Int J Biol Macromol 2022; 212:474-494. [PMID: 35613677 DOI: 10.1016/j.ijbiomac.2022.05.124] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/05/2022] [Accepted: 05/17/2022] [Indexed: 12/20/2022]
Abstract
Energy metabolism is a universal process occurring in all life forms. In Mycobacterium tuberculosis (Mtb), energy production is carried out in two possible ways, oxidative phosphorylation (OxPhos) and substrate-level phosphorylation. Mtb is an obligate aerobic bacterium, making it dependent on OxPhos for ATP synthesis and growth. Mtb inhabits varied micro-niches during the infection cycle, outside and within the host cells, which alters its primary metabolic pathways during the pathogenesis. In this review, we discuss cellular respiration in the context of the mechanism and structural importance of the proteins and enzyme complexes involved. These protein-protein complexes have been proven to be essential for Mtb virulence as they aid the bacteria's survival during aerobic and hypoxic conditions. ATP synthase, a crucial component of the electron transport chain, has been in the limelight, as a prominent drug target against tuberculosis. Likewise, in this review, we have explored other protein-protein complexes of the OxPhos pathway, their functional essentiality, and their mechanism in Mtb's diverse lifecycle. The review summarises crucial target proteins and reported inhibitors of the electron transport chain pathway of Mtb.
Collapse
Affiliation(s)
- Pragya Anand
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Lucknow, Uttar Pradesh 226025, India
| | - Yusuf Akhter
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Lucknow, Uttar Pradesh 226025, India.
| |
Collapse
|
12
|
Shu Q, Liu S, Alonzi T, LaCourse SM, Singh DK, Bao D, Wamalwa D, Jiang L, Lyon CJ, John-Stewart G, Kaushal D, Goletti D, Hu T. Assay design for unambiguous identification and quantification of circulating pathogen-derived peptide biomarkers. Theranostics 2022; 12:2948-2962. [PMID: 35401822 PMCID: PMC8965485 DOI: 10.7150/thno.70373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/25/2022] [Indexed: 11/05/2022] Open
Abstract
Rationale: Circulating pathogen-derived proteins can serve as useful biomarkers for infections but may be detected with poor sensitivity and specificity by standard immunoassays due to masking effects and cross-reactivity. Mass spectrometry (MS)-read immunoassays for biomarker-derived peptides can resolve these issues, but lack standard workflows to select species-specific peptides with strong MS signal that are suitable for antibody generation. Methods:Using a Mycobacterium tuberculosis (Mtb) protein as an example, candidate peptides were selected by length, species-specificity, MS intensity, and antigenicity score. MS data from spiked healthy serum was employed to define MS feature thresholds, including a novel measure of internal MS data correlation, to produce a peak detection algorithm. Results: This algorithm performed better in rejecting false positive signal than each of its criteria, including those currently employed for this purpose. Analysis of an Mtb peptide biomarker (CFP-10pep) by this approach identified tuberculosis cases not detected by microbiologic assays, including extrapulmonary tuberculosis and tuberculosis cases in children infected with HIV-1. Circulating CFP-10pep levels measured in a non-human primate model of tuberculosis distinguished disease from asymptomatic infection and tended to correspond with Mtb granuloma size, suggesting that it could also serve as a surrogate marker for Mtb burden and possibly treatment response. Conclusions: These biomarker selection and analysis approach appears to have strong potential utility for infectious disease diagnosis, including cryptic infections, and possibly to monitor changes in Mtb burden that may reflect disease progression or a response to treatment, which are critical needs for more effective disease control.
Collapse
Affiliation(s)
- Qingbo Shu
- Center for Cellular and Molecular Diagnostics, Department of Biochemistry and Molecular Biology, School of Medicine, Tulane University, New Orleans, Louisiana, USA
| | - Shan Liu
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Medical Genetics, Department of Laboratory medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China
| | - Tonino Alonzi
- Translational Research Unit, National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, Rome, Italy
| | - Sylvia M. LaCourse
- Departments of Medicine, Division of Allergy and Infectious Diseases, and Global Health, University of Washington, Seattle, USA
| | - Dhiraj Kumar Singh
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Duran Bao
- Center for Cellular and Molecular Diagnostics, Department of Biochemistry and Molecular Biology, School of Medicine, Tulane University, New Orleans, Louisiana, USA
| | - Dalton Wamalwa
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Li Jiang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Medical Genetics, Department of Laboratory medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China
| | - Christopher J. Lyon
- Center for Cellular and Molecular Diagnostics, Department of Biochemistry and Molecular Biology, School of Medicine, Tulane University, New Orleans, Louisiana, USA
| | - Grace John-Stewart
- Departments of Medicine, Division of Allergy and Infectious Diseases, and Global Health, University of Washington, Seattle, USA
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Delia Goletti
- Translational Research Unit, National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, Rome, Italy
| | - Tony Hu
- Center for Cellular and Molecular Diagnostics, Department of Biochemistry and Molecular Biology, School of Medicine, Tulane University, New Orleans, Louisiana, USA.,✉ Corresponding author: Tony Hu.
| |
Collapse
|
13
|
Geographically dispersed zoonotic tuberculosis in pre-contact South American human populations. Nat Commun 2022; 13:1195. [PMID: 35256608 PMCID: PMC8901693 DOI: 10.1038/s41467-022-28562-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 01/25/2022] [Indexed: 12/30/2022] Open
Abstract
AbstractPrevious ancient DNA research has shown that Mycobacterium pinnipedii, which today causes tuberculosis (TB) primarily in pinnipeds, infected human populations living in the coastal areas of Peru prior to European colonization. Skeletal evidence indicates the presence of TB in several pre-colonial South and North American populations with minimal access to marine resources— a scenario incompatible with TB transmission directly from infected pinnipeds or their tissues. In this study, we investigate the causative agent of TB in ten pre-colonial, non-coastal individuals from South America. We reconstruct M. pinnipedii genomes (10- to 15-fold mean coverage) from three contemporaneous individuals from inland Peru and Colombia, demonstrating the widespread dissemination of M. pinnipedii beyond the coast, either through human-to-human and/or animal-mediated routes. Overall, our study suggests that TB transmission in the pre-colonial era Americas involved a more complex transmission pathway than simple pinniped-to-human transfer.
Collapse
|
14
|
Grey ABJ, Cadelis MM, Diao Y, Park D, Lumley T, Weir BS, Copp BR, Wiles S. Screening of Fungi for Antimycobacterial Activity Using a Medium-Throughput Bioluminescence-Based Assay. Front Microbiol 2021; 12:739995. [PMID: 34552577 PMCID: PMC8450596 DOI: 10.3389/fmicb.2021.739995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/10/2021] [Indexed: 11/16/2022] Open
Abstract
There is a real and urgent need for new antibiotics able to kill Mycobacteria, acid-fast bacilli capable of causing multiple deadly diseases. These include members of the Mycobacterium tuberculosis complex, which causes the lung disease tuberculosis (TB) as well as non-tuberculous Mycobacteria (NTM) a growing cause of lung, skin, soft tissue, and other infections. Here we describe a medium-throughput bioluminescence-based pipeline to screen fungi for activity against Mycobacteria using the NTM species Mycobacterium abscessus and Mycobacterium marinum. We used this pipeline to screen 36 diverse fungal isolates from the International Collection of Microorganisms from Plants (ICMP) grown on a wide variety of nutrient-rich and nutrient-poor media and discovered that almost all the tested isolates produced considerable anti-mycobacterial activity. Our data also provides strong statistical evidence for the impact of growth media on antibacterial activity. Chemical extraction and fractionation of a subset of the ICMP isolates revealed that much of the activity we observed may be due to the production of the known anti-mycobacterial compound linoleic acid. However, we have identified several ICMP isolates that retained their anti-mycobacterial activity in non-linoleic acid containing fractions. These include isolates of Lophodermium culmigenum, Pseudaegerita viridis, and Trametes coccinea, as well as an unknown species of Boeremia and an isolate of an unknown genus and species in the family Phanerochaetaceae. Investigations are ongoing to identify the sources of their anti-mycobacterial activity and to determine whether any may be due to the production of novel bioactive compounds.
Collapse
Affiliation(s)
- Alexander B J Grey
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, School of Medical Sciences, The University of Auckland - Waipapa Taumata Rau, Auckland, New Zealand
| | - Melissa M Cadelis
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, School of Medical Sciences, The University of Auckland - Waipapa Taumata Rau, Auckland, New Zealand.,School of Chemical Sciences, The University of Auckland - Waipapa Taumata Rau, Auckland, New Zealand
| | - Yiwei Diao
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, School of Medical Sciences, The University of Auckland - Waipapa Taumata Rau, Auckland, New Zealand
| | - Duckchul Park
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
| | - Thomas Lumley
- Department of Statistics, The University of Auckland - Waipapa Taumata Rau, Auckland, New Zealand
| | - Bevan S Weir
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
| | - Brent R Copp
- School of Chemical Sciences, The University of Auckland - Waipapa Taumata Rau, Auckland, New Zealand
| | - Siouxsie Wiles
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, School of Medical Sciences, The University of Auckland - Waipapa Taumata Rau, Auckland, New Zealand
| |
Collapse
|
15
|
Maeda T, Kawada M, Sakata N, Kotani H, Furusawa C. Laboratory evolution of Mycobacterium on agar plates for analysis of resistance acquisition and drug sensitivity profiles. Sci Rep 2021; 11:15136. [PMID: 34302035 PMCID: PMC8302736 DOI: 10.1038/s41598-021-94645-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 07/14/2021] [Indexed: 11/09/2022] Open
Abstract
Drug-resistant tuberculosis (TB) is a growing public health problem. There is an urgent need for information regarding cross-resistance and collateral sensitivity relationships among drugs and the genetic determinants of anti-TB drug resistance for developing strategies to suppress the emergence of drug-resistant pathogens. To identify mutations that confer resistance to anti-TB drugs in Mycobacterium species, we performed the laboratory evolution of nonpathogenic Mycobacterium smegmatis, which is closely related to Mycobacterium tuberculosis, against ten anti-TB drugs. Next, we performed whole-genome sequencing and quantified the resistance profiles of each drug-resistant strain against 24 drugs. We identified the genes with novel meropenem (MP) and linezolid (LZD) resistance-conferring mutation, which also have orthologs, in M. tuberculosis H37Rv. Among the 240 possible drug combinations, we identified 24 pairs that confer cross-resistance and 18 pairs that confer collateral sensitivity. The acquisition of bedaquiline or linezolid resistance resulted in collateral sensitivity to several drugs, while the acquisition of MP resistance led to multidrug resistance. The MP-evolved strains showed cross-resistance to rifampicin and clarithromycin owing to the acquisition of a mutation in the intergenic region of the Rv2864c ortholog, which encodes a penicillin-binding protein, at an early stage. These results provide a new insight to tackle drug-resistant TB.
Collapse
Affiliation(s)
- Tomoya Maeda
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan. .,Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan.
| | - Masako Kawada
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Natsue Sakata
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Hazuki Kotani
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Chikara Furusawa
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.,Universal Biology Institute, The University of Tokyo, 7-3-1 Hongo, Tokyo, 113-0033, Japan
| |
Collapse
|
16
|
Cornejo-Granados F, Kohl TA, Sotomayor FV, Andres S, Hernández-Pando R, Hurtado-Ramirez JM, Utpatel C, Niemann S, Maurer FP, Ochoa-Leyva A. Secretome characterization of clinical isolates from the Mycobacterium abscessus complex provides insight into antigenic differences. BMC Genomics 2021; 22:385. [PMID: 34034663 PMCID: PMC8152154 DOI: 10.1186/s12864-021-07670-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/27/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycobacterium abscessus (MAB) is a widely disseminated pathogenic non-tuberculous mycobacterium (NTM). Like with the M. tuberculosis complex (MTBC), excreted / secreted (ES) proteins play an essential role for its virulence and survival inside the host. Here, we used a robust bioinformatics pipeline to predict the secretome of the M. abscessus ATCC 19977 reference strain and 15 clinical isolates belonging to all three MAB subspecies, M. abscessus subsp. abscessus, M. abscessus subsp. bolletii, and M. abscessus subsp. massiliense. RESULTS We found that ~ 18% of the proteins encoded in the MAB genomes were predicted as secreted and that the three MAB subspecies shared > 85% of the predicted secretomes. MAB isolates with a rough (R) colony morphotype showed larger predicted secretomes than isolates with a smooth (S) morphotype. Additionally, proteins exclusive to the secretomes of MAB R variants had higher antigenic densities than those exclusive to S variants, independent of the subspecies. For all investigated isolates, ES proteins had a significantly higher antigenic density than non-ES proteins. We identified 337 MAB ES proteins with homologues in previously investigated M. tuberculosis secretomes. Among these, 222 have previous experimental support of secretion, and some proteins showed homology with protein drug targets reported in the DrugBank database. The predicted MAB secretomes showed a higher abundance of proteins related to quorum-sensing and Mce domains as compared to MTBC indicating the importance of these pathways for MAB pathogenicity and virulence. Comparison of the predicted secretome of M. abscessus ATCC 19977 with the list of essential genes revealed that 99 secreted proteins corresponded to essential proteins required for in vitro growth. CONCLUSIONS This study represents the first systematic prediction and in silico characterization of the MAB secretome. Our study demonstrates that bioinformatics strategies can help to broadly explore mycobacterial secretomes including those of clinical isolates and to tailor subsequent, complex and time-consuming experimental approaches accordingly. This approach can support systematic investigation exploring candidate proteins for new vaccines and diagnostic markers to distinguish between colonization and infection. All predicted secretomes were deposited in the Secret-AAR web-server ( http://microbiomics.ibt.unam.mx/tools/aar/index.php ).
Collapse
Affiliation(s)
- Fernanda Cornejo-Granados
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autonoma de México, Cuernavaca, Morelos, Mexico
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel, Borstel, Germany
| | - Flor Vásquez Sotomayor
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Sönke Andres
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Rogelio Hernández-Pando
- Experimental Pathology Section, National Institute of Medical Sciences and Nutrition Salvador Zubirán, Mexico City, Mexico
| | - Juan Manuel Hurtado-Ramirez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autonoma de México, Cuernavaca, Morelos, Mexico
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel, Borstel, Germany
| | - Florian P Maurer
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel, Borstel, Germany.
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany.
- Institute of Medical Microbiology, Virology and Hospital Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Adrian Ochoa-Leyva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autonoma de México, Cuernavaca, Morelos, Mexico.
| |
Collapse
|
17
|
Vedithi SC, Malhotra S, Acebrón-García-de-Eulate M, Matusevicius M, Torres PHM, Blundell TL. Structure-Guided Computational Approaches to Unravel Druggable Proteomic Landscape of Mycobacterium leprae. Front Mol Biosci 2021; 8:663301. [PMID: 34026836 PMCID: PMC8138464 DOI: 10.3389/fmolb.2021.663301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/12/2021] [Indexed: 02/02/2023] Open
Abstract
Leprosy, caused by Mycobacterium leprae (M. leprae), is treated with a multidrug regimen comprising Dapsone, Rifampicin, and Clofazimine. These drugs exhibit bacteriostatic, bactericidal and anti-inflammatory properties, respectively, and control the dissemination of infection in the host. However, the current treatment is not cost-effective, does not favor patient compliance due to its long duration (12 months) and does not protect against the incumbent nerve damage, which is a severe leprosy complication. The chronic infectious peripheral neuropathy associated with the disease is primarily due to the bacterial components infiltrating the Schwann cells that protect neuronal axons, thereby inducing a demyelinating phenotype. There is a need to discover novel/repurposed drugs that can act as short duration and effective alternatives to the existing treatment regimens, preventing nerve damage and consequent disability associated with the disease. Mycobacterium leprae is an obligate pathogen resulting in experimental intractability to cultivate the bacillus in vitro and limiting drug discovery efforts to repositioning screens in mouse footpad models. The dearth of knowledge related to structural proteomics of M. leprae, coupled with emerging antimicrobial resistance to all the three drugs in the multidrug therapy, poses a need for concerted novel drug discovery efforts. A comprehensive understanding of the proteomic landscape of M. leprae is indispensable to unravel druggable targets that are essential for bacterial survival and predilection of human neuronal Schwann cells. Of the 1,614 protein-coding genes in the genome of M. leprae, only 17 protein structures are available in the Protein Data Bank. In this review, we discussed efforts made to model the proteome of M. leprae using a suite of software for protein modeling that has been developed in the Blundell laboratory. Precise template selection by employing sequence-structure homology recognition software, multi-template modeling of the monomeric models and accurate quality assessment are the hallmarks of the modeling process. Tools that map interfaces and enable building of homo-oligomers are discussed in the context of interface stability. Other software is described to determine the druggable proteome by using information related to the chokepoint analysis of the metabolic pathways, gene essentiality, homology to human proteins, functional sites, druggable pockets and fragment hotspot maps.
Collapse
Affiliation(s)
- Sundeep Chaitanya Vedithi
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom,*Correspondence: Sundeep Chaitanya Vedithi,
| | - Sony Malhotra
- Rutherford Appleton Laboratory, Science and Technology Facilities Council, Oxon, United Kingdom
| | | | | | - Pedro Henrique Monteiro Torres
- Laboratório de Modelagem e Dinâmica Molecular, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tom L. Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom,Tom L. Blundell,
| |
Collapse
|
18
|
Strategies for drug target identification in Mycobacterium leprae. Drug Discov Today 2021; 26:1569-1573. [PMID: 33798649 DOI: 10.1016/j.drudis.2021.03.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/01/2021] [Accepted: 03/23/2021] [Indexed: 11/22/2022]
Abstract
Hansen's disease (HD), or leprosy, continues to be endemic in many parts of the world. Although multidrug therapy (MDT) is successful in curing a large number of patients, some of them abandon it because it is a long-term treatment. Therefore, identification of new drug targets in Mycobacterium leprae is considered of high importance. Here, we introduce an overview of in silico and in vitro studies that might be of help in this endeavor. The essentiality of M. leprae proteins is reviewed with discussion of flux balance analysis, gene expression, and knockout articles. Finally, druggability techniques are proposed for the validation of new M. leprae protein targets (see Fig. 1).
Collapse
|
19
|
Saxena S, Spaink HP, Forn-Cuní G. Drug Resistance in Nontuberculous Mycobacteria: Mechanisms and Models. BIOLOGY 2021; 10:biology10020096. [PMID: 33573039 PMCID: PMC7911849 DOI: 10.3390/biology10020096] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 02/07/2023]
Abstract
The genus Mycobacteria comprises a multitude of species known to cause serious disease in humans, including Mycobacterium tuberculosis and M. leprae, the responsible agents for tuberculosis and leprosy, respectively. In addition, there is a worldwide spike in the number of infections caused by a mixed group of species such as the M. avium, M. abscessus and M. ulcerans complexes, collectively called nontuberculous mycobacteria (NTMs). The situation is forecasted to worsen because, like tuberculosis, NTMs either naturally possess or are developing high resistance against conventional antibiotics. It is, therefore, important to implement and develop models that allow us to effectively examine the fundamental questions of NTM virulence, as well as to apply them for the discovery of new and improved therapies. This literature review will focus on the known molecular mechanisms behind drug resistance in NTM and the current models that may be used to test new effective antimicrobial therapies.
Collapse
|
20
|
Bahuguna A, Rawat S, Rawat DS. QcrB in Mycobacterium tuberculosis: The new drug target of antitubercular agents. Med Res Rev 2021; 41:2565-2581. [PMID: 33400275 DOI: 10.1002/med.21779] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/23/2020] [Accepted: 12/12/2020] [Indexed: 11/08/2022]
Abstract
Drug-resistance in mycobacterial infections is a major global health problem that leads to high mortality and socioeconomic pressure in developing countries around the world. From finding new targets to discovering novel chemical scaffolds, there is an urgent need for the development of better approaches for the cure of tuberculosis. Recently, energy metabolism in mycobacteria, particularly the oxidative phosphorylation pathway of cellular respiration, has emerged as a novel target pathway in drug discovery. New classes of antibacterials which target oxidative phosphorylation pathway either by interacting with a protein or any step in the pathway of oxidative phosphorylation can combat dormant mycobacterial infections leading to shortening of tuberculosis chemotherapy. Adenosine triphosphate synthase is one such recently discovered target of the newly approved antitubercular drug bedaquiline. Cytochrome bcc is another new target of the antitubercular drug candidate Q203, currently in phase II clinical trial. Research suggests that b subunit of cytochrome bcc, QcrB, is the target of Q203. The review article describes the structure, function, and importance of targeting QcrB throwing light on all chemical classes of QcrB inhibitors discovered to date. An understanding of the structure and function of validated targets and their inhibitors would enable the development of new chemical entities.
Collapse
Affiliation(s)
| | - Srishti Rawat
- Department of Chemistry, University of Delhi, Delhi, India
| | - Diwan S Rawat
- Department of Chemistry, University of Delhi, Delhi, India
| |
Collapse
|
21
|
Yadav R, Rajput V, Gohil K, Khairnar K, Dharne M. Comprehensive metagenomic insights into a unique mass gathering and bathing event reveals transient influence on a riverine ecosystem. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 202:110938. [PMID: 32800221 DOI: 10.1016/j.ecoenv.2020.110938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/21/2020] [Accepted: 06/23/2020] [Indexed: 05/04/2023]
Abstract
The religious mass gathering and bathing can pose a multitude of significant public health challenges and lead to severe alterations in the river microbial ecology. The Pandharpur Wari is an annual pilgrimage of Maharashtra, India, where millions of devotees carry the footprints of the saint-poets and pay their obeisance to Lord Vitthal on the 11th day of moon's waxing phase (Ashadi Ekadashi). As a part of the ritual, the engrossed devotees, walk over 250 km, take a first holy dip in a sacred river Indrayani at Alandi and secondly in Bhima River at Pandharpur. The MinION-based shotgun metagenomic approach was employed to examine the impact of spiritual mass bathing on environmental changes (concerning the river microbial community structure and functions); and public health aspects (in terms of changes in the pathogenic potential and antibiotic resistance). The analysis of bathing and post-bathing samples of both the rivers revealed alterations in the alpha and beta diversity, indicating significant spatiotemporal variations in the overall microbial structure and function. Furthermore, the analysis revealed up to 80% of differences in the abundance of virulence genes between the bathing and post bathing samples. We observed parallel increase of priority skin and enteric pathogens (ranging from 11% to 80%) such as Acinetobacter baumannii, Staphylococcus aureus, Streptococcus pyogenes, Mycobacterium tuberculosis, and Pseudomonas aeruginosa during the bathing event. Moreover, we observed a significant increase in the antibiotic resistance in the bathing samples of Bhima and Indrayani rivers respectively. Altogether, this is the first comprehensive metagenomic study unravelling the influence of religious mass-bathing on the riverine ecosystem.
Collapse
Affiliation(s)
- Rakeshkumar Yadav
- National Collection of Industrial Microorganisms (NCIM), CSIR-National Chemical Laboratory (CSIR-NCL), Pune, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
| | - Vinay Rajput
- National Collection of Industrial Microorganisms (NCIM), CSIR-National Chemical Laboratory (CSIR-NCL), Pune, India.
| | - Kushal Gohil
- National Collection of Industrial Microorganisms (NCIM), CSIR-National Chemical Laboratory (CSIR-NCL), Pune, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
| | - Krishna Khairnar
- Environmental Virology Cell (EVC), CSIR- National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur, India.
| | - Mahesh Dharne
- National Collection of Industrial Microorganisms (NCIM), CSIR-National Chemical Laboratory (CSIR-NCL), Pune, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India. http://
| |
Collapse
|
22
|
Swain A, Gnanasekar P, Prava J, Rajeev AC, Kesarwani P, Lahiri C, Pan A. A Comparative Genomics Approach for Shortlisting Broad-Spectrum Drug Targets in Nontuberculous Mycobacteria. Microb Drug Resist 2020; 27:212-226. [PMID: 32936741 DOI: 10.1089/mdr.2020.0161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Many members of nontuberculous mycobacteria (NTM) are opportunistic pathogens causing several infections in animals. The incidence of NTM infections and emergence of drug-resistant NTM strains are rising worldwide, emphasizing the need to develop novel anti-NTM drugs. The present study is aimed to identify broad-spectrum drug targets in NTM using a comparative genomics approach. The study identified 537 core proteins in NTM of which 45 were pathogen specific and essential for the survival of pathogens. Furthermore, druggability analysis indicated that 15 were druggable among those 45 proteins. These 15 proteins, which were core proteins, pathogen-specific, essential, and druggable, were considered as potential broad-spectrum candidates. Based on their locations in cytoplasm and membrane, targets were classified as drug and vaccine targets. The identified 15 targets were different enzymes, carrier proteins, transcriptional regulator, two-component system protein, ribosomal, and binding proteins. The identified targets could further be utilized by researchers to design inhibitors for the discovery of antimicrobial agents.
Collapse
Affiliation(s)
- Aishwarya Swain
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | | | - Jyoti Prava
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Athira C Rajeev
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Pragya Kesarwani
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Chandrajit Lahiri
- Department of Biological Sciences, Sunway University, Petaling Jaya, Malaysia
| | - Archana Pan
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| |
Collapse
|
23
|
Van Wijk RC, van der Sar AM, Krekels EHJ, Verboom T, Spaink HP, Simonsson USH, van der Graaf PH. Quantification of Natural Growth of Two Strains of Mycobacterium Marinum for Translational Antituberculosis Drug Development. Clin Transl Sci 2020; 13:1060-1064. [PMID: 32267997 PMCID: PMC7719371 DOI: 10.1111/cts.12793] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/14/2020] [Indexed: 12/22/2022] Open
Abstract
The zebrafish infected with Mycobacterium marinum (M. marinum) is an attractive tuberculosis disease model, showing similar pathogenesis to Mycobacterium tuberculosis (M. tuberculosis) infections in humans. To translate pharmacological findings from this disease model to higher vertebrates, a quantitative understanding of the natural growth of M. marinum in comparison to the natural growth of M. tuberculosis is essential. Here, the natural growth of two strains of M. marinum, E11 and MUSA, is studied over an extended period using an established model‐based approach, the multistate tuberculosis pharmacometric (MTP) model, for comparison to that of M. tuberculosis. Poikilotherm‐derived strain E11 and human‐derived strain MUSA were grown undisturbed up to 221 days and viability of cultures (colony forming unit (CFU)/mL) was determined by plating at different time points. Nonlinear mixed effects modeling using the MTP model quantified the bacterial growth, the transfer among fast, slow, and non‐multiplying states, and the inoculi. Both strains showed initial logistic growth, reaching a maximum after 20–25 days for E11 and MUSA, respectively, followed by a decrease to a new plateau. Natural growth of both E11 and MUSA was best described with Gompertz growth functions. For E11, the inoculum was best described in the slow‐multiplying state, for MUSA in the fast‐multiplying state. Natural growth of E11 was most similar to that of M. tuberculosis, whereas MUSA showed more aggressive growth behavior. Characterization of natural growth of M. marinum and quantitative comparison with M. tuberculosis brings the zebrafish tuberculosis disease model closer to the quantitative translational pipeline of antituberculosis drug development.
Collapse
Affiliation(s)
- Rob C Van Wijk
- Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Astrid M van der Sar
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
| | - Elke H J Krekels
- Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Theo Verboom
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
| | - Herman P Spaink
- Division of Animal Sciences and Health, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | | | - Piet H van der Graaf
- Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands.,Certara QSP, Canterbury, UK
| |
Collapse
|
24
|
Ivanchenko DA, Hrytsenko LM. In vitro synergy testing of prodigiosin in combination with inhibitors of cell wall synthesis against Mycobacterium smegmatis. REGULATORY MECHANISMS IN BIOSYSTEMS 2020. [DOI: 10.15421/022019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The cell wall is not a target of currently used therapeutics as Mycobacterium are considered naturally resistant to most β-lactam antibiotics. Therefore, combinations of conventional antibiotics with antibiotic activity-enhancing compounds offer a productive treatment strategy and address the widespread emergence of antibiotic-resistant strains. The first area of research was the study of a comparative analysis of disk diffusion testing and the broth dilution method for evaluating the susceptibility of M. smegmatis to antimicrobial agents. A comparative analysis of the susceptibility to antimicrobial agents alone showed that M. smegmatis was the most susceptible to ceftriaxone and kanamycin, and moderately sensitive to vancomycin and prodigiosin. Compared to the susceptibility of the antibacterial combinations, the isolate was not susceptible to antibacterial combinations with prodigiosin in disk diffusion testing. The second area of research was the study of the synergic activity of prodigiosin of S. marcescens and inhibitors of cell wall synthesis manifested by their simultaneous effect on M. smegmatis. The greatest increase in the sensitivity of test-culture of mycobacteria occurred with ampicillin, benzylpenicillin, cephazolin and ceftriaxone in combination with prodigiosin of S. marcescens. The presented combination of antibiotics and prodigiosin reduce the required concentration of the antibiotic and by amplifying the effect of compounds inhibiting cell wall synthesis, thereby giving lower FICI values. These data indicate the possibility of using prodigiosin as a promising candidate for the development of "accompaniment-preparations" for antibiotics for the additional therapy of infectious diseases caused by Mycobacterium spp. and can suspend the likelihood of developing resistance to antibiotics.
The cell wall is not a target of currently used therapeutics as Mycobacterium are considered naturally resistant to most β-lactam antibiotics. Therefore, combinations of conventional antibiotics with antibiotic activity-enhancing compounds offer a productive treatment strategy and address the widespread emergence of antibiotic-resistant strains. The first area of research was the study of a comparative analysis of disk diffusion testing and the broth dilution method for evaluating the susceptibility of M. smegmatis to antimicrobial agents. A comparative analysis of the susceptibility to antimicrobial agents alone showed that M. smegmatis was the most susceptible to ceftriaxone and kanamycin, and moderately sensitive to vancomycin and prodigiosin. Compared to the susceptibility of the antibacterial combinations, the isolate was not susceptible to antibacterial combinations with prodigiosin in disk diffusion testing. The second area of research was the study of the synergic activity of prodigiosin of S. marcescens and inhibitors of cell wall synthesis manifested by their simultaneous effect on M. smegmatis. The greatest increase in the sensitivity of test-culture of mycobacteria occurred with ampicillin, benzylpenicillin, cephazolin and ceftriaxone in combination with prodigiosin of S. marcescens. The presented combination of antibiotics and prodigiosin reduce the required concentration of the antibiotic and by amplifying the effect of compounds inhibiting cell wall synthesis, thereby giving lower FICI values. These data indicate the possibility of using prodigiosin as a promising candidate for the development of "accompaniment-preparations" for antibiotics for the additional therapy of infectious diseases caused by Mycobacterium spp. and can suspend the likelihood of developing resistance to antibiotics.
Collapse
|
25
|
Dual delivery of tuberculosis drugs via cyclodextrin conjugated curdlan nanoparticles to infected macrophages. Carbohydr Polym 2019; 218:53-62. [DOI: 10.1016/j.carbpol.2019.04.056] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/22/2019] [Accepted: 04/15/2019] [Indexed: 01/14/2023]
|
26
|
Mashabela GT, de Wet TJ, Warner DF. Mycobacterium tuberculosis Metabolism. Microbiol Spectr 2019; 7:10.1128/microbiolspec.gpp3-0067-2019. [PMID: 31350832 PMCID: PMC10957194 DOI: 10.1128/microbiolspec.gpp3-0067-2019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Indexed: 02/06/2023] Open
Abstract
Mycobacterium tuberculosis is the cause of tuberculosis (TB), a disease which continues to overwhelm health systems in endemic regions despite the existence of effective combination chemotherapy and the widespread use of a neonatal anti-TB vaccine. For a professional pathogen, M. tuberculosis retains a surprisingly large proportion of the metabolic repertoire found in nonpathogenic mycobacteria with very different lifestyles. Moreover, evidence that additional functions were acquired during the early evolution of the M. tuberculosis complex suggests the organism has adapted (and augmented) the metabolic pathways of its environmental ancestor to persistence and propagation within its obligate human host. A better understanding of M. tuberculosis pathogenicity, however, requires the elucidation of metabolic functions under disease-relevant conditions, a challenge complicated by limited knowledge of the microenvironments occupied and nutrients accessed by bacilli during host infection, as well as the reliance in experimental mycobacteriology on a restricted number of experimental models with variable relevance to clinical disease. Here, we consider M. tuberculosis metabolism within the framework of an intimate host-pathogen coevolution. Focusing on recent advances in our understanding of mycobacterial metabolic function, we highlight unusual adaptations or departures from the better-characterized model intracellular pathogens. We also discuss the impact of these mycobacterial "innovations" on the susceptibility of M. tuberculosis to existing and experimental anti-TB drugs, as well as strategies for targeting metabolic pathways. Finally, we offer some perspectives on the key gaps in the current knowledge of fundamental mycobacterial metabolism and the lessons which might be learned from other systems.
Collapse
Affiliation(s)
- Gabriel T Mashabela
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
- Current address: Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, University of Stellenbosch, South Africa
| | - Timothy J de Wet
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
- Department of Integrative Biomedical Sciences, University of Cape Town, South Africa
| | - Digby F Warner
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
- Wellcome Centre for Infectious Disease Research in Africa, University of Cape Town, South Africa
| |
Collapse
|
27
|
Waman VP, Vedithi SC, Thomas SE, Bannerman BP, Munir A, Skwark MJ, Malhotra S, Blundell TL. Mycobacterial genomics and structural bioinformatics: opportunities and challenges in drug discovery. Emerg Microbes Infect 2019; 8:109-118. [PMID: 30866765 PMCID: PMC6334779 DOI: 10.1080/22221751.2018.1561158] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/03/2018] [Accepted: 12/09/2018] [Indexed: 01/08/2023]
Abstract
Of the more than 190 distinct species of Mycobacterium genus, many are economically and clinically important pathogens of humans or animals. Among those mycobacteria that infect humans, three species namely Mycobacterium tuberculosis (causative agent of tuberculosis), Mycobacterium leprae (causative agent of leprosy) and Mycobacterium abscessus (causative agent of chronic pulmonary infections) pose concern to global public health. Although antibiotics have been successfully developed to combat each of these, the emergence of drug-resistant strains is an increasing challenge for treatment and drug discovery. Here we describe the impact of the rapid expansion of genome sequencing and genome/pathway annotations that have greatly improved the progress of structure-guided drug discovery. We focus on the applications of comparative genomics, metabolomics, evolutionary bioinformatics and structural proteomics to identify potential drug targets. The opportunities and challenges for the design of drugs for M. tuberculosis, M. leprae and M. abscessus to combat resistance are discussed.
Collapse
Affiliation(s)
| | | | | | | | - Asma Munir
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Marcin J. Skwark
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Sony Malhotra
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, UK
| | - Tom L. Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| |
Collapse
|
28
|
Nyinoh IW. Spontaneous mutations conferring antibiotic resistance to antitubercular drugs at a range of concentrations in Mycobacterium smegmatis. Drug Dev Res 2018; 80:147-154. [PMID: 30511362 DOI: 10.1002/ddr.21497] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 11/07/2018] [Accepted: 11/09/2018] [Indexed: 11/06/2022]
Abstract
Mycobacteria populations can undergo mutations in their DNA sequence during replication, which if not repaired would be transferred to future generations. Earlier studies have tackled the estimation of mutation rate in mycobacteria at fixed concentrations. However, in this study, in vitro spontaneous mutations in Mycobacterium smegmatis (Msm) mc2 155 (Msm) that confers resistance to some of the most important antitubercular drugs; isoniazid (INHr ), rifampicin (RIFr ), kanamycin (KANr ) and streptomycin (STRr ) were first determined at several highly lethal concentrations, a few of which have not been previously investigated, in a fluctuation assay. Thereafter, mutation rate was estimated using the most commonly adopted Po method, and estimates were then compared concurrently with the Lea-Coulson method of the median and Ma-Sandri-Sarkar Maximum Likelihood Estimator method available on the Fluctuation AnaLysis CalculatOR (FALCOR). The mutation rates of RIFr ranged from 9.24 × 10-8 to 2.18 × 10-10 , INHr 1.2 × 10-7 -1.20 × 10-9 , STRr 2.77 × 10-8 -5.31 × 10-8 and KANr 1.7 × 10-8 mutations per cell division. Data obtained in this study provide mutation rate estimates to key antitubercular drugs at a range of concentrations while also validating a number of the frequent approaches for estimating mutation rates.
Collapse
Affiliation(s)
- Iveren Winifred Nyinoh
- Department of Biological Sciences, Benue State University, Makurdi, Benue State, Nigeria
| |
Collapse
|
29
|
Vedithi SC, Malhotra S, Das M, Daniel S, Kishore N, George A, Arumugam S, Rajan L, Ebenezer M, Ascher DB, Arnold E, Blundell TL. Structural Implications of Mutations Conferring Rifampin Resistance in Mycobacterium leprae. Sci Rep 2018; 8:5016. [PMID: 29567948 PMCID: PMC5864748 DOI: 10.1038/s41598-018-23423-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/09/2018] [Indexed: 11/09/2022] Open
Abstract
The rpoB gene encodes the β subunit of RNA polymerase holoenzyme in Mycobacterium leprae (M. leprae). Missense mutations in the rpoB gene were identified as etiological factors for rifampin resistance in leprosy. In the present study, we identified mutations corresponding to rifampin resistance in relapsed leprosy cases from three hospitals in southern India which treat leprosy patients. DNA was extracted from skin biopsies of 35 relapse/multidrug therapy non-respondent leprosy cases, and PCR was performed to amplify the 276 bp rifampin resistance-determining region of the rpoB gene. PCR products were sequenced, and mutations were identified in four out of the 35 cases at codon positions D441Y, D441V, S437L and H476R. The structural and functional effects of these mutations were assessed in the context of three-dimensional comparative models of wild-type and mutant M. leprae RNA polymerase holoenzyme (RNAP), based on the recently solved crystal structures of RNAP of Mycobacterium tuberculosis, containing a synthetic nucleic acid scaffold and rifampin. The resistance mutations were observed to alter the hydrogen-bonding and hydrophobic interactions of rifampin and the 5' ribonucleotide of the growing RNA transcript. This study demonstrates that rifampin-resistant strains of M. leprae among leprosy patients in southern India are likely to arise from mutations that affect the drug-binding site and stability of RNAP.
Collapse
Affiliation(s)
- Sundeep Chaitanya Vedithi
- Department of Biochemistry, University of Cambridge, Tennis Court Rd., Cambridge, CB2 1GA, UK. .,Molecular Biology and Immunology Division, Schieffelin Institute of Health Research & Leprosy Center (SIH R & LC), Karigiri, Vellore, Tamil Nadu, 632106, India.
| | - Sony Malhotra
- Department of Biochemistry, University of Cambridge, Tennis Court Rd., Cambridge, CB2 1GA, UK
| | - Madhusmita Das
- Molecular Biology and Immunology Division, Schieffelin Institute of Health Research & Leprosy Center (SIH R & LC), Karigiri, Vellore, Tamil Nadu, 632106, India
| | - Sheela Daniel
- Molecular Biology and Immunology Division, Schieffelin Institute of Health Research & Leprosy Center (SIH R & LC), Karigiri, Vellore, Tamil Nadu, 632106, India
| | - Nanda Kishore
- Department of Dermatology, Father Muller Medical College & Hospital, Mangalore, Karnataka, 575 002, India
| | - Anuja George
- Department of Dermatology, Trivandrum Medical College, Trivandrum, Kerala, 695011, India
| | - Shantha Arumugam
- Molecular Biology and Immunology Division, Schieffelin Institute of Health Research & Leprosy Center (SIH R & LC), Karigiri, Vellore, Tamil Nadu, 632106, India
| | - Lakshmi Rajan
- Molecular Biology and Immunology Division, Schieffelin Institute of Health Research & Leprosy Center (SIH R & LC), Karigiri, Vellore, Tamil Nadu, 632106, India
| | - Mannam Ebenezer
- Molecular Biology and Immunology Division, Schieffelin Institute of Health Research & Leprosy Center (SIH R & LC), Karigiri, Vellore, Tamil Nadu, 632106, India
| | - David B Ascher
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, VIC 3052, Australia
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine (CABM), and Rutgers University Department of Chemistry and Chemical Biology, 679 Hoes Lane, Piscataway, NJ, 08854, USA
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Rd., Cambridge, CB2 1GA, UK.
| |
Collapse
|
30
|
Abstract
Nontuberculous mycobacteria (NTM) include species that colonize human epithelia, as well as species that are ubiquitous in soil and aquatic environments. NTM that primarily inhabit soil and aquatic environments include the Mycobacterium avium complex (MAC, M. avium and Mycobacterium intracellulare) and the Mycobacterium abscessus complex (MABSC, M. abscessus subspecies abscessus, massiliense, and bolletii), and can be free-living, biofilm-associated, or amoeba-associated. Although NTM are rarely pathogenic in immunocompetent individuals, those who are immunocompromised - due to either an inherited or acquired immunodeficiency - are highly susceptible to NTM infection (NTMI). Several characteristics such as biofilm formation and the ability of select NTM species to form distinct colony morphotypes all may play a role in pathogenesis not observed in the related, well-characterized pathogen Mycobacterium tuberculosis The recognition of different morphotypes of NTM has been established and characterized since the 1950s, but the mechanisms that underlie colony phenotype change and subsequent differences in pathogenicity are just beginning to be explored. Advances in genomic analysis have led to progress in identifying genes important to the pathogenesis and persistence of MAC disease as well as illuminating genetic aspects of different colony morphotypes. Here we review recent literature regarding NTM ecology and transmission, as well as the factors which regulate colony morphotype and pathogenicity.
Collapse
Affiliation(s)
- Tiffany A Claeys
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Richard T Robinson
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.
| |
Collapse
|