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Chouhan M, Tiwari PK, Mishra R, Gupta S, Kumar M, Almuqri EA, Ibrahim NA, Basher NS, Chaudhary AA, Dwivedi VD, Verma D, Kumar S. Unearthing phytochemicals as natural inhibitors for pantothenate synthetase in Mycobacterium tuberculosis: A computational approach. Front Pharmacol 2024; 15:1403900. [PMID: 39135797 PMCID: PMC11317409 DOI: 10.3389/fphar.2024.1403900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 06/18/2024] [Indexed: 08/15/2024] Open
Abstract
Pantothenate synthetase protein plays a pivotal role in the biosynthesis of coenzyme A (CoA), which is a crucial molecule involved in a number of cellular processes including the metabolism of fatty acid, energy production, and the synthesis of various biomolecules, which is necessary for the survival of Mycobacterium tuberculosis (Mtb). Therefore, inhibiting this protein could disrupt CoA synthesis, leading to the impairment of vital metabolic processes within the bacterium, ultimately inhibiting its growth and survival. This study employed molecular docking, structure-based virtual screening, and molecular dynamics (MD) simulation to identify promising phytochemical compounds targeting pantothenate synthetase for tuberculosis (TB) treatment. Among 239 compounds, the top three (rutin, sesamin, and catechin gallate) were selected, with binding energy values ranging from -11 to -10.3 kcal/mol, and the selected complexes showed RMSD (<3 Å) for 100 ns MD simulation time. Furthermore, molecular mechanics generalized Born surface area (MM/GBSA) binding free energy calculations affirmed the stability of these three selected phytochemicals with binding energy ranges from -82.24 ± 9.35 to -66.83 ± 4.5 kcal/mol. Hence, these identified natural plant-derived compounds as potential inhibitors of pantothenate synthetase could be used to inhibit TB infection in humans.
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Affiliation(s)
- Mandeep Chouhan
- Biological and Bio-computational Lab, Department of Life Science, School of Basic Sciences and Research, Sharda University, Greater Noida, India
| | - Prashant Kumar Tiwari
- Biological and Bio-computational Lab, Department of Life Science, School of Basic Sciences and Research, Sharda University, Greater Noida, India
| | - Richa Mishra
- Department of Computer Engineering, Parul University, Vadodara, Gujarat, India
| | - Saurabh Gupta
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, India
| | - Mukesh Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Eman Abdullah Almuqri
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Nasir A. Ibrahim
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Nosiba Suliman Basher
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Vivek Dhar Dwivedi
- Center for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
- Bioinformatics Research Division, Quanta Calculus, Greater Noida, India
| | - Devvret Verma
- Department of Biotechnology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand, India
| | - Sanjay Kumar
- Biological and Bio-computational Lab, Department of Life Science, School of Basic Sciences and Research, Sharda University, Greater Noida, India
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Khan MF, Ali A, Rehman HM, Noor Khan S, Hammad HM, Waseem M, Wu Y, Clark TG, Jabbar A. Exploring optimal drug targets through subtractive proteomics analysis and pangenomic insights for tailored drug design in tuberculosis. Sci Rep 2024; 14:10904. [PMID: 38740859 DOI: 10.1038/s41598-024-61752-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 05/09/2024] [Indexed: 05/16/2024] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis, ranks among the top causes of global human mortality, as reported by the World Health Organization's 2022 TB report. The prevalence of M. tuberculosis strains that are multiple and extensive-drug resistant represents a significant barrier to TB eradication. Fortunately, having many completely sequenced M. tuberculosis genomes available has made it possible to investigate the species pangenome, conduct a pan-phylogenetic investigation, and find potential new drug targets. The 442 complete genome dataset was used to estimate the pangenome of M. tuberculosis. This study involved phylogenomic classification and in-depth analyses. Sequential filters were applied to the conserved core genome containing 2754 proteins. These filters assessed non-human homology, virulence, essentiality, physiochemical properties, and pathway analysis. Through these intensive filtering approaches, promising broad-spectrum therapeutic targets were identified. These targets were docked with FDA-approved compounds readily available on the ZINC database. Selected highly ranked ligands with inhibitory potential include dihydroergotamine and abiraterone acetate. The effectiveness of the ligands has been supported by molecular dynamics simulation of the ligand-protein complexes, instilling optimism that the identified lead compounds may serve as a robust basis for the development of safe and efficient drugs for TB treatment, subject to further lead optimization and subsequent experimental validation.
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Affiliation(s)
- Muhammad Fayaz Khan
- Department of Medical Laboratory Technology, The University of Haripur, Haripur, KP, Pakistan
| | - Amjad Ali
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
| | - Sadiq Noor Khan
- Department of Medical Laboratory Technology, The University of Haripur, Haripur, KP, Pakistan
| | - Hafiz Muhammad Hammad
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
| | - Maaz Waseem
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Yurong Wu
- Department of Chemistry, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Taane G Clark
- London School of Hygiene and Tropical Medicine, Keppel Street, London, UK.
| | - Abdul Jabbar
- Department of Medical Laboratory Technology, The University of Haripur, Haripur, KP, Pakistan.
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Naorem RS, Pangabam BD, Bora SS, Goswami G, Barooah M, Hazarika DJ, Fekete C. Identification of Putative Vaccine and Drug Targets against the Methicillin-Resistant Staphylococcus aureus by Reverse Vaccinology and Subtractive Genomics Approaches. Molecules 2022; 27:2083. [PMID: 35408485 PMCID: PMC9000511 DOI: 10.3390/molecules27072083] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 01/23/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is an opportunistic pathogen and responsible for causing life-threatening infections. The emergence of hypervirulent and multidrug-resistant (MDR) S. aureus strains led to challenging issues in antibiotic therapy. Consequently, the morbidity and mortality rates caused by S. aureus infections have a substantial impact on health concerns. The current worldwide prevalence of MRSA infections highlights the need for long-lasting preventive measures and strategies. Unfortunately, effective measures are limited. In this study, we focus on the identification of vaccine candidates and drug target proteins against the 16 strains of MRSA using reverse vaccinology and subtractive genomics approaches. Using the reverse vaccinology approach, 4 putative antigenic proteins were identified; among these, PrsA and EssA proteins were found to be more promising vaccine candidates. We applied a molecular docking approach of selected 8 drug target proteins with the drug-like molecules, revealing that the ZINC4235426 as potential drug molecule with favorable interactions with the target active site residues of 5 drug target proteins viz., biotin protein ligase, HPr kinase/phosphorylase, thymidylate kinase, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-L-lysine ligase, and pantothenate synthetase. Thus, the identified proteins can be used for further rational drug or vaccine design to identify novel therapeutic agents for the treatment of multidrug-resistant staphylococcal infection.
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Affiliation(s)
- Romen Singh Naorem
- Department of General and Environmental Microbiology, Institute of Biology and Sport Biology, University of Pécs, Ifusag utja. 6, 7624 Pecs, Hungary; (R.S.N.); (B.D.P.)
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, India; (M.B.); (D.J.H.)
| | - Bandana Devi Pangabam
- Department of General and Environmental Microbiology, Institute of Biology and Sport Biology, University of Pécs, Ifusag utja. 6, 7624 Pecs, Hungary; (R.S.N.); (B.D.P.)
| | - Sudipta Sankar Bora
- DBT—North East Centre for Agricultural Biotechnology (DBT-AAU Center), Assam Agricultural University, Jorhat 785013, India;
| | - Gunajit Goswami
- Multidisciplinary Research Unit, Jorhat Medical College and Hospital, Jorhat 785008, India;
| | - Madhumita Barooah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, India; (M.B.); (D.J.H.)
- DBT—North East Centre for Agricultural Biotechnology (DBT-AAU Center), Assam Agricultural University, Jorhat 785013, India;
| | - Dibya Jyoti Hazarika
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, India; (M.B.); (D.J.H.)
| | - Csaba Fekete
- Department of General and Environmental Microbiology, Institute of Biology and Sport Biology, University of Pécs, Ifusag utja. 6, 7624 Pecs, Hungary; (R.S.N.); (B.D.P.)
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Zhou W, Yang B, Zou Y, Rahman K, Cao X, Lei Y, Lai R, Fu ZF, Chen X, Cao G. Screening of Compounds for Anti-tuberculosis Activity, and in vitro and in vivo Evaluation of Potential Candidates. Front Microbiol 2021; 12:658637. [PMID: 34276592 PMCID: PMC8278749 DOI: 10.3389/fmicb.2021.658637] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/26/2021] [Indexed: 12/12/2022] Open
Abstract
Tuberculosis (TB) is a debilitating infectious disease responsible for more than one million deaths per year. The emergence of drug-resistant TB poses an urgent need for the development of new anti-TB drugs. In this study, we screened a library of over 4,000 small molecules and found that orbifloxacin and the peptide AK15 possess significant bactericidal activity against Mycobacterium tuberculosis (Mtb) in vitro. Orbifloxacin also showed an effective ability on the clearance of intracellular Mtb and protect mice from a strong inflammatory response but not AK15. Moreover, we identified 17 nucleotide mutations responsible for orbifloxacin resistance by whole-genome sequencing. A critical point mutation (D94G) of the DNA gyrase (gyrA) gene was found to be the key role of resistance to orbifloxacin. The computational docking revealed that GyrA D94G point mutation can disrupt the orbifloxacin–protein gyrase interactions mediated by magnesium ion bridge. Overall, this study indicated the potential ability of orbifloxacin as an anti-tuberculosis drug, which can be used either alone or in combination with first-line antibiotics to achieve more effective therapy on TB.
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Affiliation(s)
- Wei Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Bing Yang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yanyan Zou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Khaista Rahman
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xiaojian Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yingying Lei
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Ren Lai
- Key Laboratory of Animal Models and Human Disease Mechanisms, Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, China
| | - Zhen F Fu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xi Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Bio-Medical Center, Huazhong Agricultural University, Wuhan, China.,Cooperative Innovation Center for Sustainable Pig Production (CICSPPS), Huazhong Agricultural University, Wuhan, China
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Butman HS, Kotzé TJ, Dowd CS, Strauss E. Vitamin in the Crosshairs: Targeting Pantothenate and Coenzyme A Biosynthesis for New Antituberculosis Agents. Front Cell Infect Microbiol 2020; 10:605662. [PMID: 33384970 PMCID: PMC7770189 DOI: 10.3389/fcimb.2020.605662] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 10/23/2020] [Indexed: 01/05/2023] Open
Abstract
Despite decades of dedicated research, there remains a dire need for new drugs against tuberculosis (TB). Current therapies are generations old and problematic. Resistance to these existing therapies results in an ever-increasing burden of patients with disease that is difficult or impossible to treat. Novel chemical entities with new mechanisms of action are therefore earnestly required. The biosynthesis of coenzyme A (CoA) has long been known to be essential in Mycobacterium tuberculosis (Mtb), the causative agent of TB. The pathway has been genetically validated by seminal studies in vitro and in vivo. In Mtb, the CoA biosynthetic pathway is comprised of nine enzymes: four to synthesize pantothenate (Pan) from l-aspartate and α-ketoisovalerate; five to synthesize CoA from Pan and pantetheine (PantSH). This review gathers literature reports on the structure/mechanism, inhibitors, and vulnerability of each enzyme in the CoA pathway. In addition to traditional inhibition of a single enzyme, the CoA pathway offers an antimetabolite strategy as a promising alternative. In this review, we provide our assessment of what appear to be the best targets, and, thus, which CoA pathway enzymes present the best opportunities for antitubercular drug discovery moving forward.
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Affiliation(s)
- Hailey S. Butman
- Department of Chemistry, George Washington University, Washington, DC, United States
| | - Timothy J. Kotzé
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
| | - Cynthia S. Dowd
- Department of Chemistry, George Washington University, Washington, DC, United States
| | - Erick Strauss
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
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Suresh A, Srinivasarao S, Khetmalis YM, Nizalapur S, Sankaranarayanan M, Gowri Chandra Sekhar KV. Inhibitors of pantothenate synthetase of Mycobacterium tuberculosis - a medicinal chemist perspective. RSC Adv 2020; 10:37098-37115. [PMID: 35521286 PMCID: PMC9057165 DOI: 10.1039/d0ra07398a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 09/30/2020] [Indexed: 01/27/2023] Open
Abstract
Tuberculosis (TB), one of the most prevalent infections, is on the rise today. Although there are drugs available in the market to combat this lethal disorder, there are several shortcomings with the current drug regimen, such as prolonged treatment period, drug resistance, high cost, etc. Hence, it is inevitable for the current researchers across the globe to embark on new strategies for TB drug discovery, which will yield highly active low cost drugs with a shorter treatment period. To achieve this, novel strategies need to be adopted to discover new drugs. Pantothenate Synthetase (PS) is one such striking drug target in Mycobacterium tuberculosis (MTB). It was observed that the pantothenate biosynthetic pathway is crucial for the pathogenicity of MTB. Pantothenate is absent in mammals and needs to be obtained from dietary sources. Hence, the pantothenate biosynthesis pathway is an impending target for emerging new therapeutics to treat TB. Worldwide, several approaches have been implemented by researchers in the quest for these inhibitors such as high-throughput screening, simulating the reaction intermediate pantoyl adenylate, use of vibrant combinatorial chemistry, hybridization approach, virtual screening of databases, inhibitors based on the crystal structure of MTB PS, etc. The present review recapitulates current developments in PS inhibitors, important analogues of numerous metabolic intermediates, and newly established inhibitors with innumerable chemical structures.
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Affiliation(s)
- Amaroju Suresh
- Department of Chemistry, Birla Institute of Technology & Science-Pilani Hyderabad Campus, Medchal District Hyderabad-500078 Telangana India +91 40 66303527
| | - Singireddi Srinivasarao
- Department of Chemistry, Birla Institute of Technology & Science-Pilani Hyderabad Campus, Medchal District Hyderabad-500078 Telangana India +91 40 66303527
| | - Yogesh Mahadu Khetmalis
- Department of Chemistry, Birla Institute of Technology & Science-Pilani Hyderabad Campus, Medchal District Hyderabad-500078 Telangana India +91 40 66303527
| | | | - Murugesan Sankaranarayanan
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science-Pilani Pilani Campus Pilani 333031 Rajasthan India
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