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Alam A, Alqarni MH, Alotaibi BS, Khan FR, Alam MS, Aba Alkhayl FF, Alhafi AA, Almutairi TM, Alharbi ZM, Alshehri FF. Cheminformatics-enhanced discovery of therapeutic agents targeting isocitrate lyase in Mycobacterium tuberculosis infections. J Biomol Struct Dyn 2024:1-18. [PMID: 39295212 DOI: 10.1080/07391102.2024.2404145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/22/2024] [Indexed: 09/21/2024]
Abstract
Tuberculosis (TB) is a global health challenge; therefore, there is an urgent requirement to develop a novel and more effective anti-TB therapeutic. This study targeted the isocitrate lyase (ICL) protein due to its pivotal role in the pathogenicity of Mycobacterium tuberculosis (Mtb). Virtual screening of 8752 bioactive compounds used an ML-based QSAR model and molecular docking. ADMET testing was performed on the top three hits to identify the compound most closely mimicking a drug molecule. The top hits, 648 and 2785758, showed high binding affinity towards ICL with -7.3 and -7 kcal/mol, comparable to the control. These molecules also showed strong binding with the residue Asp108, which plays a vital role in ICL activity. Molecular dynamics simulations showed stability for 648 and 2785758, comparable to the control compound used in this study. It was found that 648 bound to the protein maintained the RMSD constant and consistent at 0.3 nm for a complete 100 ns simulation. 2785758 showed a comparable RMSD trend to the control. Both 648 and 2785758 showed high RMSF for critical residue Asp108. Further, PCA and FEL confirmed the formation of a stable complex. MM/GBSA estimations of binding free energy indicated that compounds 648 had an elevated level of stability (ΔGTOTAL = -28.11 kcal/mol) and 2785758 (ΔGTOTAL = -21.05 kcal/mol). This study suggests that compounds 648 and 2785758 can potentially affect the activity of ICL, leading to its inactivation and ultimately preventing the progression of tuberculosis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aftab Alam
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Mohammed H Alqarni
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Bader S Alotaibi
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Farhan R Khan
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Md Shamsher Alam
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Faris F Aba Alkhayl
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Ali A Alhafi
- Department of Pharmaceutical Sciences, College of Pharmacy, Shaqra University, Al-Dawadmi, Saudi Arabia
| | - Turki M Almutairi
- Department of Pharmaceutical Sciences, College of Pharmacy, Shaqra University, Al-Dawadmi, Saudi Arabia
| | - Zeyad M Alharbi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Faez Falah Alshehri
- Department of Medical Laboratories, College of Applied Medical Sciences, Shaqra University, Ad Dawadimi, Saudi Arabia
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2
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Gao Y, Shang B, He Y, Deng W, Wang L, Sui S. The mechanism of Gejie Zhilao Pill in treating tuberculosis based on network pharmacology and molecular docking verification. Front Cell Infect Microbiol 2024; 14:1405627. [PMID: 39015338 PMCID: PMC11250621 DOI: 10.3389/fcimb.2024.1405627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 06/17/2024] [Indexed: 07/18/2024] Open
Abstract
Introduction Gejie Zhilao Pill (GJZLP), a traditional Chinese medicine formula is known for its unique therapeutic effects in treating pulmonary tuberculosis. The aim of this study is to further investigate its underlying mechanisms by utilizing network pharmacology and molecular docking techniques. Methods Using TCMSP database the components, potential targets of GJZLP were identified. Animal-derived components were supplemented through the TCMID and BATMAN-TCM databases. Tuberculosis-related targets were collected from the TTD, OMIM, and GeneCards databases. The intersection target was imported into the String database to build the PPI network. The Metascape platform was employed to carry out Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Heatmaps were generated through an online platform (https://www.bioinformatics.com.cn). Molecular docking was conducted between the core targets and core compounds to explore their binding strengths and patterns at the molecular level. Results 61 active ingredients and 118 therapeutic targets were identified. Quercetin, Luteolin, epigallocatechin gallate, and beta-sitosterol showed relatively high degrees in the network. IL6, TNF, JUN, TP53, IL1B, STAT3, AKT1, RELA, IFNG, and MAPK3 are important core targets. GO and KEGG revealed that the effects of GJZLP on tuberculosis mainly involve reactions to bacterial molecules, lipopolysaccharides, and cytokine stimulation. Key signaling pathways include TNF, IL-17, Toll-like receptor and C-type lectin receptor signaling. Molecular docking analysis demonstrated a robust binding affinity between the core compounds and the core proteins. Stigmasterol exhibited the lowest binding energy with AKT1, indicating the most stable binding interaction. Discussion This study has delved into the efficacious components and molecular mechanisms of GJZLP in treating tuberculosis, thereby highlighting its potential as a promising therapeutic candidate for the treatment of tuberculosis.
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Affiliation(s)
- Yuhui Gao
- Emergency Department, The Second Affiliated Hospital, Dalian Medical University, Dalian, Liaoning, China
| | - Bingbing Shang
- Emergency Department, The Second Affiliated Hospital, Dalian Medical University, Dalian, Liaoning, China
| | - Yanyao He
- Research and Teaching Department of Comparative Medicine, Dalian Medical University, Dalian, Liaoning, China
| | - Wen Deng
- Research and Teaching Department of Comparative Medicine, Dalian Medical University, Dalian, Liaoning, China
| | - Liang Wang
- Research and Teaching Department of Comparative Medicine, Dalian Medical University, Dalian, Liaoning, China
| | - Shaoguang Sui
- Emergency Department, The Second Affiliated Hospital, Dalian Medical University, Dalian, Liaoning, China
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3
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Mi J, Wu X, Liang J. The advances in adjuvant therapy for tuberculosis with immunoregulatory compounds. Front Microbiol 2024; 15:1380848. [PMID: 38966394 PMCID: PMC11222340 DOI: 10.3389/fmicb.2024.1380848] [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: 02/02/2024] [Accepted: 06/10/2024] [Indexed: 07/06/2024] Open
Abstract
Tuberculosis (TB) is a chronic bacterial disease, as well as a complex immune disease. The occurrence, development, and prognosis of TB are not only related to the pathogenicity of Mycobacterium tuberculosis (Mtb), but also related to the patient's own immune state. The research and development of immunotherapy drugs can effectively regulate the body's anti-TB immune responses, inhibit or eliminate Mtb, alleviate pathological damage, and facilitate rehabilitation. This paper reviews the research progress of immunotherapeutic compounds for TB, including immunoregulatory compounds and repurposing drugs, and points out the existing problems and future research directions, which lays the foundation for studying new agents for host-directed therapies of TB.
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Affiliation(s)
- Jie Mi
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Institute of Tuberculosis Research, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China
| | - Xueqiong Wu
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Institute of Tuberculosis Research, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China
| | - Jianqin Liang
- Department of Tuberculosis, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China
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4
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Niculescu AG, Mük GR, Avram S, Vlad IM, Limban C, Nuta D, Grumezescu AM, Chifiriuc MC. Novel strategies based on natural products and synthetic derivatives to overcome resistance in Mycobacterium tuberculosis. Eur J Med Chem 2024; 269:116268. [PMID: 38460268 DOI: 10.1016/j.ejmech.2024.116268] [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: 12/27/2023] [Revised: 02/09/2024] [Accepted: 02/18/2024] [Indexed: 03/11/2024]
Abstract
One of the biggest health challenges of today's world is the emergence of antimicrobial resistance (AMR), which renders conventional therapeutics insufficient and urgently demands the generation of novel antimicrobial strategies. Mycobacterium tuberculosis (M. tuberculosis), the pathogen causing tuberculosis (TB), is among the most successful bacteria producing drug-resistant infections. The versatility of M. tuberculosis allows it to evade traditional anti-TB agents through various acquired and intrinsic mechanisms, rendering TB among the leading causes of infectious disease-related mortality. In this context, researchers worldwide focused on establishing novel approaches to address drug resistance in M. tuberculosis, developing diverse alternative treatments with varying effectiveness and in different testing phases. Overviewing the current progress, this paper aims to briefly present the mechanisms involved in M. tuberculosis drug-resistance, further reviewing in more detail the under-development antibiotics, nanotechnological approaches, and natural therapeutic solutions that promise to overcome current treatment limitations.
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Affiliation(s)
- Adelina-Gabriela Niculescu
- Research Institute of the University of Bucharest, University of Bucharest, 90 Panduri Road, Bucharest, Romania; Department of Science and Engineering of Oxide Materials and Nanomaterials, National University of Science and Technology Politehnica Bucharest, 011061, Bucharest, Romania.
| | - Georgiana Ramona Mük
- Faculty of Biology, University of Bucharest, Splaiul Independenței 91-95, Bucharest, R-050095, Romania; St. Stephen's Pneumoftiziology Hospital, Șoseaua Ștefan cel Mare 11, Bucharest, 020122, Romania.
| | - Speranta Avram
- Faculty of Biology, University of Bucharest, Splaiul Independenței 91-95, Bucharest, R-050095, Romania.
| | - Ilinca Margareta Vlad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, 6 Traian Vuia, 020956, Bucharest, Romania.
| | - Carmen Limban
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, 6 Traian Vuia, 020956, Bucharest, Romania.
| | - Diana Nuta
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, 6 Traian Vuia, 020956, Bucharest, Romania.
| | - Alexandru Mihai Grumezescu
- Research Institute of the University of Bucharest, University of Bucharest, 90 Panduri Road, Bucharest, Romania; Department of Science and Engineering of Oxide Materials and Nanomaterials, National University of Science and Technology Politehnica Bucharest, 011061, Bucharest, Romania.
| | - Mariana-Carmen Chifiriuc
- Research Institute of the University of Bucharest, University of Bucharest, 90 Panduri Road, Bucharest, Romania; Faculty of Biology, University of Bucharest, Splaiul Independenței 91-95, Bucharest, R-050095, Romania.
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5
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Rana HK, Singh AK, Kumar R, Pandey AK. Antitubercular drugs: possible role of natural products acting as antituberculosis medication in overcoming drug resistance and drug-induced hepatotoxicity. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:1251-1273. [PMID: 37665346 DOI: 10.1007/s00210-023-02679-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/16/2023] [Indexed: 09/05/2023]
Abstract
Mycobacterium tuberculosis (Mtb) is a pathogenic bacterium which causes tuberculosis (TB). TB control programmes are facing threats from drug resistance. Multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mtb strains need longer and more expensive treatment with many medications resulting in more adverse effects and decreased chances of treatment outcomes. The World Health Organization (WHO) has emphasised the development of not just new individual anti-TB drugs, but also novel medication regimens as an alternative treatment option for the drug-resistant Mtb strains. Many plants, as well as marine creatures (sponge; Haliclona sp.) and fungi, have been continuously used to treat TB in various traditional treatment systems around the world, providing an almost limitless supply of active components. Natural products, in addition to their anti-mycobacterial action, can be used as adjuvant therapy to increase the efficacy of conventional anti-mycobacterial medications, reduce their side effects, and reverse MDR Mtb strain due to Mycobacterium's genetic flexibility and environmental adaptation. Several natural compounds such as quercetin, ursolic acid, berberine, thymoquinone, curcumin, phloretin, and propolis have shown potential anti-mycobacterial efficacy and are still being explored in preclinical and clinical investigations for confirmation of their efficacy and safety as anti-TB medication. However, more high-level randomized clinical trials are desperately required. The current review provides an overview of drug-resistant TB along with the latest anti-TB medications, drug-induced hepatotoxicity and oxidative stress. Further, the role and mechanisms of action of first and second-line anti-TB drugs and new drugs have been highlighted. Finally, the role of natural compounds as anti-TB medication and hepatoprotectants have been described and their mechanisms discussed.
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Affiliation(s)
- Harvesh Kumar Rana
- Department of Biochemistry, University of Allahabad, Prayagraj (Allahabad), 211002, India
- Department of Zoology, Feroze Gandhi College, Raebareli, 229001, India
| | - Amit Kumar Singh
- Department of Biochemistry, University of Allahabad, Prayagraj (Allahabad), 211002, India
- Department of Botany, BMK Government. Girls College, Balod, Chhattisgarh, 491226, India
| | - Ramesh Kumar
- Department of Biochemistry, University of Allahabad, Prayagraj (Allahabad), 211002, India
- Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, 151401, India
| | - Abhay K Pandey
- Department of Biochemistry, University of Allahabad, Prayagraj (Allahabad), 211002, India.
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Zhao T, Zhang Y, Liu L, Deng X, Guo J, Cao S, Zhu D, Xu J, Nikolaevna UV, Maratbek S, Wang Z, Sun Z, Gu X, Zhang H. Systemic Pharmacology Reveals the Potential Targets and Signaling Mechanisms in the Adjuvant Treatment of Brucellosis with Traditional Chinese Medicine. ACS OMEGA 2023; 8:28797-28812. [PMID: 37576692 PMCID: PMC10413447 DOI: 10.1021/acsomega.3c03716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/19/2023] [Indexed: 08/15/2023]
Abstract
Human brucellosis is one of the world's most common zoonoses, caused by Brucella infection and characterized by induced inflammation, which in severe cases can lead to abortion and sterility in humans and animals. There is growing evidence that traditional Chinese medicine (TCM) is beneficial as an adjunct to the treatment of brucellosis. However, its specific targets of action and molecular mechanisms remain unclear. In this study, a systematic pharmacological approach was applied to demonstrate pharmacological targets, biological functions, and signaling pathways of TCM as an adjunct to the treatment of brucellosis (TCMTB). The results of network pharmacology were further verified by in vitro experiments. Network analysis revealed that 133 active ingredients and 247 targets were screened in TCMTB. Further data analysis identified 21 core targets and 5 core compounds in TCMTB, including beta-sitosterol, quercetin, kaempferol, luteolin, and paeoniflorin. Gene ontology and the Kyoto Encyclopedia of Gene and Genome analysis showed that TCMTB might actively treat brucellosis by regulating inflammatory response, enhancing immune function, and targeting signaling pathways such as tuberculosis and TNF. Molecular docking results showed that multiple compounds could bind to multiple targets. Further, in vitro experiments confirmed that quercetin, among the active compounds screened, induced the strongest immunomodulatory and pro-inflammatory cytokine production during Brucella abortus infection. Further, quercetin induced nitric oxide production, which attenuated the ability of B. abortus to internalize THP-1 cells as well as intracellular survival. This study reveals the mechanism by which TCMTB aids in the treatment of brucellosis through a synergistic multicomponent, multipathway, and multitarget action. The contribution of quercetin treatment to B. abortus infection was demonstrated for the first time, which may be related to the quercetin-induced production of nitric oxide and immunomodulatory and inflammatory cytokines. These predictions of the core compounds and targets may be used in the future for the clinical treatment of brucellosis.
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Affiliation(s)
- Tianyi Zhao
- State
International Joint Research Center for Animal Health Breeding, College
of Animal Science and Technology, Shihezi
University, Shihezi, Xinjiang 832003, China
| | - Yu Zhang
- State
International Joint Research Center for Animal Health Breeding, College
of Animal Science and Technology, Shihezi
University, Shihezi, Xinjiang 832003, China
| | - Liangbo Liu
- State
International Joint Research Center for Animal Health Breeding, College
of Animal Science and Technology, Shihezi
University, Shihezi, Xinjiang 832003, China
| | - Xingmei Deng
- State
International Joint Research Center for Animal Health Breeding, College
of Animal Science and Technology, Shihezi
University, Shihezi, Xinjiang 832003, China
| | - Jia Guo
- State
International Joint Research Center for Animal Health Breeding, College
of Animal Science and Technology, Shihezi
University, Shihezi, Xinjiang 832003, China
| | - Shuzhu Cao
- State
International Joint Research Center for Animal Health Breeding, College
of Animal Science and Technology, Shihezi
University, Shihezi, Xinjiang 832003, China
| | - Dexin Zhu
- State
International Joint Research Center for Animal Health Breeding, College
of Animal Science and Technology, Shihezi
University, Shihezi, Xinjiang 832003, China
| | - Jian Xu
- Herbivorous
Animal Bacterial Disease Innovation Team, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural
Sciences, Lanzhou, Gansu 730046, China
| | - Usevich Vera Nikolaevna
- State
International Joint Research Center for Animal Health Breeding, College
of Animal Science and Technology, Shihezi
University, Shihezi, Xinjiang 832003, China
- College
of Veterinary, Ural State Agricultural University, Yekaterinburg 620000, Russia
| | - Suleimenov Maratbek
- State
International Joint Research Center for Animal Health Breeding, College
of Animal Science and Technology, Shihezi
University, Shihezi, Xinjiang 832003, China
- College
of Veterinary, Kazakh National Agricultural
University, Nur Sultan 050001, Kazakhstan
| | - Zhen Wang
- State
International Joint Research Center for Animal Health Breeding, College
of Animal Science and Technology, Shihezi
University, Shihezi, Xinjiang 832003, China
| | - Zhihua Sun
- State
International Joint Research Center for Animal Health Breeding, College
of Animal Science and Technology, Shihezi
University, Shihezi, Xinjiang 832003, China
| | - Xinli Gu
- State
International Joint Research Center for Animal Health Breeding, College
of Animal Science and Technology, Shihezi
University, Shihezi, Xinjiang 832003, China
| | - Hui Zhang
- State
International Joint Research Center for Animal Health Breeding, College
of Animal Science and Technology, Shihezi
University, Shihezi, Xinjiang 832003, China
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7
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Siddiqui AJ, Kumar V, Jahan S, Alshahrani MM, Al Awadh AA, Siddiqui MA, Hamadou WS, Abdelgadir A, Saxena J, Badraoui R, Snoussi M, Adnan M. Computational insight into structural basis of human ELOVL1 inhibition. Comput Biol Med 2023; 157:106786. [PMID: 36924735 DOI: 10.1016/j.compbiomed.2023.106786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 02/17/2023] [Accepted: 03/10/2023] [Indexed: 03/13/2023]
Abstract
Very long-chain fatty acids (VLCFAs) play a direct role in the development of a neurological disorder, X-linked adrenoleukodystrophy (X-ALD). Since ELOVL1 catalyzes the rate-limiting step of the synthesis of VLCFAs, it has emerged as an attractive target for the treatment of X-ALD. Recently two potent inhibitors, compound 22 (C22) and compound 27 (C27) have been reported to specifically inhibit human ELOVL1 but their structural basis of inhibition has not been explored. In the present study, we have used a homology model of human ELOVL1 to deduce the binding site and binding modes of C22 and C27. We have employed computational approaches to characterize the binding of C22 and C27. Initially, binding of hexacosanoyl-CoA (C26:0-CoA) to ELOVL1 was modelled and further validated by molecular dynamics (MD) simulation. We observed that the fatty acid tail of C26: CoA protrudes from a unique opening located at the occluded end of ELOVL1. Structural comparison of ELOVL1 with the crystal structure of ELOVL7 revealed that the unique opening was not present in human ELOVL7. Combined blind and focused molecular docking approaches revealed that C22 and C27 exhibit favourable binding in the same unique opening. Further, MD simulations and free binding energy calculations confirmed that C22 and C27 maintain the favourable binding in the unique opening of ELOVL1. Overall, our findings suggest that selective human ELOVL1 inhibitors block the binding of long tails of VLCFAs near the occluded end of ELOVL1. Present study will be helpful in the discovery and design of novel, selective and potent inhibitors of human ELOVL1.
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Affiliation(s)
- Arif Jamal Siddiqui
- Department of Biology, College of Science, University of Ha'il, Ha'il, P.O. Box 2440, Saudi Arabia; Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha'il, Ha'il, P O Box 2440, Saudi Arabia.
| | - Vikash Kumar
- JeevikaSilicoBio, Lucknow, Uttar Pradesh, 226014, India.
| | - Sadaf Jahan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, 11952, Saudi Arabia.
| | - Mohammed Merae Alshahrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, 1988, Najran, 61441, Saudi Arabia.
| | - Ahmed Abdullah Al Awadh
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, 1988, Najran, 61441, Saudi Arabia.
| | - Maqsood Ahmed Siddiqui
- Department of Zoology, College of Science, King Saud University, P.O. Box: 2455, Riyadh, 11451, Saudi Arabia.
| | - Walid Sabri Hamadou
- Department of Biology, College of Science, University of Ha'il, Ha'il, P.O. Box 2440, Saudi Arabia; Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha'il, Ha'il, P O Box 2440, Saudi Arabia.
| | - Abdelmushin Abdelgadir
- Department of Biology, College of Science, University of Ha'il, Ha'il, P.O. Box 2440, Saudi Arabia; Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha'il, Ha'il, P O Box 2440, Saudi Arabia.
| | - Juhi Saxena
- Department of Biotechnology, University Institute of Biotechnology, Chandigarh University, Gharuan, NH- 95, Ludhiana - Chandigarh State Hwy, Punjab, 140413, India.
| | - Riadh Badraoui
- Department of Biology, College of Science, University of Ha'il, Ha'il, P.O. Box 2440, Saudi Arabia; Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha'il, Ha'il, P O Box 2440, Saudi Arabia.
| | - Mejdi Snoussi
- Department of Biology, College of Science, University of Ha'il, Ha'il, P.O. Box 2440, Saudi Arabia; Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha'il, Ha'il, P O Box 2440, Saudi Arabia.
| | - Mohd Adnan
- Department of Biology, College of Science, University of Ha'il, Ha'il, P.O. Box 2440, Saudi Arabia; Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha'il, Ha'il, P O Box 2440, Saudi Arabia.
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8
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Jiang Y, Zhang JX, Liu R. Systematic comparison of differential expression networks in MTB mono-, HIV mono- and MTB/HIV co-infections for drug repurposing. PLoS Comput Biol 2022; 18:e1010744. [PMID: 36534703 PMCID: PMC9810203 DOI: 10.1371/journal.pcbi.1010744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 01/03/2023] [Accepted: 11/17/2022] [Indexed: 12/24/2022] Open
Abstract
The synergy between human immunodeficiency virus (HIV) and Mycobacterium tuberculosis (MTB) could accelerate the deterioration of immunological functions. Previous studies have explored the pathogenic mechanisms of HIV mono-infection (HMI), MTB mono-infection (MMI) and MTB/HIV co-infection (MHCI), but their similarities and specificities remain to be profoundly investigated. We thus designed a computational framework named IDEN to identify gene pairs related to these states, which were then compared from different perspectives. MMI-related genes showed the highest enrichment level on a greater number of chromosomes. Genes shared by more states tended to be more evolutionarily conserved, posttranslationally modified and topologically important. At the expression level, HMI-specific gene pairs yielded higher correlations, while the overlapping pairs involved in MHCI had significantly lower correlations. The correlation changes of common gene pairs showed that MHCI shared more similarities with MMI. Moreover, MMI- and MHCI-related genes were enriched in more identical pathways and biological processes, further illustrating that MTB may play a dominant role in co-infection. Hub genes specific to each state could promote pathogen infections, while those shared by two states could enhance immune responses. Finally, we improved the network proximity measure for drug repurposing by considering the importance of gene pairs, and approximately ten drug candidates were identified for each disease state.
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Affiliation(s)
- Yao Jiang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China
| | - Jia-Xuan Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China
| | - Rong Liu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China
- * E-mail:
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9
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Parwani D, Bhattacharya S, Rathore A, Mallick C, Asati V, Agarwal S, Rajoriya V, Das R, Kashaw SK. Current Insights into the Chemistry and Antitubercular Potential of Benzimidazole and Imidazole Derivatives. Mini Rev Med Chem 2021; 21:643-657. [PMID: 33138762 DOI: 10.2174/1389557520666201102094401] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/27/2020] [Accepted: 09/09/2020] [Indexed: 11/22/2022]
Abstract
Tuberculosis is a disease caused by Mycobacterium tuberculosis (Mtb), affecting millions of people worldwide. The emergence of drug resistance is a major problem in the successful treatment of tuberculosis. Due to the commencement of MDR-TB (multi-drug resistance) and XDR-TB (extensively drug resistance), there is a crucial need for the development of novel anti-tubercular agents with improved characteristics such as low toxicity, enhanced inhibitory activity and short duration of treatment. In this direction, various heterocyclic compounds have been synthesized and screened against Mycobacterium tuberculosis. Among them, benzimidazole and imidazole containing derivatives have been found to have potential anti-tubercular activity. The present review focuses on various imidazole and benzimidazole derivatives (from 2015-2019) with their structure-activity relationships in the treatment of tuberculosis.
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Affiliation(s)
- Deepa Parwani
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar (MP), India
| | - Sushanta Bhattacharya
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar (MP), India
| | - Akash Rathore
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar (MP), India
| | - Chaitali Mallick
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar (MP), India
| | - Vivek Asati
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar (MP), India
| | - Shivangi Agarwal
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar (MP), India
| | - Vaibhav Rajoriya
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar (MP), India
| | - Ratnesh Das
- Department of Chemistry, Dr. Harisingh Gour University (A Central University), Sagar (MP), India
| | - Sushil Kumar Kashaw
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar (MP), India
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10
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Demystifying the catalytic pathway of Mycobacterium tuberculosis isocitrate lyase. Sci Rep 2020; 10:18925. [PMID: 33144641 PMCID: PMC7609661 DOI: 10.1038/s41598-020-75799-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 10/07/2020] [Indexed: 02/04/2023] Open
Abstract
Pulmonary tuberculosis, caused by Mycobacterium tuberculosis, is one of the most persistent diseases leading to death in humans. As one of the key targets during the latent/dormant stage of M. tuberculosis, isocitrate lyase (ICL) has been a subject of interest for new tuberculosis therapeutics. In this work, the cleavage of the isocitrate by M. tuberculosis ICL was studied using quantum mechanics/molecular mechanics method at M06-2X/6-31+G(d,p): AMBER level of theory. The electronic embedding approach was applied to provide a better depiction of electrostatic interactions between MM and QM regions. Two possible pathways (pathway I that involves Asp108 and pathway II that involves Glu182) that could lead to the metabolism of isocitrate was studied in this study. The results suggested that the core residues involved in isocitrate catalytic cleavage mechanism are Asp108, Cys191 and Arg228. A water molecule bonded to Mg2+ acts as the catalytic base for the deprotonation of isocitrate C(2)–OH group, while Cys191 acts as the catalytic acid. Our observation suggests that the shuttle proton from isocitrate hydroxyl group C(2) atom is favourably transferred to Asp108 instead of Glu182 with a lower activation energy of 6.2 kcal/mol. Natural bond analysis also demonstrated that pathway I involving the transfer of proton to Asp108 has a higher intermolecular interaction and charge transfer that were associated with higher stabilization energy. The QM/MM transition state stepwise catalytic mechanism of ICL agrees with the in vitro enzymatic assay whereby Asp108Ala and Cys191Ser ICL mutants lost their isocitrate cleavage activities.
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11
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Sartor P, Bock J, Hennecke U, Thierbach S, Fetzner S. Modification of the Pseudomonas aeruginosa toxin 2-heptyl-1-hydroxyquinolin-4(1H)-one and other secondary metabolites by methyltransferases from mycobacteria. FEBS J 2020; 288:2360-2376. [PMID: 33064871 DOI: 10.1111/febs.15595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 09/22/2020] [Accepted: 10/12/2020] [Indexed: 11/26/2022]
Abstract
The opportunistic pathogen Pseudomonas aeruginosa, one of the most prevalent species in infections of the cystic fibrosis lung, produces a range of secondary metabolites, among them the respiratory toxin 2-heptyl-1-hydroxyquinolin-4(1H)-one (2-heptyl-4-hydroxyquinoline N-oxide, HQNO). Cultures of the emerging cystic fibrosis pathogen Mycobacteroides abscessus detoxify HQNO by methylating the N-hydroxy moiety. In this study, the class I methyltransferase MAB_2834c and its orthologue from Mycobacterium tuberculosis, Rv0560c, were identified as HQNO O-methyltransferases. The P. aeruginosa exoproducts 4-hydroxyquinolin-2(1H)-one (DHQ), 2-heptylquinolin-4(1H)-one (HHQ), and 2-heptyl-3-hydroxyquinolin-4(1H)-one (the 'Pseudomonas quinolone signal', PQS), some structurally related (iso)quinolones, and the flavonol quercetin were also methylated; however, HQNO was by far the preferred substrate. Both enzymes converted a benzimidazole[1,2-a]pyridine-4-carbonitrile-based compound, representing the scaffold of antimycobacterial substances, to an N-methylated derivative. We suggest that these promiscuous methyltransferases, newly termed as heterocyclic toxin methyltransferases (Htm), are involved in cellular response to chemical stress and possibly contribute to resistance of mycobacteria toward antimicrobial natural compounds as well as drugs. Thus, synthetic antimycobacterial agents may be designed to be unamenable to methyl transfer. ENZYMES: S-adenosyl-l-methionine:2-heptyl-1-hydroxyquinolin-4(1H)-one O-methyl-transferase, EC 2.1.1.
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Affiliation(s)
- Pascal Sartor
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Germany
| | - Jonathan Bock
- Organic Chemistry Research Group, Department of Chemistry and Department of Bioengineering Sciences, Vrije Universiteit Brussels, Belgium
| | - Ulrich Hennecke
- Organic Chemistry Research Group, Department of Chemistry and Department of Bioengineering Sciences, Vrije Universiteit Brussels, Belgium
| | - Sven Thierbach
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Germany
| | - Susanne Fetzner
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Germany
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12
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Maiolini M, Gause S, Taylor J, Steakin T, Shipp G, Lamichhane P, Deshmukh B, Shinde V, Bishayee A, Deshmukh RR. The War against Tuberculosis: A Review of Natural Compounds and Their Derivatives. Molecules 2020; 25:molecules25133011. [PMID: 32630150 PMCID: PMC7412169 DOI: 10.3390/molecules25133011] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/12/2022] Open
Abstract
Tuberculosis (TB), caused by the bacterial organism Mycobacterium tuberculosis, pose a major threat to public health, especially in middle and low-income countries. Worldwide in 2018, approximately 10 million new cases of TB were reported to the World Health Organization (WHO). There are a limited number of medications available to treat TB; additionally, multi-drug resistant TB and extensively-drug resistant TB strains are becoming more prevalent. As a result of various factors, such as increased costs of developing new medications and adverse side effects from current medications, researchers continue to evaluate natural compounds for additional treatment options. These substances have the potential to target bacterial cell structures and may contribute to successful treatment. For example, a study reported that green and black tea, which contains epigallocatechin gallate (a phenolic antioxidant), may decrease the risk of contracting TB in experimental subjects; cumin (a seed from the parsley plant) has been demonstrated to improve the bioavailability of rifampicin, an important anti-TB medication, and propolis (a natural substance produced by honeybees) has been shown to improve the binding affinity of anti-TB medications to bacterial cell structures. In this article, we review the opportunistic pathogen M. tuberculosis, various potential therapeutic targets, available therapies, and natural compounds that may have anti-TB properties. In conclusion, different natural compounds alone as well as in combination with already approved medication regimens should continue to be investigated as treatment options for TB.
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Affiliation(s)
- Morgan Maiolini
- School of Pharmacy, Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA; (M.M.); (S.G.); (J.T.); (T.S.)
| | - Stacey Gause
- School of Pharmacy, Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA; (M.M.); (S.G.); (J.T.); (T.S.)
| | - Jerika Taylor
- School of Pharmacy, Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA; (M.M.); (S.G.); (J.T.); (T.S.)
| | - Tara Steakin
- School of Pharmacy, Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA; (M.M.); (S.G.); (J.T.); (T.S.)
| | - Ginger Shipp
- Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA;
| | - Purushottam Lamichhane
- School of Dental Medicine, Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA;
| | - Bhushan Deshmukh
- Department of Chemistry, Kavayitri Bahinabai Chaudhari North Maharashtra University, Jalgaon 425 001, Maharashtra, India;
| | - Vaibhav Shinde
- Department of Pharmacognosy, Poona College of Pharmacy, Bharati Vidyapeeth (Deemed to be University), Pune-411 038, Maharashtra, India;
| | - Anupam Bishayee
- Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA;
- Correspondence: or (A.B.); (R.R.D.); Tel.: +1-941-782-5950 (A.B.); +1-941-782-5646 (R.R.D.)
| | - Rahul R. Deshmukh
- Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA;
- Correspondence: or (A.B.); (R.R.D.); Tel.: +1-941-782-5950 (A.B.); +1-941-782-5646 (R.R.D.)
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Allosteric inhibition and kinetic characterization of Klebsiella pneumoniae CysE: An emerging drug target. Int J Biol Macromol 2019; 151:1240-1249. [PMID: 31751684 DOI: 10.1016/j.ijbiomac.2019.10.170] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 10/22/2019] [Accepted: 10/22/2019] [Indexed: 12/31/2022]
Abstract
The emergence and spread of multidrug-resistant strains of Klebsiella pneumoniae is a major concern that necessitates the development of unique therapeutics. The essential requirement of serine acetyltransferase (SAT/CysE) for survival of several human pathogens makes it a very promising target for inhibitor designing and drug discovery. In this study, as an initial step to structure-based drug discovery, CysE from K. pneumonia was structurally and biochemically characterized. Subsequently, blind docking of selected natural products into the X-ray crystallography determined 3D structure of the target was carried out. Experimental validation of the inhibitory potential of the top-scorers established quercetin as an uncompetitive inhibitor of Kpn CysE. Molecular dynamics simulations carried out to elucidate the binding mode of quercetin reveal that this small molecule binds at the trimer-trimer interface of hexameric CysE, a site physically distinct from the active site of the enzyme. Detailed analysis of conformational differences incurred in Kpn CysE structure on binding to quercetin provides mechanistic understanding of allosteric modulation. Binding of quercetin to CysE leads to conformation changes in the active site loops and proximal loops that affect its internal dynamics and consequently its affinity for substrate/co-factor binding, justifying the reduced enzyme activity.
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14
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Zhang H, Pan J, Wu X, Zuo AR, Wei Y, Ji ZL. Large-Scale Target Identification of Herbal Medicine Using a Reverse Docking Approach. ACS OMEGA 2019; 4:9710-9719. [PMID: 31460061 PMCID: PMC6648299 DOI: 10.1021/acsomega.9b00020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 04/17/2019] [Indexed: 06/10/2023]
Abstract
Herbal medicine has been used to countermine various diseases for centuries. However, most of the therapeutic targets underlying herbal therapy remain unclear, which largely slow down the novel drug discovery process from natural products. In this study, we developed a novel computational pipeline for assisting de novo identification of protein targets for herbal ingredients. The pipeline involves pharmacophore comparison and reverse ligand-protein docking simulation in a high throughput manner. We evaluated the pipeline using three traditional Chinese medicine ingredients such as acteoside, quercetin, and epigallocatechin gallate as examples. A majority of current known targets of these ingredients were successfully identified by the pipeline. Structural comparative analyses confirmed that the predicted ligand-target interactions used the same binding pockets and binding modes as those of known ligand-target interactions. Furthermore, we illustrated the mechanism of actions of the ingredients by constructing the pharmacological networks on the basis of the predicted target profiles. In summary, we proposed an efficient and economic option for large-scale target exploration in the herb study. This pipeline will be particularly valuable in aiding precise drug discovery and drug repurposing from natural products.
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Affiliation(s)
- Haiping Zhang
- State
Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, PR China
- Joint
Engineering Research Center for Health Big Data Intelligent Analysis
Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong Province 518055, People’s Republic
of China
| | - Jianbo Pan
- Department
of Ophthalmology, Johns Hopkins School of
Medicine, Baltimore, Maryland 21205, United States
| | - Xuli Wu
- School
of Medicine, Shenzhen University, Shenzhen, Guangdong Province 518060, People’s Republic
of China
| | - Ai-Ren Zuo
- Jiangxi
University of Traditional Chinese Medicine, Nanchang, Jiangxi, 330004, China
| | - Yanjie Wei
- Joint
Engineering Research Center for Health Big Data Intelligent Analysis
Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong Province 518055, People’s Republic
of China
| | - Zhi-Liang Ji
- State
Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, PR China
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15
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Gupta S, Shukla H, Kumar A, Shukla R, Kumari R, Tripathi T, Singh RK, Anupurba S. Mycobacterium tuberculosis nucleoside diphosphate kinase shows interaction with putative ATP binding cassette (ABC) transporter, Rv1273c. J Biomol Struct Dyn 2019; 38:1083-1093. [PMID: 30898047 DOI: 10.1080/07391102.2019.1595150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Protein-protein interactions are crucial for all biological processes. Compiling this network provides many new insights into protein function and gives directions for the development of new drugs targeted to the pathogen. Mycobacterium tuberculosis Nucleoside diphosphate kinase (Mtb Ndk) has been reported to promote survival of mycobacterium within the macrophage and contribute significantly to mycobacterium virulence. Hence, the present study was aimed to identify and characterize the interacting partner for Ndk. The in vitro experiments, pull down and far western blotting have demonstrated that Mtb Ndk interacts with Rv1273c, a probable drug ABC transporter ATP-binding protein annotated to export drugs across the membrane. This observation was further confirmed by molecular docking and dynamic simulations studies. The homology model of Rv1273c was constructed and docked with Mtb Ndk for protein-protein interaction analysis. The critical residues involved at interface of Rv1273c-Ndk interaction were identified. MDS and Principal Component analysis carried out for conformational feasibility and stability concluded that the complex between the two proteins is more stable as compared to apo proteins. Our findings would be expected to improve the dissection of protein-protein interaction network and significantly advance our understanding of tuberculosis infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Smita Gupta
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Harish Shukla
- Department of Biochemistry, North Eastern Hill University, Shillong, India
| | - Arun Kumar
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Rohit Shukla
- Department of Biochemistry, North Eastern Hill University, Shillong, India
| | - Richa Kumari
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Timir Tripathi
- Department of Biochemistry, North Eastern Hill University, Shillong, India
| | - Rakesh K Singh
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Shampa Anupurba
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
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16
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Tiwari A, Kumar A, Srivastava G, Sharma A. Screening of Anti-mycobacterial Phytochemical Compounds for Potential Inhibitors against Mycobacterium Tuberculosis Isocitrate Lyase. Curr Top Med Chem 2019; 19:600-608. [PMID: 30836915 DOI: 10.2174/1568026619666190304125603] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 10/12/2018] [Accepted: 11/05/2018] [Indexed: 11/22/2022]
Abstract
Background and Introduction: Tuberculosis (TB) is a leading infectious disease caused by Mycobacterium tuberculosiswith high morbidity and mortality. Isocitrate lyase (MtbICL), a key enzyme of glyoxylate pathway has been shown to be involved in mycobacterial persistence, is attractive drug target against persistent tuberculosis. METHODS Virtual screening, molecular docking and MD simulation study has been integrated for screening of phytochemical based anti-mycobacterial compounds. Docking study of reported MtbICL inhibitors has shown an average binding affinity score -7.30 Kcal/mol. In virtual screening, compounds exhibiting lower binding energy than calculated average binding energy were selected as top hit compounds followed by calculation of drug likeness property. Relationship between experimental IC50 value and calculated binding gibbs free energy of reported inhibitors was also calculated through regression analysis to predict IC50 value of potential inhibitors. RESULTS Docking and MD simulation studies of top hit compounds have identified shinjudilactone (quassinoid), lecheronol A (pimarane) and caniojane (diterpene) as potential MtbICL inhibitors. CONCLUSION Phytochemical based anti-mycobacterial compound can further developed into effective drugs against persistence tuberculosis with lesser toxicity and side effects.
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Affiliation(s)
- Ashish Tiwari
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plant (CIMAP), Lucknow-226015, Uttar Pradesh, India
| | - Akhil Kumar
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plant (CIMAP), Lucknow-226015, Uttar Pradesh, India
| | - Gaurava Srivastava
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plant (CIMAP), Lucknow-226015, Uttar Pradesh, India
| | - Ashok Sharma
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plant (CIMAP), Lucknow-226015, Uttar Pradesh, India
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17
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Shukla R, Shukla H, Tripathi T. Structural and energetic understanding of novel natural inhibitors of Mycobacterium tuberculosis malate synthase. J Cell Biochem 2019; 120:2469-2482. [PMID: 30206985 DOI: 10.1002/jcb.27538] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/06/2018] [Indexed: 01/24/2023]
Abstract
Persistent infection by Mycobacterium tuberculosis requires the glyoxylate shunt. This is a bypass to the tricarboxylic acid cycle in which isocitrate lyase (ICL) and malate synthase (MS) catalyze the net incorporation of carbon during mycobacterial growth on acetate or fatty acids as the primary carbon source. To identify a potential antitubercular compound, we performed a structure-based screening of natural compounds from the ZINC database (n = 1 67 740) against the M tuberculosis MS (MtbMS) structure. The ligands were screened against MtbMS, and 354 ligands were found to have better docking score. These compounds were assessed for Lipinski and absorption, distribution, metabolism, excretion, and toxicity prediction where 15 compounds were found to fit well for redocking studies. After refinement by molecular docking and drug-likeness analysis, four potential inhibitors (ZINC1483899, ZINC1754310, ZINC2269664, and ZINC15729522) were identified. These four ligands with phenyl-diketo acid were further subjected to molecular dynamics simulation to compare the dynamics and stability of the protein structure after ligand binding. The binding energy analysis was calculated to determine the intermolecular interactions. Our results suggested that the four compounds had a binding free energy of -201.96, -242.02, -187.03, and -169.02 kJ·mol-1 , for compounds with IDs ZINC1483899, ZINC1754310, ZINC2269664, and ZINC15729522, respectively. We concluded that two compounds (ZINC1483899 and ZINC1754310) displayed considerable structural and pharmacological properties and could be probable drug candidates to fight against M tuberculosis parasites.
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Affiliation(s)
- Rohit Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Umshing, Shillong, India
| | - Harish Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Umshing, Shillong, India
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Umshing, Shillong, India
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18
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Uddin R, Zahra NUA, Azam SS. Identification of glucosyl-3-phosphoglycerate phosphatase as a novel drug target against resistant strain of Mycobacterium tuberculosis (XDR1219) by using comparative metabolic pathway approach. Comput Biol Chem 2019; 79:91-102. [PMID: 30743161 DOI: 10.1016/j.compbiolchem.2019.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 01/13/2019] [Accepted: 01/23/2019] [Indexed: 10/27/2022]
Abstract
Tuberculosis (TB) is a major global health challenge. It has been afflicting human for thousands of years and is still severely affecting a huge population. The etiological agent of the disease is Mycobacterium tuberculosis (MTB) that survives in the human host in latent, dormant, and non-replicative state by evading the immune system. It is one of the leading causes of infection related death worldwide. The situation is exacerbated by the massive increase in the resistant strains such as multi-drug resistant TB (MDR-TB) and extensive drug-resistant TB (XDR-TB). The resistance is as severe that it resulted in failure of the current chemotherapy regimens (i.e. anti-tubercular drugs). It is therefore imperative to discover the new anti-tuberculosis drug targets and their potential inhibitors. Current study has made the use of in silico approaches to perform the comparative metabolic pathway analysis of the MTBXDR1219 with the host i.e. H. sapiens. We identified several metabolic pathways which are unique to pathogen only. By performing subtractive genomic analysis 05 proteins as potential drug target are retrieved. This study suggested that the identified proteins are essential for the bacterial survival and non-homolog to the host proteins. Furthermore, we selected glucosyl-3-phosoglycerate phosphatase (GpgP, EC 5.4.2.1) out of the 05 proteins for molecular docking analysis and virtual screening. The protein is involved in the biosynthesis of methylglucose lipopolysaccharides (MGLPs) which regulate the biosynthesis of mycolic acid. Mycolic acid is the building block of the unique cell wall of the MTB which is responsible for the resistance and pathogenicity. A relatively larger library consisting of 10,431 compounds was screened using AutoDock Vina to predict the binding modes and to rank the potential inhibitors. No potent inhibitor against MTB GpgP has been reported yet, therefore ranking of compounds is performed by making a comparison with the substrate i.e. glucosyl-3-phosphoglycerate. The obtained results provide the understanding of underlying mechanism of interactions of ligands with protein. Follow up study will include the study of the Protein-Protein Interactions (PPIs), and to propose the potential inhibitors against them.
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Affiliation(s)
- Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Pakistan.
| | - Noor-Ul-Ain Zahra
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
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19
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Uddin R, Masood F, Azam SS, Wadood A. Identification of putative non-host essential genes and novel drug targets against Acinetobacter baumannii by in silico comparative genome analysis. Microb Pathog 2018; 128:28-35. [PMID: 30550846 DOI: 10.1016/j.micpath.2018.12.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 12/10/2018] [Accepted: 12/10/2018] [Indexed: 10/27/2022]
Abstract
Acinetobacter baumannii, the gram-negative bacteria emerged as an extremely critical pathogen causing nosocomial and different kinds of infections. A. baumannii exhibit resistivity towards various classes of antibiotics that shows that there is a dire need to search more drug targets by exploiting the full genome of the bacteria. In doing so, a strategy is made with the combination of computational biology, pathogen informatics and cheminformatics. Comparative genomics analysis, modeling and docking studies have been performed for the prediction of non-host essential genes and novel drug candidates against A. baumannii. Among 37 unique and 82 common metabolic pathways, 92 genes were predicted as non-host genes. Similarly, using homology search between A. baumannii genome and essential genes of different bacteria, 293 genes were predicted as essential genes of A. baumannii. Among these predicted non-host and essential genes, 86 genes were predicted as non-host essential genes which could serve as potential novel drug and vaccine targets. Additional drug-target like physicochemical properties were estimated such as the molecular weight, subcellular localization and druggability potential. On the structural part, the crystal structures of all the non-host essential genes of A. baumannii were found except the three genes. Out of these three, a homology model of Undecaprenyl-diphosphatase was built using a PDB template by MODELLER [version 9.18]. The quality of the model was assessed by the ProSA and RAMPAGE. The built model was subjected as a receptor for the molecular docking with Adenosine diphosphate (ADP) as a ligand. The molecular docking was performed by AutoDock4 and the best conformation with lowest binding energy (-4.39 kcal/mol) was obtained. The LigPlot was used to identify the close interactions between the ligand the receptor's residues. This study will further aid for the selection of putative inhibitors against a novel drug target identified against A. baumannii and hence could lead to the better therapeutics.
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Affiliation(s)
- Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Pakistan.
| | - Fareha Masood
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Pakistan
| | - Syed Sikander Azam
- National Centre for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
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Sasikumar K, Ghosh AR, Dusthackeer A. Antimycobacterial potentials of quercetin and rutin against Mycobacterium tuberculosis H37Rv. 3 Biotech 2018; 8:427. [PMID: 30305996 DOI: 10.1007/s13205-018-1450-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 09/24/2018] [Indexed: 11/30/2022] Open
Abstract
Quercetin and rutin, two flavonoids were examined for antimycobacterial activities against M. tuberculosis H37Rv (ATCC 27294). The quercetin exhibited (99.30 ± 0.268%) in (LRP) assay at 200 µg/ml and 56.21 ± 0.97% inhibition in (BMD) at 50 µg/ml, whereas rutin exhibited (90.40 ± 0.68%) in LRP assay at 200 µg/ml and 56.10 ± 0.67% inhibition in BMD at 50 µg/ml. The minimum inhibitory concentration (MIC) was found to be 6.25 µg ml-1 and 25 µg ml-1 respectively. The current investigation suggests that quercetin has better inhibitory activity than rutin.
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Affiliation(s)
- Kandasamy Sasikumar
- 1Department of Integrative Biology, School of BioSciences and Technology (SBST), VIT University, Vellore, Tamilnadu 632014 India
| | - Asit Ranjan Ghosh
- 1Department of Integrative Biology, School of BioSciences and Technology (SBST), VIT University, Vellore, Tamilnadu 632014 India
| | - Azger Dusthackeer
- 2Department of Bacteriology, National Institute for Research in Tuberculosis (NIRT-ICMR), Chennai, Tamilnadu 600031 India
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21
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Shukla H, Khan SR, Shukla R, Krishnan MY, Akhtar MS, Tripathi T. Alternate pathway to ascorbate induced inhibition of Mycobacterium tuberculosis. Tuberculosis (Edinb) 2018; 111:161-169. [DOI: 10.1016/j.tube.2018.06.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 06/12/2018] [Accepted: 06/16/2018] [Indexed: 11/28/2022]
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22
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Kalita J, Shukla R, Shukla H, Gadhave K, Giri R, Tripathi T. Comprehensive analysis of the catalytic and structural properties of a mu-class glutathione s-transferase from Fasciola gigantica. Sci Rep 2017; 7:17547. [PMID: 29235505 PMCID: PMC5727538 DOI: 10.1038/s41598-017-17678-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 11/28/2017] [Indexed: 01/12/2023] Open
Abstract
Glutathione S‒transferases (GSTs) play an important role in the detoxification of xenobiotics. They catalyze the nucleophilic addition of glutathione (GSH) to nonpolar compounds, rendering the products water-soluble. In the present study, we investigated the catalytic and structural properties of a mu-class GST from Fasciola gigantica (FgGST1). The purified recombinant FgGST1 formed a homodimer composed of 25 kDa subunit. Kinetic analysis revealed that FgGST1 displays broad substrate specificity and shows high GSH conjugation activity toward 1-chloro-2,4-dinitrobenzene, 4-nitroquinoline-1-oxide, and trans-4-phenyl-3-butene-2-one and peroxidase activity towards trans-2-nonenal and hexa-2,4-dienal. The FgGST1 was highly sensitive to inhibition by cibacron blue. The cofactor (GSH) and inhibitor (cibacron blue) were docked, and binding sites were identified. The molecular dynamics studies and principal component analysis indicated the stability of the systems and the collective motions, respectively. Unfolding studies suggest that FgGST1 is a highly cooperative molecule because, during GdnHCl-induced denaturation, a simultaneous unfolding of the protein without stabilization of any partially folded intermediate is observed. The protein is stabilized with a conformational free energy of about 10 ± 0.3 kcal mol-1. Additionally, the presence of conserved Pro-53 and structural motifs such as N-capping box and hydrophobic staple, further aided in the stability and proper folding of FgGST1.
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Affiliation(s)
- Jupitara Kalita
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Rohit Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Harish Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Kundlik Gadhave
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, 175005, India
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, 175005, India
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India.
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Shukla R, Shukla H, Tripathi T. Activity loss by H46A mutation in Mycobacterium tuberculosis isocitrate lyase is due to decrease in structural plasticity and collective motions of the active site. Tuberculosis (Edinb) 2017. [PMID: 29523315 DOI: 10.1016/j.tube.2017.11.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Mycobacterium tuberculosis isocitrate lyase (MtbICL) is a crucial enzyme of the glyoxylate cycle and is a validated anti-tuberculosis drug target. Structurally distant, non-active site mutation (H46A) in MtbICL has been found to cause loss of enzyme activity. The aim of the present work was to explore the structural alterations induced by H46A mutation that caused the loss of enzyme activity. The structural and dynamic consequences of H46A mutation were studied using multiple computational methods such as docking, molecular dynamics simulation and residue interaction network analysis (RIN). Principal component analysis and cross correlation analysis revealed the difference in conformational flexibility and collective modes of motions between the wild-type and mutant enzyme, particularly in the active site region. RIN analysis revealed that the active site geometry was disturbed in the mutant enzyme. Thus, the dynamic perturbation of the active site led to enzyme transition from its active form to inactive form upon mutation. The computational analyses elucidated the mutant-specific conformational alterations, differential dominant motions, and anomalous residue level interactions that contributed to the abrogated function of mutant MtbICL. An understanding of interactions of mutant enzymes may help in modifying the existing drugs and designing improved drugs for successful control of tuberculosis.
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Affiliation(s)
- Rohit Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Harish Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India.
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Safwat NA, Kashef MT, Aziz RK, Amer KF, Ramadan MA. Quercetin 3-O-glucoside recovered from the wild Egyptian Sahara plant, Euphorbia paralias L., inhibits glutamine synthetase and has antimycobacterial activity. Tuberculosis (Edinb) 2017. [PMID: 29523309 DOI: 10.1016/j.tube.2017.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Tuberculosis remains a major health problem accentuated by the rise of resistance to all available drugs. Therefore, this study was launched to discover a novel antituberculosis agent from wild Egyptian Sahara plants. Twelve such plants were screened, in vitro, for their activity against various Mycobacterium species. The most active plant, Euphorbia paralias, was further fractionated with different organic solvents, and the activity of the obtained fractions was determined by the agar diffusion and broth microdilution methods. The methanol fraction was the most active against Mycobacterium spp., and was non-toxic in doses up to 10 g/kg of animal weight. Its main component was separated by column chromatography, and then identified by ultraviolet spectroscopy and nuclear magnetic resonance analysis as quercetin-3-O-β-D-glucoside. Docking analysis suggested that quercetin-3-O-β-D-glucoside inhibits the glutamine synthetase enzyme, a promising target for the development of antituberculosis drugs. This prediction was confirmed by an in vitro glutamine synthetase biosynthetic assay. To the best of our knowledge, and based on bioinformatics mining of the BioPhytMol database, this is the first report on the antimycobacterial activity of Euphorbia paralias plant. It is also the first report on the inhibition of mycobacterial glutamine synthetase by the flavonoid quercetin.
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Affiliation(s)
- Nesreen A Safwat
- Department of Medicinal Plants, Desert Research Center, Matareya, Cairo, 11753, Egypt.
| | - Mona T Kashef
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt.
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt.
| | - Khadiga F Amer
- Department of Medicinal Plants, Desert Research Center, Matareya, Cairo, 11753, Egypt.
| | - Mohammed A Ramadan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt.
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Salt-regulated reversible fibrillation of Mycobacterium tuberculosis isocitrate lyase: Concurrent restoration of structure and activity. Int J Biol Macromol 2017; 104:89-96. [DOI: 10.1016/j.ijbiomac.2017.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 05/30/2017] [Accepted: 06/02/2017] [Indexed: 02/03/2023]
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26
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Lee YV, Choi SB, Wahab HA, Choong YS. Active Site Flexibility of Mycobacterium tuberculosis Isocitrate Lyase in Dimer Form. J Chem Inf Model 2017; 57:2351-2357. [PMID: 28820943 DOI: 10.1021/acs.jcim.7b00265] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tuberculosis (TB) still remains a global threat due to the emergence of a drug-resistant strain. Instead of focusing on the drug target of active stage TB, we are highlighting the isocitrate lyase (ICL) at the dormant stage TB. ICL is one of the persistent factors for Mycobacterium tuberculosis (MTB) to survive during the dormant phase. In addition, the absence of ICL in human has made ICL a potential drug target for TB therapy. However, the dynamic details of ICL which could give insights to the ICL-ligand interaction have yet to be solved. Therefore, a series of ICL dimer dynamics studies through molecular dynamics simulation were performed in this work. The ICL active site entrance gate closure is contributed to by hydrogen bonding and electrostatic interactions with the C-terminal. Analysis suggested that the open-closed behavior of the ICL active site entrance depends on the type of ligand present in the active site. We also observed four residues (Ser91, Asp108, Asp153, and Cys191) which could possibly be the nucleophiles for nucleophilic attack on the cleavage of isocitrate at the C2-C3 bond. We hope that the elucidation of ICL dynamics can benefit future works such as lead identification or antibody design against ICL for TB therapeutics.
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Affiliation(s)
- Yie-Vern Lee
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia , 11800 Minden, Penang, Malaysia
| | - Sy Bing Choi
- Pharmaceutical Design and Simulation Laboratory, School of Pharmaceutical Sciences, Universiti Sains Malaysia , 11800 Minden, Penang, Malaysia
| | - Habibah A Wahab
- Pharmaceutical Design and Simulation Laboratory, School of Pharmaceutical Sciences, Universiti Sains Malaysia , 11800 Minden, Penang, Malaysia
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia , 11800 Minden, Penang, Malaysia
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Shukla H, Shukla R, Sonkar A, Tripathi T. Alterations in conformational topology and interaction dynamics caused by L418A mutation leads to activity loss of Mycobacterium tuberculosis isocitrate lyase. Biochem Biophys Res Commun 2017; 490:276-282. [DOI: 10.1016/j.bbrc.2017.06.036] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 06/09/2017] [Indexed: 11/17/2022]
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28
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Shukla R, Shukla H, Sonkar A, Pandey T, Tripathi T. Structure-based screening and molecular dynamics simulations offer novel natural compounds as potential inhibitors of Mycobacterium tuberculosis isocitrate lyase. J Biomol Struct Dyn 2017; 36:2045-2057. [DOI: 10.1080/07391102.2017.1341337] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Rohit Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Harish Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Amit Sonkar
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Tripti Pandey
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
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Shukla H, Shukla R, Sonkar A, Pandey T, Tripathi T. Distant Phe345 mutation compromises the stability and activity of Mycobacterium tuberculosis isocitrate lyase by modulating its structural flexibility. Sci Rep 2017; 7:1058. [PMID: 28432345 PMCID: PMC5430663 DOI: 10.1038/s41598-017-01235-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 03/23/2017] [Indexed: 11/24/2022] Open
Abstract
Isocitrate lyase (ICL), a potential anti-tubercular drug target, catalyzes the first step of the glyoxylate shunt. In the present investigation, we studied the conformational flexibility of MtbICL to better understand its stability and catalytic activity. Our biochemical results showed that a point mutation at Phe345, which is topologically distant (>10 Å) to the active site signature sequence (189KKCGH193), completely abolishes the activity of the enzyme. In depth computational analyses were carried out for understanding the structural alterations using molecular dynamics, time-dependent secondary structure and principal component analysis. The results showed that the mutated residue increased the structural flexibility and induced conformational changes near the active site (residues 170–210) and in the C-terminal lid region (residues 411–428). Both these regions are involved in the catalytic activity of MtbICL. Upon mutation, the residual mobility of the enzyme increased, resulting in a decrease in the stability, which was confirmed by the lower free energy of stabilization in the mutant enzyme suggesting the destabilization in the structure. Our results have both biological importance and chemical novelty. It reveals internal dynamics of the enzyme structure and also suggests that regions other than the active site should be exploited for targeting MtbICL inhibition and development of novel anti-tuberculosis compounds.
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Affiliation(s)
- Harish Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Rohit Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Amit Sonkar
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Tripti Pandey
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India.
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Song L, Wu X. Development of efflux pump inhibitors in antituberculosis therapy. Int J Antimicrob Agents 2016; 47:421-9. [DOI: 10.1016/j.ijantimicag.2016.04.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 03/25/2016] [Accepted: 04/02/2016] [Indexed: 12/18/2022]
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