Computer-aided identification of Mycobacterium tuberculosis resuscitation-promoting factor B (RpfB) inhibitors from Gymnema sylvestre natural products
Tuberculosis (TB), an infectious disease caused by multi-drug resistant Mycobacterium tuberculosis (Mtb), has been a global health concern. Mtb affects over a third of the world’s population, causing two million deaths annually due to its dormancy and propensity to spread infection during this perio...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-11-01
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| Series: | Frontiers in Pharmacology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fphar.2023.1325227/full |
| _version_ | 1797448619788337152 |
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| author | Mohibullah Shah Fatiha Khan Iqra Ahmad Cun-Liang Deng Asia Perveen Anwar Iqbal Umar Nishan Aqal Zaman Riaz Ullah Essam A. Ali Ke Chen |
| author_facet | Mohibullah Shah Fatiha Khan Iqra Ahmad Cun-Liang Deng Asia Perveen Anwar Iqbal Umar Nishan Aqal Zaman Riaz Ullah Essam A. Ali Ke Chen |
| author_sort | Mohibullah Shah |
| collection | DOAJ |
| description | Tuberculosis (TB), an infectious disease caused by multi-drug resistant Mycobacterium tuberculosis (Mtb), has been a global health concern. Mtb affects over a third of the world’s population, causing two million deaths annually due to its dormancy and propensity to spread infection during this period. Resuscitation-promoting factor B (RpfB) plays a pivotal role in the growth of Mtb during dormant periods, making it a critical target for eliminating Mtb and curing TB. Gymnema sylvestre is a famous medicinal plant with several medicinal properties, including antimicrobial activity; however, the therapeutic potential of the various reported metabolites of this plant against Mtb has not yet been explored. The aim of this study was to explore the reported natural products of G. sylvestre against the RpfB of the Mtb. A total of 131 reported secondary metabolites of this plant were collected and virtually screened against the RpfB. We particularly targeted the Glu292 residue of RpfB as it is crucial for the catalysis of this protein. From our in-house library, 114 compounds showed a binding affinity higher than the standard drug. The binding stability of the top three lead compounds was further confirmed through MD simulation analysis. Drug likeness analyses indicated that the ten hits had zero violations of the Lipinski rule of five. In addition, analyses of pharmacokinetics, toxicity, and target prediction revealed that the top compounds are devoid of toxicity and do not affect human proteins. Additionally, they reflect multifaceted approach as anti-TB agents. Our selected hits not only exhibit molecular properties favoring physiological compatibility but also exhibit properties enhancing their potential efficacy as therapeutic candidates. The compounds investigated here are worthy of experimental validation for the discovery of novel treatments against TB. Further, this study also provides a promising avenue for research on the pharmacological potential of G. sylvestre. |
| first_indexed | 2024-03-09T14:14:05Z |
| format | Article |
| id | doaj.art-c218f8f6156741ae984115c4e1fc0219 |
| institution | Directory Open Access Journal |
| issn | 1663-9812 |
| language | English |
| last_indexed | 2024-03-09T14:14:05Z |
| publishDate | 2023-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Pharmacology |
| spelling | doaj.art-c218f8f6156741ae984115c4e1fc02192023-11-29T05:44:21ZengFrontiers Media S.A.Frontiers in Pharmacology1663-98122023-11-011410.3389/fphar.2023.13252271325227Computer-aided identification of Mycobacterium tuberculosis resuscitation-promoting factor B (RpfB) inhibitors from Gymnema sylvestre natural productsMohibullah Shah0Fatiha Khan1Iqra Ahmad2Cun-Liang Deng3Asia Perveen4Anwar Iqbal5Umar Nishan6Aqal Zaman7Riaz Ullah8Essam A. Ali9Ke Chen10Department of Biochemistry, Bahauddin Zakariya University, Multan, PakistanDepartment of Biochemistry, Bahauddin Zakariya University, Multan, PakistanDepartment of Biochemistry, Bahauddin Zakariya University, Multan, PakistanDepartment of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, ChinaDepartment of Biochemistry, Bahauddin Zakariya University, Multan, PakistanDepartment of Chemical Sciences, University of Lakki Marwat, Lakki Marwat, PakistanDepartment of Chemistry, Kohat University of Science and Technology, Kohat, PakistanDepartment of Microbiology and Molecular Genetics, Bahauddin Zakariya University, Multan, PakistanDepartment of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi ArabiaDepartment of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi ArabiaDepartment of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, ChinaTuberculosis (TB), an infectious disease caused by multi-drug resistant Mycobacterium tuberculosis (Mtb), has been a global health concern. Mtb affects over a third of the world’s population, causing two million deaths annually due to its dormancy and propensity to spread infection during this period. Resuscitation-promoting factor B (RpfB) plays a pivotal role in the growth of Mtb during dormant periods, making it a critical target for eliminating Mtb and curing TB. Gymnema sylvestre is a famous medicinal plant with several medicinal properties, including antimicrobial activity; however, the therapeutic potential of the various reported metabolites of this plant against Mtb has not yet been explored. The aim of this study was to explore the reported natural products of G. sylvestre against the RpfB of the Mtb. A total of 131 reported secondary metabolites of this plant were collected and virtually screened against the RpfB. We particularly targeted the Glu292 residue of RpfB as it is crucial for the catalysis of this protein. From our in-house library, 114 compounds showed a binding affinity higher than the standard drug. The binding stability of the top three lead compounds was further confirmed through MD simulation analysis. Drug likeness analyses indicated that the ten hits had zero violations of the Lipinski rule of five. In addition, analyses of pharmacokinetics, toxicity, and target prediction revealed that the top compounds are devoid of toxicity and do not affect human proteins. Additionally, they reflect multifaceted approach as anti-TB agents. Our selected hits not only exhibit molecular properties favoring physiological compatibility but also exhibit properties enhancing their potential efficacy as therapeutic candidates. The compounds investigated here are worthy of experimental validation for the discovery of novel treatments against TB. Further, this study also provides a promising avenue for research on the pharmacological potential of G. sylvestre.https://www.frontiersin.org/articles/10.3389/fphar.2023.1325227/fullmulti-drug resistancetuberculosisRpfBdormancyGymnema sylvestrein-silico |
| spellingShingle | Mohibullah Shah Fatiha Khan Iqra Ahmad Cun-Liang Deng Asia Perveen Anwar Iqbal Umar Nishan Aqal Zaman Riaz Ullah Essam A. Ali Ke Chen Computer-aided identification of Mycobacterium tuberculosis resuscitation-promoting factor B (RpfB) inhibitors from Gymnema sylvestre natural products Frontiers in Pharmacology multi-drug resistance tuberculosis RpfB dormancy Gymnema sylvestre in-silico |
| title | Computer-aided identification of Mycobacterium tuberculosis resuscitation-promoting factor B (RpfB) inhibitors from Gymnema sylvestre natural products |
| title_full | Computer-aided identification of Mycobacterium tuberculosis resuscitation-promoting factor B (RpfB) inhibitors from Gymnema sylvestre natural products |
| title_fullStr | Computer-aided identification of Mycobacterium tuberculosis resuscitation-promoting factor B (RpfB) inhibitors from Gymnema sylvestre natural products |
| title_full_unstemmed | Computer-aided identification of Mycobacterium tuberculosis resuscitation-promoting factor B (RpfB) inhibitors from Gymnema sylvestre natural products |
| title_short | Computer-aided identification of Mycobacterium tuberculosis resuscitation-promoting factor B (RpfB) inhibitors from Gymnema sylvestre natural products |
| title_sort | computer aided identification of mycobacterium tuberculosis resuscitation promoting factor b rpfb inhibitors from gymnema sylvestre natural products |
| topic | multi-drug resistance tuberculosis RpfB dormancy Gymnema sylvestre in-silico |
| url | https://www.frontiersin.org/articles/10.3389/fphar.2023.1325227/full |
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