nach oben

Network Modeling Analysis in Health Informatics and Bioinformatics

Erschienen in:

01.12.2021 | Original Article

Inhibitory effect of anti-HIV compounds extracted from Indian medicinal plants to retard the replication and transcription process of SARS-CoV-2: an insight from molecular docking and MD-simulation studies

verfasst von: Tanmoy Dutta, Nabajyoti Baildya, Abdul Ashik Khan, Narendra Nath Ghosh

Erschienen in: Network Modeling Analysis in Health Informatics and Bioinformatics | Ausgabe 1/2021

Einloggen

Aktivieren Sie unsere intelligente Suche, um passende Fachinhalte oder Patente zu finden.

search-config

KI-gestützte Suche

Aus

Abstract

Outbreak of Coronavirus (SARS-CoV-2) has thrown a big challenge to the globe by snatching millions of human lives from the world. In this study, inhibitory efficiency of ten anti-HIV compounds from different Indian medicinal plant parts have been virtually screened against Mpro, PLpro and RdRp proteins of SARS-CoV-2. The molecular docking study reflected that among these compounds, Proptine (PTP) has the highest binding affinity for the three cases. Introduction of PTP molecules within the binding pocket of these proteins showed a large structural and conformational changes on the structure of proteins which is revealed from molecular dynamics (MD) simulation studies. RMSD, RMSF and analysis of thermodynamic parameters also revealed that PTP makes a huge impact on the structures of the respective proteins which will pave an opportunity for doing advanced experimental research to evaluate the potential drug to combat COVID-19.

Graphic abstract

Vorheriger Artikel Guest Editorial: Intelligent solutions for green computing in internet of medical things

Nächster Artikel Swarm optimization-based neural network model for secondary structure prediction of proteins

Sie haben noch keine Lizenz? Dann Informieren Sie sich jetzt über unsere Produkte:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

über 102.000 Bücher
über 537 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Finance + Banking
Management + Führung
Marketing + Vertrieb
Maschinenbau + Werkstoffe
Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Jetzt informieren

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

über 67.000 Bücher
über 390 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Maschinenbau + Werkstoffe

Jetzt Wissensvorsprung sichern!

Jetzt informieren

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

über 67.000 Bücher
über 340 Zeitschriften

aus folgenden Fachgebieten:

Bauwesen + Immobilien
Business IT + Informatik
Finance + Banking
Management + Führung
Marketing + Vertrieb
Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Jetzt informieren

Nur mit Berechtigung zugänglich

Abraham MJ, Gready JE (2011) Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.5. J Comput Chem 32(9):2031–2040. https://doi.org/10.1002/jcc.21773CrossRef

Baden LR, El Sahly HM, Essink B, Kotloff K, Frey S, Novak R, Diemert D, Spector SA, Rouphael N, Creech CB (2021) Efficacy and safety of the mRNA-1273 SARS-CoV-2 vaccine. N Engl J Med 384(5):403–416. https://doi.org/10.1056/NEJMoa2035389CrossRef

Baildya N, Ghosh NN, Chattopadhyay AP (2020) Inhibitory activity of hydroxychloroquine on COVID-19 main protease: an insight from MD-simulation studies. J Mol Struct 1219:128595. https://doi.org/10.1016/j.molstruc.2020.128595CrossRef

Baildya N, Ghosh NN, Chattopadhyay AP (2021a) Inhibitory capacity of Chloroquine against SARS-COV-2 by effective binding with Angiotensin converting enzyme-2 receptor: an insight from molecular docking and MD-simulation studies. J Mol Struct 1230:129891. https://doi.org/10.1016/j.molstruc.2021.129891CrossRef

Baildya N, Khan AA, Ghosh NN, Dutta T, Chattopadhyay AP (2021b) Screening of potential drug from Azadirachta Indica (Neem) extracts for SARS-CoV-2: an insight from molecular docking and MD-simulation studies. J Mol Struct 1227:129390. https://doi.org/10.1016/j.molstruc.2020.129390CrossRef

Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci 98(18):10037–10041. https://doi.org/10.1073/pnas.181342398CrossRef

Bedoya L, Sanchez-Palomino S, Abad M, Bermejo P, Alcami J (2001) Anti-HIV activity of medicinal plant extracts. J Ethnopharmacol 77(1):113–116. https://doi.org/10.1016/S0378-8741(01)00265-3CrossRef

Berendsen HJ, van der Spoel D, van Drunen R (1995) GROMACS: a message-passing parallel molecular dynamics implementation. Comput PhysCommun 91(1–3):43–56. https://doi.org/10.1016/0010-4655(95)00042-ECrossRef

Boonstra S, Onck PR, van der Giessen E (2016) CHARMM TIP3P water model suppresses peptide folding by solvating the unfolded state. J Phys Chem B 120(15):3692–3698. https://doi.org/10.1021/acs.jpcb.6b01316CrossRef

Borkotoky S, Banerjee M (2020) A computational prediction of SARS-CoV-2 structural protein inhibitors from Azadirachta indica (Neem). J BiomolStruct Dyn. https://doi.org/10.1080/07391102.2020.1774419CrossRef

Davies NG, Abbott S, Barnard RC, Jarvis CI, Kucharski AJ, Munday JD, Pearson CA, Russell TW, Tully DC, Washburne AD (2021) Estimated transmissibility and impact of SARS-CoV-2 lineage B. 1.1. 7 in England. Science. https://doi.org/10.1126/science.abg3055CrossRef

Dutta T, Ghorai S, Khan AA, Baildya N, Ghosh NN (2021) Screening of potential anti-HIV compounds from Achyranthes aspera extracts for SARS-CoV-2: an insight from molecular docking study. J PhysConfSer. https://doi.org/10.1088/1742-6596/1797/1/012042CrossRef

Elfiky AA (2020) Ribavirin, remdesivir, sofosbuvir, galidesivir, and tenofovir against SARS-CoV-2 RNA dependent RNA polymerase (RdRp): a molecular docking study. Life Sci. https://doi.org/10.1016/j.lfs.2020.117592CrossRef

Fontanet A, Autran B, Lina B, Kieny MP, Karim SSA, Sridhar D (2021) SARS-CoV-2 variants and ending the COVID-19 pandemic. Lancet. https://doi.org/10.1016/S0140-6736(21)00370-6CrossRef

Graham MS, Sudre CH, May A, Antonelli M, Murray B, Varsavsky T, Klaser K, Canas LDS, Molteni E, Modat M (2021) The effect of SARS-CoV-2 variant B. 1.1. 7 on symptomatology, re-infection and transmissibility. medRxiv. https://doi.org/10.1101/2021.01.28.21250680CrossRef

Gu H, Chen Q, Yang G, He L, Fan H, Deng Y-Q, Wang Y, Teng Y, Zhao Z, Cui Y (2020) Adaptation of SARS-CoV-2 in BALB/c mice for testing vaccine efficacy. Science 369(6511):1603–1607. https://doi.org/10.1126/science.abc4730CrossRef

Guerriero G, Berni R, Muñoz-Sanchez JA, Apone F, Abdel-Salam EM, Qahtan AA, Alatar AA, Cantini C, Cai G, Hausman J-F (2018) Production of plant secondary metabolites: Examples, tips and suggestions for biotechnologists. Genes 9(6):309. https://doi.org/10.3390/genes9060309CrossRef

Indwiani Astuti Y (2020) Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): an overview of viral structure and host response. Diabetes MetabSyndr 14(4):407–412. https://doi.org/10.1016/j.dsx.2020.04.020CrossRef

Jiang F, Deng L, Zhang L, Cai Y, Cheung CW, Xia Z (2020) Review of the clinical characteristics of coronavirus disease 2019 (COVID-19). J Gen Intern Med. https://doi.org/10.1007/s11606-020-05762-wCrossRef

Kandeel M, Al-Nazawi M (2020) Virtual screening and repurposing of FDA approved drugs against COVID-19 main protease. Life Sci 251:117627. https://doi.org/10.1016/j.lfs.2020.117627CrossRef

Khan AA, Baildya N, Dutta T, Ghosh NN (2021) Inhibitory efficiency of potential drugs against SARS-CoV-2 by blocking human angiotensin converting enzyme-2: Virtual screening and molecular dynamics study. MicrobPathog 152:104762. https://doi.org/10.1016/j.micpath.2021.104762CrossRef

Kirby T (2021) New variant of SARS-CoV-2 in UK causes surge of COVID-19. Lancet Respir Med 9(2):e20–e21. https://doi.org/10.1016/S2213-2600(21)00005-9MathSciNetCrossRef

Kumari R, Kumar R, Lynn A, Consortium O S D D (2014) g_mmpbsa-A GROMACS tool for high-throughput MM-PBSA calculations. J Chem Inf Model 54(7):1951–1962. https://doi.org/10.1021/ci500020mCrossRef

Lee S, Tran A, Allsopp M, Lim JB, Hénin JRM, Klauda JB (2014) CHARMM36 united atom chain model for lipids and surfactants. J Phys Chem B 118(2):547–556. https://doi.org/10.1021/jp410344gCrossRef

Lu H, Stratton CW, Tang YW (2020) Outbreak of pneumonia of unknown etiology in Wuhan, China: the mystery and the miracle. J Med Virol 92(4):401–402. https://doi.org/10.1002/jmv.25678CrossRef

Mandal M, Chowdhury SK, Khan AA, Baildya N, Dutta T, Misra D, Ghosh NN (2021) Inhibitory efficacy of RNA virus drugs against SARS-CoV-2 proteins: an extensive study. J Mol Struct 1234:130152. https://doi.org/10.1016/j.molstruc.2021.130152CrossRef

Mascola JR, Graham BS, Fauci AS (2021) SARS-CoV-2 viral variants—tackling a moving target. JAMA. https://doi.org/10.1001/jama.2021.2088CrossRef

Min BS, Bae KH, Kim YH, Miyashiro H, Hattori M, Shimotohno K (1999) Screening of Korean plants against human immunodeficiency virus type 1 protease. Phytother Res 13(8):680–682. https://doi.org/10.1002/(SICI)1099-1573(199912)13:8%3c680::AID-PTR501%3e3.0.CO;2-HCrossRef

Min BS, Kim YH, Tomiyama M, Nakamura N, Miyashiro H, Otake T, Hattori M (2001) Inhibitory effects of Korean plants on HIV-1 activities. Phytother Res 15(6):481–486. https://doi.org/10.1002/ptr.751CrossRef

Murgueitio MS, Bermudez M, Mortier J, Wolber G (2012) In silico virtual screening approaches for anti-viral drug discovery. Drug Discov Today Technol 9(3):e219–e225. https://doi.org/10.1016/j.ddtec.2012.07.009CrossRef

Pal M, Berhanu G, Desalegn C, Kandi V (2020) Severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2): an update. Cureus. https://doi.org/10.7759/cureus.7423CrossRef

Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera—a visualization system for exploratory research and analysis. J Comput Chem 25(13):1605–1612. https://doi.org/10.1002/jcc.20084CrossRef

Pires DE, Blundell TL, Ascher DB (2015) pkCSM: predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. J Med Chem 58(9):4066–4072. https://doi.org/10.1021/acs.jmedchem.5b00104CrossRef

Polack FP, Thomas SJ, Kitchin N, Absalon J, Gurtman A, Lockhart S, Perez JL, Pérez Marc G, Moreira ED, Zerbini C (2020) Safety and efficacy of the BNT162b2 mRNA Covid-19 vaccine. N Engl J Med 383(27):2603–2615. https://doi.org/10.1056/NEJMoa2034577CrossRef

Sabde S, Bodiwala HS, Karmase A, Deshpande PJ, Kaur A, Ahmed N, Chauthe SK, Brahmbhatt KG, Phadke RU, Mitra D (2011) Anti-HIV activity of Indian medicinal plants. J Nat Med 65(3–4):662–669. https://doi.org/10.1007/s11418-011-0513-2CrossRef

Sahin AR, Erdogan A, Agaoglu PM, Dineri Y, Cakirci AY, Senel ME, Okyay RA, Tasdogan AM (2020) 2019 novel coronavirus (COVID-19) outbreak: a review of the current literature. EJMO 4(1):1–7. https://doi.org/10.14744/ejmo.2020.12220CrossRef

Shekerdemian LS, Mahmood NR, Wolfe KK, Riggs BJ, Ross CE, McKiernan CA, Heidemann SM, Kleinman LC, Sen AI, Hall MW (2020) Characteristics and outcomes of children with coronavirus disease 2019 (COVID-19) infection admitted to US and Canadian pediatric intensive care units. JAMAPediatr 174(9):868–873. https://doi.org/10.1001/jamapediatrics.2020.1948CrossRef

Tang JW, Tambyah PA, Hui DS (2020) Emergence of a new SARS-CoV-2 variant in the UK. J Infect. https://doi.org/10.1016/j.jinf.2020.12.024CrossRef

Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V, Giandhari J, Doolabh D, Pillay S, San EJ, Msomi N (2020) Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa. medRxiv. https://doi.org/10.1101/2020.12.21.20248640CrossRef

Trott O, Olson AJ (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31(2):455–461. https://doi.org/10.1002/jcc.21334CrossRef

Varshney KK, Varshney M, Nath B (2020) Molecular Modeling of Isolated Phytochemicals from Ocimum sanctum Towards Exploring Potential Inhibitors of SARS Coronavirus Main Protease and Papain-Like Protease to Treat COVID-19. SSRN 3554371. https://ssrn.com/abstract=3554371

Volz E, Mishra S, Chand M, Barrett JC, Johnson R, Geidelberg L, Hinsley WR, Laydon DJ, Dabrera G, O’Toole Á (2021) Transmission of SARS-CoV-2 Lineage B. 1.1. 7 in England: Insights from linking epidemiological and genetic data. medRxiv. https://doi.org/10.1101/2020.12.30.20249034CrossRef

Wang C, Horby PW, Hayden FG, Gao GF (2020) A novel coronavirus outbreak of global health concern. Lancet 395(10223):470–473. https://doi.org/10.1016/S0140-6736(20)30185-9CrossRef

Xie X, Liu Y, Liu J, Zhang X, Zou J, Fontes-Garfias CR, Xia H, Swanson KA, Cutler M, Cooper D (2021) Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K and N501Y variants by BNT162b2 vaccine-elicited sera. Nat Med. https://doi.org/10.1038/s41591-021-01270-4CrossRef

Yang L, Wen K-S, Ruan X, Zhao Y-X, Wei F, Wang Q (2018) Response of plant secondary metabolites to environmental factors. Molecules 23(4):762. https://doi.org/10.3390/molecules23040762CrossRef

Zhang H, Penninger JM, Li Y, Zhong N, Slutsky AS (2020) Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 receptor: molecular mechanisms and potential therapeutic target. Intensive Care Med 46(4):586–590. https://doi.org/10.1007/s00134-020-05985-9CrossRef

Titel: Inhibitory effect of anti-HIV compounds extracted from Indian medicinal plants to retard the replication and transcription process of SARS-CoV-2: an insight from molecular docking and MD-simulation studies
verfasst von: Tanmoy Dutta
Nabajyoti Baildya
Abdul Ashik Khan
Narendra Nath Ghosh
Publikationsdatum: 01.12.2021
Verlag: Springer Vienna
Erschienen in: Network Modeling Analysis in Health Informatics and Bioinformatics / Ausgabe 1/2021
Print ISSN: 2192-6662
Elektronische ISSN: 2192-6670
DOI: https://doi.org/10.1007/s13721-021-00309-3

Springer Professional

Abstract

Graphic abstract

Bitte loggen Sie sich ein, um Zugang zu Ihrer Lizenz zu erhalten.

Sie haben noch keine Lizenz? Dann Informieren Sie sich jetzt über unsere Produkte:

Springer Professional "Wirtschaft+Technik"

Springer Professional "Technik"

Springer Professional "Wirtschaft"

Weitere Artikel der Ausgabe 1/2021

Stenosis diagnosis based on peripheral arterial and artificial neural network

Hybrid image encryption scheme for secure E-health systems

A novel enhanced decision tree model for detecting chronic kidney disease

Computational design of novel AKT inhibitors

In silico studies of selected multi-drug targeting against 3CLpro and nsp12 RNA-dependent RNA-polymerase proteins of SARS-CoV-2 and SARS-CoV

A hybrid feature selection model based on improved squirrel search algorithm and rank aggregation using fuzzy techniques for biomedical data classification

Premium Partner