دورية أكاديمية
Identification of potent food constituents as SARS-CoV-2 papain-like protease modulators through advanced pharmacoinformatics approaches.
العنوان: | Identification of potent food constituents as SARS-CoV-2 papain-like protease modulators through advanced pharmacoinformatics approaches. |
---|---|
المؤلفون: | Bhowmick S; Department of Chemical Technology, University of Calcutta, 92, A.P.C. Road, Kolkata, 700009, India., Saha A; Department of Chemical Technology, University of Calcutta, 92, A.P.C. Road, Kolkata, 700009, India. Electronic address: achintya_saha@yahoo.com., AlFaris NA; Nutrition and Food Science, Department of Physical Sport Science, Princess Nourah bint Abdulrahman University, P. O. Box 84428, Riyadh, 11671, Saudi Arabia., ALTamimi JZ; Nutrition and Food Science, Department of Physical Sport Science, Princess Nourah bint Abdulrahman University, P. O. Box 84428, Riyadh, 11671, Saudi Arabia., ALOthman ZA; Department of Chemistry, P.O. Box 2455, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia., Aldayel TS; Nutrition and Food Science, Department of Physical Sport Science, Princess Nourah bint Abdulrahman University, P. O. Box 84428, Riyadh, 11671, Saudi Arabia., Wabaidur SM; Department of Chemistry, P.O. Box 2455, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia., Islam MA; Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. Electronic address: ataul.islam80@gmail.com. |
المصدر: | Journal of molecular graphics & modelling [J Mol Graph Model] 2022 Mar; Vol. 111, pp. 108113. Date of Electronic Publication: 2021 Dec 21. |
نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't |
اللغة: | English |
بيانات الدورية: | Publisher: Elsevier Science, Inc Country of Publication: United States NLM ID: 9716237 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1873-4243 (Electronic) Linking ISSN: 10933263 NLM ISO Abbreviation: J Mol Graph Model Subsets: MEDLINE |
أسماء مطبوعة: | Original Publication: New York, NY : Elsevier Science, Inc., c1997- |
مواضيع طبية MeSH: | COVID-19*, Antiviral Agents/pharmacology ; Coronavirus Papain-Like Proteases ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; SARS-CoV-2 |
مستخلص: | The current ongoing pandemic of COVID-19 urges immediate treatment measures for controlling the highly contagious SARS-CoV-2 infections. The papain-like protease (PLpro), which is released from nsp3, is presently being evaluated as a significant anti-viral drug target for COVID-19 therapy development. Particularly, PLpro is implicated in the cleavage of viral polyproteins and antagonizes the host innate immune response through its deubiquitinating and deISGylating actions, thus making it a high-profile antiviral therapeutic target. The present study reports a few specific food compounds that can bind tightly with the SARS-CoV-2 PLpro protein identified through extensive computational screening techniques. Precisely, extensive advanced computational approaches combining target-based virtual screening, particularly employing sub-structure based similarity search, molecular docking, molecular dynamics (MD) simulations, and MM-GBSA based binding free energy calculations have been employed for the identification of the most promising food compounds with substantial functional implications as SARS-CoV-2 PLpro protein inhibitors/modulators. Observations from the present research investigation also provide a deeper understanding of the binding modes of the proposed four food compounds with SARS-CoV-2 PLpro protein. In docking analyses, all compounds have established essential inter-molecular interaction profiles at the active site cavity of the SARS-CoV-2 PLpro protein. Similarly, the long-range 100 ns conventional MD simulation studies also provided an in-depth understanding of probable interactions and dynamic behaviour of the SARS-CoV-2 PLpro protein-food compound complexes. Binding free energies of all molecular systems revealed a strong interaction affinity of food compounds towards the SARS-CoV-2 PLpro protein. Moreover, clear-cut comparative analyses against the known standard inhibitor also suggest that proposed food compounds may act as potential active chemical entities for modulating the action of the SARS-CoV-2 PLpro protein. (Copyright © 2021 Elsevier Inc. All rights reserved.) |
References: | Cell Biosci. 2021 Feb 28;11(1):45. (PMID: 33640032) Nutrients. 2020 Aug 28;12(9):. (PMID: 32872374) J Cheminform. 2016 Jul 05;8:36. (PMID: 27382417) J Cheminform. 2015 May 20;7:20. (PMID: 26052348) Crit Rev Food Sci Nutr. 2020;60(13):2174-2211. (PMID: 31267783) RSC Adv. 2021 Oct 12;11(53):33380-33398. (PMID: 35497510) J Biomol Struct Dyn. 2022 Apr;40(7):3071-3081. (PMID: 33200683) ACS Infect Dis. 2021 Jun 11;7(6):1457-1468. (PMID: 33570381) ACS Pharmacol Transl Sci. 2020 Aug 04;3(5):1017-1019. (PMID: 33062954) J Pharm Anal. 2020 Dec;10(6):546-559. (PMID: 32874702) Proteins. 2004 May 1;55(2):383-94. (PMID: 15048829) J Comput Chem. 2005 Dec;26(16):1668-88. (PMID: 16200636) J Pharm Drug Res. 2020;3(2):341-361. (PMID: 32617527) Comput Biol Chem. 2020 Oct;88:107319. (PMID: 32801062) Nat Commun. 2021 Feb 2;12(1):743. (PMID: 33531496) ChemMedChem. 2021 Jan 19;16(2):340-354. (PMID: 32930481) Epigenomics. 2011 Aug;3(4):503-18. (PMID: 22022340) PLoS Pathog. 2014 May 22;10(5):e1004113. (PMID: 24854014) Nat Microbiol. 2021 Apr;6(4):467-478. (PMID: 33727702) Front Mol Biosci. 2020 Aug 04;7:174. (PMID: 32850963) PLoS One. 2021 May 19;16(5):e0251910. (PMID: 34010326) Adv Nutr. 2010 Nov;1(1):8-16. (PMID: 22043447) J Chem Phys. 2020 Sep 21;153(11):115101. (PMID: 32962355) J Med Virol. 2020 Sep;92(9):1542-1548. (PMID: 32181901) J Mol Recognit. 2020 Jul;33(7):e2838. (PMID: 32060998) N Engl J Med. 2020 Apr 30;382(18):1708-1720. (PMID: 32109013) J Med Virol. 2021 May;93(5):2722-2734. (PMID: 33475167) Compr Rev Food Sci Food Saf. 2018 May;17(3):754-768. (PMID: 33350126) Circulation. 2016 Jan 12;133(2):187-225. (PMID: 26746178) ACS Cent Sci. 2021 Jul 28;7(7):1245-1260. (PMID: 34341772) Precis Clin Med. 2021 Jan 18;4(1):1-16. (PMID: 33842834) Heliyon. 2021 Jan;7(1):e05957. (PMID: 33462562) Antiviral Res. 2015 Mar;115:21-38. (PMID: 25554382) J Chem Theory Comput. 2015 Aug 11;11(8):3696-713. (PMID: 26574453) Int J Mol Sci. 2018 Nov 01;19(11):. (PMID: 30388784) Food Res Int. 2019 Nov;125:108646. (PMID: 31554120) Curr Res Struct Biol. 2021;3:9-18. (PMID: 33319212) Eur J Pharmacol. 2021 Jan 15;891:173759. (PMID: 33249077) Front Chem. 2020 Nov 16;8:594009. (PMID: 33304884) Nature. 2020 Nov;587(7835):657-662. (PMID: 32726803) J Chem Inf Model. 2020 Jan 27;60(1):204-211. (PMID: 31887035) Chem Phys Lett. 2021 Jan 16;763:138193. (PMID: 33223560) Medicines (Basel). 2019 Sep 09;6(3):. (PMID: 31505825) Expert Opin Drug Discov. 2015 May;10(5):449-61. (PMID: 25835573) Adv Nutr. 2016 Jan 15;7(1):44-65. (PMID: 26773014) J Chem Inf Model. 2018 Feb 26;58(2):287-296. (PMID: 29309725) Antioxidants (Basel). 2019 Nov 22;8(12):. (PMID: 31766676) Int J Biol Macromol. 2021 Oct 1;188:137-146. (PMID: 34364941) J Nutr. 2004 Sep;134(9):2492S-2498S. (PMID: 15333748) J Comput Chem. 2010 Jan 30;31(2):455-61. (PMID: 19499576) Mol Nutr Food Res. 2019 Jan;63(1):e1800384. (PMID: 30176196) Comput Biol Med. 2020 Sep;124:103936. (PMID: 32738628) J Med Virol. 2021 Apr;93(4):2406-2419. (PMID: 33347622) J Mol Model. 2019 Jan 18;25(2):39. (PMID: 30659357) EMBO J. 2020 Sep 15;39(18):e106275. (PMID: 32845033) J Mol Struct. 2021 Mar 5;1227:129390. (PMID: 33041371) J Proteome Res. 2021 Jan 1;20(1):1015-1026. (PMID: 33350309) Nucleic Acids Res. 2015 Jul 1;43(W1):W443-7. (PMID: 25873628) Nat Commun. 2021 Jan 20;12(1):488. (PMID: 33473130) Front Nutr. 2018 Sep 21;5:87. (PMID: 30298133) Sci Adv. 2020 Oct 16;6(42):. (PMID: 33067239) Mol Divers. 2022 Feb;26(1):309-329. (PMID: 33825097) |
فهرسة مساهمة: | Keywords: Food compounds; MM-GBSA; Molecular docking; Molecular dynamics; SARS-CoV-2 PLpro; Virtual screening |
المشرفين على المادة: | 0 (Antiviral Agents) EC 3.4.22.2 (Coronavirus Papain-Like Proteases) EC 3.4.22.2 (papain-like protease, SARS-CoV-2) |
تواريخ الأحداث: | Date Created: 20211227 Date Completed: 20220125 Latest Revision: 20221221 |
رمز التحديث: | 20240628 |
مُعرف محوري في PubMed: | PMC8688376 |
DOI: | 10.1016/j.jmgm.2021.108113 |
PMID: | 34959151 |
قاعدة البيانات: | MEDLINE |
تدمد: | 1873-4243 |
---|---|
DOI: | 10.1016/j.jmgm.2021.108113 |