دورية أكاديمية
أعرض في EDS

Identification of bio-active food compounds as potential SARS-CoV-2 PLpro inhibitors-modulators via negative image-based screening and computational simulations.

التفاصيل البيبلوغرافية
العنوان: Identification of bio-active food compounds as potential SARS-CoV-2 PLpro inhibitors-modulators via negative image-based screening and computational simulations.
المؤلفون: Bhowmick S; Department of Chemical Technology, University of Calcutta, 92 A.P.C. Road, Kolkata, India., AlFaris NA; Nutrition and Food Science, Department of Physical Sport Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia. Electronic address: naalfaris@pnu.edu.sa., Zaidan ALTamimi J; Nutrition and Food Science, Department of Physical Sport Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia., ALOthman ZA; Chemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia., Patil PC; Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth Deemed University, Pune-Satara Road, Pune, India., Aldayel TS; Nutrition and Food Science, Department of Physical Sport Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia., Wabaidur SM; Chemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia., Saha A; Department of Chemical Technology, University of Calcutta, 92 A.P.C. Road, Kolkata, India. Electronic address: achintya_saha@yahoo.com.
المصدر: Computers in biology and medicine [Comput Biol Med] 2022 Jun; Vol. 145, pp. 105474. Date of Electronic Publication: 2022 Apr 01.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Elsevier Country of Publication: United States NLM ID: 1250250 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1879-0534 (Electronic) Linking ISSN: 00104825 NLM ISO Abbreviation: Comput Biol Med Subsets: MEDLINE
أسماء مطبوعة: Publication: New York : Elsevier
Original Publication: New York, Pergamon Press.
مواضيع طبية MeSH: SARS-CoV-2* , COVID-19 Drug Treatment*, Aniline Compounds ; Benzamides ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Naphthalenes ; Pandemics
مستخلص: Despite significant studies on the COVID-19 pandemic, scientists around the world are still battling to find a definitive therapy against the ongoing severe global health crisis. In this study, advanced computational approaches have been employed to identify bioactive food constituents as potential SARS-CoV-2 PLpro inhibitors-modulators. As a validated antiviral drug target, PLpro has gained tremendous attention for therapeutics developments. Therefore, targeting the multifunctional SARS-CoV-2 PLpro protein, ∼1039 bioactive dietary compounds have been screened extensively through novel techniques like negative image-based (NIB) screening and molecular docking approaches. In particular, the three different models of NIB screening have been generated and used to re-score the dietary compounds based on the negative image which is created by reversing the shape and electrostatics features of PLpro protein's ligand-binding cavity. Further, 100 ns molecular dynamics simulation has been performed and MM-GBSA based binding free energies have been estimated for the final proposed four dietary compounds (PC000550, PC000361, PC000558, and PC000573) as potential inhibitors/modulators of SARS-CoV-2 PLpro protein. Employed computational study outcome also has been compared with respect to the earlier experimentally investigated compound GRL0617 against SARS-CoV-2 PLpro protein, which suggests much greater interaction potential in terms of binding affinity and other energetic contributions for the proposed dietary compounds. Hence, the present study suggests that proposed dietary compounds can be suitable chemical entities for modulating the activity of PLpro protein or can be further utilized for optimizing or screening of novel chemical surrogates, however also needs experimental evaluation for entry in clinical studies for better assessment.
(Copyright © 2022 Elsevier Ltd. All rights reserved.)
References: J Comput Chem. 2005 Dec;26(16):1668-88. (PMID: 16200636)
J Med Chem. 2015 May 14;58(9):4066-72. (PMID: 25860834)
Antioxidants (Basel). 2019 Nov 22;8(12):. (PMID: 31766676)
Biophys Chem. 2021 Mar;270:106537. (PMID: 33450550)
ChemMedChem. 2022 Jan 5;17(1):e202100455. (PMID: 34423563)
ACS Pharmacol Transl Sci. 2020 Aug 04;3(5):1017-1019. (PMID: 33062954)
J Biomol Struct Dyn. 2022;40(20):9833-9847. (PMID: 34096457)
J Pharm Anal. 2020 Dec;10(6):546-559. (PMID: 32874702)
Proteins. 2004 May 1;55(2):383-94. (PMID: 15048829)
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)
Nat Microbiol. 2021 Apr;6(4):467-478. (PMID: 33727702)
Front Mol Biosci. 2020 Aug 04;7:174. (PMID: 32850963)
Adv Nutr. 2010 Nov;1(1):8-16. (PMID: 22043447)
J Chem Phys. 2020 Sep 21;153(11):115101. (PMID: 32962355)
J Mol Graph Model. 2022 Mar;111:108113. (PMID: 34959151)
PLoS One. 2021 May 19;16(5):e0251910. (PMID: 34010326)
Mil Med Res. 2020 Mar 13;7(1):11. (PMID: 32169119)
J Chem Inf Model. 2019 Aug 26;59(8):3584-3599. (PMID: 31290660)
Int J Mol Sci. 2019 Jun 06;20(11):. (PMID: 31174295)
J Med Virol. 2020 Sep;92(9):1542-1548. (PMID: 32181901)
J Mol Recognit. 2020 Jul;33(7):e2838. (PMID: 32060998)
Protein J. 2021 Apr;40(2):148-165. (PMID: 33421024)
J Gastroenterol Hepatol. 2017 Mar;32 Suppl 1:73-77. (PMID: 28244660)
Struct Chem. 2021;32(2):879-886. (PMID: 33106741)
Circulation. 2016 Jan 12;133(2):187-225. (PMID: 26746178)
J Comput Chem. 2009 Dec;30(16):2785-91. (PMID: 19399780)
ACS Cent Sci. 2021 Jul 28;7(7):1245-1260. (PMID: 34341772)
Precis Clin Med. 2021 Jan 18;4(1):1-16. (PMID: 33842834)
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)
Nucleic Acids Res. 2000 Jan 1;28(1):235-42. (PMID: 10592235)
Food Res Int. 2019 Nov;125:108646. (PMID: 31554120)
Mol Divers. 2021 Aug;25(3):1979-1997. (PMID: 33844135)
Curr Res Struct Biol. 2021;3:9-18. (PMID: 33319212)
Biochim Biophys Acta Mol Basis Dis. 2020 Oct 1;1866(10):165878. (PMID: 32544429)
Lancet Infect Dis. 2020 Jun;20(6):669-677. (PMID: 32240634)
Eur J Pharmacol. 2021 Jan 15;891:173759. (PMID: 33249077)
Front Chem. 2020 Nov 16;8:594009. (PMID: 33304884)
J Chem Inf Model. 2012 Aug 27;52(8):2079-88. (PMID: 22817270)
ACS Chem Neurosci. 2018 May 16;9(5):1128-1140. (PMID: 29300091)
Sci Rep. 2017 Mar 03;7:42717. (PMID: 28256516)
Chem Biol Drug Des. 2019 Oct;94(4):1799-1812. (PMID: 31260165)
Adv Drug Deliv Rev. 2001 Mar 1;46(1-3):3-26. (PMID: 11259830)
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)
Arch Biochem Biophys. 2021 Mar 30;700:108771. (PMID: 33485847)
Nature. 2020 Nov;587(7835):657-662. (PMID: 32726803)
Int J Biol Macromol. 2021 Oct 1;188:137-146. (PMID: 34364941)
Eur J Pharm Sci. 2019 Jun 15;134:31-59. (PMID: 30974173)
J Nutr. 2004 Sep;134(9):2492S-2498S. (PMID: 15333748)
Front Pharmacol. 2018 Mar 26;9:260. (PMID: 29632488)
J Mol Biol. 2016 Feb 22;428(4):720-725. (PMID: 26410586)
Nat Struct Biol. 2002 Sep;9(9):646-52. (PMID: 12198485)
Mol Nutr Food Res. 2019 Jan;63(1):e1800384. (PMID: 30176196)
J Biomol Struct Dyn. 2022 Apr;40(6):2395-2406. (PMID: 33103598)
Mol Divers. 2022 Aug;26(4):2189-2209. (PMID: 34591234)
Int J Mol Sci. 2020 May 23;21(10):. (PMID: 32456257)
J Comput Chem. 2010 Jan 30;31(2):455-61. (PMID: 19499576)
Comput Biol Med. 2020 Sep;124:103936. (PMID: 32738628)
J Med Virol. 2021 Apr;93(4):2406-2419. (PMID: 33347622)
Lancet. 2020 Feb 15;395(10223):497-506. (PMID: 31986264)
J Cheminform. 2011 Oct 07;3:33. (PMID: 21982300)
Crit Rev Food Sci Nutr. 2020;60(13):2174-2211. (PMID: 31267783)
RSC Adv. 2021 Oct 12;11(53):33380-33398. (PMID: 35497510)
J Mol Biol. 2003 Jul 18;330(4):891-913. (PMID: 12850155)
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)
J Biomol Struct Dyn. 2022 Apr;40(7):3071-3081. (PMID: 33200683)
Food Funct. 2018 Dec 13;9(12):6081-6095. (PMID: 30403220)
Mol Divers. 2022 Feb;26(1):389-407. (PMID: 34008129)
ACS Infect Dis. 2021 Jun 11;7(6):1457-1468. (PMID: 33570381)
Nucleic Acids Res. 2015 Jul 1;43(W1):W443-7. (PMID: 25873628)
Nat Commun. 2021 Jan 20;12(1):488. (PMID: 33473130)
J Chem Inf Model. 2009 Feb;49(2):492-502. (PMID: 19434847)
Front Nutr. 2018 Sep 21;5:87. (PMID: 30298133)
J Comput Aided Mol Des. 2015 Oct;29(10):989-1006. (PMID: 26407559)
Sci Adv. 2020 Oct 16;6(42):. (PMID: 33067239)
Mol Divers. 2022 Feb;26(1):309-329. (PMID: 33825097)
Am J Med. 2002 Dec 30;113 Suppl 9B:71S-88S. (PMID: 12566142)
فهرسة مساهمة: Keywords: Food compounds; MM-GBSA; Molecular docking; Molecular dynamics; SARS-CoV-2 PLpro; Virtual screening
المشرفين على المادة: 0 (5-amino-2-methyl-N-((R)-1-(1-naphthyl)ethyl)benzamide)
0 (Aniline Compounds)
0 (Benzamides)
0 (Naphthalenes)
تواريخ الأحداث: Date Created: 20220408 Date Completed: 20220519 Latest Revision: 20221216
رمز التحديث: 20240628
مُعرف محوري في PubMed: PMC8973019
DOI: 10.1016/j.compbiomed.2022.105474
PMID: 35395517
قاعدة البيانات: MEDLINE
الوصف
تدمد:1879-0534
DOI:10.1016/j.compbiomed.2022.105474