دورية أكاديمية
أعرض في EDS

Rational Approach toward COVID-19's Main Protease Inhibitors: A Hierarchical Biochemoinformatics Analysis.

التفاصيل البيبلوغرافية
العنوان: Rational Approach toward COVID-19's Main Protease Inhibitors: A Hierarchical Biochemoinformatics Analysis.
المؤلفون: Bastos RS; Graduate Program in Medicinal Chemistry and Molecular Modeling, Federal University of Pará, Belém 66075-110, PA, Brazil.; Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapa 68903-419, AP, Brazil., de Aguiar CPO; Graduate Program in Medicinal Chemistry and Molecular Modeling, Federal University of Pará, Belém 66075-110, PA, Brazil., Cruz JN; Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapa 68903-419, AP, Brazil., Ramos RS; Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapa 68903-419, AP, Brazil., Kimani NM; Department of Physical Sciences, University of Embu, Embu P.O. Box 6-60100, Kenya.; Natural Product Chemistry and Computational Drug Discovery Laboratory, Embu P.O. Box 6-60100, Kenya., de Souza JSN; Chemistry Department, Federal University of Piauí, Teresina 64049-550, PI, Brazil., Chaves MH; Chemistry Department, Federal University of Piauí, Teresina 64049-550, PI, Brazil., de Freitas HF; Laboratory of Bioinformatics and Molecular Modeling (LaBiMM), Federal University of Bahia, Av. Barão de Jeremoabo, 147, Pharmacy College, Ondina, Salvador 40170-115, BA, Brazil., Pita SSR; Laboratory of Bioinformatics and Molecular Modeling (LaBiMM), Federal University of Bahia, Av. Barão de Jeremoabo, 147, Pharmacy College, Ondina, Salvador 40170-115, BA, Brazil., Santos CBRD; Graduate Program in Medicinal Chemistry and Molecular Modeling, Federal University of Pará, Belém 66075-110, PA, Brazil.; Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapa 68903-419, AP, Brazil.
المصدر: International journal of molecular sciences [Int J Mol Sci] 2024 Jun 18; Vol. 25 (12). Date of Electronic Publication: 2024 Jun 18.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Basel, Switzerland : MDPI, [2000-
مواضيع طبية MeSH: Molecular Docking Simulation* , SARS-CoV-2*/drug effects , Molecular Dynamics Simulation* , COVID-19 Drug Treatment* , Coronavirus 3C Proteases*/antagonists & inhibitors , Coronavirus 3C Proteases*/chemistry , Coronavirus 3C Proteases*/metabolism, Humans ; Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; Protease Inhibitors/chemistry ; Protease Inhibitors/pharmacology ; Hydrogen Bonding ; Ligands ; COVID-19/virology ; Protein Binding
مستخلص: This study investigated the potential of selected compounds as inhibitors of SARS-CoV-2 M pro through pharmacokinetic and toxicological analyses, molecular docking, and molecular dynamics simulations. In silico molecular docking simulations revealed promising ligands with favorable binding affinities for M pro , ranging from -6.2 to -9.5 kcal/mol. Moreover, molecular dynamics simulations demonstrated the stability of protein-ligand complexes over 200 ns, maintaining protein secondary structures. MM-PBSA analysis revealed favorable interactions between ligands and M pro , with negative binding energy values. Hydrogen bond formation capacity during molecular dynamics was confirmed, indicating consistent interactions with M pro catalytic residues. Based on these findings, selected ligands show promise for future studies in developing COVID-19 treatments.
Competing Interests: The authors declare no conflicts of interest.
References: BMC Complement Altern Med. 2018 Feb 05;18(1):50. (PMID: 29402248)
Cell Res. 2020 Aug;30(8):678-692. (PMID: 32541865)
Curr Opin Microbiol. 2004 Aug;7(4):412-9. (PMID: 15358261)
Biopolymers. 2006;84(6):595-604. (PMID: 17041919)
Proteins. 1991;9(1):56-68. (PMID: 2017436)
Proc Natl Acad Sci U S A. 2001 Aug 28;98(18):10037-41. (PMID: 11517324)
JAMA. 2020 May 12;323(18):1824-1836. (PMID: 32282022)
J Comput Aided Mol Des. 2023 Aug;37(8):357-371. (PMID: 37310542)
Science. 2020 Jun 19;368(6497):1331-1335. (PMID: 32321856)
J Comput Chem. 2005 Dec;26(16):1701-18. (PMID: 16211538)
Eur Biophys J. 2011 Jul;40(7):843-56. (PMID: 21533652)
Comput Biol Chem. 2020 May 28;87:107292. (PMID: 32485652)
J Phys Chem Lett. 2020 Jun 4;11(11):4413-4420. (PMID: 32406687)
Methods Mol Biol. 2015;1263:243-50. (PMID: 25618350)
Viruses. 2020 Apr 06;12(4):. (PMID: 32268515)
Bioinformatics. 2013 Apr 1;29(7):845-54. (PMID: 23407358)
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W486-91. (PMID: 21576229)
Int J Mol Sci. 2021 Oct 29;22(21):. (PMID: 34769170)
J Comput Chem. 2009 Dec;30(16):2785-91. (PMID: 19399780)
Molecules. 2019 Aug 14;24(16):. (PMID: 31416180)
J Mol Biol. 2005 Oct 14;353(1):38-52. (PMID: 16169013)
Comput Struct Biotechnol J. 2022;20:3336-3346. (PMID: 35720615)
Int J Mol Sci. 2023 May 16;24(10):. (PMID: 37240165)
J Korean Med Sci. 2020 Feb 17;35(6):e79. (PMID: 32056407)
Methods Mol Biol. 2018;1762:271-284. (PMID: 29594777)
Biosci Rep. 2020 Jun 26;40(6):. (PMID: 32441299)
Science. 2003 Jun 13;300(5626):1763-7. (PMID: 12746549)
J Biomol Struct Dyn. 2021 May;39(8):2904-2913. (PMID: 32306822)
Pharmaceuticals (Basel). 2023 Jan 09;16(1):. (PMID: 36678592)
Eur J Med Chem. 2014 Feb 12;73:225-32. (PMID: 24412498)
Anal Biochem. 2016 Sep 1;508:97-103. (PMID: 27365221)
Science. 2020 Apr 24;368(6489):409-412. (PMID: 32198291)
Genome Biol. 2016 May 09;17:99. (PMID: 27161042)
Rev Panam Salud Publica. 2020 Mar 20;44:e40. (PMID: 32256547)
Sci Rep. 2017 May 18;7(1):2118. (PMID: 28522849)
J Biomol Struct Dyn. 2021 Apr;39(7):2607-2616. (PMID: 32238094)
J Cheminform. 2011 Oct 07;3:33. (PMID: 21982300)
Biopolymers. 1983 Dec;22(12):2577-637. (PMID: 6667333)
J Phys Chem B. 2006 Mar 9;110(9):4393-8. (PMID: 16509740)
ACS Omega. 2023 Mar 24;8(13):11674-11699. (PMID: 37033812)
PLoS Biol. 2005 Oct;3(10):e324. (PMID: 16128623)
Nucleic Acids Res. 2015 Jan;43(Database issue):D364-8. (PMID: 25352545)
Molecules. 2023 Jan 19;28(3):. (PMID: 36770702)
J Chem Inf Model. 2014 Jul 28;54(7):1951-62. (PMID: 24850022)
Pharmaceuticals (Basel). 2023 Apr 18;16(4):. (PMID: 37111369)
Nature. 2020 Jun;582(7811):289-293. (PMID: 32272481)
Molecules. 2020 Mar 10;25(5):. (PMID: 32164183)
J Chem Inf Model. 2012 Nov 26;52(11):3099-105. (PMID: 23092397)
Wiley Interdiscip Rev Comput Mol Sci. 2016 Mar;6(2):147-172. (PMID: 27066112)
Cell. 2020 Apr 16;181(2):271-280.e8. (PMID: 32142651)
J Phys Chem Lett. 2020 Dec 17;11(24):10446-10453. (PMID: 33269932)
J Chem Phys. 2007 Jan 7;126(1):014101. (PMID: 17212484)
J Chem Theory Comput. 2011 Feb 8;7(2):525-37. (PMID: 26596171)
Curr Pharm Des. 2018;24(5):576-594. (PMID: 28699538)
Biophys J. 1998 Apr;74(4):1622-39. (PMID: 9545028)
فهرسة مساهمة: Keywords: SARS-CoV-2; binding affinity; drug development; molecular docking; molecular dynamics
المشرفين على المادة: EC 3.4.22.28 (Coronavirus 3C Proteases)
0 (Antiviral Agents)
0 (Protease Inhibitors)
0 (Ligands)
تواريخ الأحداث: Date Created: 20240627 Date Completed: 20240627 Latest Revision: 20240629
رمز التحديث: 20240629
مُعرف محوري في PubMed: PMC11204165
DOI: 10.3390/ijms25126715
PMID: 38928422
قاعدة البيانات: MEDLINE
الوصف
تدمد:1422-0067
DOI:10.3390/ijms25126715