دورية أكاديمية
Interactions between carbon nanotubes and external structures of SARS-CoV-2 using molecular docking and molecular dynamics.
العنوان: | Interactions between carbon nanotubes and external structures of SARS-CoV-2 using molecular docking and molecular dynamics. |
---|---|
المؤلفون: | Lobato JCM; Laboratory of Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, C. P. 479, 66075-110, Belém, PA, Brazil.; Proderna, Federal University of Pará, C. P. 479, 66075-110, Belém, PA, Brazil., Arouche TDS; Laboratory of Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, C. P. 479, 66075-110, Belém, PA, Brazil., Nero JD; Physics Faculty, Science Institute of Sciences (ICEN), Federal University of Pará, 66075-110, Belém, PA, Brazil., Filho T; Federal University of the South and Southeast of Pará. 68507-590, Marabá - PA, Brazil., Borges RDS; Pharmacy Faculty, Science Institute of Sciences (ICEN), Federal University of Pará, C. P. 479, 66075-110, Belém, PA, Brazil., Neto AMJC; Laboratory of Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, C. P. 479, 66075-110, Belém, PA, Brazil.; Physics Faculty, Science Institute of Sciences (ICEN), Federal University of Pará, 66075-110, Belém, PA, Brazil.; Chemistry and Biochemistry, The University of Texas at Arlington, Box 19065, 700 Planetarium Place, Room 130, Arlington, TX 76019-0065. |
المصدر: | Journal of molecular structure [J Mol Struct] 2023 Aug 15; Vol. 1286, pp. 135604. Date of Electronic Publication: 2023 Apr 18. |
نوع المنشور: | Journal Article |
اللغة: | English |
بيانات الدورية: | Publisher: Elsevier Country of Publication: Netherlands NLM ID: 0141747 Publication Model: Print-Electronic Cited Medium: Print ISSN: 0022-2860 (Print) Linking ISSN: 00222860 NLM ISO Abbreviation: J Mol Struct Subsets: PubMed not MEDLINE |
أسماء مطبوعة: | Original Publication: Amsterdam : Elsevier |
مستخلص: | Molecular modeling techniques are used to describe the process of interaction between nanotubes and the main structures of the Covid-19 virus: the envelope protein, the main protease, and the Spike glycoprotein. Molecular docking studies show that the ligands have interaction characteristics capable of adsorbing the structures. Molecular dynamics simulations provide information on the mean squared deviation of atomic positions between 0.5 and 3.0 Å. The Gibbs free energy model and solvent accessible surface area approaches are used. Through the results obtained through molecular dynamics simulations, it is noted that the zig-zag nanotube prefers to interact with E-pro, M-pro, and S-gly, respectively. Molecular couplings and free energy showed that the S-gly active site residues strongly interact with zigzag, chiral, and armchair nanotubes, in this order. The interactions demonstrated in this manuscript may predict some promising candidates for virus antagonists, which may be confirmed through experimental approaches. Competing Interests: The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: (© 2023 Published by Elsevier B.V.) |
References: | J Am Chem Soc. 2021 Mar 17;143(10):3959-3966. (PMID: 33657316) J Biomol Struct Dyn. 2021 Jul;39(10):3787-3792. (PMID: 32396771) J Phys Chem A. 2005 Mar 31;109(12):2937-41. (PMID: 16833612) Sci Rep. 2017 Feb 23;7:43286. (PMID: 28230179) J Comput Chem. 2010 Jan 30;31(2):455-61. (PMID: 19499576) J Am Chem Soc. 2002 Dec 18;124(50):15076-80. (PMID: 12475352) Phys Rev Lett. 2006 Feb 10;96(5):057001. (PMID: 16486971) In Silico Pharmacol. 2021 Jan 6;9(1):10. (PMID: 33432283) J Biomol Struct Dyn. 2022 Feb;40(3):1230-1245. (PMID: 32960159) IDrugs. 2010 Dec;13(12):938-48. (PMID: 21154154) Int J Occup Environ Med. 2020 Feb 5;11(2):65-71. (PMID: 32020915) J Am Chem Soc. 2004 Sep 15;126(36):11182-8. (PMID: 15355099) Ann Rheum Dis. 2020 Jun;79(6):734-736. (PMID: 32295786) J Am Chem Soc. 2005 May 25;127(20):7538-42. (PMID: 15898805) Nat Struct Biol. 2003 Dec;10(12):980. (PMID: 14634627) J Org Chem. 2012 Dec 7;77(23):10824-34. (PMID: 23153035) J Comput Chem. 2005 Dec;26(16):1668-88. (PMID: 16200636) Infez Med. 2020 Ahead of print Jun 1;28(2):174-184. (PMID: 32275259) Ann Hepatol. 2014 Jul-Aug;13(4):364-75. (PMID: 24927607) Nature. 2001 Jun 7;411(6838):665-9. (PMID: 11395762) Proc Natl Acad Sci U S A. 2010 Jul 6;107(27):12369-74. (PMID: 20566862) Drugs. 2006;66(9):1275-99. (PMID: 16827606) Ann Intensive Care. 2020 May 20;10(1):61. (PMID: 32436029) Sci Rep. 2021 Feb 10;11(1):3459. (PMID: 33568738) Amino Acids. 2022 Feb;54(2):205-213. (PMID: 34807314) Proc Natl Acad Sci U S A. 2006 Feb 28;103(9):3357-62. (PMID: 16492781) J Biol Chem. 1990 Aug 5;265(22):13240-7. (PMID: 2376594) Nutrition. 2021 Feb;82:111048. (PMID: 33277149) J Biomol Struct Dyn. 2021 Aug;39(13):4671-4685. (PMID: 32567995) J Am Chem Soc. 2001 Dec 26;123(51):12849-56. (PMID: 11749543) Clin Pharmacol Ther. 2020 Oct;108(4):762-765. (PMID: 32378737) J Chem Inf Model. 2022 Mar 28;62(6):1425-1436. (PMID: 35239339) J Am Chem Soc. 2010 Dec 1;132(47):16790-5. (PMID: 21062058) RSC Adv. 2021 Feb 2;11(10):5785-5800. (PMID: 35423109) J Am Chem Soc. 2021 Aug 4;143(30):11404-11422. (PMID: 34283611) Sci Rep. 2016 Apr 13;6:24027. (PMID: 27071308) Toxicol Lett. 2007 Jan 30;168(2):121-31. (PMID: 17169512) PLoS One. 2015 Mar 27;10(3):e0119264. (PMID: 25816325) Expert Opin Drug Discov. 2015 May;10(5):449-61. (PMID: 25835573) J Phys Chem B. 2015 Mar 19;119(11):4220-9. (PMID: 25692537) J Chem Inf Model. 2019 Jan 28;59(1):441-452. (PMID: 30516994) Drugs. 2003;63(8):769-802. (PMID: 12662125) Nutrition. 2021 Feb;82:111052. (PMID: 33290970) Biomaterials. 2011 Jan;32(1):144-51. (PMID: 20888630) Nat Rev Drug Discov. 2015 Feb;14(2):111-29. (PMID: 25614221) Nutrition. 2021 Mar;83:111089. (PMID: 33412367) Sci Rep. 2018 May 16;8(1):7711. (PMID: 29769553) J Enzyme Inhib Med Chem. 2020 Dec;35(1):145-151. (PMID: 31724441) Life Sci. 2020 Sep 1;256:117963. (PMID: 32535080) J Virol. 2013 Apr;87(7):3741-51. (PMID: 23325689) J Biomol Struct Dyn. 2022 Feb;40(2):696-711. (PMID: 32897138) Phys Chem Chem Phys. 2021 Jan 21;23(2):753-776. (PMID: 33427250) Expert Rev Anti Infect Ther. 2005 Feb;3(1):9-21. (PMID: 15757454) Mol Divers. 2022 Feb;26(1):171-181. (PMID: 33389441) J Nanosci Nanotechnol. 2020 Dec 1;20(12):7311-7323. (PMID: 32711596) J Comput Chem. 2010 Jul 15;31(9):1911-8. (PMID: 20082382) J Comput Chem. 2010 Mar;31(4):797-810. (PMID: 19569205) J Am Chem Soc. 2005 Mar 30;127(12):4388-96. (PMID: 15783221) J Am Chem Soc. 2019 Mar 20;141(11):4711-4720. (PMID: 30834751) Biophys J. 2006 Jun 15;90(12):4558-73. (PMID: 16565070) J Chem Theory Comput. 2017 Jul 11;13(7):3378-3387. (PMID: 28553983) Biophys J. 2006 Feb 15;90(4):1156-63. (PMID: 16299086) N Engl J Med. 2020 Nov 19;383(21):2041-2052. (PMID: 32706953) J Am Chem Soc. 2021 Jun 9;143(22):8333-8343. (PMID: 34039006) Sci Rep. 2021 Mar 2;11(1):4930. (PMID: 33654230) Nanomaterials (Basel). 2021 Feb 11;11(2):. (PMID: 33670119) Nature. 2020 May;581(7807):215-220. (PMID: 32225176) J Am Chem Soc. 2022 Feb 23;144(7):2905-2920. (PMID: 35142215) Math Program. 2016 Sep;159(1):81-107. (PMID: 27765996) Nat Nanotechnol. 2007 Feb;2(2):108-13. (PMID: 18654229) |
فهرسة مساهمة: | Keywords: Antiviral effect; Carbon nanotube; Molecular docking, Molecular dynamics, DFT, In silico study; SARS–CoV-2 |
تواريخ الأحداث: | Date Created: 20230424 Latest Revision: 20230516 |
رمز التحديث: | 20240628 |
مُعرف محوري في PubMed: | PMC10111146 |
DOI: | 10.1016/j.molstruc.2023.135604 |
PMID: | 37089815 |
قاعدة البيانات: | MEDLINE |
تدمد: | 0022-2860 |
---|---|
DOI: | 10.1016/j.molstruc.2023.135604 |