Understanding the electronic structure of the alkaloid in scorpion venom through drug adsorption and molecular docking studies on COVID-19 proteins
Electronic structure analysis of the alkaloid from scorpion venom (ASV) was studied at the B3LYP/6-311++G (d, p) level of theory. Vibrational analysis, molecular orbital analysis and the MEP and contour plot analysis show the reactivity and molecular stability of the compound. The measured frontier...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-12-01
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| Series: | Chemical Physics Impact |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2667022423001299 |
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| author | Anbumani Velmurugan Ilavarasi Francisxavier Paularokiadoss L. Mary Novena T. Pooventhiran Sultan Erkan Christian A. Celaya Renjith Thomas Dinakara Rao Ampasala Thayalaraj Christopher Jeyakumar |
| author_facet | Anbumani Velmurugan Ilavarasi Francisxavier Paularokiadoss L. Mary Novena T. Pooventhiran Sultan Erkan Christian A. Celaya Renjith Thomas Dinakara Rao Ampasala Thayalaraj Christopher Jeyakumar |
| author_sort | Anbumani Velmurugan Ilavarasi |
| collection | DOAJ |
| description | Electronic structure analysis of the alkaloid from scorpion venom (ASV) was studied at the B3LYP/6-311++G (d, p) level of theory. Vibrational analysis, molecular orbital analysis and the MEP and contour plot analysis show the reactivity and molecular stability of the compound. The measured frontier molecular orbital energy distance (ELUMO-EHOMO) is 4.12 eV. The reactive descriptors research found that the ASV molecule has a chemical hardness of 2.205 eV and an electronegativity of 3.325 eV, consistent with its biological activity. The calculated NLA parameters μo, αo, and β° values of the title molecule are 1.5009 Debye, −5.718 × 10-24 e.s.u, 2.984 × 10-30 e.s.u, respectively. The alkaloid from scorpion venom is found to form stable complexes with cyclodextrin. ASV was docked against the main proteases (MPro) and papain-like proteases (PLpro) of COVID-19. ASV has a Glide docking score of -8.017 kcal/mol with MPro and -5.091 kcal/mol with PLpro. ASV has a Prime MM-GBSA binding score of -51.74 kcal/mol with MPro and -32.19 kcal/mol with PLpro. The Glide and Prime results demonstrated that ASV has a stronger binding for MPro than PLpro protein. Furthermore, the major pharmacokinetic characteristics of ASV were predicted. ASV was found to have good drug-like properties with no violations. Since ASV binds to COVID-19 proteases, it could be used as an anti-COVID-19 agent. The outcomes of the study may have a substantial impact on the development of COVID-19 therapies. |
| first_indexed | 2024-03-09T02:01:40Z |
| format | Article |
| id | doaj.art-49a06201a5d6470abbf1d626bc77af7c |
| institution | Directory Open Access Journal |
| issn | 2667-0224 |
| language | English |
| last_indexed | 2024-03-09T02:01:40Z |
| publishDate | 2023-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Chemical Physics Impact |
| spelling | doaj.art-49a06201a5d6470abbf1d626bc77af7c2023-12-08T04:46:30ZengElsevierChemical Physics Impact2667-02242023-12-017100289Understanding the electronic structure of the alkaloid in scorpion venom through drug adsorption and molecular docking studies on COVID-19 proteinsAnbumani Velmurugan Ilavarasi0Francisxavier Paularokiadoss1L. Mary Novena2T. Pooventhiran3Sultan Erkan4Christian A. Celaya5Renjith Thomas6Dinakara Rao Ampasala7Thayalaraj Christopher Jeyakumar8Department of Bioinformatics, Pondicherry University, Puducherry, IndiaPG&Research Department of Chemistry, St. Joseph's College of Arts & Science (Autonomous), Cuddalore, IndiaDepartment of Physics, Stella Mary's College of Engineering, Azhikal, Kanniyakumari District, IndiaDepartment Chemistry, St Berchmans College (Autonomous), Changanassery, Kerala, IndiaDepartment Chemistry, Faculty of Science, Sivas Cumhuriyet University, Sivas, TurkeyCentro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Km 107 Carretera Tijuana-Ensenada, Ensenada, BC, C.P. 22800, MexicoDepartment Chemistry, St Berchmans College (Autonomous), Changanassery, Kerala, India; Corresponding authors.Department of Bioinformatics, Pondicherry University, Puducherry, IndiaPG&Research Department of chemistry, The American College (Autonomous), Madurai, India; Corresponding authors.Electronic structure analysis of the alkaloid from scorpion venom (ASV) was studied at the B3LYP/6-311++G (d, p) level of theory. Vibrational analysis, molecular orbital analysis and the MEP and contour plot analysis show the reactivity and molecular stability of the compound. The measured frontier molecular orbital energy distance (ELUMO-EHOMO) is 4.12 eV. The reactive descriptors research found that the ASV molecule has a chemical hardness of 2.205 eV and an electronegativity of 3.325 eV, consistent with its biological activity. The calculated NLA parameters μo, αo, and β° values of the title molecule are 1.5009 Debye, −5.718 × 10-24 e.s.u, 2.984 × 10-30 e.s.u, respectively. The alkaloid from scorpion venom is found to form stable complexes with cyclodextrin. ASV was docked against the main proteases (MPro) and papain-like proteases (PLpro) of COVID-19. ASV has a Glide docking score of -8.017 kcal/mol with MPro and -5.091 kcal/mol with PLpro. ASV has a Prime MM-GBSA binding score of -51.74 kcal/mol with MPro and -32.19 kcal/mol with PLpro. The Glide and Prime results demonstrated that ASV has a stronger binding for MPro than PLpro protein. Furthermore, the major pharmacokinetic characteristics of ASV were predicted. ASV was found to have good drug-like properties with no violations. Since ASV binds to COVID-19 proteases, it could be used as an anti-COVID-19 agent. The outcomes of the study may have a substantial impact on the development of COVID-19 therapies.http://www.sciencedirect.com/science/article/pii/S2667022423001299VenomAlkaloidDFTCOVID-19Molecular docking |
| spellingShingle | Anbumani Velmurugan Ilavarasi Francisxavier Paularokiadoss L. Mary Novena T. Pooventhiran Sultan Erkan Christian A. Celaya Renjith Thomas Dinakara Rao Ampasala Thayalaraj Christopher Jeyakumar Understanding the electronic structure of the alkaloid in scorpion venom through drug adsorption and molecular docking studies on COVID-19 proteins Chemical Physics Impact Venom Alkaloid DFT COVID-19 Molecular docking |
| title | Understanding the electronic structure of the alkaloid in scorpion venom through drug adsorption and molecular docking studies on COVID-19 proteins |
| title_full | Understanding the electronic structure of the alkaloid in scorpion venom through drug adsorption and molecular docking studies on COVID-19 proteins |
| title_fullStr | Understanding the electronic structure of the alkaloid in scorpion venom through drug adsorption and molecular docking studies on COVID-19 proteins |
| title_full_unstemmed | Understanding the electronic structure of the alkaloid in scorpion venom through drug adsorption and molecular docking studies on COVID-19 proteins |
| title_short | Understanding the electronic structure of the alkaloid in scorpion venom through drug adsorption and molecular docking studies on COVID-19 proteins |
| title_sort | understanding the electronic structure of the alkaloid in scorpion venom through drug adsorption and molecular docking studies on covid 19 proteins |
| topic | Venom Alkaloid DFT COVID-19 Molecular docking |
| url | http://www.sciencedirect.com/science/article/pii/S2667022423001299 |
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