Targeting mutation sites in the omicron variant of SARS-CoV-2 as potential therapeutic strategy against COVID-19 by antiretroviral drugs
The multiple mutation of the spike (S) protein of the Omicron SARS-CoV-2 variant is a major concern, as it has been implicated in the severity of COVID-19 and its complications. These mutations have been attributed to COVID-19-infected immune-compromised individuals, with HIV patients being suspecte...
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Elsevier
2024-12-01
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| Series: | Toxicology Reports |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2214750024002087 |
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| author | Ochuko L. Erukainure Aliyu Muhammad Rahul Ravichandran Musa M. Abarshi Sanusi B. Katsayal Murtala B. Abubakar Ya'qub U. Abiodun Olubunmi Atolani Robert Preissner Priyanka Banerjee |
| author_facet | Ochuko L. Erukainure Aliyu Muhammad Rahul Ravichandran Musa M. Abarshi Sanusi B. Katsayal Murtala B. Abubakar Ya'qub U. Abiodun Olubunmi Atolani Robert Preissner Priyanka Banerjee |
| author_sort | Ochuko L. Erukainure |
| collection | DOAJ |
| description | The multiple mutation of the spike (S) protein of the Omicron SARS-CoV-2 variant is a major concern, as it has been implicated in the severity of COVID-19 and its complications. These mutations have been attributed to COVID-19-infected immune-compromised individuals, with HIV patients being suspected to top the list. The present study investigated the mutation of the S protein of the omicron variant in comparison to the Delta and Wuhan variants. It also investigated the molecular interactions of antiretroviral drugs (ARVd) vis-à-vis dolutegravir, lamivudine, tenofovir-disoproxilfumarate and lenacapavir with the initiation and termination codons of the mRNAs of the mutated proteins of the omicron variant using computational tools. The complete genome sequences of the respective S proteins for omicron (OM066778.1), Delta (OK091006.1) and Wuhan (NC 045512.2) SARS-CoV-2 variants were retrieved from the National Center for Biotechnology Information (NCBI) database. Evolutionary analysis revealed high trends of mutations in the S protein of the omicron SARS-CoV-2 variant compared to the delta and Wuhan variants coupled with 68 % homology. The sequences of the translation initiation sites (TISs), translation termination sites (TTSs), high mutation region-1 (HMR1) and high region mutation-2 (HMR2) mRNAs were retrieved from the full genome of the omicron variant S protein. Molecular docking analysis revealed strong molecular interactions of ARVd with TISs, TTSs, HMR1 and HMR2 of the S protein mRNA. These results indicate mutations in the S protein of the Omicron SARS-CoV-2 variant compared to the Delta and Wuhan variants. These mutation points may present new therapeutic targets for COVID-19. |
| format | Article |
| id | doaj-art-00f7229047e248788e2a1f705839d9ac |
| institution | Kabale University |
| issn | 2214-7500 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Toxicology Reports |
| spelling | doaj-art-00f7229047e248788e2a1f705839d9ac2024-12-19T10:54:56ZengElsevierToxicology Reports2214-75002024-12-0113101825Targeting mutation sites in the omicron variant of SARS-CoV-2 as potential therapeutic strategy against COVID-19 by antiretroviral drugsOchuko L. Erukainure0Aliyu Muhammad1Rahul Ravichandran2Musa M. Abarshi3Sanusi B. Katsayal4Murtala B. Abubakar5Ya'qub U. Abiodun6Olubunmi Atolani7Robert Preissner8Priyanka Banerjee9Laser Research Centre, Faculty of Health Sciences, University of Johannesburg, Doornfontein 2028, South Africa; Corresponding authors.Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, Zaria, Kaduna State, Nigeria; Corresponding authors.DiSTABiF, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, Caserta 81100, ItalyDepartment of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, Zaria, Kaduna State, NigeriaDepartment of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, Zaria, Kaduna State, NigeriaCenter for Advanced Medical Research and Training (CAMRET), Usmanu Danfodiyo University, Sokoto, Nigeria; Department of Physiology, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria; Department of Physiology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat 123, OmanCenter for Advanced Medical Research and Training (CAMRET), Usmanu Danfodiyo University, Sokoto, Nigeria; Department of Physiology, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, NigeriaDepartment of Chemistry, University of Ilorin, Ilorin, NigeriaInstitute for Physiology, Charité and Science-IT– University Medicine Berlin, Berlin, GermanyInstitute for Physiology, Charité and Science-IT– University Medicine Berlin, Berlin, GermanyThe multiple mutation of the spike (S) protein of the Omicron SARS-CoV-2 variant is a major concern, as it has been implicated in the severity of COVID-19 and its complications. These mutations have been attributed to COVID-19-infected immune-compromised individuals, with HIV patients being suspected to top the list. The present study investigated the mutation of the S protein of the omicron variant in comparison to the Delta and Wuhan variants. It also investigated the molecular interactions of antiretroviral drugs (ARVd) vis-à-vis dolutegravir, lamivudine, tenofovir-disoproxilfumarate and lenacapavir with the initiation and termination codons of the mRNAs of the mutated proteins of the omicron variant using computational tools. The complete genome sequences of the respective S proteins for omicron (OM066778.1), Delta (OK091006.1) and Wuhan (NC 045512.2) SARS-CoV-2 variants were retrieved from the National Center for Biotechnology Information (NCBI) database. Evolutionary analysis revealed high trends of mutations in the S protein of the omicron SARS-CoV-2 variant compared to the delta and Wuhan variants coupled with 68 % homology. The sequences of the translation initiation sites (TISs), translation termination sites (TTSs), high mutation region-1 (HMR1) and high region mutation-2 (HMR2) mRNAs were retrieved from the full genome of the omicron variant S protein. Molecular docking analysis revealed strong molecular interactions of ARVd with TISs, TTSs, HMR1 and HMR2 of the S protein mRNA. These results indicate mutations in the S protein of the Omicron SARS-CoV-2 variant compared to the Delta and Wuhan variants. These mutation points may present new therapeutic targets for COVID-19.http://www.sciencedirect.com/science/article/pii/S2214750024002087AntiretroviralCOVID-19OmicronAnd SARS-CoV-2 |
| spellingShingle | Ochuko L. Erukainure Aliyu Muhammad Rahul Ravichandran Musa M. Abarshi Sanusi B. Katsayal Murtala B. Abubakar Ya'qub U. Abiodun Olubunmi Atolani Robert Preissner Priyanka Banerjee Targeting mutation sites in the omicron variant of SARS-CoV-2 as potential therapeutic strategy against COVID-19 by antiretroviral drugs Toxicology Reports Antiretroviral COVID-19 Omicron And SARS-CoV-2 |
| title | Targeting mutation sites in the omicron variant of SARS-CoV-2 as potential therapeutic strategy against COVID-19 by antiretroviral drugs |
| title_full | Targeting mutation sites in the omicron variant of SARS-CoV-2 as potential therapeutic strategy against COVID-19 by antiretroviral drugs |
| title_fullStr | Targeting mutation sites in the omicron variant of SARS-CoV-2 as potential therapeutic strategy against COVID-19 by antiretroviral drugs |
| title_full_unstemmed | Targeting mutation sites in the omicron variant of SARS-CoV-2 as potential therapeutic strategy against COVID-19 by antiretroviral drugs |
| title_short | Targeting mutation sites in the omicron variant of SARS-CoV-2 as potential therapeutic strategy against COVID-19 by antiretroviral drugs |
| title_sort | targeting mutation sites in the omicron variant of sars cov 2 as potential therapeutic strategy against covid 19 by antiretroviral drugs |
| topic | Antiretroviral COVID-19 Omicron And SARS-CoV-2 |
| url | http://www.sciencedirect.com/science/article/pii/S2214750024002087 |
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