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Shafiq A, Khalid U, Abdur Rehman U, Abdullah Almuqri E, Muddassir M, Ahmad S, Khan MI, Khan A, Wei DQ. Structural basis for the mechanism of interaction of SARS-CoV-2 B.1.640.2 variant RBD with the host receptors hACE2 and GRP78. J Biomol Struct Dyn 2024; 42:2034-2042. [PMID: 37286365 DOI: 10.1080/07391102.2023.2220053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/09/2023] [Indexed: 06/09/2023]
Abstract
The inflicted chaos instigated by the SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) globally continues with the emergence of novel variants. The current global outbreak is aggravated by the manifestation of novel variants, which affect the effectiveness of the vaccine, attachment with hACE2 (human Angiotensin-converting enzyme 2) and immune evasion. Recently, a new variant named University Hospital Institute (IHU) (B.1.640.2) was reported in France in November 2021 and is spreading globally affecting public healthcare. The B.1.640.2 SARS-CoV-2 strain revealed 14 mutations and 9 deletions in spike protein. Thus, it is important to understand how these variations in the spike protein impact the communication with the host. A protein coupling approach along with molecular simulation protocols was used to interpret the variation in the binding of the wild type (WT) and B.1.640.2 variant with hACE2 and Glucose-regulating protein 78 (GRP78) receptors. The initial docking scores revealed a stronger binding of the B.1.640.2-RBD with both the hACE2 and GRP78. To further understand the crucial dynamic changes, we looked at the structural and dynamic characteristics and also explored the variations in the bonding networks between the WT and B.1.640.2-RBD (receptor-binding domain) in association with hACE2 and GRP78, respectively. Our findings revealed that the variant complex demonstrated distinct dynamic properties in contrast to the wild type due to the acquired mutations. Finally, to provide conclusive evidence on the higher binding by the B.1.640.2 variant the TBE was computed for each complex. For the WT with hACE2 the TBE was quantified to be-61.38 ± 0.96 kcal/mol and for B.1.640.2 variant the TBE was estimated to be -70.47 ± 1.00 kcal/mol. For the WT-RBD-GRP78 the TBE -was computed to be 32.32 ± 0.56 kcal/mol and for the B.1.640.2-RBD a TBE of -50.39 ± 0.88 kcal/mol was reported. This show that these mutations are the basis for higher binding and infectivity produced by B.1.640.2 variant and can be targeted for drug designing against it.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Athar Shafiq
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Ujala Khalid
- Fatima Jinnah Medical University, Lahore, Punjab, Pakistan
| | - Umar Abdur Rehman
- Aziz Fatimah Medical and Dental College, Faisalabad, Punjab, Pakistan
| | - Eman Abdullah Almuqri
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Maria Muddassir
- Institute of Molecular Biology & Biotechnology, The University of Lahore (UOL), Lahore, Punjab, Pakistan
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Idrees Khan
- Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Nayang, Henan, P.R. China
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Nayang, Henan, P.R. China
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Laboratory of Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
- Peng Cheng Laboratory, Shenzhen, Guangdong, P.R. China
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Petrof O, Fajgenblat M, Neyens T, Molenberghs G, Faes C. The doubling effect of COVID-19 cases on key health indicators. PLoS One 2022; 17:e0275523. [PMID: 36417418 PMCID: PMC9683546 DOI: 10.1371/journal.pone.0275523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 09/19/2022] [Indexed: 11/25/2022] Open
Abstract
From the beginning of the COVID-19 pandemic, researchers advised policy makers to make informed decisions towards the adoption of mitigating interventions. Key easy-to-interpret metrics applied over time can measure the public health impact of epidemic outbreaks. We propose a novel method which quantifies the effect of hospitalizations or mortality when the number of COVID-19 cases doubles. Two analyses are used, a country-by-country analysis and a multi-country approach which considers all countries simultaneously. The new measure is applied to several European countries, where the presence of different variants, vaccination rates and intervention measures taken over time leads to a different risk. Based on our results, the vaccination campaign has a clear effect for all countries analyzed, reducing the risk over time. However, the constant emergence of new variants combined with distinct intervention measures impacts differently the risk per country.
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Affiliation(s)
- Oana Petrof
- I-Biostat, DSI, Hasselt University, Diepenbeek, Belgium
- * E-mail:
| | - Maxime Fajgenblat
- Laboratory of Freshwater Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Thomas Neyens
- I-Biostat, DSI, Hasselt University, Diepenbeek, Belgium
- Leuven Biostatistics and Statistical Bioinformatics Centre (L-BioStat), KU Leuven, Leuven, Belgium
| | - Geert Molenberghs
- I-Biostat, DSI, Hasselt University, Diepenbeek, Belgium
- I-BioStat, KU Leuven University of Leuven, Leuven, Belgium
| | - Christel Faes
- I-Biostat, DSI, Hasselt University, Diepenbeek, Belgium
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Guérin P, Yahi N, Azzaz F, Chahinian H, Sabatier JM, Fantini J. Structural Dynamics of the SARS-CoV-2 Spike Protein: A 2-Year Retrospective Analysis of SARS-CoV-2 Variants (from Alpha to Omicron) Reveals an Early Divergence between Conserved and Variable Epitopes. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123851. [PMID: 35744971 PMCID: PMC9230616 DOI: 10.3390/molecules27123851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/09/2022] [Accepted: 06/13/2022] [Indexed: 12/17/2022]
Abstract
We analyzed the epitope evolution of the spike protein in 1,860,489 SARS-CoV-2 genomes. The structural dynamics of these epitopes was determined by molecular modeling approaches. The D614G mutation, selected in the first months of the pandemic, is still present in currently circulating SARS-CoV-2 strains. This mutation facilitates the conformational change leading to the demasking of the ACE2 binding domain. D614G also abrogated the binding of facilitating antibodies to a linear epitope common to SARS-CoV-1 and SARS-CoV-2. The main neutralizing epitope of the N-terminal domain (NTD) of the spike protein showed extensive structural variability in SARS-CoV-2 variants, especially Delta and Omicron. This epitope is located on the flat surface of the NTD, a large electropositive area which binds to electronegatively charged lipid rafts of host cells. A facilitating epitope located on the lower part of the NTD appeared to be highly conserved among most SARS-CoV-2 variants, which may represent a risk of antibody-dependent enhancement (ADE). Overall, this retrospective analysis revealed an early divergence between conserved (facilitating) and variable (neutralizing) epitopes of the spike protein. These data aid in the designing of new antiviral strategies that could help to control COVID-19 infection by mimicking neutralizing antibodies or by blocking facilitating antibodies.
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Affiliation(s)
| | - Nouara Yahi
- INSERM UMR_S 1072, Aix-Marseille University, CEDEX, 13015 Marseille, France; (N.Y.); (F.A.); (H.C.)
| | - Fodil Azzaz
- INSERM UMR_S 1072, Aix-Marseille University, CEDEX, 13015 Marseille, France; (N.Y.); (F.A.); (H.C.)
| | - Henri Chahinian
- INSERM UMR_S 1072, Aix-Marseille University, CEDEX, 13015 Marseille, France; (N.Y.); (F.A.); (H.C.)
| | - Jean-Marc Sabatier
- Inst Neurophysiopathol, Aix-Marseille University, CNRS, INP, CEDEX, 13005 Marseille, France;
| | - Jacques Fantini
- INSERM UMR_S 1072, Aix-Marseille University, CEDEX, 13015 Marseille, France; (N.Y.); (F.A.); (H.C.)
- Correspondence:
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Sokhna C, Brah S, Djimde A, Mouffok N, Zahraoui M, Ould Mohamed Salem Boukhary A, Bitam I, Cisse B, Thera M, Lekana-Douki JB, Adehossi E, Seydi M, Akiana J, Heikel J, Lagier JC, Mboup S, Mouyembe-Tamfum JJ, Parola P. COVID-19 in africa: what else? New Microbes New Infect 2022; 47:100982. [PMID: 35573042 PMCID: PMC9081042 DOI: 10.1016/j.nmni.2022.100982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 04/29/2022] [Accepted: 05/02/2022] [Indexed: 11/15/2022] Open
Affiliation(s)
- C. Sokhna
- VITROME, Campus International IRD-UCAD, Dakar, Senegal
| | - S. Brah
- Service de Médecine Interne, Hôpital Général de Référence, Niamey, Niger
| | - A. Djimde
- Malaria Research and Training Center, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - N. Mouffok
- Service des Maladies Infectieuses, Centre Hospitalier Universitaire, Oran, Algeria
| | - M. Zahraoui
- Service de Médecine Interne, Clinique De Vinci, Casablanca, Morocco
| | | | - I. Bitam
- Ecole Supérieure en Sciences de L'Aliment et des Industries Agroalimentaire, Direction Générale de La Recherche Scientifique et Développement Technologique, Ministère de L'enseignement Supérieur et de La Recherche Scientifique, Alger, Algeria
| | - B. Cisse
- Institut de Recherche en Santé, de Surveillance Epidemiologique et de Formation (IRESSEF), Dakar, Senegal
| | - M.A. Thera
- Malaria Research and Training Center, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - J.-B. Lekana-Douki
- Département de Parasitologie-Mycologie, Université des Sciences de La Santé (USS) Libreville, UNEEREP-CIRMF, Franceville, Gabon
| | | | - M. Seydi
- Service de Maladies Infectieuses et Tropicale, Centre Hospitalier Universitaire de Fann, Université Cheikh Anta Diop, Dakar, Senegal
| | - J. Akiana
- Faculté des Sciences et Techniques/Université Marien NGOUABI de Brazzaville, Democratic Republic of the Congo
| | - J. Heikel
- Service de Médecine Interne, Clinique De Vinci, Casablanca, Morocco
| | - J.-C. Lagier
- University Hospital Institute IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - S. Mboup
- Institut de Recherche en Santé, de Surveillance Epidemiologique et de Formation (IRESSEF), Dakar, Senegal
| | - J.-J. Mouyembe-Tamfum
- Département de Microbiologie, Faculté de Médecine, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - P. Parola
- University Hospital Institute IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
- Corresponding author: Philippe Parola, University Hospital Institute IHU-Méditerranée Infection, Marseille, France.
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