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Sultana N, Nagesha SN, Reddy CNL, Ramesh BN, Shyamalamma S, Shashidhara KS, Satish KM, Pradeep C, Vidyadhar GD. Computational analysis of affinity dynamics between the variants of SARS-CoV-2 spike protein (RBD) and human ACE-2 receptor. Virol J 2024; 21:88. [PMID: 38641844 PMCID: PMC11031966 DOI: 10.1186/s12985-024-02365-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 04/13/2024] [Indexed: 04/21/2024] Open
Abstract
The novel coronavirus SARS-CoV-2 resulted in a significant worldwide health emergency known as the COVID-19 pandemic. This crisis has been marked by the widespread of various variants, with certain ones causing notable apprehension. In this study, we harnessed computational techniques to scrutinize these Variants of Concern (VOCs), including various Omicron subvariants. Our approach involved the use of protein structure prediction algorithms and molecular docking techniques, we have investigated the effects of mutations within the Receptor Binding Domain (RBD) of SARS-CoV-2 and how these mutations influence its interactions with the human angiotensin-converting enzyme 2 (hACE-2) receptor. Further we have predicted the structural alterations in the RBD of naturally occurring SARS-CoV-2 variants using the tr-Rosetta algorithm. Subsequent docking and binding analysis employing HADDOCK and PRODIGY illuminated crucial interactions occurring at the Receptor-Binding Motif (RBM). Our findings revealed a hierarchy of increased binding affinity between the human ACE2 receptor and the various RBDs, in the order of wild type (Wuhan-strain) < Beta < Alpha < Gamma < Omicron-B.1.1.529 < Delta < Omicron-BA.2.12.1 < Omicron-BA.5.2.1 < Omicron-BA.1.1. Notably, Omicron-BA.1.1 demonstrated the highest binding affinity of -17.4 kcal mol-1 to the hACE2 receptor when compared to all the mutant complexes. Additionally, our examination indicated that mutations occurring in active residues of the Receptor Binding Domain (RBD) consistently improved the binding affinity and intermolecular interactions in all mutant complexes. Analysis of the differences among variants has laid a foundation for the structure-based drug design targeting the RBD region of SARS-CoV-2.
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Affiliation(s)
- Nishad Sultana
- Department of Plant Biotechnology, University of Agricultural Sciences, GKVK, Bangalore, 560 065, India
| | - S N Nagesha
- Department of Plant Biotechnology, College of Agriculture, Hassan, UAS, Bangalore, 573 225, India.
| | | | - B N Ramesh
- ICAR-PHT, UAS, GKVK, Bangalore, 560 065, India
| | - S Shyamalamma
- Department of Plant Biotechnology, University of Agricultural Sciences, GKVK, Bangalore, 560 065, India
| | - K S Shashidhara
- Department of Genetics and Plant Breeding, College of Agriculture, Hassan, UAS, Bangalore, 573 225, India
| | - K M Satish
- Department Biotechnology, KSNUAHS, Shivamogga, 577 412, India
| | - C Pradeep
- Department of Plant Biotechnology, University of Agricultural Sciences, GKVK, Bangalore, 560 065, India
| | - G D Vidyadhar
- Department of Plant Biotechnology, University of Agricultural Sciences, GKVK, Bangalore, 560 065, India
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Ozden B, Şamiloğlu E, Özsan A, Erguven M, Yükrük C, Koşaca M, Oktayoğlu M, Menteş M, Arslan N, Karakülah G, Barlas AB, Savaş B, Karaca E. Benchmarking the accuracy of structure-based binding affinity predictors on Spike-ACE2 deep mutational interaction set. Proteins 2024; 92:529-539. [PMID: 37991066 DOI: 10.1002/prot.26645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/25/2023] [Accepted: 11/13/2023] [Indexed: 11/23/2023]
Abstract
Since the start of COVID-19 pandemic, a huge effort has been devoted to understanding the Spike (SARS-CoV-2)-ACE2 recognition mechanism. To this end, two deep mutational scanning studies traced the impact of all possible mutations across receptor binding domain (RBD) of Spike and catalytic domain of human ACE2. By concentrating on the interface mutations of these experimental data, we benchmarked six commonly used structure-based binding affinity predictors (FoldX, EvoEF1, MutaBind2, SSIPe, HADDOCK, and UEP). These predictors were selected based on their user-friendliness, accessibility, and speed. As a result of our benchmarking efforts, we observed that none of the methods could generate a meaningful correlation with the experimental binding data. The best correlation is achieved by FoldX (R = -0.51). When we simplified the prediction problem to a binary classification, that is, whether a mutation is enriching or depleting the binding, we showed that the highest accuracy is achieved by FoldX with a 64% success rate. Surprisingly, on this set, simple energetic scoring functions performed significantly better than the ones using extra evolutionary-based terms, as in Mutabind and SSIPe. Furthermore, we demonstrated that recent AI approaches, mmCSM-PPI and TopNetTree, yielded comparable performances to the force field-based techniques. These observations suggest plenty of room to improve the binding affinity predictors in guessing the variant-induced binding profile changes of a host-pathogen system, such as Spike-ACE2. To aid such improvements we provide our benchmarking data at https://github.com/CSB-KaracaLab/RBD-ACE2-MutBench with the option to visualize our mutant models at https://rbd-ace2-mutbench.github.io/.
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Affiliation(s)
- Burcu Ozden
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Eda Şamiloğlu
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Atakan Özsan
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Mehmet Erguven
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Can Yükrük
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Mehdi Koşaca
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Melis Oktayoğlu
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Muratcan Menteş
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Nazmiye Arslan
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Gökhan Karakülah
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Ayşe Berçin Barlas
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Büşra Savaş
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Ezgi Karaca
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
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Erabi G, Faridzadeh A, Parvin A, Deravi N, Rahmanian M, Fathi M, Aleebrahim‐Dehkordi E, Rezaei N. SARS-CoV-2 Omicron (BA.4, BA.5) variant: Lessons learned from a new variant during the COVID-19 pandemic. Health Sci Rep 2024; 7:e1873. [PMID: 38332930 PMCID: PMC10851086 DOI: 10.1002/hsr2.1873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 01/05/2024] [Accepted: 01/21/2024] [Indexed: 02/10/2024] Open
Abstract
Background and Aim In late 2021, the world faced the rapid spread of the SARS-CoV-2 Omicron variant, which quickly became the variant of concern. In April 2022, two new lineages of Omicron (BA.4/BA.5) emerged from Africa, where they caused the fifth wave of infection. Method We searched PubMed, Google Scholar, and Scopus online databases up to December 2023 for founding relevant studies. Results BA.4 and BA.5 subgroups, with changes in the spike protein, have a greater ability to escape from the immune system, which was possible with the help of L452R and F486V mutations. Epidemiologically, these evolving subtypes show similarities to seasonal influenza but with higher mortality rates. The symptoms of these subgroups are different from the previous types in the form of upper respiratory symptoms. Antiviral treatments, the use of antibodies such as bebtelovimab, and the development of vaccines are promising. Conclusion Consequently, we must continue to be vigilant in our joint surveillance efforts against COVID-19 in diagnosis and treatment.
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Affiliation(s)
- Gisou Erabi
- Student Research CommitteeUrmia University of Medical SciencesUrmiaIran
| | - Arezoo Faridzadeh
- Department of Immunology and AllergyMashhad University of Medical SciencesMashhadIran
- Immunology Research CenterMashhad University of Medical SciencesMashhadIran
| | - Ali Parvin
- Student Research CommitteeUrmia University of Medical SciencesUrmiaIran
| | - Niloofar Deravi
- Student Research Committee, School of MedicineShahid Beheshti University of Medical SciencesTehranIran
- Systematic Review and Meta‐Analysis Expert Group (SRMEG)Universal Scientific Education and Research Network (USERN)TehranIran
| | - Mohammad Rahmanian
- Student Research Committee, School of MedicineShahid Beheshti University of Medical SciencesTehranIran
- Systematic Review and Meta‐Analysis Expert Group (SRMEG)Universal Scientific Education and Research Network (USERN)TehranIran
| | - Mobina Fathi
- Student Research Committee, School of MedicineShahid Beheshti University of Medical SciencesTehranIran
- Systematic Review and Meta‐Analysis Expert Group (SRMEG)Universal Scientific Education and Research Network (USERN)TehranIran
| | - Elahe Aleebrahim‐Dehkordi
- Medical Plants Research Center, Basic Health Sciences instituteShahrekord University of Medical SciencesShahrekordIran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical CenterTehran University of Medical SciencesTehranIran
- Department of Immunology, School of MedicineTehran University of Medical SciencesTehranIran
- Network of Immunity in Infection, Malignancy, and Autoimmunity (NIIMA)Universal Scientific Education and Research Network (USERN)TehranIran
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Majeed A, Tahir Ul Qamar M, Maryam A, Mirza MU, Alhussain L, Al Otaibi SO, Almatroudi A, Allemailem KS, Alrumaihi F, Aloliqi AA, Alshehri FF. Structural insights into the mechanism of resistance to bicalutamide by the clinical mutations in androgen receptor in chemo-treatment resistant prostate cancer. J Biomol Struct Dyn 2024; 42:1181-1190. [PMID: 37144757 DOI: 10.1080/07391102.2023.2208203] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 03/28/2023] [Indexed: 05/06/2023]
Abstract
Despite advanced diagnosis and detection technologies, prostate cancer (PCa) is the most prevalent neoplasms in males. Dysregulation of the androgen receptor (AR) is centrally involved in the tumorigenesis of PCa cells. Acquisition of drug resistance due to modifications in AR leads to therapeutic failure and relapse in PCa. An overhaul of comprehensive catalogues of cancer-causing mutations and their juxta positioning on 3D protein can help in guiding the exploration of small drug molecules. Among several well-studied PCa-specific mutations, T877A, T877S and H874Y are the most common substitutions in the ligand-binding domain (LBD) of the AR. In this study, we combined structure as well as dynamics-based in silico approaches to infer the mechanistic effect of amino acid substitutions on the structural stability of LBD. Molecular dynamics simulations allowed us to unveil a possible drug resistance mechanism that acts through structural alteration and changes in the molecular motions of LBD. Our findings suggest that the resistance to bicalutamide is partially due to increased flexibility in the H12 helix, which disturbs the compactness, thereby reducing the affinity for bicalutamide. In conclusion, the current study helps in understanding the structural changes caused by mutations and could assist in the drug development process.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdul Majeed
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Muhammad Tahir Ul Qamar
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Arooma Maryam
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, MA, USA
| | - Muhammad Usman Mirza
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
| | - Laila Alhussain
- Department of Biology, College of Science, Qassim University, Buraydah, Saudi Arabia
| | - Seham Obaid Al Otaibi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Khaled S Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Abdulaziz A Aloliqi
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Faez Falah Alshehri
- Department of Medical Laboratories, College of Applied Medical Sciences, Shaqra University, Aldawadmi, Saudi Arabia
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Zhao X, Gao F. Novel Omicron Variants Enhance Anchored Recognition of TMEM106B: A New Pathway for SARS-CoV-2 Cellular Invasion. J Phys Chem Lett 2024; 15:671-680. [PMID: 38206837 DOI: 10.1021/acs.jpclett.3c03296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
The recent discovery that TMEM106B serves as a receptor mediating ACE2-independent SARS-CoV-2 entry into cells deserves attention, especially in the background of the frequent emergence of mutant strains. Here, the structure-dynamic features of this novel pathway are dissected deeply. Our investigation revealed that the large loop (RBD@471-491) could anchor TMEM106B, which was then firmly locked by another loop (RBD@444-451). The novel and widely disseminated Omicron variants (BA.2.86/EG.5.1) affect the anchoring recognition of proteins, with BA.2.86 being more likely to impact cells with limited or undetectable ACE2 expression. The large loop of the EG.5.1 variant captures TMEM106B poorly due to impaired electrostatic complementarity. Furthermore, we emphasize that antibody design against these two loops could enhance the protection of ACE2 low-expressing cells according to the alanine scanning mutagenesis of multiple antibodies. We hope this study will provide a novel perspective for the prevention and treatment against this new viral invasion pathway.
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Affiliation(s)
- Xiaoyu Zhao
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
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Pashameah RA, Soltane R, Sayed AM. A novel inhibitor of SARS-CoV infection: Lactulose octasulfate interferes with ACE2-Spike protein binding. Heliyon 2024; 10:e23222. [PMID: 38163229 PMCID: PMC10754899 DOI: 10.1016/j.heliyon.2023.e23222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024] Open
Abstract
The ongoing challenge of managing coronaviruses, particularly SARS-CoV-2, necessitates the development of effective antiviral agents. This study introduces Lactulose octasulfate (LOS), a sulfated disaccharide, demonstrating significant antiviral activity against key coronaviruses including SARS-CoV-2, SARS-CoV, and MERS-CoV. We hypothesize LOS operates extracellularly, targeting the ACE2-S-protein axis, due to its low cellular permeability. Our investigation combines biolayer interferometry (BLI), isothermal titration calorimetry (ITC)-based experiments with in silico studies, revealing LOS's ability to reduce SARS-CoV-2's RBD's affinity for ACE2 in a dose-dependent manner, and bind tightly to ACE2 without inhibiting its enzymatic activity. Gaussian accelerated molecular dynamics simulations (GaMD) further supported these findings, illustrating LOS's potential as a broad-spectrum antiviral agent against current and future coronavirus strains, meriting in vivo and clinical exploration.
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Affiliation(s)
- Rami Adel Pashameah
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Raya Soltane
- Department of Biology, Adham University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Ahmed M. Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, 62513 Beni-Suef, Egypt
- Department of Pharmacognosy, collage of Pharmacy, Almaaqal University, 61014 Basra, Iraq
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Lin J, Anjum Huma F, Irfan A, Ali SS, Waheed Y, Mohammad A, Munir M, Khan A, Wei DQ. Structural plasticity of omicron BA.5 and BA.2.75 for enhanced ACE-dependent entry into cells. J Biomol Struct Dyn 2023; 41:10762-10773. [PMID: 36541923 DOI: 10.1080/07391102.2022.2158944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
The current study investigated the binding variations among the wilt type, Omicron sub-variants BA.2.75 and BA.5, using protein-protein docking, protein structural graphs (P SG), and molecular simulation methods. HADDOCK predicted docking scores and dissociation constant (KD) revealed tighter binding of these sub-variants in contrast to the WT. Further investigation revealed variations in the hub residues, protein sub-networks, and GlobalMetapath in these variants as compared to the WT. A very unusual dynamic for BA.2.75 and BA.5 was observed, and secondary structure transition can also be witnessed in the loops (44-505). The results show that the flexibility of these three loops is increased by the mutations as an allosteric effect and thus enhances the chances of bonding with the nearby residues to connect and form a stable connection. Furthermore, the additional hydrogen bonding contacts steer the robust binding of these variants in contrast to the wild type. The total binding free energy for the wild type was calculated to be -61.38 kcal/mol, while for BA.2.75 and BA.5 variants the T BE was calculated to be -70.42 kcal/mol and 69.78 kcal/mol, respectively. We observed that the binding of BA.2.75 is steered by the electrostatic interactions while the BA.5 additional contacts are due to the vdW (Van der Waal) energy. From these findings, it can be observed the Spike (S) protein is undergoing structural adjustments to bind efficiently to the hACE2 (human angiotensin-converting enzyme 2) receptor and, in turn, increase entry to the host cells. The current study will aid the development of structure-based drugs against these variants.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Junqi Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | | | - Aiza Irfan
- Rawalpindi Medical University, Punjab, Pakistan
| | - Syed Shujait Ali
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Yasir Waheed
- Office of Research, Innovation & Commercialization, Shaheed Zulfiqar Ali Bhutto Medical University (SZABMU), Islamabad, Pakistan
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
| | - 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, Zhongguancun Scientific Park, Nanyang, 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, Zhongguancun Scientific Park, Nanyang, Henan, P.R. China
- Peng Cheng Laboratory, Nashan District, Shenzhen, Guangdong, P.R China
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de Souza AS, de Souza RF, Guzzo CR. Cooperative and structural relationships of the trimeric Spike with infectivity and antibody escape of the strains Delta (B.1.617.2) and Omicron (BA.2, BA.5, and BQ.1). J Comput Aided Mol Des 2023; 37:585-606. [PMID: 37792106 DOI: 10.1007/s10822-023-00534-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/11/2023] [Indexed: 10/05/2023]
Abstract
Herein, we conducted simulations of trimeric Spike from several SARS-CoV-2 variants of concern (Delta and Omicron sub-variants BA.2, BA.5, and BQ.1) and investigated the mechanisms by which specific mutations confer resistance to neutralizing antibodies. We observed that the mutations primarily affect the cooperation between protein domains within and between protomers. The substitutions K417N and L452R expand hydrogen bonding interactions, reducing their interaction with neutralizing antibodies. By interacting with nearby residues, the K444T and N460K mutations in the SpikeBQ.1 variant potentially reduces solvent exposure, thereby promoting resistance to antibodies. We also examined the impact of D614G, P681R, and P681H substitutions on Spike protein structure that may be related to infectivity. The D614G substitution influences communication between a glycine residue and neighboring domains, affecting the transition between up- and -down RBD states. The P681R mutation, found in the Delta variant, enhances correlations between protein subunits, while the P681H mutation in Omicron sub-variants weakens long-range interactions that may be associated with reduced fusogenicity. Using a multiple linear regression model, we established a connection between inter-protomer communication and loss of sensitivity to neutralizing antibodies. Our findings underscore the importance of structural communication between protein domains and provide insights into potential mechanisms of immune evasion by SARS-CoV-2. Overall, this study deepens our understanding of how specific mutations impact SARS-CoV-2 infectivity and shed light on how the virus evades the immune system.
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Affiliation(s)
- Anacleto Silva de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, Cidade Universitária, Sao Paulo, SP, 5508-900, Brazil.
| | - Robson Francisco de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, Cidade Universitária, Sao Paulo, SP, 5508-900, Brazil
| | - Cristiane Rodrigues Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, Cidade Universitária, Sao Paulo, SP, 5508-900, Brazil.
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Wu F, Lin C, Han Y, Zhou D, Chen K, Yang M, Xiao Q, Zhang H, Li W. Multi-omic analysis characterizes molecular susceptibility of receptors to SARS-CoV-2 spike protein. Comput Struct Biotechnol J 2023; 21:5583-5600. [PMID: 38034398 PMCID: PMC10681948 DOI: 10.1016/j.csbj.2023.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 11/05/2023] [Accepted: 11/05/2023] [Indexed: 12/02/2023] Open
Abstract
In the post COVID-19 era, new SARS-CoV-2 variant strains may continue emerging and long COVID is poised to be another public health challenge. Deciphering the molecular susceptibility of receptors to SARS-CoV-2 spike protein is critical for understanding the immune responses in COVID-19 and the rationale of multi-organ injuries. Currently, such systematic exploration remains limited. Here, we conduct multi-omic analysis of protein binding affinities, transcriptomic expressions, and single-cell atlases to characterize the molecular susceptibility of receptors to SARS-CoV-2 spike protein. Initial affinity analysis explains the domination of delta and omicron variants and demonstrates the strongest affinities between BSG (CD147) receptor and most variants. Further transcriptomic data analysis on 4100 experimental samples and single-cell atlases of 1.4 million cells suggest the potential involvement of BSG in multi-organ injuries and long COVID, and explain the high prevalence of COVID-19 in elders as well as the different risks for patients with underlying diseases. Correlation analysis validated moderate associations between BSG and viral RNA abundance in multiple cell types. Moreover, similar patterns were observed in primates and validated in proteomic expressions. Overall, our findings implicate important therapeutic targets for the development of receptor-specific vaccines and drugs for COVID-19.
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Affiliation(s)
- Fanjie Wu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Chenghao Lin
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Yutong Han
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Dingli Zhou
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Kang Chen
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Minglei Yang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Department of Pathology, First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Qinyuan Xiao
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Haiyue Zhang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Weizhong Li
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China
- Center for Precision Medicine, Sun Yat-sen University, Guangzhou 510080, China
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11
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de Souza AS, Amorim VMDF, de Souza RF, Guzzo CR. Molecular dynamics simulations of the spike trimeric ectodomain of the SARS-CoV-2 Omicron variant: structural relationships with infectivity, evasion to immune system and transmissibility. J Biomol Struct Dyn 2023; 41:9326-9343. [PMID: 36345794 DOI: 10.1080/07391102.2022.2142296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 10/24/2022] [Indexed: 11/11/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron is currently the most prevalent SARS-CoV-2 variant worldwide. Herein, we calculated molecular dynamics simulations of the trimeric spikeWT and SpikeBA.1 for 300 ns. Our results show that SpikeBA.1 has more conformational flexibility than SpikeWT. Our principal component analysis (PCA) allowed us to observe a broader spectrum of different conformations for SpikeBA.1, mainly at N-terminal domain (NTD) and receptor-binding domain (RBD). Such increased flexibility could contribute to decreased neutralizing antibody recognition of this variant. Our molecular dynamics data show that the RBDBA.1 easily visits an up-conformational state and the prevalent D614G mutation is pivotal to explain molecular dynamics results for this variant because to lost hydrogen bonding interactions between the residue pairs K854SC/D614SC, Y837MC/D614MC, K835SC/D614SC, T859SC/D614SC. In addition, SpikeBA.1 residues near the furin cleavage site are more flexible than in SpikeWT, probably due to P681H and D614G substitutions. Finally, dynamical cross-correlation matrix (DCCM) analysis reveals that D614G and P681H may allosterically affect the cleavage site S1/S2. Conversely, S2' site may be influenced by residues located between NTD and RBD of a neighboring protomer of the SpikeWT. Such communication may be lost in SpikeBA.1, explaining the changes of the cell tropism in the viral infection. In addition, the movements of the NTDWT and NTDBA.1 may modulate the RBD conformation through allosteric effects. Taken together, our results explain how the structural aspects may explain the observed gains in infectivity, immune system evasion and transmissibility of the Omicron variant.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anacleto Silva de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Robson Francisco de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Cristiane Rodrigues Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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12
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Nguyen H, Nguyen HL, Lan PD, Thai NQ, Sikora M, Li MS. Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation. Chem Soc Rev 2023; 52:6497-6553. [PMID: 37650302 DOI: 10.1039/d1cs01170g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the devastating global COVID-19 pandemic announced by WHO in March 2020. Through unprecedented scientific effort, several vaccines, drugs and antibodies have been developed, saving millions of lives, but the fight against COVID-19 continues as immune escape variants of concern such as Delta and Omicron emerge. To develop more effective treatments and to elucidate the side effects caused by vaccines and therapeutic agents, a deeper understanding of the molecular interactions of SARS-CoV-2 with them and human cells is required. With special interest in computational approaches, we will focus on the structure of SARS-CoV-2 and the interaction of its spike protein with human angiotensin-converting enzyme-2 (ACE2) as a prime entry point of the virus into host cells. In addition, other possible viral receptors will be considered. The fusion of viral and human membranes and the interaction of the spike protein with antibodies and nanobodies will be discussed, as well as the effect of SARS-CoV-2 on protein synthesis in host cells.
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Affiliation(s)
- Hung Nguyen
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
| | - Hoang Linh Nguyen
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty of Environmental and Natural Sciences, Duy Tan University, Da Nang 550000, Vietnam
| | - Pham Dang Lan
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, 729110 Ho Chi Minh City, Vietnam
- Faculty of Physics and Engineering Physics, VNUHCM-University of Science, 227, Nguyen Van Cu Street, District 5, 749000 Ho Chi Minh City, Vietnam
| | - Nguyen Quoc Thai
- Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Vietnam
| | - Mateusz Sikora
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
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13
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Pashameah RA, Soltane R, Sayed AM. Discovery of raffinose sulfate as a potential SARS CoV-2 inhibitor via blocking its binding with angiotensin converting enzyme 2. Int J Biol Macromol 2023; 248:125818. [PMID: 37473891 DOI: 10.1016/j.ijbiomac.2023.125818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/23/2023] [Accepted: 07/11/2023] [Indexed: 07/22/2023]
Abstract
The present study aimed to characterize the possible binding sites on the SARS CoV-2 RBD-ACE2 complex and to highlight sulfated oligosaccharides as potential anti-SARS CoV-2 via inducing RBD-ACE2 complex destabilization and dissociation. By combining pharmacophore-based and structural-based virtual screening approaches we were able to discover raffinose sulfate (RS) as a potential antiviral sulfated oligosaccharide against two SARS CoV-2 variants (i.e., wild type and Omicron) (IC50 = 4.45 ± 0.28 μM and 4.65 ± 0.32 μM, respectively). Upon MD simulation, RS was able to establish stable binding at the RBD-ACE2 interface inducing a rapid dissociation. Accordingly, and by using bio-layer interferometry (BLI) assays, RS was able to significantly weaken the affinity between RBD (of both variants) and ACE2. Additionally, we found that RS has a poor cellular permeability indicating that its interaction with the RBD-ACE2 complex may be the main mechanism by which it mediates its antiviral activity against SARS CoV-2. Despite its proposed interaction with the RBD-ACE2 complex, RS did not show any inhibitory activity against ACE2 catalytic activity. In light of these findings, the RS scaffold can be further developed into a novel anti-SARS CoV-2 drug with improved activity and tolerability in comparison with other sulfated polysaccharides e.g., heparin and heparan.
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Affiliation(s)
- Rami Adel Pashameah
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah 21955, Saudi Arabia.
| | - Raya Soltane
- Department of Basic Sciences, Adham University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia.
| | - Ahmed M Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, 62513 Beni-Suef, Egypt.
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Wang J, Fatima Muhammad S, Aman S, Khan A, Munir S, Khan M, Mohammad A, Waheed Y, Munir M, Guo L, Chen L, Wei DQ. Structural communication fingerprinting and dynamic investigation of RBD-hACE2 complex from BA.1 × AY.4 recombinant variant (Deltacron) of SARS-CoV-2 to decipher the structural basis for enhanced transmission. J Biomol Struct Dyn 2023; 41:7665-7676. [PMID: 36129018 DOI: 10.1080/07391102.2022.2123399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/05/2022] [Indexed: 10/14/2022]
Abstract
The BA.1 × AY.4 recombinant variant (Deltacron) continues to inflict chaos globally due to its rapid transmission and infectivity. To decipher the mechanism of pathogenesis by the BA.1 × AY.4 recombinant variant (Deltacron), a protein coupling, protein structural graphs (PSG), residue communication and all atoms simulation protocols were used. We observed that the bonding network is altered by this variant; engaging new residues that helps to robustly bind. HADDOCK docking score for the wild type has been previously reported to be -111.8 ± 1.5 kcal/mol while the docking score for the Deltacron variant was calculated to be -128.3 ± 2.5 kcal/mol. The protein structural graphs revealed variations in the hub residues, number of nodes, inter and intra residues communities, and path communication perturbation caused by the acquired mutations in the Deltacron-RBD thus alter the binding approach and infectivity. Moreover, the dynamic behaviour reported a highly flexible structure with enhanced residues flexibility particularly by the loops required for interaction with ACE2. It was observed that these mutations have altered the secondary structure of the RBD mostly transited to the loops thus acquired higher flexible dynamics than the native structure during the simulation. The total binding free energy for each of these complexes, that is, WT-RBD and Deltacron-RBD were reported to be -61.38 kcal/mol and -70.47 kcal/mol. Protein's motion revealed a high trace value in the Deltacron variant that clearly depict more structural flexibility. The broad range of phase space covered by the Deltacron variant along PC1 and PC2 suggests that these mutations are important in contributing conformational heterogeneity or flexibility that consequently help the variant to bind more efficiently than the wild type. The current study provides a basis for structure-based drug designing against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jiangang Wang
- The Nanyang Central Hospital, Gongnong Road, Nanyang, Henan, China
| | | | - Shafaq Aman
- King Edward Medical University, Lahore, Punjab, Pakistan
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
- Zhongguancun Scientific Park, Meixi, Zhongjing Research and Industrialization Institute of Chinese Medicine, Nanyang, Henan, P.R. China
| | - Sadaf Munir
- Combined Military Hospital (CMH), Lahore, Punjab, Pakistan
| | - Mazhar Khan
- The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China (USTC), Collaborative Innovation Center of Genetics and Development, Hefei, Anhui, China
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Kuwait
| | - Yasir Waheed
- Office of Research, Innovation, and Commercialization (ORIC), Shaheed Zulfiqar Ali Bhutto Medical University (SZABMU), Islamabad, Pakistan
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Lancaster University, United Kingdom
| | - Lisha Guo
- Zhongjing Chinese Medicine College, Nayang Institute of Technology, Nanyang, China
| | - Lei Chen
- Biyang First High School, Wenming Road, Biyang, Henan, China
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
- Zhongguancun Scientific Park, Meixi, Zhongjing Research and Industrialization Institute of Chinese Medicine, Nanyang, Henan, P.R. China
- Peng Cheng Laboratory, Shenzhen, Guangdong, P.R China
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Suleman M, Murtaza A, Khan H, Rashid F, Alshammari A, Ali L, Khan A, Wei DQ. The XBB.1.5 slightly increase the binding affinity for host receptor ACE2 and exhibit strongest immune escaping features: molecular modeling and free energy calculation. Front Mol Biosci 2023; 10:1153046. [PMID: 37325478 PMCID: PMC10264657 DOI: 10.3389/fmolb.2023.1153046] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/15/2023] [Indexed: 06/17/2023] Open
Abstract
Introduction: The current XBB variant of SARS-CoV-2 with the strongest immune escaping properties is currently the most dominant variant circulating around the world. With the emergence of XBB global morbidities and mortalities have raised again. In the current scenario, it was highly required to delineate the binding capabilities of NTD of XBB subvariant towards human neutralizing antibodies and to dig out the binding affinity of RBD of XBB subvariant with ACE2 receptor. Materials and Methods: The current study uses molecular interaction and simulation-based approaches to decipher the binding mechanism of RBD with ACE2 and mAb interaction with NTD of the spike protein. Results: Molecular docking of the Wild type NTD with mAb revealed a docking score of -113.2 ± 0.7 kcal/mol while XBB NTD docking with mAb reported -76.2 ± 2.3 kcal/mol. On the other hand, wild-type RBD and XBB RBD with ACE2 receptor demonstrated docking scores of -115.0 ± 1.5 kcal/mol and -120.8 ± 3.4 kcal/mol respectively. Moreover, the interaction network analysis also revealed significant variations in the number of hydrogen bonds, salt-bridges, and non-bonded contacts. These findings were further validated by computing the dissociation constant (KD). Molecular simulation analysis such as RMSD, RMSF, Rg and hydrogen bonding analysis revealed variation in the dynamics features of the RBD and NTD complexes due to the acquired mutations. Furthermore, the total binding energy for the wild-type RBD in complex with ACE2 reported -50.10 kcal/mol while XBB-RBD coupled with ACE2 reported -52.66 kcal/mol respectively. This shows though the binding of XBB is slightly increased but due to the variation in the bonding network and other factors makes the XBB variant to enter into the host cell efficiently than the wild type. On the other hand, the total binding free energy for the wildtype NTD-mAb was calculated to be -65.94 kcal/mol while for XBB NTD-mAb was reported to be -35.06 kcal/mol respectively. The significant difference in the total binding energy factors explains that the XBB variant possess stronger immune evasion properties than the others variants and wild type. Conclusions: The current study provides structural features for the XBB variant binding and immune evasion which can be used to design novel therapeutics.
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Affiliation(s)
- Muhammad Suleman
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | | | - Maria
- D. G. Khan Medical College, D. G. Khan, Punjab, Pakistan
| | - Haji Khan
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Farooq Rashid
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Liaqat Ali
- Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, TX, United States
| | - Abbas Khan
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nayang, Henan, China
| | - Dong-Qing Wei
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nayang, Henan, China
- Peng Cheng Laboratory, Shenzhen, Guangdong, China
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Shahab M, Akter S, Sarkar MMH, Banu TA, Goswami B, Chowdhury SF, Naser SR, Habib MA, Shaikh AA, Saki M, Zheng G, Khan MS. Computational design of medicinal compounds to inhibit RBD-hACE2 interaction in the Omicron variant: unveiling a vulnerable target site. Inform Med Unlocked 2023; 40:101281. [PMID: 37265644 PMCID: PMC10210851 DOI: 10.1016/j.imu.2023.101281] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/22/2023] [Accepted: 05/22/2023] [Indexed: 06/03/2023] Open
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, has globally affected both human health and economy. Several variants with a high potential for reinfection and the ability to evade immunity were detected shortly after the initial reported case of COVID-19. A total of 30 mutations in the spike protein (S) have been reported in the SARS-CoV-2 (BA.2) variant in India and South Africa, while half of these mutations are in the receptor-binding domain and have spread rapidly throughout the world. Drug repurposing offers potential advantages over the discovery of novel drugs, and one is that it can be delivered quickly without lengthy assessments and time-consuming clinical trials. In this study, computational drug design, such as pharmacophore-based virtual screening and MD simulation has been concentrated, in order to find a novel small molecular inhibitor that prevents hACE2 from binding to the receptor binding domain (RBD). three medicinal compound databases: North-East African, North African, and East African were screened and carried out a multi-step screening approach that identified three compounds, which are thymoquinol 2-O-beta-glucopyranoside (C1), lanneaflavonol (C2), and naringenin-4'-methoxy-7-O-Alpha-L-rhamnoside (C3), with excellent anti-viral properties against the RBD of the omicron variant. Furthermore, PAIN assay interference, computation bioactivity prediction, binding free energy, and dissociation constant were used to validate the top hits, which indicated good antiviral activity. The three compounds that were found may be useful against COVID-19, though more research is required. These findings could aid the development of novel therapeutic drugs against the emerging Omicron variant of SARS-CoV-2.
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Affiliation(s)
- Muhammad Shahab
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Shahina Akter
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | | | - Tanjina Akhtar Banu
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Barna Goswami
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | | | - Showti Raheel Naser
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Md Ahashan Habib
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Aftab Ali Shaikh
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Morteza Saki
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Guojun Zheng
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Md Salim Khan
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
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Li Y, Yang M, Nan Y, Wang J, Wang S, Cui D, Guo J, He P, Dai W, Zhou S, Zhang Y, Ma W. SARS-CoV-2 spike host cell surface exposure promoted by a COPI sorting inhibitor. Acta Pharm Sin B 2023:S2211-3835(23)00123-5. [PMID: 37360012 PMCID: PMC10110937 DOI: 10.1016/j.apsb.2023.04.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/26/2023] [Accepted: 04/10/2023] [Indexed: 06/28/2023] Open
Abstract
Via an insufficient coat protein complex I (COPI) retrieval signal, the majority of SARS-CoV-2 spike (S) is resident in host early secretory organelles and a tiny amount is leaked out in cell surface. Only surface-exposed S can be recognized by B cell receptor (BCR) or anti-S therapeutic monoclonal antibodies (mAbs) that is the trigger step for B cell activation after S mRNA vaccination or infected cell clearance by S mAbs. Now, a drug strategy to promote S host surface exposure is absent. Here, we first combined structural and biochemical analysis to characterize S COPI sorting signals. A potent S COPI sorting inhibitor was then invented, evidently capable of promoting S surface exposure and facilitating infected cell clearance by S antibody-dependent cellular cytotoxicity (ADCC). Importantly, with the inhibitor as a probe, we revealed Omicron BA.1 S is less cell surface exposed than prototypes because of a constellation of S folding mutations, possibly corresponding to its ER chaperone association. Our findings not only suggest COPI is a druggable target against COVID-19, but also highlight SARS-CoV-2 evolution mechanism driven by S folding and trafficking mutations.
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Affiliation(s)
- Yiqun Li
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Mingrui Yang
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Yanan Nan
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Jiaming Wang
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Sanjiao Wang
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Dongxiao Cui
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Jiajian Guo
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Pengfei He
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Wenxin Dai
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Shuqi Zhou
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Yue Zhang
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Wenfu Ma
- School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China
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18
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Singh JK, Anand S, Srivastava SK. Is BF.7 more infectious than other Omicron subtypes: Insights from structural and simulation studies of BF.7 spike RBD variant. Int J Biol Macromol 2023; 238:124154. [PMID: 36965551 PMCID: PMC10036297 DOI: 10.1016/j.ijbiomac.2023.124154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 03/26/2023]
Abstract
Fear of a fresh infection wave and a global health issue in the ongoing COVID-19 pandemic have been rekindled by the appearance of two new novel variants BF.7 and BA.4/5 of Omicron lineages. Predictions of increased antibody evasion capabilities and transmissibility have been recognised in addition to the existing lineages (BA.1.1, BA.2, BA.2.12.1 and BA.3) as cause for worry. In comparison to Omicron, BA.4 and BF.7 share nine mutations in the spike protein, Leu371Phe, Thr376Ala, Asp405Asn, Arg408Ser, Ser446Gly, Leu452Arg, Phe486Val, Arg493Gln, Ser496Gly, whereas BF.7 contains an additional mutation, Arg346Thr, in the receptor binding domain (RBD) region. Due to the critical need for analysis and data on the BA.4 and BF.7 variants, we have computationally analyzed the interaction pattern between the Omicron, BA.4 and BF.7 RBD and angiotensin-converting enzyme 2 (ACE2) to determine the influence of these unique mutations on the structures, functions, and binding affinity of RBD towards ACE2. These analyses also allow to compare molecular models to previously reported data to evaluate the robustness of our methods for quick prediction of emerging future variants. The docking results reveal that BA.4 and BF.7 have particularly strong interactions with ACE2 when compared to Omicron, as shown by several parameters such as salt bridge, hydrogen bond, and non-bonded interactions. In addition, the estimations of binding free energy corroborated the findings further. BA.4 and BF.7 were found to bind to ACE2 with similar affinities (-72.14 and - 71.54 kcal/mol, respectively) and slightly stronger than Omicron (-70.04 kcal/mol). The differences in the binding pattern between the Omicron, BA.4 and BF.7 variant complexes indicated that the BA.4 and BF.7 RBD substitutions Asp405Asn, Ser446Gly, Leu452Arg, Phe486Val and Arg493Gln caused additional interactions with ACE2. In addition, normal mode analyses also indicate more stable conformations of BA.4 and BF.7 RBDs against human ACE2. Based on these structural and simulation analyses, we hypothesized that these changes may affect the binding affinity of BA.4 and BF.7 with ACE2.
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Affiliation(s)
- Jaikee Kumar Singh
- Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Off Jaipur-Ajmer Expressway, Jaipur, Rajasthan 303007, India
| | - Shashi Anand
- Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Off Jaipur-Ajmer Expressway, Jaipur, Rajasthan 303007, India
| | - Sandeep Kumar Srivastava
- Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Off Jaipur-Ajmer Expressway, Jaipur, Rajasthan 303007, India.
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Alhadrami HA, Sayed AM, Hassan HM, Rateb ME. Aloin A inhibits SARS CoV-2 replication by targeting its binding with ACE2 - Evidence from modeling-supported molecular dynamics simulation. J Biomol Struct Dyn 2023; 41:11647-11656. [PMID: 36755429 DOI: 10.1080/07391102.2023.2175262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/01/2023] [Indexed: 02/10/2023]
Abstract
The current study aimed to expand on the recently published results and assess the inhibitory efficacy of aloin A against SARS CoV-2. In vitro testing of aloin A against SARS CoV-2 proteases (i.e., MPro and PLPro) showed weak to moderate activity (IC50 = 68.56 ± 1.13 µM and 24.77 ± 1.57 µM, respectively). However, aloin A was able to inhibit the replication of SARS CoV-2 in Vero E6 cells efficiently with an IC50 of 0.095 ± 0.022 µM. Depending on the reported poor permeability of aloin A alongside its insignificant protease inhibitory activities presented in this study, we ran a number of extensive virtual screenings and physics-based simulations to determine the compound's potential mode of action. As a result, RBD-ACE2 was identified as a key target for aloin A. Results from 600 ns-long molecular dynamics (MD) simulation experiments pointed to aloin A's role as an RBD-ACE2 destabilizer. Therefore, the results of this work may pave the way for further development of this scaffold and the eventual production of innovative anti-SARS CoV-2 medicines with several mechanisms of action.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hani A Alhadrami
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Molecular Diagnostic Laboratory, King Abdulaziz University Hospital, King Abdulaziz University, Jeddah, Saudi Arabia
- King Fahd Medical Research Center, King Abdulaziz University Hospital, King Abdulaziz University , Jeddah, Saudi Arabia
| | - Ahmed M Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt
| | - Hossam M Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Mostafa E Rateb
- School of Computing, Engineering & Physical Sciences, University of the West of Scotland, Paisley, Scotland
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Khan A, Heng W, Imran K, Zhu G, Ji J, Zhang Y, Guan X, Ge G, Wei DQ. Discovery of Isojacareubin as a covalent inhibitor of SARS-CoV-2 main protease using structural and experimental approaches. J Med Virol 2023; 95:e28542. [PMID: 36727647 DOI: 10.1002/jmv.28542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 02/03/2023]
Abstract
The ongoing pandemic with the emergence of immune evasion potential and, particularly, the current omicron subvariants intensified the situation further. Although vaccines are available, the immune evasion capabilities of the recent variants demand further efficient therapeutic choices to control the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Hence, considering the necessity of the small molecule inhibitor, we target the main protease (3CLpro), which is an appealing target for the development of antiviral drugs against SARS-CoV-2. High-throughput molecular in silico screening of South African natural compounds database reported Isojacareubin and Glabranin as the potential inhibitors for the main protease. The calculated docking scores were reported to be -8.47 and -8.03 kcal/mol, respectively. Moreover, the structural dynamic assessment reported that Isojacareubin in complex with 3CLpro exhibit a more stable dynamic behavior than Glabranin. Inhibition assay indicated that Isojacareubin could inhibit SARS-CoV-2 3CLpro in a time- and dose-dependent manner, with half maximal inhibitory concentration values of 16.00 ± 1.35 μM (60 min incubation). Next, the covalent binding sites of Isojacareubin on SARS-CoV-2 3CLpro was identified by biomass spectrometry, which reported that Isojacareubin can covalently bind to thiols or Cysteine through Michael addition. To evaluate the inactivation potency of Isojacareubin, the inactivation kinetics was further investigated. The inactivation kinetic curves were plotted according to various concentrations with gradient-ascending incubation times. The KI value of Isojacareubin was determined as 30.71 μM, whereas the Kinact value was calculated as 0.054 min-1 . These results suggest that Isojacareubin is a covalent inhibitor of SARS-CoV-2 3CLpro .
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Affiliation(s)
- 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, Zhongguancun Scientific Park, Meixi, Nayang, Henan, P.R., China
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R., China
| | - Wang Heng
- International School of Cosmetics, School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, P.R., China
| | - Kashif Imran
- Services Institute of Medical Sciences, Lahore, Punjab, Pakistan
| | - Guanghao Zhu
- Shanghai Frontiers Science Center for Chinese Medicine Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jun Ji
- Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, P.R., China
| | - Yani Zhang
- Peng Cheng Laboratory, Vanke Cloud City, Nashan District, Shenzhen, Guangdong, P.R., China
| | - Xiaoqing Guan
- Shanghai Frontiers Science Center for Chinese Medicine Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Guangbo Ge
- Shanghai Frontiers Science Center for Chinese Medicine Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 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, Zhongguancun Scientific Park, Meixi, Nayang, Henan, P.R., China
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R., China
- Peng Cheng Laboratory, Vanke Cloud City, Nashan District, Shenzhen, Guangdong, P.R., China
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21
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Hanifa M, Salman M, Fatima M, Mukhtar N, Almajhdi FN, Zaman N, Suleman M, Ali SS, Waheed Y, Khan A. Mutational analysis of the spike protein of SARS-COV-2 isolates revealed atomistic features responsible for higher binding and infectivity. Front Cell Dev Biol 2023; 10:940863. [PMID: 36733340 PMCID: PMC9888553 DOI: 10.3389/fcell.2022.940863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 12/30/2022] [Indexed: 01/18/2023] Open
Abstract
Introduction: The perpetual appearance of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-COV-2), and its new variants devastated the public health and social fabric around the world. Understanding the genomic patterns and connecting them to phenotypic attributes is of great interest to devise a treatment strategy to control this pandemic. Materials and Methods: In this regard, computational methods to understand the evolution, dynamics and mutational spectrum of SARS-CoV-2 and its new variants are significantly important. Thus, herein, we used computational methods to screen the genomes of SARS-CoV-2 isolated from Pakistan and connect them to the phenotypic attributes of spike protein; we used stability-function correlation methods, protein-protein docking, and molecular dynamics simulation. Results: Using the Global initiative on sharing all influenza data (GISAID) a total of 21 unique mutations were identified, among which five were reported as stabilizing while 16 were destabilizing revealed through mCSM, DynaMut 2.0, and I-Mutant servers. Protein-protein docking with Angiotensin-converting enzyme 2 (ACE2) and monoclonal antibody (4A8) revealed that mutation G446V in the receptor-binding domain; R102S and G181V in the N-terminal domain (NTD) significantly affected the binding and thus increased the infectivity. The interaction pattern also revealed significant variations in the hydrogen bonding, salt bridges and non-bonded contact networks. The structural-dynamic features of these mutations revealed the global dynamic trend and the finding energy calculation further established that the G446V mutation increases the binding affinity towards ACE2 while R102S and G181V help in evading the host immune response. The other mutations reported supplement these processes indirectly. The binding free energy results revealed that wild type-RBD has a TBE of -60.55 kcal/mol while G446V-RBD reported a TBE of -73.49 kcal/mol. On the other hand, wild type-NTD reported -67.77 kcal/mol of TBE, R102S-NTD reported -51.25 kcal/mol of TBE while G181V-NTD reported a TBE of -63.68 kcal/mol. Conclusions: In conclusion, the current findings revealed basis for higher infectivity and immune evasion associated with the aforementioned mutations and structure-based drug discovery against such variants.
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Affiliation(s)
- Muhammad Hanifa
- Centre for Biotechnology and Microbiology, University of Swat, Charbagh, Khyber Pakhtunkhwa, Pakistan
| | | | | | - Naila Mukhtar
- Department of Botany, University of Okara, Punjab, Pakistan
| | - Fahad N. Almajhdi
- COVID-19 Virus Research Chair, Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Nasib Zaman
- Centre for Biotechnology and Microbiology, University of Swat, Charbagh, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Suleman
- Centre for Biotechnology and Microbiology, University of Swat, Charbagh, Khyber Pakhtunkhwa, Pakistan
| | - Syed Shujait Ali
- Centre for Biotechnology and Microbiology, University of Swat, Charbagh, Khyber Pakhtunkhwa, Pakistan
| | - Yasir Waheed
- Office of Research, Innovation and Commercialization, Shaheed Zulfiqar Ali Bhutto Medical University (SZABMU), Islamabad, Pakistan,Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon,*Correspondence: Yasir Waheed, ; Abbas Khan,
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China,*Correspondence: Yasir Waheed, ; Abbas Khan,
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22
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Wang H, Wang Z, Ma L, Zhu X, Li B, Huang Y, Li J, Sun M, Shi L, Yao Y. S Trimer Derived from SARS-CoV-2 B.1.351 and B.1.618 Induced Effective Immune Response against Multiple SARS-CoV-2 Variants. Vaccines (Basel) 2023; 11:193. [PMID: 36680037 DOI: 10.3390/vaccines11010193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/30/2022] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
The spread of SARS-CoV-2 and its variants leads to a heavy burden on healthcare and the global economy, highlighting the need for developing vaccines that induce broad immunity against coronavirus. Here, we explored the immunogenicity of monovalent or bivalent spike (S) trimer subunit vaccines derived from SARS-CoV-2 B.1.351 (S1-2P) or/and B.1. 618 (S2-2P) in Balb/c mice. Both S1-2P and S2-2P elicited anti-spike antibody responses, and alum adjuvant induced higher levels of antibodies than Addavax adjuvant. The dose responses of the vaccines on immunogenicity were evaluated in vivo. A low dose of 5 μg monovalent recombinant protein or 2.5 μg bivalent vaccine triggered high-titer antibodies that showed cross-activity to Beta, Delta, and Gamma RBD in mice. The third immunization dose could boost (1.1 to 40.6 times) high levels of cross-binding antibodies and elicit high titers of neutralizing antibodies (64 to 1024) prototype, Beta, Delta, and Omicron variants. Furthermore, the vaccines were able to provoke a Th1-biased cellular immune response. Significantly, at the same antigen dose, S1-2P immune sera induced stronger broadly neutralizing antibodies against prototype, Beta, Delta, and Omicron variants compared to that induced by S2-2P. At the same time, the low dose of bivalent vaccine containing S2-2P and S1-2P (2.5 μg for each antigen) significantly improved the cross-neutralizing antibody responses. In conclusion, our results showed that monovalent S1-2P subunit vaccine or bivalent vaccine (S1-2P and S2-2P) induced potent humoral and cellular responses against multiple SARS-CoV-2 variants and provided valuable information for the development of recombinant protein-based SARS-CoV-2 vaccines that protect against emerging SARS-CoV-2 variants.
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23
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Abeywardhana S, Premathilaka M, Bandaranayake U, Perera D, Peiris LDC. In silico study of SARS-CoV-2 spike protein RBD and human ACE-2 affinity dynamics across variants and Omicron subvariants. J Med Virol 2023; 95:e28406. [PMID: 36519577 PMCID: PMC9877981 DOI: 10.1002/jmv.28406] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 11/07/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022]
Abstract
The coronavirus disease 2019 virus outbreak continues worldwide, with many variants emerging, some of which are considered variants of concern (VOCs). The WHO designated Omicron as a VOC and assigned it under variant B.1.1.529. Here, we used computational studies to examine the VOCs, including Omicron subvariants, and one variant of interest. Here we found that the binding affinity of human receptor angiotensin-converting enzyme 2 (hACE2) and receptor-binding domain (RBDs) increased in the order of wild type (Wuhan-strain) < Beta < Alpha < OmicronBA.5 < Gamma < Delta < Omicron BA.2.75 < BA.1 < BA.3 < BA.2. Interactions between docked complexes revealed that the RBD residue positions like 452, 478, 493, 498, 501, and 505 are crucial in creating strong interactions with hACE2. Omicron BA.2 shows the highest binding capacity to the hACE2 receptor among all the mutant complexes. The BA.5's L452R, F486V, and T478K mutation significantly impact the interaction network in the BA.5 RBD-hACE2 interface. Here for the first time, we report the His505, an active residue on the RBD forming a salt bridge in the BA.2, leading to increased mutation stability. When the active RBD residues are mutated, binding affinity and intermolecular interactions increase across all mutant complexes. By examining the differences in different variants, this study may provide a solid foundation for structure-based drug design for newly emerging variants.
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Affiliation(s)
- Shamali Abeywardhana
- Department of Zoology, Faculty of Applied SciencesUniversity of Sri JayewardenepuraNugegodaSri Lanka
| | - Malinda Premathilaka
- Department of Chemistry, Faculty of Applied SciencesUniversity of Sri JayewardenepuraNugegodaSri Lanka
| | - Upeka Bandaranayake
- Genetics & Molecular Biology Unit (Center for Biotechnology), Faculty of Applied SciencesUniversity of Sri JayewardenepuraNugegodaSri Lanka
| | - Deshan Perera
- Department of Biochemistry & Molecular Biology, Cumming School of MedicineUniversity of CalgaryCalgaryAlbertaCanada
| | - L. Dinithi C. Peiris
- Department of Zoology/Genetics & Molecular Biology Unit (Center for Biotechnology), Faculty of Applied SciencesUniversity of Sri JayewardenepuraNugegodaSri Lanka
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24
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Semenov VA, Krivdin LB. The Development of Pharmacophore Models for the Search of New Natural Inhibitors of SARS-CoV-2 Spike RBD-ACE2 Binding Interface. Molecules 2022; 27. [PMID: 36558067 DOI: 10.3390/molecules27248938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
To date, some succeeding variants of SARS-CoV-2 have become more contagious. This virus is known to enter human cells by binding the receptor-binding domain (RBD) of spike protein with the angiotensin-converting enzyme 2 (ACE2), the latter being a membrane protein that regulates the renin-angiotensin system. Since the host cell receptor plays a critical role in viral entry, inhibition of the RBD-ACE2 complex is a promising strategy for preventing COVID-19 infection. In the present communication, we propose and utilize an approach based on the generation of a complex of pharmacophore models and subsequent Induced Fit Docking (IFD) to identify potential inhibitors of the main binding sites of the Omicron SARS-CoV-2 RBD(S1)-ACE2 complex (PDB ID: 7T9L) among a number of natural products of various types and origins. Several natural compounds have been found to provide a high affinity for the receptor of interest. It is expected that the present results will stimulate further research aimed at the development of specialized drugs against this virus.
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25
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Sharma H, Ilyas A, Chowdhury A, Poddar NK, Chaudhary AA, Shilbayeh SAR, Ibrahim AA, Khan S. Does COVID-19 lockdowns have impacted on global dengue burden? A special focus to India. BMC Public Health 2022; 22:1402. [PMID: 35869470 PMCID: PMC9304795 DOI: 10.1186/s12889-022-13720-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/27/2022] [Indexed: 12/12/2022] Open
Abstract
Background The world has been battling several vector-borne diseases since time immemorial. Socio-economic marginality, precipitation variations and human behavioral attributes play a major role in the proliferation of these diseases. Lockdown and social distancing have affected social behavioral aspects of human life and somehow impact on the spread of vector borne diseases. This article sheds light into the relationship between COVID-19 lockdown and global dengue burden with special focus on India. It also focuses on the interconnection of the COVID-19 pandemic (waves 1 and 2) and the alteration of human behavioral patterns in dengue cases. Methods We performed a systematic search using various resources from different platforms and websites, such as Medline; Pubmed; PAHO; WHO; CDC; ECDC; Epidemiology Unit Ministry of Health (Sri Lanka Government); NASA; NVBDCP from 2015 until 2021. We have included many factors, such as different geographical conditions (tropical climate, semitropic and arid conditions); GDP rate (developed nations, developing nations, and underdeveloped nations). We also categorized our data in order to conform to COVID-19 duration from 2019 to 2021. Data was extracted for the complete duration of 10 years (2012 to 2021) from various countries with different geographical region (arid region, semitropic/semiarid region and tropical region). Results There was a noticeable reduction in dengue cases in underdeveloped (70–85%), developing (50–90%), and developed nations (75%) in the years 2019 and 2021. The dengue cases drastically reduced by 55–65% with the advent of COVID-19 s wave in the year 2021 across the globe. Conclusions At present, we can conclude that COVID-19 and dengue show an inverse relationship. These preliminary, data-based observations should guide clinical practice until more data are made public and basis for further medical research. • COVID-19 has increased the burden on the health care system across the globe. • COVID-19 has inverse relation with the occurrence of Dengue cases. • Dengue situation is worse in countries with low GDP. • Human behavior and social distancing have direct correlation with the number of Dengue cases. • Cross-reactivity or overlap between Dengue and COVID-19, has proportional effect on each other.
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26
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Asghar A, Imran HM, Bano N, Maalik S, Mushtaq S, Hussain A, Varjani S, Aleya L, Iqbal HMN, Bilal M. SARS-COV-2/COVID-19: scenario, epidemiology, adaptive mutations, and environmental factors. Environ Sci Pollut Res Int 2022; 29:69117-69136. [PMID: 35947257 PMCID: PMC9363873 DOI: 10.1007/s11356-022-22333-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
The coronavirus pandemic of 2019 has already exerted an enormous impact. For over a year, the worldwide pandemic has ravaged the whole globe, with approximately 250 million verified human infection cases and a mortality rate surpassing 4 million. While the genetic makeup of the related pathogen (SARS-CoV-2) was identified, many unknown facets remain a mystery, comprising the virus's origin and evolutionary trend. There were many rumors that SARS-CoV-2 was human-borne and its evolution was predicted many years ago, but scientific investigation proved them wrong and concluded that bats might be the origin of SARS-CoV-2 and pangolins act as intermediary species to transmit the virus from bats to humans. Airborne droplets were found to be the leading cause of human-to-human transmission of this virus, but later studies showed that contaminated surfaces and other environmental factors are also involved in its transmission. The evolution of different SARS-CoV-2 variants worsens the condition and has become a challenge to overcome this pandemic. The emergence of COVID-19 is still a mystery, and scientists are unable to explain the exact origin of SARS-CoV-2. This review sheds light on the possible origin of SARS-CoV-2, its transmission, and the key factors that worsen the situation.
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Affiliation(s)
- Asma Asghar
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Hafiz Muhammad Imran
- Department of Biochemistry, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Naheed Bano
- Department of Fisheries & Aquaculture, MNS-University of Agriculture, Multan, Pakistan
| | - Sadia Maalik
- Department of Zoology, Government College Women University, Sialkot, Pakistan
| | - Sajida Mushtaq
- Department of Zoology, Government College Women University, Sialkot, Pakistan
| | - Asim Hussain
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Sunita Varjani
- Gujarat Pollution Control Board, Gandhinagar, 382 010, Gujarat, India
| | - Lotfi Aleya
- Chrono-Environment Laboratory, UMR CNRS 6249, Bourgogne Franche-Comté University, Besançon, France
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, 64849, Monterrey, Mexico
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, China.
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27
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Barozi V, Edkins AL, Tastan Bishop Ö. Evolutionary progression of collective mutations in Omicron sub-lineages towards efficient RBD-hACE2: Allosteric communications between and within viral and human proteins. Comput Struct Biotechnol J 2022; 20:4562-78. [PMID: 35989699 DOI: 10.1016/j.csbj.2022.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/06/2022] [Accepted: 08/07/2022] [Indexed: 11/23/2022] Open
Abstract
The interaction between the Spike (S) protein of SARS-CoV-2 and the human angiotensin converting enzyme 2 (hACE2) is essential for infection, and is a target for neutralizing antibodies. Consequently, selection of mutations in the S protein is expected to be driven by the impact on the interaction with hACE2 and antibody escape. Here, for the first time, we systematically characterized the collective effects of mutations in each of the Omicron sub-lineages (BA.1, BA.2, BA.3 and BA.4) on both the viral S protein receptor binding domain (RBD) and the hACE2 protein using post molecular dynamics studies and dynamic residue network (DRN) analysis. Our analysis suggested that Omicron sub-lineage mutations result in altered physicochemical properties that change conformational flexibility compared to the reference structure, and may contribute to antibody escape. We also observed changes in the hACE2 substrate binding groove in some sub-lineages. Notably, we identified unique allosteric communication paths in the reference protein complex formed by the DRN metrics betweenness centrality and eigencentrality hubs, originating from the RBD core traversing the receptor binding motif of the S protein and the N-terminal domain of the hACE2 to the active site. We showed allosteric changes in residue network paths in both the RBD and hACE2 proteins due to Omicron sub-lineage mutations. Taken together, these data suggest progressive evolution of the Omicron S protein RBD in sub-lineages towards a more efficient interaction with the hACE2 receptor which may account for the increased transmissibility of Omicron variants.
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28
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Yamacli S, Avci M. Density functional theory computation of the binding free energies between various mutations of SARS-CoV-2 RBD and human ACE2: molecular level roots of the contagiousness. Heliyon 2022; 8:e10128. [PMID: 35971531 PMCID: PMC9365710 DOI: 10.1016/j.heliyon.2022.e10128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/27/2022] [Accepted: 07/27/2022] [Indexed: 12/13/2022] Open
Abstract
The receptor-binding domain (RBD) of SARS-CoV-2 attaches to the human ACE2 to initiate binding of SARS-CoV-2 to human cell and leads to the infection process afterwards. In this study, various mutations of SARS-CoV-2 spike RBD and human ACE2 complexes are investigated via density functional theory (DFT) computations to obtain binding free energies. The DFT computations are performed without fragmenting the interfaces to involve longer-range quantum mechanical interactions for improving accuracy. The vibrational free energies, van der Waals dispersion forces and basis set superposition error corrections are also included in the calculations. The results show that the absolute value of the binding energy of B.1.1.7 mutated spike RBD-ACE2 complex is more than five times higher than that of the original strain. The results of this study are expected to be useful for a deeper understanding of the relation of the binding free energies and the level of contagiousness.
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Affiliation(s)
- Serhan Yamacli
- Nuh Naci Yazgan University, Department of Electrical-Electronics Engineering, 38090, Kayseri, Turkey
| | - Mutlu Avci
- Cukurova University, Department of Biomedical Engineering, 01330, Adana, Turkey
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29
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Shafiq A, Zubair F, Ambreen A, Suleman M, Yousafi Q, Rasul Niazi Z, Anwar Z, Khan A, Mohammad A, Wei DQ. Investigation of the binding and dynamic features of A.30 variant revealed higher binding of RBD for hACE2 and escapes the neutralizing antibody: A molecular simulation approach. Comput Biol Med 2022; 146:105574. [PMID: 35533461 PMCID: PMC9055381 DOI: 10.1016/j.compbiomed.2022.105574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 01/17/2023]
Abstract
With the emergence of Delta and Omicron variants, many other important variants of SARS-CoV-2, which cause Coronavirus disease-2019, including A.30, are reported to increase the concern created by the global pandemic. The A.30 variant, reported in Tanzania and other countries, harbors spike gene mutations that help this strain to bind more robustly and to escape neutralizing antibodies. The present study uses molecular modelling and simulation-based approaches to investigate the key features of this strain that result in greater infectivity. The protein-protein docking results for the spike protein demonstrated that additional interactions, particularly two salt-bridges formed by the mutated residue Lys484, increase binding affinity, while the loss of key residues at the N terminal domain (NTD) result in a change to binding conformation with monoclonal antibodies, thus escaping their neutralizing effects. Moreover, we deeply studied the atomic features of these binding complexes through molecular simulation, which revealed differential dynamics when compared to wild type. Analysis of the binding free energy using MM/GBSA revealed that the total binding free energy (TBE) for the wild type receptor-binding domain (RBD) complex was -58.25 kcal/mol in contrast to the A.30 RBD complex, which reported -65.59 kcal/mol. The higher TBE for the A.30 RBD complex signifies a more robust interaction between A.30 variant RBD with ACE2 than the wild type, allowing the variant to bind and spread more promptly. The BFE for the wild type NTD complex was calculated to be -65.76 kcal/mol, while the A.30 NTD complex was estimated to be -49.35 kcal/mol. This shows the impact of the reported substitutions and deletions in the NTD of A.30 variant, which consequently reduce the binding of mAb, allowing it to evade the immune response of the host. The reported results will aid the development of cross-protective drugs against SARS-CoV-2 and its variants.
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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, 200240, PR China
| | | | - Amna Ambreen
- Amna Inayat Medical College, Lahore, Punjab, Pakistan
| | - Muhammad Suleman
- Center for Biotechnology and Microbiology, University of Swat, Khyber Pakhtunkhwa, Pakistan
| | - Qudsia Yousafi
- Department of Biosciences, COMSATS University Islamabad-Sahiwal Campus, Punjab, Pakistan
| | - Zahid Rasul Niazi
- Department of Pharmacy, Faculty of Pharmacy, Gomal University, D I Khan, KPK, Pakistan
| | - Zeeshan Anwar
- Department of Pharmacy, Abdul Wali Khan University, Mardan, KPK, Pakistan
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China,Corresponding author
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Kuwait
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR 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, 200030, PR China,Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong, 518055, PR China,Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nayang, Henan, 473006, PR China,Corresponding author. Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
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30
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Khan A, Khan SA, Zia K, Altowyan MS, Barakat A, Ul-Haq Z. Deciphering the Impact of Mutations on the Binding Efficacy of SARS-CoV-2 Omicron and Delta Variants With Human ACE2 Receptor. Front Chem 2022; 10:892093. [PMID: 35755247 PMCID: PMC9213841 DOI: 10.3389/fchem.2022.892093] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/28/2022] [Indexed: 12/26/2022] Open
Abstract
The pandemic of COVID-19, caused by SARS-CoV-2, has globally affected the human health and economy. Since the emergence of the novel coronavirus SARS-CoV-2, the life-threatening virus continues to mutate and evolve. Irrespective of acquired natural immunity and vaccine-induced immunity, the emerging multiple variants are growing exponentially, crossing the territorial barriers of the modern world. The rapid emergence of SARS-CoV-2 multiple variants challenges global researchers regarding the efficacy of available vaccines and variant transmissibility. SARS-CoV-2 surface-anchored S-protein recognizes and interacts with the host-cell ACE2, facilitating viral adherence and entrance into the cell. Understanding the interfacial interactions between the spike protein of SARS-CoV-2 variants and human ACE2 receptor is important for the design and development of antiviral therapeutics against SARS-CoV-2 emerging variants. Despite extensive research, the crucial determinants related to the molecular interactions between the spike protein of SARS-CoV-2 variants and host receptors are poorly understood. Thus, in this study, we explore the comparative interfacial binding pattern of SARS-CoV-2 spike RBD of wild type, Delta, and Omicron with the human ACE2 receptor to determine the crucial determinants at the atomistic level, using MD simulation and MM/GBSA energy calculations. Based on our findings, the substitution of Q493R, G496S, Q498R, and Y505H induced internal conformational changes in Omicron spike RBD, which leads to higher binding affinity than Delta spike RBD with the human ACE2 receptor, eventually contributing to higher transmission and infectivity. Taken together, these results could be used for the structure-based design of effective antiviral therapeutics against SARS-CoV-2 variants.
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Affiliation(s)
- Alamgir Khan
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Salman Ali Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Komal Zia
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Mezna Saleh Altowyan
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Assem Barakat
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia.,Department of Chemistry, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Zaheer Ul-Haq
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan.,Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
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Ward B, Yombi JC, Balligand JL, Cani PD, Collet JF, de Greef J, Dewulf JP, Gatto L, Haufroid V, Jodogne S, Kabamba B, Pyr dit Ruys S, Vertommen D, Elens L, Belkhir L. HYGIEIA: HYpothesizing the Genesis of Infectious Diseases and Epidemics through an Integrated Systems Biology Approach. Viruses 2022; 14:v14071373. [PMID: 35891354 PMCID: PMC9318602 DOI: 10.3390/v14071373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/13/2022] [Accepted: 06/21/2022] [Indexed: 12/13/2022] Open
Abstract
More than two years on, the COVID-19 pandemic continues to wreak havoc around the world and has battle-tested the pandemic-situation responses of all major global governments. Two key areas of investigation that are still unclear are: the molecular mechanisms that lead to heterogenic patient outcomes, and the causes of Post COVID condition (AKA Long-COVID). In this paper, we introduce the HYGIEIA project, designed to respond to the enormous challenges of the COVID-19 pandemic through a multi-omic approach supported by network medicine. It is hoped that in addition to investigating COVID-19, the logistics deployed within this project will be applicable to other infectious agents, pandemic-type situations, and also other complex, non-infectious diseases. Here, we first look at previous research into COVID-19 in the context of the proteome, metabolome, transcriptome, microbiome, host genome, and viral genome. We then discuss a proposed methodology for a large-scale multi-omic longitudinal study to investigate the aforementioned biological strata through high-throughput sequencing (HTS) and mass-spectrometry (MS) technologies. Lastly, we discuss how a network medicine approach can be used to analyze the data and make meaningful discoveries, with the final aim being the translation of these discoveries into the clinics to improve patient care.
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Affiliation(s)
- Bradley Ward
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (B.W.); (S.P.d.R.)
- Louvain Center for Toxicology and Applied Pharmacology (LTAP), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.d.G.); (J.P.D.); (V.H.)
| | - Jean Cyr Yombi
- Department of Internal Medicine, Cliniques Universitaires Saint-Luc, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Jean-Luc Balligand
- WELBIO (Walloon Excellence in Life Sciences and Biotechnology), Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Experimentale et Clinique (IREC), Cliniques Universitaires Saint-Luc, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Patrice D. Cani
- WELBIO (Walloon Excellence in Life Sciences and Biotechnology), Metabolism and Nutrition Research Group, Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Jean-François Collet
- WELBIO (Walloon Excellence in Life Sciences and Biotechnology), de Duve Institute, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Julien de Greef
- Louvain Center for Toxicology and Applied Pharmacology (LTAP), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.d.G.); (J.P.D.); (V.H.)
- Department of Internal Medicine, Cliniques Universitaires Saint-Luc, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Joseph P. Dewulf
- Louvain Center for Toxicology and Applied Pharmacology (LTAP), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.d.G.); (J.P.D.); (V.H.)
- Department of Laboratory Medicine, Cliniques Universitaires Saint-Luc, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
- Department of Biochemistry, de Duve Institute, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Laurent Gatto
- Computational Biology and Bioinformatics Unit (CBIO), de Duve Institute, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Vincent Haufroid
- Louvain Center for Toxicology and Applied Pharmacology (LTAP), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.d.G.); (J.P.D.); (V.H.)
- Department of Laboratory Medicine, Cliniques Universitaires Saint-Luc, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Sébastien Jodogne
- Computer Science and Engineering Department (INGI), Institute of Information and Communication Technologies, Electronics and Applied Mathematics (ICTEAM), UCLouvain, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium;
| | - Benoît Kabamba
- Department of Laboratory Medicine, Cliniques Universitaires Saint-Luc, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
- Pôle de Microbiologie, Institut de Recherche Expérimentale et Clinique, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Sébastien Pyr dit Ruys
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (B.W.); (S.P.d.R.)
| | - Didier Vertommen
- De Duve Institute, and MASSPROT Platform, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Laure Elens
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (B.W.); (S.P.d.R.)
- Louvain Center for Toxicology and Applied Pharmacology (LTAP), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.d.G.); (J.P.D.); (V.H.)
- Correspondence: (L.E.); (L.B.)
| | - Leïla Belkhir
- Louvain Center for Toxicology and Applied Pharmacology (LTAP), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.d.G.); (J.P.D.); (V.H.)
- Department of Internal Medicine, Cliniques Universitaires Saint-Luc, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
- Correspondence: (L.E.); (L.B.)
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32
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Lata S, Akif M. Probing structural basis for enhanced binding of SARS-CoV-2 P.1 variant spike protein with the human ACE2 receptor. J Cell Biochem 2022; 123:1207-1221. [PMID: 35620980 PMCID: PMC9347910 DOI: 10.1002/jcb.30276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/22/2022] [Accepted: 05/10/2022] [Indexed: 11/25/2022]
Abstract
The initial step of infection by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) involves the binding of receptor binding domain (RBD) of the spike protein to the angiotensin converting enzyme 2 (ACE2) receptor. Each successive wave of SARS‐CoV‐2 reports emergence of many new variants, which is associated with mutations in the RBD as well as other parts of the spike protein. These mutations are reported to have enhanced affinity towards the ACE2 receptor as well as are also crucial for the virus transmission. Many computational and experimental studies have demonstrated the effect of individual mutation on the RBD‐ACE2 binding. However, the cumulative effect of mutations on the RBD and away from the RBD was not investigated in detail. We report here a comparative analysis on the structural communication and dynamics of the RBD and truncated S1 domain of spike protein in complex with the ACE2 receptor from SARS‐CoV‐2 wild type and its P.1 variant. Our integrative network and dynamics approaches highlighted a subtle conformational changes in the RBD as well as truncated S1 domain of spike protein at the protein contact level, responsible for the increased affinity with the ACE2 receptor. Moreover, our study also identified the commonalities and differences in the dynamics of the interactions between spike protein of SARS‐CoV‐2 wild type and its P.1 variant with the ACE2 receptor. Further, our investigation yielded an understanding towards identification of the unique RBD residues crucial for the interaction with the ACE2 host receptor. Overall, the study provides an insight for designing better therapeutics against the circulating P.1 variants as well as other future variants.
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Affiliation(s)
- Surabhi Lata
- Laboratory of Structural Biology, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Mohd Akif
- Laboratory of Structural Biology, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
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33
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Suleman M, Balouch AR, Randhawa AW, Khan T, Mudassir M, Ullah A, Jan AU, Zia MA, Ali SS, Khan A. Characterization of proteome wide antigenic epitopes to design proteins specific and proteome-wide ensemble vaccines against heartland virus using structural vaccinology and immune simulation approaches. Microb Pathog 2022; 168:105592. [PMID: 35595178 DOI: 10.1016/j.micpath.2022.105592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/13/2022] [Accepted: 05/13/2022] [Indexed: 11/29/2022]
Abstract
Heartland virus is a single-stranded negative-sense RNA virus that infects humans and causes lethargy, myalgia, headaches, nausea, diarrhea, weight loss, arthralgia, loss of appetite, leukopenia, and easy bruising due thrombocytopenia. The unavailability of antiviral drugs for HRTV infection is a major obstacle to treat this infection, therefore supportive care management is adopted in the case of a severe ailment. In this scientific study, proteins specific and proteome-wide Helper T-cell (HTL), linear B cell, and cytotoxic T-cell (CTL) epitopes mapping joined together with suitable linkers to design multi-epitopes subunit vaccine (MEVC). The constructed four vaccines from nucleocapsid protein, replicase, glycoprotein and finally whole proteome-wide constructs demonstrated stronger antigenic and non-allergenic behavior. Physiochemical properties evaluation also reported easy and efficient expression and downstream analysis of the constructs. Molecular docking of these constructs with toll-like receptor 7 (TLR7) revealed good binding and further validation based on MM/GBSA also demonstrated stronger interaction between the vaccine constructs and TLR7. Moreover, in silico cloning reported CAI value of 0.96 for each construct and excellent GC contents percentage required for experimental analysis. Furthermore, immune simulation-based immune response surveillance revealed that upon the injection of antigen the primary and secondary antibodies were produced between 5-15 days, and a more robust neutralization of the antigen by the proteome-wide vaccine construct was observed. This research could pave the way for the development of dynamic and efficient vaccines that contain a unique mix of numerous HRTV derived antigenic peptides to control HRTV infection.
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Affiliation(s)
- Muhammad Suleman
- Centre for Biotechnology and Microbiology, University of Swat, Kanju, Khyber Pakhtunkhwa, Pakistan
| | | | | | - Taimoor Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Maria Mudassir
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, Lahore, Pakistan.
| | - Asad Ullah
- Department of Health and Biological Sciences, Abasyn University, Peshawar, 25000, Pakistan
| | - Amin Ullah Jan
- Department of Biotechnology, Faculty of Sciences, Shaheed Benazir Bhutto University, Sheringal Dir (U), 18000, Pakistan.
| | - Muhammad Amir Zia
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Center (NARC), Islamabad, Pakistan.
| | - Syed Shujait Ali
- Centre for Biotechnology and Microbiology, University of Swat, Kanju, Khyber Pakhtunkhwa, Pakistan
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China.
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Abstract
The Angiotensin Converting Enzyme 2 (ACE2) assists the regulation of blood pressure and is the main target of the coronaviruses responsible for SARS and COVID19. The catalytic function of ACE2 relies on the opening and closing motion of its peptidase domain (PD). In this study, we investigated the possibility of allosterically controlling the ACE2 PD functional dynamics. After confirming that ACE2 PD binding site opening-closing motion is dominant in characterizing its conformational landscape, we observed that few mutations in the viral receptor binding domain fragments were able to impart different effects on the binding site opening of ACE2 PD. This showed that binding to the solvent exposed area of ACE2 PD can effectively alter the conformational profile of the protein, and thus likely its catalytic function. Using a targeted machine learning model and relative entropy-based statistical analysis, we proposed the mechanism for the allosteric perturbation that regulates the ACE2 PD binding site dynamics at atomistic level. The key residues and the source of the allosteric regulation of ACE PD dynamics are also presented.
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Affiliation(s)
- Francesco Trozzi
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, USA.
| | - Nischal Karki
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, USA.
| | - Zilin Song
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, USA.
| | - Niraj Verma
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, USA.
| | - Elfi Kraka
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, USA.
| | - Brian D Zoltowski
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, USA.
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, USA.
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Popovic M. Strain wars 2: Binding constants, enthalpies, entropies, Gibbs energies and rates of binding of SARS-CoV-2 variants. Virology 2022; 570:35-44. [PMID: 35366482 PMCID: PMC8961312 DOI: 10.1016/j.virol.2022.03.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 03/04/2022] [Accepted: 03/24/2022] [Indexed: 12/30/2022]
Abstract
SARS-CoV-2 virus is the cause of COVID-19 pandemic and belongs to RNA viruses, showing great tendency to mutate. Several dozens of mutations have been observed on the SARS-CoV-2 virus, during the last two years. Some of the mutated strains show a greater infectivity and are capable of suppressing the earlier strains, through interference. In this work, kinetic and thermodynamic properties were calculated for strains characterized by various numbers and locations of mutations. It was shown that mutations lead to changes in chemical composition, thermodynamic properties and infectivity. Through competition, the phenomenon of interference of various SARS-CoV-2 strains was explained, which results in suppression of the wild type by mutant strains. Standard Gibbs energy of binding and binding constant for the Omicron (B.1.1.529) strain were found to be ΔBG⁰ = −45.96 kJ/mol and KB = 1.13 ∙ 10+8 M−1, respectively.
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Khan A, Randhawa AW, Balouch AR, Mukhtar N, Sayaf AM, Suleman M, Khan T, Ali S, Ali SS, Wang Y, Mohammad A, Wei DQ. Blocking key mutated hotspot residues in the RBD of the omicron variant (B.1.1.529) with medicinal compounds to disrupt the RBD-hACE2 complex using molecular screening and simulation approaches. RSC Adv 2022; 12:7318-7327. [PMID: 35424688 PMCID: PMC8982251 DOI: 10.1039/d2ra00277a] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 02/14/2022] [Indexed: 12/30/2022] Open
Abstract
A new variant of SARS-CoV-2 known as the omicron variant (B.1.1.529) reported in South Africa with 30 mutations in the whole spike protein, among which 15 mutations are in the receptor-binding domain, is continuously spreading exponentially around the world. The omicron variant is reported to be highly contagious with antibody-escaping activity. The emergence of antibody-escaping variants is alarming, and thus the quick discovery of small molecule inhibitors is needed. Hence, the current study uses computational drug screening and molecular dynamics simulation approaches (replicated) to identify novel drugs that can inhibit the binding of the receptor-binding domain (RBD) with hACE2. Screening of the North African, East African and North-East African medicinal compound databases by employing a multi-step screening approach revealed four compounds, namely (-)-pipoxide (C1), 2-(p-hydroxybenzyl) benzofuran-6-ol (C2), 1-(4-hydroxy-3-methoxyphenyl)-2-{4-[(E)-3-hydroxy-1-propenyl]-2-methoxyphenoxy}-1,3-propanediol (C3), and Rhein (C4), with excellent anti-viral properties against the RBD of the omicron variant. Investigation of the dynamics demonstrates stable behavior, good residue flexibility profiles, and structural compactness. Validation of the top hits using computational bioactivity analysis, binding free energy calculations and dissociation constant (K D) analysis also indicated the anti-viral properties of these compounds. In conclusion, this study will help in the design and discovery of novel drug therapeutics, which may be used against the emerging omicron variant of SARS-CoV-2.
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Affiliation(s)
- Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 P.R. China
| | | | | | - Naila Mukhtar
- Department of Botany, University of Okara Punjab Pakistan
| | - Abrar Mohammad Sayaf
- School of Chemical Sciences, Universiti Sains Malaysia Pulau Pinang 11800 Malaysia
| | - Muhammad Suleman
- Centre for Biotechnology and Microbiology, University of Swat Kanju Khyber Pakhtunkhwa Pakistan
| | - Taimoor Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 P.R. China
| | - Shahid Ali
- Centre for Biotechnology and Microbiology, University of Swat Kanju Khyber Pakhtunkhwa Pakistan
| | - Syed Shujait Ali
- Centre for Biotechnology and Microbiology, University of Swat Kanju Khyber Pakhtunkhwa Pakistan
| | - Yanjing Wang
- Engineering Research Center of Cell and Therapeutics Antibody, School of Pharmacy, Shanghai Jiao Tong University Shanghai 200240 P.R. China
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute Dasman Kuwait
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 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 200030 P.R. China
- Peng Cheng Laboratory Vanke Cloud City Phase I Building 8, Xili Street, Nashan District Shenzhen Guangdong 518055 P.R China
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Khan A, Waris H, Rafique M, Suleman M, Mohammad A, Ali SS, Khan T, Waheed Y, Liao C, Wei DQ. The Omicron (B.1.1.529) variant of SARS-CoV-2 binds to the hACE2 receptor more strongly and escapes the antibody response: Insights from structural and simulation data. Int J Biol Macromol 2022; 200:438-448. [PMID: 35063482 PMCID: PMC8767976 DOI: 10.1016/j.ijbiomac.2022.01.059] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/10/2022] [Accepted: 01/10/2022] [Indexed: 02/07/2023]
Abstract
As SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) continues to inflict chaos globally, a new variant officially known as B.1.1.529 was reported in South Africa and was found to harbor 30 mutations in the spike protein. It is too early to speculate on transmission and hospitalizations. Hence, more analyses are required, particularly to connect the genomic patterns to the phenotypic attributes to reveal the binding differences and antibody response for this variant, which can then be used for therapeutic interventions. Given the urgency of the required analysis and data on the B.1.1.529 variant, we have performed a detailed investigation to provide an understanding of the impact of these novel mutations on the structure, function, and binding of RBD to hACE2 and mAb to the NTD of the spike protein. The differences in the binding pattern between the wild type and B.1.1.529 variant complexes revealed that the key substitutions Asn417, Ser446, Arg493, and Arg498 in the B.1.1.529 RBD caused additional interactions with hACE2 and the loss of key residues in the B.1.1.529 NTD resulted in decreased interactions with three CDR regions (1-3) in the mAb. Further investigation revealed that B.1.1.529 displayed a stable dynamic that follows a global stability trend. In addition, the dissociation constant (KD), hydrogen bonding analysis, and binding free energy calculations further validated the findings. Hydrogen bonding analysis demonstrated that significant hydrogen bonding reprogramming took place, which revealed key differences in the binding. The total binding free energy using MM/GBSA and MM/PBSA further validated the docking results and demonstrated significant variations in the binding. This study is the first to provide a basis for the higher infectivity of the new SARS-CoV-2 variants and provides a strong impetus for the development of novel drugs against them.
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Affiliation(s)
- Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Hira Waris
- Rawalpindi Medical College, Rawalpindi, Punjab, Pakistan
| | | | - Muhammad Suleman
- Center for Biotechnology and Microbiology, University of Swat, Khyber Pakhtunkhwa, Pakistan
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Kuwait
| | - Syed Shujait Ali
- Center for Biotechnology and Microbiology, University of Swat, Khyber Pakhtunkhwa, Pakistan
| | - Taimoor Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Yasir Waheed
- Foundation University Medical College, Foundation University Islamabad, Islamabad, Pakistan
| | - Chenguang Liao
- College of Software, Zhengzhou University, Daxue Road, Zhengzhou, China
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR 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 200030, PR China; Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong 518055, PR China.
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Hakami AR. Targeting the RBD of Omicron Variant (B.1.1.529) with Medicinal Phytocompounds to Abrogate the Binding of Spike Glycoprotein with the hACE2 Using Computational Molecular Search and Simulation Approach. Biology (Basel) 2022; 11:258. [PMID: 35205124 DOI: 10.3390/biology11020258] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 01/29/2022] [Accepted: 01/31/2022] [Indexed: 01/23/2023]
Abstract
Simple Summary The current study based on virtual drugs screening and simulations identified novel drugs to target the RBD of the spike protein from Omicron variant of SARS-CoV-2. Using molecular modeling tools to search for a good binding drugs we identified SANC00944, SANC01032, SANC00992, and SANC00317 from South African natural compounds database as potential inhibitor of the Spike-ACE2 complex. In sum, this study will help in the design and discovery of novel drug therapeutics, which may be used against the emerging Omicron variant of SARS-CoV-2. Abstract The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus continues to inflict chaos globally. The emergence of a novel Omicron variant (B.1.1.529) in South Africa harbors 30 mutations in the spike protein. The variant is distinguished from other variants of concern (VOCs) with an increased (15) number of mutations in the receptor-binding domain (RBD) and suggests higher chances of causing reinfections. Initial reports also claimed that this variant escapes all the neutralizing antibodies, thus demanding a novel strategy against it. Thus, in this study, we performed a computational molecular screening against the RBD of the Omicron (B.1.1.529) variant and assessed the binding affinity of potent drugs against the RBD. The multi-steps screening of the South African Natural Compounds Database (SANCDB) revealed four medicinal compounds as excellent (potential) anti-viral agents against the Omicron variant, namely SANC00944, SANC01032, SANC00992, and SANC00317. The simulation analysis of these compounds in complex with the RBD demonstrated stable dynamics and structural compactness. Moreover, the residual flexibility analysis revealed that the flexibility of three loops required for interaction with hACE2 has been reduced by the binding of these drugs. The post-simulation validation of these compounds such as binding free energy, in silico bioactivity, and dissociation constant prediction validated the anti-viral potency of these compounds. The total binding free energy (TBFE) for the SANC01032–RBD complex was reported to be −46.54 kcal/mol; for the SANC01032–RBD complex, the TBFE was −41.88 kcal/mol; for the SANC00992–RBD complex the TBFE was −29.05 kcal/mol, while for the SANC00317–RBD complex the TBFE was −31.03 kcal/mol. The results showed the inhibition potential of these compounds by targeting the RBD. In conclusion, this study will help in the design and discovery of novel drug therapeutics, which may be used against the emerging Omicron variant of SARS-CoV-2.
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Alatawi EA, Alshabrmi FM. Structural and Dynamic Insights into the W68L, L85P, and T87A Mutations of Mycobacterium tuberculosis Inducing Resistance to Pyrazinamide. IJERPH 2022; 19:1615. [PMID: 35162636 PMCID: PMC8835092 DOI: 10.3390/ijerph19031615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/05/2022] [Accepted: 01/19/2022] [Indexed: 12/10/2022]
Abstract
Tuberculosis (TB), the most frequent bacterium-mediated infectious disease caused by Mycobacterium tuberculosis, has been known to infect humans since ancient times. Although TB is common worldwide, the most recent report by the WHO (World Health Organization) listed the three countries of India, China, and Russia with 27%, 14%, and 8% of the global burden of TB, respectively. It has been reported that resistance to TB drugs, particularly by the pncA gene to the pyrazinamide drug due to mutations, significantly affects the effective treatment of TB. Understanding the mechanism of drug resistance using computational methods is of great interest to design effective TB treatment, exploring the structural features with these tools. Thus, keeping in view the importance of these methods, we employed state-of-the-art computational methods to study the mechanism of resistance caused by the W68L, L85P, and T87A mutations recently reported in 2021. We employed a molecular docking approach to predict the binding conformation and studied the dynamic properties of each complex using molecular dynamics simulation approaches. Our analysis revealed that compared to the wildtype, these three mutations altered the binding pattern and reduced the binding affinity. Moreover, the structural dynamic features also showed that these mutations significantly reduced the structural stability and packing, particularly by the W68L and L85P mutations. Moreover, principal component analysis, free energy landscape, and the binding free energy results revealed variation in the protein’s motion and the binding energy. The total binding free energy was for the wildtype −9.61 kcal/mol, W68L −7.57 kcal/mol, L85P −6.99 kcal/mol, and T87A −7.77 kcal/mol. Our findings can help to design a structure-based drug against the MDR (multiple drug-resistant) TB.
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Tetz G, Tetz V. Prion-Like Domains in Spike Protein of SARS-CoV-2 Differ across Its Variants and Enable Changes in Affinity to ACE2. Microorganisms 2022; 10:280. [PMID: 35208734 PMCID: PMC8878784 DOI: 10.3390/microorganisms10020280] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 12/10/2022] Open
Abstract
Currently, the world is struggling with the coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Prions are proteins that possess a unique conformational conversion, with the ability to rapidly shift between multiple conformations due to residue hydrophobicity and net sequence charge, and viral prion-like proteins are known as potential regulators of viral infections. However, the prion-like domains (PrD) in the SARS-CoV-2 proteome have not been analyzed. In this in silico study, using the PLAAC algorithm, we identified the presence of prion-like domains in the SARS-CoV-2 spike protein. Compared with other viruses, a striking difference was observed in the distribution of prion-like domains in the spike protein since SARS-CoV-2 is the only coronavirus with a prion-like domain found in the receptor-binding domain of the S1 region of the spike protein. The presence and unique distribution of prion-like domains in the SARS-CoV-2 receptor-binding domains of the spike protein are particularly interesting since although the SARS-CoV-2 and SARS-CoV S proteins share the same host cell receptor, angiotensin-converting enzyme 2 (ACE2), SARS-CoV-2 demonstrates a 10- to 20-fold higher affinity for ACE2. We identified prion-like domains in the α1 helix of the ACE2 receptor that interact with the viral receptor-binding domain of SARS-CoV-2. Finally, we found substantial differences in the prion-like domain of the S1 region of the spike protein across emerging variants including Omicron (B.1.1.529). Taken together, the present findings indicate that the identified PrDs in the SARS-CoV-2 receptor-binding domain (RBD) and ACE2 region that interact with RBD play important functional roles in viral adhesion and entry.
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Khan A, Hussain S, Ahmad S, Suleman M, Bukhari I, Khan T, Rashid F, Azad AK, Waseem M, Khan W, Hussain Z, Khan A, Ali SS, Qin Q, Wei DQ. Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. Comput Biol Med 2022; 141:105163. [PMID: 34979405 PMCID: PMC8716154 DOI: 10.1016/j.compbiomed.2021.105163] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/16/2021] [Accepted: 12/19/2021] [Indexed: 12/28/2022]
Abstract
The spike protein of SARS-CoV-2 and the host ACE2 receptor plays a vital role in the entry to the cell. Among which the hotspot residue 501 is continuously subjected to positive selection pressure and induces unusual virulence. Keeping in view the importance of the hot spot residue 501, we predicted the potentially emerging structural variants of 501 residue. We analyzed the binding pattern of wild type and mutants (Spike RBD) to the ACE2 receptor by deciphering variations in the amino acids’ interaction networks by graph kernels along with evolutionary, network metrics, and energetic information. Our analysis revealed that N501I, N501T, and N501V increase the binding affinity and alter the intra and inter-residue bonding networks. The N501T has shown strong positive selection and fitness in other animals. Docking results and repeated simulations (three times) confirmed the structural stability and tighter binding of these three variants, correlated with the previous results following the global stability trend. Consequently, we reported three variants N501I, N501T, and N501V could worsen the situation further if they emerged. The relations between the viral fitness and binding affinity is a complicated game thus the emergence of high affinity mutations in the SARS-CoV-2 RBD brings up the question of whether or not positive selection favours these mutations or not?
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Affiliation(s)
- Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Sarfaraz Hussain
- Institute of Food Sciences and Technology, Chinese Academy of Agriculture Sciences, Beijing, 100193, China
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, 25000, Pakistan
| | - Muhammad Suleman
- Center for Biotechnology and Microbiology, University of Swat, Swat, KP, Pakistan
| | - Imrana Bukhari
- Department of Botany, University of Okara, Punjab, Pakistan
| | - Taimoor Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Farooq Rashid
- School of Public Health, Department of Epidemiology, Southern Medical University, Dermatology Hospital, Guangzhou, China
| | - Abul Kalam Azad
- Advanced Drug Delivery Laboratory, Department of Pharmaceutical Technology, Faculty of Pharmacy, International Islamic University Malaysia, 25200, Kuantan, Pahang, Malaysia
| | - Muhammad Waseem
- Faculty of Rehabilitation and Allied Health Science, Riphah International University, Islamabad, Pakistan
| | - Wajid Khan
- Center for Biotechnology and Microbiology, University of Swat, Swat, KP, Pakistan
| | - Zahid Hussain
- Center for Biotechnology and Microbiology, University of Swat, Swat, KP, Pakistan
| | - Asghar Khan
- Saidu Teaching Hospital, Saidu Sharif, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Syed Shujait Ali
- Center for Biotechnology and Microbiology, University of Swat, Swat, KP, Pakistan
| | - Qiyao Qin
- School of Statistics, Renmin University of China, PR China
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China; Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong, 518055, PR China; State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, PR China.
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Karlebach G, Aronow B, Baylin SB, Butler D, Foox J, Levy S, Meydan C, Mozsary C, Saravia-Butler AM, Taylor DM, Wurtele E, Mason CE, Beheshti A, Robinson PN. Betacoronavirus-specific alternate splicing. Genomics 2022; 114:110270. [PMID: 35074468 PMCID: PMC8782732 DOI: 10.1016/j.ygeno.2022.110270] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/15/2021] [Accepted: 01/16/2022] [Indexed: 11/04/2022]
Abstract
Viruses can subvert a number of cellular processes including splicing in order to block innate antiviral responses, and many viruses interact with cellular splicing machinery. SARS-CoV-2 infection was shown to suppress global mRNA splicing, and at least 10 SARS-CoV-2 proteins bind specifically to one or more human RNAs. Here, we investigate 17 published experimental and clinical datasets related to SARS-CoV-2 infection, datasets from the betacoronaviruses SARS-CoV and MERS, as well as Streptococcus pneumonia, HCV, Zika virus, Dengue virus, influenza H3N2, and RSV. We show that genes showing differential alternative splicing in SARS-CoV-2 have a similar functional profile to those of SARS-CoV and MERS and affect a diverse set of genes and biological functions, including many closely related to virus biology. Additionally, the differentially spliced transcripts of cells infected by coronaviruses were more likely to undergo intron-retention, contain a pseudouridine modification, and have a smaller number of exons as compared with differentially spliced transcripts in the control groups. Viral load in clinical COVID-19 samples was correlated with isoform distribution of differentially spliced genes. A significantly higher number of ribosomal genes are affected by differential alternative splicing and gene expression in betacoronavirus samples, and the betacoronavirus differentially spliced genes are depleted for binding sites of RNA-binding proteins. Our results demonstrate characteristic patterns of differential splicing in cells infected by SARS-CoV-2, SARS-CoV, and MERS. The alternative splicing changes observed in betacoronaviruses infection potentially modify a broad range of cellular functions, via changes in the functions of the products of a diverse set of genes involved in different biological processes.
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Yang Q, Jian X, Syed AAS, Fahira A, Zheng C, Zhu Z, Wang K, Zhang J, Wen Y, Li Z, Pan D, Lu T, Wang Z, Shi Y. Structural Comparison and Drug Screening of Spike Proteins of Ten SARS-CoV-2 Variants. Research (Wash D C) 2022; 2022:9781758. [PMID: 35198984 PMCID: PMC8829538 DOI: 10.34133/2022/9781758] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/30/2021] [Indexed: 12/14/2022]
Abstract
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) has evolved many variants with stronger infectivity and immune evasion than the original strain, including Alpha, Beta, Gamma, Delta, Epsilon, Kappa, Iota, Lambda, and 21H strains. Amino acid mutations are enriched in the spike protein of SARS-CoV-2, which plays a crucial role in cell infection. However, the impact of these mutations on protein structure and function is unclear. Understanding the pathophysiology and pandemic features of these SARS-CoV-2 variants requires knowledge of the spike protein structures. Here, we obtained the spike protein structures of 10 main globally endemic SARS-CoV-2 strains using AlphaFold2. The clustering analysis based on structural similarity revealed the unique features of the mainly pandemic SARS-CoV-2 Delta variants, indicating that structural clusters can reflect the current characteristics of the epidemic more accurately than those based on the protein sequence. The analysis of the binding affinities of ACE2-RBD, antibody-NTD, and antibody-RBD complexes in the different variants revealed that the recognition of antibodies against S1 NTD and RBD was decreased in the variants, especially the Delta variant compared with the original strain, which may induce the immune evasion of SARS-CoV-2 variants. Furthermore, by virtual screening the ZINC database against a high-accuracy predicted structure of Delta spike protein and experimental validation, we identified multiple compounds that target S1 NTD and RBD, which might contribute towards the development of clinical anti-SARS-CoV-2 medicines. Our findings provided a basic foundation for future in vitro and in vivo investigations that might speed up the development of potential therapies for the SARS-CoV-2 variants.
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Affiliation(s)
- Qiangzhen Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Xuemin Jian
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Ali Alamdar Shah Syed
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Aamir Fahira
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Chenxiang Zheng
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Zijia Zhu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Ke Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Jinmai Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Yanqin Wen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Zhiqiang Li
- Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao 266003, China
| | - Dun Pan
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Tingting Lu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Zhuo Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
- Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao 266003, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
- Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
- Department of Psychiatry, First Teaching Hospital of Xinjiang Medical University, Urumqi 830046, China
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Farahani M, Niknam Z, Mohammadi Amirabad L, Amiri-Dashatan N, Koushki M, Nemati M, Danesh Pouya F, Rezaei-Tavirani M, Rasmi Y, Tayebi L. Molecular pathways involved in COVID-19 and potential pathway-based therapeutic targets. Biomed Pharmacother 2022; 145:112420. [PMID: 34801852 PMCID: PMC8585639 DOI: 10.1016/j.biopha.2021.112420] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/05/2021] [Accepted: 11/10/2021] [Indexed: 01/08/2023] Open
Abstract
Deciphering the molecular downstream consequences of severe acute respiratory syndrome coronavirus (SARS-CoV)- 2 infection is important for a greater understanding of the disease and treatment planning. Furthermore, greater understanding of the underlying mechanisms of diagnostic and therapeutic strategies can help in the development of vaccines and drugs against COVID-19. At present, the molecular mechanisms of SARS-CoV-2 in the host cells are not sufficiently comprehended. Some of the mechanisms are proposed considering the existing similarities between SARS-CoV-2 and the other members of the β-CoVs, and others are explained based on studies advanced in the structure and function of SARS-CoV-2. In this review, we endeavored to map the possible mechanisms of the host response following SARS-CoV-2 infection and surveyed current research conducted by in vitro, in vivo and human observations, as well as existing suggestions. We addressed the specific signaling events that can cause cytokine storm and demonstrated three forms of cell death signaling following virus infection, including apoptosis, pyroptosis, and necroptosis. Given the elicited signaling pathways, we introduced possible pathway-based therapeutic targets; ADAM17 was especially highlighted as one of the most important elements of several signaling pathways involved in the immunopathogenesis of COVID-19. We also provided the possible drug candidates against these targets. Moreover, the cytokine-cytokine receptor interaction pathway was found as one of the important cross-talk pathways through a pathway-pathway interaction analysis for SARS-CoV-2 infection.
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Affiliation(s)
- Masoumeh Farahani
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Niknam
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Nasrin Amiri-Dashatan
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran,Zanjan Metabolic Diseases Research Center, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mehdi Koushki
- Department of Clinical Biochemistry, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mohadeseh Nemati
- Department of Biochemistry, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Fahima Danesh Pouya
- Department of Biochemistry, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Mostafa Rezaei-Tavirani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Yousef Rasmi
- Department of Biochemistry, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran; Cellular and Molecular Research Center, Urmia University of Medical Sciences, Urmia, Iran.
| | - Lobat Tayebi
- Marquette University School of Dentistry, Milwaukee, WI 53233, USA
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Shah A, Rehmat S, Aslam I, Suleman M, Batool F, Aziz A, Rashid F, Midrarullah, Nawaz MA, Ali SS, Junaid M, Khan A, Wei DQ. Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. Comput Biol Med 2021; 141:105170. [PMID: 34968862 DOI: 10.1016/j.compbiomed.2021.105170] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 01/08/2023]
Abstract
SARS-CoV-2, an RNA virus, has been prone to high mutations since its first emergence in Wuhan, China, and throughout its spread. Its genome has been sequenced continuously by many countries, including Pakistan, but the results vary. Understanding its genomic patterns and connecting them with phenotypic features will help in devising therapeutic strategies. Thus, in this study, we explored the mutation landscape of 250 Pakistani isolates of SARS-CoV-2 genomes to check the genome diversity and examine the impact of these mutations on protein stability and viral pathogenesis in comparison with a reference sequence (Wuhan NC 045512.2). Our results revealed that structural proteins mainly exhibit more mutations than others in the Pakistani isolates; in particular, the nucleocapsid protein is highly mutated. In comparison, the spike protein is the most mutated protein globally. Furthermore, nsp12 was found to be the most mutated NSP in the Pakistani isolates and worldwide. Regarding accessory proteins, ORF3A is the most mutated in the Pakistani isolates, whereas ORF8 is highly mutated in world isolates. These mutations decrease the structural stability of their proteins and alter different biological pathways. Molecular docking, the dissociation constant (KD), and MM/GBSA analysis showed that mutations in the S protein alter its binding with ACE2. The spike protein mutations D614G-S943T-V622F (−75.17 kcal/mol), D614G-Q677H (−75.78 kcal/mol), and N74K-D614G (−73.84 kcal/mol) exhibit stronger binding energy than the wild type (−66.34 kcal/mol), thus increasing infectivity. Furthermore, the simulation results strongly corroborated the predicted protein servers. Our analysis findings also showed that E, M, ORF6, ORF7A, ORF7B, and ORF10 are the most stable coding genes; they may be suitable targets for vaccine and drug development.
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Muhseen ZT, Kadhim S, Yahiya YI, Alatawi EA, Aba Alkhayl FF, Almatroudi A. Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches. Biology (Basel) 2021; 10:1310. [PMID: 34943225 PMCID: PMC8698945 DOI: 10.3390/biology10121310] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 12/13/2022]
Abstract
Recently, a new variant, B.1620, with mutations (S477N-E484K) in the spike protein's receptor-binding domain (RBD) has been reported in Europe. In order to design therapeutic strategies suitable for B.1.620, further studies are required. A detailed investigation of the structural features and variations caused by these substitutions, that is, a molecular level investigation, is essential to uncover the role of these changes. To determine whether and how the binding affinity of ACE2-RBD is affected, we used protein-protein docking and all-atom simulation approaches. Our analysis revealed that B.1.620 binds more strongly than the wild type and alters the hydrogen bonding network. The docking score for the wild type was reported to be -122.6 +/- 0.7 kcal/mol, while for B.1.620, the docking score was -124.9 +/- 3.8 kcal/mol. A comparative binding investigation showed that the wild-type complex has 11 hydrogen bonds and one salt bridge, while the B.1.620 complex has 14 hydrogen bonds and one salt bridge, among which most of the interactions are preserved between the wild type and B.1.620. A dynamic analysis of the two complexes revealed stable dynamics, which corroborated the global stability trend, compactness, and flexibility of the three essential loops, providing a better conformational optimization opportunity and binding. Furthermore, binding free energy revealed that the wild type had a total binding energy of -51.14 kcal/mol, while for B.1.628, the total binding energy was -68.25 kcal/mol. The current findings based on protein complex modeling and bio-simulation methods revealed the atomic features of the B.1.620 variant harboring S477N and E484K mutations in the RBD and the basis for infectivity. In conclusion, the current study presents distinguishing features of B.1.620, which can be used to design structure-based drugs against the B.1.620 variant.
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Affiliation(s)
- Ziyad Tariq Muhseen
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210093, China
- School of Life Sciences, Shaanxi Normal University, Xi’an 710062, China
| | - Salim Kadhim
- Department of Pharmacology, College of Pharmacy, University of Alkafeel, Najaf 61001, Iraq; (S.K.); (Y.I.Y.)
| | - Yahiya Ibrahim Yahiya
- Department of Pharmacology, College of Pharmacy, University of Alkafeel, Najaf 61001, Iraq; (S.K.); (Y.I.Y.)
| | - Eid A. Alatawi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia;
| | - Faris F. Aba Alkhayl
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia;
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Dentistry and Pharmacy, Buraydah Colleges, Buraydah 51418, Saudi Arabia
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia;
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Rashid F, Suleman M, Shah A, Dzakah EE, Chen S, Wang H, Tang S. Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. Front Microbiol 2021; 12:789062. [PMID: 34925297 PMCID: PMC8671833 DOI: 10.3389/fmicb.2021.789062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 10/29/2021] [Indexed: 01/12/2023] Open
Abstract
Mutations in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have made this virus more infectious. Previous studies have confirmed that non-structural protein 13 (NSP13) plays an important role in immune evasion by physically interacting with TANK binding kinase 1 (TBK1) to inhibit IFNβ production. Mutations have been reported in NSP13; hence, in the current study, biophysical and structural modeling methodologies were adapted to dissect the influence of major mutations in NSP13, i.e., P77L, Q88H, D260Y, E341D, and M429I, on its binding to the TBK1 and to escape the human immune system. The results revealed that these mutations significantly affected the binding of NSP13 and TBK1 by altering the hydrogen bonding network and dynamic structural features. The stability, flexibility, and compactness of these mutants displayed different dynamic features, which are the basis for immune evasion. Moreover, the binding was further validated using the MM/GBSA approach, revealing that these mutations have higher binding energies than the wild-type (WT) NSP13 protein. These findings thus justify the basis of stronger interactions and evasion for these NSP13 mutants. In conclusion, the current findings explored the key features of the NSP13 WT and its mutant complexes, which can be used to design structure-based inhibitors against the SARS-CoV-2 new variants to rescue the host immune system.
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Affiliation(s)
- Farooq Rashid
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Muhammad Suleman
- Centre for Biotechnology and Microbiology, University of Swat, Mingora, Pakistan
| | - Abdullah Shah
- Department of Biotechnology, Shaheed Benazir Bhutto University, Sheringal, Dir, Pakistan
| | - Emmanuel Enoch Dzakah
- Department of Molecular Biology and Biotechnology, School of Biological Sciences, College of Agriculture and Natural Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Shuyi Chen
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Haiying Wang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Shixing Tang
- Dermatology Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
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Khan A, Mohammad A, Haq I, Nasar M, Ahmad W, Yousafi Q, Suleman M, Ahmad S, Albutti A, Khan T, Marafie SK, Alshawaf E, Ali SS, Abubaker J, Wei DQ. Structural-Dynamics and Binding Analysis of RBD from SARS-CoV-2 Variants of Concern (VOCs) and GRP78 Receptor Revealed Basis for Higher Infectivity. Microorganisms 2021; 9:2331. [PMID: 34835456 PMCID: PMC8619099 DOI: 10.3390/microorganisms9112331] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/01/2021] [Accepted: 11/01/2021] [Indexed: 01/21/2023] Open
Abstract
Glucose-regulated protein 78 (GRP78) might be a receptor for SARS-CoV-2 to bind and enter the host cell. Recently reported mutations in the spike glycoprotein unique to the receptor-binding domain (RBD) of different variants might increase the binding and pathogenesis. However, it is still not known how these mutations affect the binding of RBD to GRP78. The current study provides a structural basis for the binding of GRP78 to the different variants, i.e., B.1.1.7, B.1.351, B.1.617, and P.1 (spike RBD), of SARS-CoV-2 using a biomolecular simulation approach. Docking results showed that the new variants bound stronger than the wild-type, which was further confirmed through the free energy calculation results. All-atom simulation confirmed structural stability, which was consistent with previous results by following the global stability trend. We concluded that the increased binding affinity of the B.1.1.7, B.1.351, and P.1 variants was due to a variation in the bonding network that helped the virus induce a higher infectivity and disease severity. Consequently, we reported that the aforementioned new variants use GRP78 as an alternate receptor to enhance their seriousness.
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Affiliation(s)
- Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (A.K.); (T.K.)
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman 15462, Kuwait; (A.M.); (S.K.M.); (E.A.); (J.A.)
| | - Inamul Haq
- Department of Animal Sciences, Jeonbuk National University, 567 Baekji-Daero, Deokjin-gu, Jeonju-si, Jeollabuk-do, Jeonju 54896, Korea;
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Wanju-gun 55365, Korea
| | - Mohammad Nasar
- Department of Biosciences, COMSATS University, Islamabad-Sahiwal Campus, Punjab 57000, Pakistan; (M.N.); (Q.Y.)
| | - Waqar Ahmad
- Department of Microbiology, Abdul Wali Khan University (AWKUM), Mardan 23200, Khyber Pakhtunkhwa, Pakistan;
| | - Qudsia Yousafi
- Department of Biosciences, COMSATS University, Islamabad-Sahiwal Campus, Punjab 57000, Pakistan; (M.N.); (Q.Y.)
| | - Muhammad Suleman
- Center for Biotechnology and Microbiology, University of Swat, Swat 19200, KP, Pakistan; (M.S.); (S.S.A.)
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25120, Pakistan;
| | - Aqel Albutti
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia;
| | - Taimoor Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (A.K.); (T.K.)
| | - Sulaiman K. Marafie
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman 15462, Kuwait; (A.M.); (S.K.M.); (E.A.); (J.A.)
| | - Eman Alshawaf
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman 15462, Kuwait; (A.M.); (S.K.M.); (E.A.); (J.A.)
| | - Syed Shujait Ali
- Center for Biotechnology and Microbiology, University of Swat, Swat 19200, KP, Pakistan; (M.S.); (S.S.A.)
| | - Jehad Abubaker
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman 15462, Kuwait; (A.M.); (S.K.M.); (E.A.); (J.A.)
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (A.K.); (T.K.)
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen 518055, China
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Suleman M, Yousafi Q, Ali J, Ali SS, Hussain Z, Ali S, Waseem M, Iqbal A, Ahmad S, Khan A, Wang Y, Wei DQ. Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. Comput Biol Med 2021; 138:104936. [PMID: 34655895 DOI: 10.1016/j.compbiomed.2021.104936] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/08/2021] [Accepted: 10/08/2021] [Indexed: 12/26/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). Reports of new variants that potentially increase virulence and viral transmission, as well as reduce the efficacy of available vaccines, have recently emerged. In this study, we computationally analyzed the N439K, S477 N, and T478K variants for their ability to bind Angiotensin-converting enzyme 2 (ACE2). We used the protein-protein docking approach to explore whether the three variants displayed a higher binding affinity to the ACE2 receptor than the wild type. We found that these variants alter the hydrogen bonding network and the cluster of interactions. Additional salt bridges, hydrogen bonds, and a high number of non-bonded contacts (i.e., non-bonded interactions between atoms in the same molecule and those in other molecules) were observed only in the mutant complexes, allowing efficient binding to the ACE2 receptor. Furthermore, we used a 2.0-μs all-atoms simulation approach to detect differences in the structural dynamic features of the resulting protein complexes. Our findings revealed that the mutant complexes possessed stable dynamics, consistent with the global trend of mutations yielding variants with improved stability and enhanced affinity. Binding energy calculations based on molecular mechanics/generalized Born surface area (MM/GBSA) further revealed that electrostatic interactions principally increased net binding energies. The stability and binding energies of N439K, S477 N, and T478K variants were enhanced compared to the wild-type-ACE2 complex. The net binding energy of the systems was -31.86 kcal/mol for the wild-type-ACE2 complex, -67.85 kcal/mol for N439K, -69.82 kcal/mol for S477 N, and -69.64 kcal/mol for T478K. The current study provides a basis for exploring the enhanced binding abilities and structural features of SARS-CoV-2 variants to design novel therapeutics against the virus.
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Khan A, Khan T, Ali S, Aftab S, Wang Y, Qiankun W, Khan M, Suleman M, Ali S, Heng W, Ali SS, Wei DQ, Mohammad A. SARS-CoV-2 new variants: Characteristic features and impact on the efficacy of different vaccines. Biomed Pharmacother 2021; 143:112176. [PMID: 34562770 PMCID: PMC8433040 DOI: 10.1016/j.biopha.2021.112176] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 01/10/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its new variants reported in different countries have posed a serious threat to human health and social fabrics worldwide. In addition, these new variants hindered the efforts of vaccines and other therapeutic developments. In this review article, we explained the emergence of new variants of SARS-CoV-2, their transmission risk, mortality rate, and, more importantly, the impact of each new variant on the efficacy of the developed vaccines reported in different literature and findings. The literature reported that with the emergence of new variants, the efficacy of different vaccines is declined, hospitalization and the risk of reinfection is increased. The reports concluded that the emergence of a variant that entirely evades the immune response triggered by the vaccine is improbable. The emergence of new variants and reports of re-infections are creating a more distressing situation and therefore demands further investigation to formulate an effective therapeutic strategy.
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Affiliation(s)
- Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Taimoor Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Shughla Ali
- Department of Zoology, Swat College of Science and Technology (SCST), Swat, Khyber Pakhtunkhwa, Pakistan
| | - Summiya Aftab
- Department of Zoology, Government Girls Degree College, Thana, Khyber Pakhtunkhwa, Pakistan
| | - Yanjing Wang
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Wang Qiankun
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Mazhar Khan
- The CAS Key Laboratory of Innate Immunity and Chronic Diseases, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China (USTC), Collaborative Innovation Center of Genetics and Development, Hefei 230027, Anhui, PR China
| | - Muhammad Suleman
- Center for Biotechnology and Microbiology, University of Swat, Kanju Campus, Swat, Pakistan
| | - Shahid Ali
- Center for Biotechnology and Microbiology, University of Swat, Kanju Campus, Swat, Pakistan
| | - Wang Heng
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China.
| | - Syed Shujait Ali
- Center for Biotechnology and Microbiology, University of Swat, Kanju Campus, Swat, Pakistan
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China; Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong 518055, PR China; State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, PR China.
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Kuwait
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