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Dhami LS, Dahal P, Thapa B, Gautam N, Pantha N, Adhikari R, Adhikari NP. Insights from in silico study of receptor energetics of SARS-CoV-2 variants. Phys Chem Chem Phys 2024; 26:8794-8806. [PMID: 38420855 DOI: 10.1039/d3cp04997c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
The emergence of new variants of the novel coronavirus SARS-CoV-2 with increased infectivity, superior virulence, high transmissibility, and unmatched immune escape has demonstrated the adaptability and evolutionary fitness of the virus. The subject of relative order of the binding affinity of SARS-CoV-2 variants with the human ACE2 (hACE2) receptor is hotly debated and its resolution has implications for drug design and development. In this work, we have investigated the energetics of the binding of receptor binding domain (RBD) of SARS-CoV-2 variants of concern (VOCs): Beta (B.1.351), Delta (B.1.617.2), Omicron (B.1.1.529), variant of interest (VOI): Kappa (B.1.617.1), and Delta Plus (B.1.617.2.1) variant with the human ACE2 receptor by using the umbrella sampling (US) method. Our work indicates that Delta and Delta Plus variants have greater values of the US binding free energy than Wild-type (WT), whereas Beta, Kappa, and Omicron variants have lower values. Further analysis of hydrogen bonding, salt bridges, non-bonded interaction energy, and contact surface area at the RBD-hACE2 interface establish Delta as the variant with the highest binding affinity among these variants.
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Affiliation(s)
- Lokendra Singh Dhami
- Central Department of Physics, Tribhuvan University, Kirtipur, Kathmandu 44613, Nepal.
| | - Prabin Dahal
- Central Department of Physics, Tribhuvan University, Kirtipur, Kathmandu 44613, Nepal.
| | - Bidhya Thapa
- Central Department of Physics, Tribhuvan University, Kirtipur, Kathmandu 44613, Nepal.
- Padma Kanya Multiple Campus, Tribhuvan University, Bagbazar, Kathmandu 44613, Nepal
| | - Narayan Gautam
- Central Department of Physics, Tribhuvan University, Kirtipur, Kathmandu 44613, Nepal.
- Tri-chandra Multiple Campus, Tribhuvan University, Ghantaghar, Kathmandu 44613, Nepal
| | - Nurapati Pantha
- Central Department of Physics, Tribhuvan University, Kirtipur, Kathmandu 44613, Nepal.
| | - Rameshwar Adhikari
- Research Centre for Applied Science and Technology (RECAST), Tribhuvan University, Kirtipur, Kathmandu 44613, Nepal
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2
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Shankar M, Rani MSS, Gopi P, P A, Pandya P. Structure and energetics of serum protein complex of tea adulterant dye Bismarck brown Y using experimental and computational methods. Comput Biol Chem 2024; 108:107976. [PMID: 37956472 DOI: 10.1016/j.compbiolchem.2023.107976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023]
Abstract
Tea, a widely consumed aromatic beverage, is often adulterated with dyes such as Bismarck brown Y (C.I. 21000) (BBY), Prussian blue, and Plumbago, which pose potential health risks. The objective of this study is to analyze how the food dye BBY interacts with serum protein, bovine serum albumin (BSA). This study investigated the BBY-BSA interaction at the molecular level. Fluorescence spectroscopy results showed that the quenching of BSA by BBY is carried out by dynamic quenching mechanism. The displacement assay and molecular docking studies revealed that BBY binds at the flavanone binding site of BSA with hydrophobic interactions. Circular Dichroism results indicate the structural stability of the protein upon BBY binding. Molecular dynamics simulations demonstrated the stability of the complex in a dynamic solvent system, and quantum mechanics calculations showed slight conformational changes of the diaminophenyl ring due to increased hydrophobic interaction. The energetics of gas phase optimized and stable MD structures of BBY indicated similar values which further confirmed that the conformational changes were minor, and it also exhibited a moderate binding with BSA as shown by the MM/PBSA results. This study enhances our understanding of the molecular-level interactions between BBY and BSA, emphasizing the critical role of hydrophobic interactions.
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Affiliation(s)
- Manwi Shankar
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh 201303, India.
| | - Majji Sai Sudha Rani
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh 201303, India.
| | - Priyanka Gopi
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh 201303, India.
| | - Arsha P
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh 201303, India.
| | - Prateek Pandya
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh 201303, India.
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3
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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: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [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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4
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Zeng Z, Geng X, Wen X, Chen Y, Zhu Y, Dong Z, Hao L, Wang T, Yang J, Zhang R, Zheng K, Sun Z, Zhang Y. Novel receptor, mutation, vaccine, and establishment of coping mode for SARS-CoV-2: current status and future. Front Microbiol 2023; 14:1232453. [PMID: 37645223 PMCID: PMC10461067 DOI: 10.3389/fmicb.2023.1232453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/25/2023] [Indexed: 08/31/2023] Open
Abstract
Since the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its resultant pneumonia in December 2019, the cumulative number of infected people worldwide has exceeded 670 million, with over 6.8 million deaths. Despite the marketing of multiple series of vaccines and the implementation of strict prevention and control measures in many countries, the spread and prevalence of SARS-CoV-2 have not been completely and effectively controlled. The latest research shows that in addition to angiotensin converting enzyme II (ACE2), dozens of protein molecules, including AXL, can act as host receptors for SARS-CoV-2 infecting human cells, and virus mutation and immune evasion never seem to stop. To sum up, this review summarizes and organizes the latest relevant literature, comprehensively reviews the genome characteristics of SARS-CoV-2 as well as receptor-based pathogenesis (including ACE2 and other new receptors), mutation and immune evasion, vaccine development and other aspects, and proposes a series of prevention and treatment opinions. It is expected to provide a theoretical basis for an in-depth understanding of the pathogenic mechanism of SARS-CoV-2 along with a research basis and new ideas for the diagnosis and classification, of COVID-19-related disease and for drug and vaccine research and development.
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Affiliation(s)
- Zhaomu Zeng
- Department of Neurosurgery, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China
- Department of Neurosurgery, Xiangya Hospital Jiangxi Hospital of Central South University, National Regional Medical Center for Nervous System Diseases, Nanchang, China
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Xiuchao Geng
- Department of Nursing, School of Medicine, Taizhou University, Taizhou, China
| | - Xichao Wen
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Yueyue Chen
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, China
| | - Yixi Zhu
- Department of Pharmacy, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zishu Dong
- Department of Zoology, Advanced Research Institute, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Liangchao Hao
- Department of Plastic Surgery, Shaoxing People’s Hospital, Shaoxing, China
| | - Tingting Wang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Jifeng Yang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Ruobing Zhang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Kebin Zheng
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Zhiwei Sun
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, China
| | - Yuhao Zhang
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, China
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Sharma T, Gerstman B, Chapagain P. Distinctive Features of the XBB.1.5 and XBB.1.16 Spike Protein Receptor-Binding Domains and Their Roles in Conformational Changes and Angiotensin-Converting Enzyme 2 Binding. Int J Mol Sci 2023; 24:12586. [PMID: 37628766 PMCID: PMC10454900 DOI: 10.3390/ijms241612586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
The emergence and the high transmissibility of the XBB.1.5 and XBB.1.16 subvariants of the SARS-CoV-2 omicron has reignited concerns over the potential impact on vaccine efficacy for these and future variants. We investigated the roles of the XBB.1.5 and XBB.1.16 mutations on the structure of the spike protein's receptor-binding domain (RBD) and its interactions with the host cell receptor ACE2. To bind to ACE2, the RBD must transition from the closed-form to the open-form configuration. We found that the XBB variants have less stable closed-form structures that may make the transition to the open-form easier. We found that the mutations enhance the RBD-ACE2 interactions in XBB.1.16 compared to XBB.1.5. We observed significant structural changes in the loop and motif regions of the RBD, altering well-known antibody-binding sites and potentially rendering primary RBD-specific antibodies ineffective. Our findings elucidate how subtle structural changes and interactions contribute to the subvariants' fitness over their predecessors.
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Affiliation(s)
- Tej Sharma
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Bernard Gerstman
- Department of Physics, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
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6
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Avelar M, Pedraza-González L, Sinicropi A, Flores-Morales V. Triterpene Derivatives as Potential Inhibitors of the RBD Spike Protein from SARS-CoV-2: An In Silico Approach. Molecules 2023; 28:molecules28052333. [PMID: 36903578 PMCID: PMC10005606 DOI: 10.3390/molecules28052333] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
The appearance of a new coronavirus, SARS-CoV-2, in 2019 kicked off an international public health emergency. Although rapid progress in vaccination has reduced the number of deaths, the development of alternative treatments to overcome the disease is still necessary. It is known that the infection begins with the interaction of the spike glycoprotein (at the virus surface) and the angiotensin-converting enzyme 2 cell receptor (ACE2). Therefore, a straightforward solution for promoting virus inhibition seems to be the search for molecules capable of abolishing such attachment. In this work, we tested 18 triterpene derivatives as potential inhibitors of SARS-CoV-2 against the receptor-binding domain (RBD) of the spike protein by means of molecular docking and molecular dynamics simulations, modeling the RBD S1 subunit from the X-ray structure of the RBD-ACE2 complex (PDB ID: 6M0J). Molecular docking revealed that at least three triterpene derivatives of each type (i.e., oleanolic, moronic and ursolic) present similar interaction energies as the reference molecule, i.e., glycyrrhizic acid. Molecular dynamics suggest that two compounds from oleanolic and ursolic acid, OA5 and UA2, can induce conformational changes capable of disrupting the RBD-ACE2 interaction. Finally, physicochemical and pharmacokinetic properties simulations revealed favorable biological activity as antivirals.
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Affiliation(s)
- Mayra Avelar
- Laboratorio de Síntesis Asimétrica y Bio-Quimioinformática (LSAyB), Ingeniería Química (UACQ), Universidad Autónoma de Zacatecas, Campus XXI Km 6 Carr. Zac-Gdl, Zacatecas 98160, Mexico
- Correspondence: (M.A.); (V.F.-M.)
| | - Laura Pedraza-González
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via Moruzzi 13, 56124 Pisa, Italy
| | - Adalgisa Sinicropi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
- Institute of Chemistry of Organometallic Compounds (CNR-ICCOM), Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
- CSGI, Consorzio per lo Sviluppo dei Sistemi a Grande Interfase, 50019 Sesto Fiorentino, Italy
| | - Virginia Flores-Morales
- Laboratorio de Síntesis Asimétrica y Bio-Quimioinformática (LSAyB), Ingeniería Química (UACQ), Universidad Autónoma de Zacatecas, Campus XXI Km 6 Carr. Zac-Gdl, Zacatecas 98160, Mexico
- Correspondence: (M.A.); (V.F.-M.)
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7
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Effect of Double Mutation (L452R and E484Q) on the Binding Affinity of Monoclonal Antibodies (mAbs) against the RBD-A Target for Vaccine Development. Vaccines (Basel) 2022; 11:vaccines11010023. [PMID: 36679867 PMCID: PMC9860914 DOI: 10.3390/vaccines11010023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, emerges as a global health problem, as the viral genome is evolving rapidly to form several variants. Advancement and progress in the development of effective vaccines and neutralizing monoclonal antibodies are promising to combat viral infections. In the current scenario, several lineages containing "co-mutations" in the receptor-binding domain (RBD) region of the spike (S) protein are imposing new challenges. Co-occurrence of some co-mutations includes delta (L452R/T478K), kappa (L452R/E484Q), and a common mutation in both beta and gamma variants (E484K/N501Y). The effect of co-mutants (L452R/E484Q) on human angiotensin-converting enzyme 2 (hACE2) binding has already been elucidated. Here, for the first time, we investigated the role of these RBD co-mutations (L452R/E484Q) on the binding affinity of mAbs by adopting molecular dynamics (MD) simulation and free-energy binding estimation. The results obtained from our study suggest that the structural and dynamic changes introduced by these co-mutations reduce the binding affinity of the viral S protein to monoclonal antibodies (mAbs). The structural changes imposed by L452R create a charged patch near the interfacial surface that alters the affinity towards mAbs. In E484Q mutation, polar negatively charged E484 helps in the formation of electrostatic interaction, while the neutrally charged Q residue affects the interaction by forming repulsive forces. MD simulations along with molecular mechanics-generalized Born surface area (MMGBSA) studies revealed that the REGN 10933, BD-368-2, and S2M11 complexes have reduced binding affinity towards the double-mutant RBD. This indicates that their mutant (MT) structures have a stronger ability to escape from most antibodies than the wild type (WT). However, EY6A Ab showed higher affinity towards the double MT-RBD complex as compared to the WT. However, no significant effect of the per-residue contribution of double-mutated residues was observed, as this mAb does not interact with the region harboring L452 and E484 residues.
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8
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Characterization and Function of Glycans on the Spike Proteins of SARS-CoV-2 Variants of Concern. Microbiol Spectr 2022; 10:e0312022. [PMID: 36318020 PMCID: PMC9769822 DOI: 10.1128/spectrum.03120-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
SARS-CoV-2 variants of concern (VOCs) pose a great challenge to viral prevention and treatment owing to spike (S) protein mutations, which enhance their infectivity and capacity for immune evasion. However, whether these S protein mutations affect glycosylation patterns and thereby influence infectivity and immunogenicity remains unclear. In this study, four VOC S proteins-S-Alpha, S-Beta, S-Delta, and S-Omicron-were expressed and purified. Lectin microarrays were performed to characterize their glycosylation patterns. Several glycans were differentially expressed among the four VOC S proteins. Furthermore, the functional examination of glycans differentially expressed on S-Omicron revealed a higher expression of fucose-containing glycans, which modestly increased the binding of S-Omicron to angiotensin converting enzyme 2 (ACE2). A higher abundance of sialic acid and galactose-containing glycan was observed on S-Omicron, which significantly reduced its sensitivity against broad S protein-neutralizing antibodies. These findings contribute to the further understanding of SARS-CoV-2 infection mechanisms and provide novel glycan targets for emerging and future variants of SARS-CoV-2. IMPORTANCE Though glycosylation sites of SARS-CoV-2 S protein remain highly conserved, we confirmed that mutations in the Spike gene affect the S protein glycan expression pattern in different variants. More importantly, we found that glycans were differentially expressed on the S protein of the Omicron variant, enabling different forms of receptor binding and neutralization resistance. This study improves our understanding of SARS-CoV-2 glycomics and glycobiology and provides novel therapeutic and preventive strategies for SARS-CoV-2 VOCs.
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Sang P, Chen YQ, Liu MT, Wang YT, Yue T, Li Y, Yin YR, Yang LQ. Electrostatic Interactions Are the Primary Determinant of the Binding Affinity of SARS-CoV-2 Spike RBD to ACE2: A Computational Case Study of Omicron Variants. Int J Mol Sci 2022; 23:ijms232314796. [PMID: 36499120 PMCID: PMC9740405 DOI: 10.3390/ijms232314796] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 12/02/2022] Open
Abstract
To explore the mechanistic origin that determines the binding affinity of SARS-CoV-2 spike receptor binding domain (RBD) to human angiotensin converting enzyme 2 (ACE2), we constructed the homology models of RBD-ACE2 complexes of four Omicron subvariants (BA.1, BA.2, BA.3 and BA.4/5), and compared them with wild type complex (RBDWT-ACE2) in terms of various structural dynamic properties by molecular dynamics (MD) simulations and binding free energy (BFE) calculations. The results of MD simulations suggest that the RBDs of all the Omicron subvariants (RBDOMIs) feature increased global structural fluctuations when compared with RBDWT. Detailed comparison of BFE components reveals that the enhanced electrostatic attractive interactions are the main determinant of the higher ACE2-binding affinity of RBDOMIs than RBDWT, while the weakened electrostatic attractive interactions determine RBD of BA.4/5 subvariant (RBDBA.4/5) lowest ACE2-binding affinity among all Omicron subvariants. The per-residue BFE decompositions and the hydrogen bond (HB) networks analyses indicate that the enhanced electrostatic attractive interactions are mainly through gain/loss of the positively/negatively charged residues, and the formation or destruction of the interfacial HBs and salt bridges can also largely affect the ACE2-binding affinity of RBD. It is worth pointing out that since Q493R plays the most important positive contribution in enhancing binding affinity, the absence of this mutation in RBDBA.4/5 results in a significantly weaker binding affinity to ACE2 than other Omicron subvariants. Our results provide insight into the role of electrostatic interactions in determining of the binding affinity of SARS-CoV-2 RBD to human ACE2.
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Affiliation(s)
- Peng Sang
- College of Agriculture and Biological Science, Dali University, Dali 671000, China
- Key Laboratory of Bioinformatics and Computational Biology, Department of Education of Yunnan Province, Dali University, Dali 671000, China
- Yunnan Key Laboratory of Screening and Research on Anti-Pathogenic Plant Resources from West Yunnan, Dali University, Dali 671000, China
| | - Yong-Qin Chen
- College of Agriculture and Biological Science, Dali University, Dali 671000, China
| | - Meng-Ting Liu
- College of Agriculture and Biological Science, Dali University, Dali 671000, China
| | - Yu-Ting Wang
- College of Agriculture and Biological Science, Dali University, Dali 671000, China
| | - Ting Yue
- College of Agriculture and Biological Science, Dali University, Dali 671000, China
| | - Yi Li
- College of Mathematics and Computer Science, Dali University, Dali 671000, China
| | - Yi-Rui Yin
- College of Agriculture and Biological Science, Dali University, Dali 671000, China
| | - Li-Quan Yang
- College of Agriculture and Biological Science, Dali University, Dali 671000, China
- Key Laboratory of Bioinformatics and Computational Biology, Department of Education of Yunnan Province, Dali University, Dali 671000, China
- Yunnan Key Laboratory of Screening and Research on Anti-Pathogenic Plant Resources from West Yunnan, Dali University, Dali 671000, China
- Correspondence:
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10
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Conformational Stability and Denaturation Processes of Proteins Investigated by Electrophoresis under Extreme Conditions. Molecules 2022; 27:molecules27206861. [PMID: 36296453 PMCID: PMC9610776 DOI: 10.3390/molecules27206861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/10/2022] [Accepted: 10/10/2022] [Indexed: 11/17/2022] Open
Abstract
The functional structure of proteins results from marginally stable folded conformations. Reversible unfolding, irreversible denaturation, and deterioration can be caused by chemical and physical agents due to changes in the physicochemical conditions of pH, ionic strength, temperature, pressure, and electric field or due to the presence of a cosolvent that perturbs the delicate balance between stabilizing and destabilizing interactions and eventually induces chemical modifications. For most proteins, denaturation is a complex process involving transient intermediates in several reversible and eventually irreversible steps. Knowledge of protein stability and denaturation processes is mandatory for the development of enzymes as industrial catalysts, biopharmaceuticals, analytical and medical bioreagents, and safe industrial food. Electrophoresis techniques operating under extreme conditions are convenient tools for analyzing unfolding transitions, trapping transient intermediates, and gaining insight into the mechanisms of denaturation processes. Moreover, quantitative analysis of electrophoretic mobility transition curves allows the estimation of the conformational stability of proteins. These approaches include polyacrylamide gel electrophoresis and capillary zone electrophoresis under cold, heat, and hydrostatic pressure and in the presence of non-ionic denaturing agents or stabilizers such as polyols and heavy water. Lastly, after exposure to extremes of physical conditions, electrophoresis under standard conditions provides information on irreversible processes, slow conformational drifts, and slow renaturation processes. The impressive developments of enzyme technology with multiple applications in fine chemistry, biopharmaceutics, and nanomedicine prompted us to revisit the potentialities of these electrophoretic approaches. This feature review is illustrated with published and unpublished results obtained by the authors on cholinesterases and paraoxonase, two physiologically and toxicologically important enzymes.
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11
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Coderc de Lacam EG, Blazhynska M, Chen H, Gumbart JC, Chipot C. When the Dust Has Settled: Calculation of Binding Affinities from First Principles for SARS-CoV-2 Variants with Quantitative Accuracy. J Chem Theory Comput 2022; 18:5890-5900. [PMID: 36108303 PMCID: PMC9518821 DOI: 10.1021/acs.jctc.2c00604] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Indexed: 11/30/2022]
Abstract
Accurate determination of binding free energy is pivotal for the study of many biological processes and has been applied in a number of theoretical investigations to compare the affinity of severe acute respiratory syndrome coronavirus 2 variants toward the host cell. Diversity of these variants challenges the development of effective general therapies, their transmissibility relying either on an increased affinity toward their dedicated human receptor, the angiotensin-converting enzyme 2 (ACE2), or on escaping the immune response. Now that robust structural data are available, we have determined with utmost accuracy the standard binding free energy of the receptor-binding domain to the most widespread variants, namely, Alpha, Beta, Delta, and Omicron BA.2, as well as the wild type (WT) in complex either with ACE2 or with antibodies, namely, S2E12 and H11-D4, using a rigorous theoretical framework that combines molecular dynamics and potential-of-mean-force calculations. Our results show that an appropriate starting structure is crucial to ensure appropriate reproduction of the binding affinity, allowing the variants to be compared. They also emphasize the necessity to apply the relevant methodology, bereft of any shortcut, to account for all the contributions to the standard binding free energy. Our estimates of the binding affinities support the view that while the Alpha and Beta variants lean on an increased affinity toward the host cell, the Delta and Omicron BA.2 variants choose immune escape. Moreover, the S2E12 antibody, already known to be active against the WT (Starr et al., 2021; Mlcochova et al., 2021), proved to be equally effective against the Delta variant. In stark contrast, H11-D4 retains a low affinity toward the WT compared to that of ACE2 for the latter. Assuming robust structural information, the methodology employed herein successfully addresses the challenging protein-protein binding problem in the context of coronavirus disease 2019 while offering promising perspectives for predictive studies of ever-emerging variants.
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Affiliation(s)
- Emma Goulard Coderc de Lacam
- Laboratoire International Associé Centre
National de la Recherche Scientifique et University of Illinois at Urbana-Champaign,
Unité Mixte de Recherche No 7019, Université de
Lorraine, B.P. 70239, Vandœuvre-lès-Nancy Cedex54506,
France
| | - Marharyta Blazhynska
- Laboratoire International Associé Centre
National de la Recherche Scientifique et University of Illinois at Urbana-Champaign,
Unité Mixte de Recherche No 7019, Université de
Lorraine, B.P. 70239, Vandœuvre-lès-Nancy Cedex54506,
France
| | - Haochuan Chen
- Laboratoire International Associé Centre
National de la Recherche Scientifique et University of Illinois at Urbana-Champaign,
Unité Mixte de Recherche No 7019, Université de
Lorraine, B.P. 70239, Vandœuvre-lès-Nancy Cedex54506,
France
| | - James C. Gumbart
- School of Physics, Georgia Institute of
Technology, Atlanta, Georgia30332, United States
| | - Christophe Chipot
- Laboratoire International Associé Centre
National de la Recherche Scientifique et University of Illinois at Urbana-Champaign,
Unité Mixte de Recherche No 7019, Université de
Lorraine, B.P. 70239, Vandœuvre-lès-Nancy Cedex54506,
France
- Theoretical and Computational Biophysics Group, Beckman
Institute, and Department of Physics, University of Illinois at
Urbana-Champaign, UrbanaIllinois61802, United
States
- Department of Biochemistry and Molecular Biology,
The University of Chicago, 929 E. 57th Street W225, Chicago,
Illinois60637, United States
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12
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Obeng EM, Fianu I, Danquah MK. Multivalent ACE2 engineering-A promising pathway for advanced coronavirus nanomedicine development. NANO TODAY 2022; 46:101580. [PMID: 35942040 PMCID: PMC9350675 DOI: 10.1016/j.nantod.2022.101580] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/26/2022] [Accepted: 07/30/2022] [Indexed: 05/06/2023]
Abstract
The spread of coronavirus diseases has resulted in a clarion call to develop potent drugs and vaccines even as different strains appear beyond human prediction. An initial step that is integral to the viral entry into host cells results from an active-targeted interaction of the viral spike (S) proteins and the cell surface receptor, called angiotensin-converting enzyme 2 (ACE2). Thus, engineered ACE2 has been an interesting decoy inhibitor against emerging coronavirus infestation. This article discusses promising innovative ACE2 engineering pathways for current and emerging coronavirus therapeutic development. First, we provide a brief discussion of some ACE2-associated human coronaviruses and their cell invasion mechanism. Then, we describe and contrast the individual spike proteins and ACE2 receptor interactions, highlighting crucial hotspots across the ACE2-associated coronaviruses. Lastly, we address the importance of multivalency in ACE2 nanomedicine engineering and discuss novel approaches to develop and achieve multivalent therapeutic outcomes. Beyond coronaviruses, these approaches will serve as a paradigm to develop new and improved treatment technologies against pathogens that use ACE2 receptor for invasion.
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Affiliation(s)
- Eugene M Obeng
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Isaac Fianu
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Michael K Danquah
- Department of Chemical Engineering, University of Tennessee, 615 McCallie Ave, Chattanooga, TN 37403, United States
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13
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Dutta S, Panthi B, Chandra A. All-Atom Simulations of Human ACE2-Spike Protein RBD Complexes for SARS-CoV-2 and Some of its Variants: Nature of Interactions and Free Energy Diagrams for Dissociation of the Protein Complexes. J Phys Chem B 2022; 126:5375-5389. [PMID: 35833966 PMCID: PMC9328126 DOI: 10.1021/acs.jpcb.2c00833] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 06/25/2022] [Indexed: 12/18/2022]
Abstract
The spike protein of SARS-CoV-2 is known to interact with the human ACE2 protein via its receptor binding domain (RBD). We have investigated the molecular nature of this interprotein interaction and the associated free energy diagrams for the unbinding of the two proteins for SARS-CoV-2 and some of its known variants through all-atom simulations. The present work involves generation and analysis of 2.5 μs of unbiased and 4.2 μs of biased molecular dynamics trajectories in total for five explicitly solvated RBD-ACE2 systems at full atomic level. First, we have made a comparative analysis of the details of residue-wise specific interactions of the spike protein with ACE2 for SARS-CoV-1 and SARS-CoV-2. It is found that the average numbers of both direct interprotein and water-bridged hydrogen bonds between the RBD and ACE2 are higher for SARS-CoV-2 than SARS-CoV-1. These higher hydrogen bonded interactions are further aided by enhanced nonspecific electrostatic attractions between the two protein surfaces for SARS-CoV-2. The free energy calculations reveal that there is an increase in the free energy barrier by ∼1.5 kcal/mol for the unbinding of RBD from ACE2 for SARS-CoV-2 compared to that for SARS-CoV-1. Subsequently, we considered the RBDs of three variants of SARS-CoV-2, namely N501Y, E484Q/L452R, and N440K. The free energy barrier of protein unbinding for the N501Y variant is found to be ∼4 kcal/mol higher than the wild type SARS-CoV-2 which can be attributed to additional specific interactions involving Tyr501 of RBD and Lys353 and Tyr42 of ACE2 and also enhanced nonspecific electrostatic interaction between the protein surfaces. For the other two mutant variants of E484Q/L452R and N440K, the free energy barrier for protein unbinding increases by ∼2 and ∼1 kcal/mol, respectively, compared with the wild type SARS-CoV-2, which can be attributed to an increase in the number of interprotein hydrogen bonds for the former and also to enhanced positive electrostatic potential on the RBD surfaces for both of the variants. The successive breaking of interprotein hydrogen bonds along the free energy pathway of the unbinding process is also found out for all five systems studied here.
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Affiliation(s)
- Saheb Dutta
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Bhavana Panthi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
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14
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Dragnea B. Viruses: A Physical Chemistry Perspective. J Phys Chem B 2022; 126:4411-4414. [PMID: 35734854 DOI: 10.1021/acs.jpcb.2c03430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Kaplonek P, Cizmeci D, Fischinger S, Collier AR, Suscovich T, Linde C, Broge T, Mann C, Amanat F, Dayal D, Rhee J, de St. Aubin M, Nilles EJ, Musk ER, Menon AS, Saphire EO, Krammer F, Lauffenburger DA, Barouch DH, Alter G. mRNA-1273 and BNT162b2 COVID-19 vaccines elicit antibodies with differences in Fc-mediated effector functions. Sci Transl Med 2022; 14:eabm2311. [PMID: 35348368 PMCID: PMC8995030 DOI: 10.1126/scitranslmed.abm2311] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 03/17/2022] [Indexed: 01/02/2023]
Abstract
The successful development of several coronavirus disease 2019 (COVID-19) vaccines has substantially reduced morbidity and mortality in regions of the world where the vaccines have been deployed. However, in the wake of the emergence of viral variants that are able to evade vaccine-induced neutralizing antibodies, real-world vaccine efficacy has begun to show differences across the two approved mRNA platforms, BNT162b2 and mRNA-1273; these findings suggest that subtle variation in immune responses induced by the BNT162b2 and mRNA-1273 vaccines may confer differential protection. Given our emerging appreciation for the importance of additional antibody functions beyond neutralization, we profiled the postboost binding and functional capacity of humoral immune responses induced by the BNT162b2 and mRNA-1273 vaccines in a cohort of hospital staff. Both vaccines induced robust humoral immune responses to wild-type severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and to variants of concern. However, differences emerged across epitope-specific responses, with higher concentrations of receptor binding domain (RBD)- and N-terminal domain-specific IgA observed in recipients of mRNA-1273. Antibodies eliciting neutrophil phagocytosis and natural killer cell activation were also increased in mRNA-1273 vaccine recipients as compared to BNT162b2 recipients. RBD-specific antibody depletion highlighted the different roles of non-RBD-specific antibody effector functions induced across the mRNA vaccines. These data provide insights into potential differences in protective immunity conferred by these vaccines.
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Affiliation(s)
- Paulina Kaplonek
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Deniz Cizmeci
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | | | - Ai-ris Collier
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | | | | | | | - Colin Mann
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Fatima Amanat
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Diana Dayal
- Space Exploration Technologies Corp, Hawthorne, CA 90250, USA
| | - Justin Rhee
- Space Exploration Technologies Corp, Hawthorne, CA 90250, USA
| | | | | | - Elon R. Musk
- Space Exploration Technologies Corp, Hawthorne, CA 90250, USA
| | - Anil S. Menon
- Space Exploration Technologies Corp, Hawthorne, CA 90250, USA
| | - Erica Ollmann Saphire
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Douglas A. Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Dan H. Barouch
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
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16
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Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. 3 Biotech 2022; 12:87. [PMID: 35265451 PMCID: PMC8893057 DOI: 10.1007/s13205-022-03151-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 02/13/2022] [Indexed: 12/26/2022] Open
Abstract
The Receptor Binding Domain (RBD) of SARS-CoV-2, located on the S1 subunit, plays a vital role in the virus binding and its entry into the host cell through angiotensin-converting enzyme 2 (ACE2) receptor. Therefore, understanding the dynamic effects of mutants on the SARS-CoV-2 RBD is essential for discovering drugs to inhibit the virus binding and disrupt its entry into the host cells. A recent study reported a double mutant of SARS-CoV-2, L452R-E484Q, located in the RBD region. Thus, this study employed various computational algorithms and methods to understand the structural impact of both individual variants L452R, E484Q, and the double mutant L452R-E484Q on the native RBD of spike glycoprotein. The effects of the mutations on native RBD structure were predicted by in silico algorithms, which predicted changes in the protein structure and function upon the mutations. Subsequently, molecular dynamics (MD) simulations were employed to understand the conformational stability and functional changes on the RBD upon the mutations. The comparative results of MD simulation parameters displayed that the double mutant induces significant conformational changes in the spike glycoprotein RBD, which may alter its biological functions. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03151-0.
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17
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Cheng MH, Krieger JM, Banerjee A, Xiang Y, Kaynak B, Shi Y, Arditi M, Bahar I. Impact of new variants on SARS-CoV-2 infectivity and neutralization: A molecular assessment of the alterations in the spike-host protein interactions. iScience 2022; 25:103939. [PMID: 35194576 PMCID: PMC8851820 DOI: 10.1016/j.isci.2022.103939] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 01/31/2022] [Accepted: 02/14/2022] [Indexed: 12/29/2022] Open
Abstract
The emergence of SARS-CoV-2 variants necessitates rational assessment of their impact on the recognition and neutralization of the virus by the host cell. We present a comparative analysis of the interactions of Alpha, Beta, Gamma, and Delta variants with cognate molecules (ACE2 and/or furin), neutralizing nanobodies (Nbs), and monoclonal antibodies (mAbs) using in silico methods, in addition to Nb-binding assays. Our study elucidates the molecular origin of the ability of Beta and Delta variants to evade selected antibodies, such as REGN10933, LY-CoV555, B38, C105, or H11-H4, while being insensitive to others including REGN10987. Experiments confirm that nanobody Nb20 retains neutralizing activity against the Delta variant. The substitutions T478K and L452R in the Delta variant enhance associations with ACE2, whereas P681R promotes recognition by proteases, thus facilitating viral entry. The Ab-specific responses of variants highlight how full-atomic structure and dynamics analyses are required for assessing the response to newly emerging variants.
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Affiliation(s)
- Mary Hongying Cheng
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - James M. Krieger
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Anupam Banerjee
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Yufei Xiang
- Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Burak Kaynak
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Yi Shi
- Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Moshe Arditi
- Department of Pediatrics, Division of Pediatric Infectious Diseases and Immunology, and Biomedical Sciences, Infectious and Immunologic Diseases Research Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
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18
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Eslami S, Glassy MC, Ghafouri-Fard S. A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. Gene 2022; 813:146113. [PMID: 34896524 PMCID: PMC8656178 DOI: 10.1016/j.gene.2021.146113] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/31/2021] [Accepted: 12/06/2021] [Indexed: 02/07/2023]
Abstract
Since late 2019, when SARS-CoV-2 was reported at Wuhan, several sequence analyses have been performed and SARS-CoV-2 genome sequences have been submitted in various databases. Moreover, the impact of these variants on infectivity and response to neutralizing antibodies has been assessed. In the present study, we retrieved a total number of 176 complete and high-quality S glycoprotein sequences of Iranian SARS-COV-2 in public database of the GISAID and GenBank from April 2020 up to May 2021. Then, we identified the number of variables, singleton and parsimony informative sites at both gene and protein levels and discussed the possible functional consequences of important mutations on the infectivity and response to neutralizing antibodies. Phylogenetic tree was constructed to represent the relationship between Iranian SARS-COV2 and variants of concern (VOC), variants of interest (VOI) and reference sequence. We found that the four current VOCs - Alpha, Beta, Gamma and Delta - are circulated in different regions in Iran. The Delta variant is notably more transmissible than other variants, and is expected to become a dominant variant. However, some of the Delta variants in Iran carry an additional mutation, namely E1202Q in the HR2 subdomain that might confer an advantage to viral/cell membrane fusion process. We also observed some more common mutations such as an N-terminal domain (NTD) deletion at position I210 and P863H in fusion peptide-heptad repeat 1 span region in Iranian SARS-COV-2. The reported mutations in the current project have practical significance in prediction of disease spread as well as design of vaccines and drugs.
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Affiliation(s)
- Solat Eslami
- Department of Medical Biotechnology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran,Dietary Supplements and Probiotic Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Mark C. Glassy
- Translational Neuro-Oncology Laboratory, San Diego (UCSD) Moores Cancer Center, University of California, CA, United States
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran,Corresponding author
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19
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Hossen ML, Baral P, Sharma T, Gerstman BS, Chapagain P. Significance of the RBD mutations in the SARS-CoV-2 Omicron: from spike opening to antibody escape and cell attachment. Phys Chem Chem Phys 2022; 24:9123-9129. [DOI: 10.1039/d2cp00169a] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We computationally investigated the role of the Omicron RBD mutations on its structure and interactions with surrounding domains in the spike trimer as well as with ACE2. Our results suggest...
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20
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Valério M, Borges-Araújo L, Melo MN, Lousa D, Soares CM. SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility. FRONTIERS IN MEDICAL TECHNOLOGY 2022; 4:1009451. [PMID: 36277437 PMCID: PMC9581196 DOI: 10.3389/fmedt.2022.1009451] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/20/2022] [Indexed: 02/05/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has killed over 6 million people and is having a devastating social and economic impact around the world. The rise of new variants of concern (VOCs) represents a difficult challenge due to the loss of vaccine and natural immunity, as well as increased transmissibility. All VOCs contain mutations in the spike glycoprotein, which mediates fusion between the viral and host cell membranes. The spike glycoprotein binds to angiotensin-converting enzyme 2 (ACE2) via its receptor binding domain (RBD) initiating the infection process. Attempting to understand the effect of RBD mutations in VOCs, a lot of attention has been given to the RBD-ACE2 interaction. However, this type of analysis ignores more indirect effects, such as the conformational dynamics of the RBD itself. Observing that some mutations occur in residues that are not in direct contact with ACE2, we hypothesized that they could affect the RBD conformational dynamics. To test this, we performed long atomistic (AA) molecular dynamics (MD) simulations to investigate the structural dynamics of wt RBD, and that of four VOCs (Alpha, Beta, Delta, and Omicron). Our results show that the wt RBD presents two distinct conformations: an "open" conformation where it is free to bind ACE2; and a "closed" conformation, where the RBM ridge blocks the binding surface. The Alpha and Beta variants shift the open/closed equilibrium towards the open conformation by roughly 20%, likely increasing ACE2 binding affinity. Simulations of the Delta and Omicron variants showed extreme results, with the closed conformation being rarely observed. The Delta variant also differed substantially from the other variants, alternating between the open conformation and an alternative "reversed" one, with a significantly changed orientation of the RBM ridge. This alternate conformation could provide a fitness advantage due to increased availability for ACE2 binding, and by aiding antibody escape through epitope occlusion. These results support the hypothesis that VOCs, and particularly the Omicron and Delta variants, impact RBD conformational dynamics in a direction that promotes efficient binding to ACE2 and, in the case of Delta, may assist antibody escape.
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Affiliation(s)
- Mariana Valério
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Luís Borges-Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Manuel N. Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
- Correspondence: Manuel N. Melo Diana Lousa Cláudio M. Soares
| | - Diana Lousa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
- Correspondence: Manuel N. Melo Diana Lousa Cláudio M. Soares
| | - Cláudio M. Soares
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
- Correspondence: Manuel N. Melo Diana Lousa Cláudio M. Soares
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21
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Kim S, Liu Y, Lei Z, Dicker J, Cao Y, Zhang XF, Im W. Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. J Chem Theory Comput 2021; 17:7972-7979. [PMID: 34856802 PMCID: PMC8672429 DOI: 10.1021/acs.jctc.1c00965] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the current coronavirus disease 2019 (COVID-19) pandemic. It is known that the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 interacts with the human angiotensin-converting enzyme 2 (ACE2) receptor, initiating the entry of SARS-CoV-2. Since its emergence, a number of SARS-CoV-2 variants have been reported, and the variants that show high infectivity are classified as variants of concern according to the United States Centers for Disease Control and Prevention. In this study, we performed both all-atom steered molecular dynamics (SMD) simulations and microscale thermophoresis (MST) experiments to characterize the binding interactions between ACE2 and RBD of all current variants of concern (Alpha, Beta, Gamma, and Delta) and two variants of interest (Epsilon and Kappa). We report that RBD of the Alpha (N501Y) variant requires the highest amount of force initially to be detached from ACE2 due to the N501Y mutation in addition to the role of N90-glycan, followed by Beta/Gamma (K417N/T, E484 K, and N501Y) or Delta (L452R and T478 K) variants. Among all variants investigated in this work, RBD of the Epsilon (L452R) variant is relatively easily detached from ACE2. Our results from both SMD simulations and MST experiments indicate what makes each variant more contagious in terms of RBD and ACE2 interactions. This study could shed light on developing new drugs to inhibit SARS-CoV-2 entry effectively.
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Affiliation(s)
- Seonghan Kim
- Department of Bioengineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA
| | - Yi Liu
- Department of Bioengineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA
| | - Zewei Lei
- Department of Bioengineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA
| | - Jeffrey Dicker
- Department of Bioengineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA
| | - Yiwei Cao
- Department of Biological Sciences, Chemistry, and Computer Science and Engineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA
| | - X. Frank Zhang
- Department of Bioengineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA
| | - Wonpil Im
- Department of Bioengineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA
- Department of Biological Sciences, Chemistry, and Computer Science and Engineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA
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22
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Hatirnaz Ng O, Akyoney S, Sahin I, Soykam HO, Bayram Akcapinar G, Ozdemir O, Kancagi DD, Sir Karakus G, Yurtsever B, Kocagoz AS, Ovali E, Ozbek U. Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. PLoS One 2021; 16:e0260438. [PMID: 34871297 PMCID: PMC8648120 DOI: 10.1371/journal.pone.0260438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/10/2021] [Indexed: 12/11/2022] Open
Abstract
The Coronavirus Disease 2019 (COVID-19) was declared a pandemic in March 2020 by the World Health Organization (WHO). As of May 25th, 2021 there were 2.059.941 SARS-COV2 genome sequences that have been submitted to the GISAID database, with numerous variations. Here, we aim to analyze the SARS-CoV-2 genome data submitted to the GISAID database from Turkey and to determine the variant and clade distributions by the end of May 2021, in accordance with their appearance timeline. We compared these findings to USA, Europe, and Asia data as well. We have also evaluated the effects of spike protein variations, detected in a group of genome sequences of 13 patients who applied to our clinic, by using 3D modeling algorithms. For this purpose, we analyzed 4607 SARS-CoV-2 genome sequences submitted by different lab centers from Turkey to the GISAID database between March 2020 and May 2021. Described mutations were also introduced in silico to the spike protein structure to analyze their isolated impacts on the protein structure. The most abundant clade was GR followed by G, GH, and GRY and we did not detect any V clade. The most common variant was B.1, followed by B.1.1, and the UK variant, B.1.1.7. Our results clearly show a concordance between the variant distributions, the number of cases, and the timelines of different variant accumulations in Turkey. The 3D simulations indicate an increase in the surface hydrophilicity of the reference spike protein and the detected mutations. There was less surface hydrophilicity increase in the Asp614Gly mutation, which exhibits a more compact conformation around the ACE-2 receptor binding domain region, rendering the structure in a “down” conformation. Our genomic findings can help to model vaccination programs and protein modeling may lead to different approaches for COVID-19 treatment strategies.
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Affiliation(s)
- Ozden Hatirnaz Ng
- Department of Medical Biology, Acibadem Mehmet Ali Aydinlar University School of Medicine, Istanbul, Turkey
- Acibadem Mehmet Ali Aydinlar University Rare Diseases and Orphan Drugs Application and Research Center (ACURARE), Istanbul, Turkey
| | - Sezer Akyoney
- Department of Medical Biology, Acibadem Mehmet Ali Aydinlar University School of Medicine, Istanbul, Turkey
- Department of Biostatistics and Bioinformatics, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Ilayda Sahin
- Department of Medical Biotechnology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Department of Medical Genetics, Acibadem Mehmet Ali Aydinlar University School of Medicine, Istanbul, Turkey
| | - Huseyin Okan Soykam
- Department of Biostatistics and Bioinformatics, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Gunseli Bayram Akcapinar
- Department of Medical Biotechnology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Ozkan Ozdemir
- Acibadem Mehmet Ali Aydinlar University Rare Diseases and Orphan Drugs Application and Research Center (ACURARE), Istanbul, Turkey
- Department of Genome Studies, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | | | | | - Bulut Yurtsever
- Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey
| | - Ayse Sesin Kocagoz
- Department of Infectious Diseases and Clinical Microbiology, Acibadem Mehmet Ali Aydinlar University School of Medicine, Istanbul, Turkey
| | - Ercument Ovali
- Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey
| | - Ugur Ozbek
- Acibadem Mehmet Ali Aydinlar University Rare Diseases and Orphan Drugs Application and Research Center (ACURARE), Istanbul, Turkey
- Department of Medical Genetics, Acibadem Mehmet Ali Aydinlar University School of Medicine, Istanbul, Turkey
- * E-mail:
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23
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Baral P, Bhattarai N, Hossen ML, Stebliankin V, Gerstman BS, Narasimhan G, Chapagain PP. Mutation-induced changes in the receptor-binding interface of the SARS-CoV-2 Delta variant B.1.617.2 and implications for immune evasion. Biochem Biophys Res Commun 2021; 574:14-19. [PMID: 34425281 PMCID: PMC8364676 DOI: 10.1016/j.bbrc.2021.08.036] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/13/2021] [Indexed: 12/15/2022]
Abstract
Following the initial surges of the Alpha (B.1.1.7) and the Beta (B.1.351) variants, a more infectious Delta variant (B.1.617.2) is now surging, further deepening the health crises caused by the pandemic. The sharp rise in cases attributed to the Delta variant has made it especially disturbing and is a variant of concern. Fortunately, current vaccines offer protection against known variants of concern, including the Delta variant. However, the Delta variant has exhibited some ability to dodge the immune system as it is found that neutralizing antibodies from prior infections or vaccines are less receptive to binding with the Delta spike protein. Here, we investigated the structural changes caused by the mutations in the Delta variant's receptor-binding interface and explored the effects on binding with the ACE2 receptor as well as with neutralizing antibodies. We find that the receptor-binding β-loop-β motif adopts an altered but stable conformation causing separation in some of the antibody binding epitopes. Our study shows reduced binding of neutralizing antibodies and provides a possible mechanism for the immune evasion exhibited by the Delta variant.
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Affiliation(s)
- Prabin Baral
- Department of Physics, Florida International University, Miami, FL, 33199, USA
| | - Nisha Bhattarai
- Department of Physics, Florida International University, Miami, FL, 33199, USA
| | - Md Lokman Hossen
- Department of Physics, Florida International University, Miami, FL, 33199, USA
| | - Vitalii Stebliankin
- Bioinformatics Research Group (BioRG), Knight Foundation School of Computing and Information Sciences, Florida International University, Miami, FL, 33199, USA
| | - Bernard S. Gerstman
- Department of Physics, Florida International University, Miami, FL, 33199, USA,Biomolecular Sciences Institute, Florida International University, Miami, FL, 33199, USA
| | - Giri Narasimhan
- Bioinformatics Research Group (BioRG), Knight Foundation School of Computing and Information Sciences, Florida International University, Miami, FL, 33199, USA,Biomolecular Sciences Institute, Florida International University, Miami, FL, 33199, USA
| | - Prem P. Chapagain
- Department of Physics, Florida International University, Miami, FL, 33199, USA,Biomolecular Sciences Institute, Florida International University, Miami, FL, 33199, USA,Corresponding author. Department of Physics, Florida International University, Miami, FL, 33199, USA
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24
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Kaplonek P, Cizmeci D, Fischinger S, Collier AR, Suscovich T, Linde C, Broge T, Mann C, Amanat F, Dayal D, Rhee J, de St. Aubin M, Nilles EJ, Musk ER, Menon AS, Saphire EO, Krammer F, Lauffenburger DA, Barouch DH, Alter G. Subtle immunological differences in mRNA-1273 and BNT162b2 COVID-19 vaccine induced Fc-functional profiles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.08.31.458247. [PMID: 34494026 PMCID: PMC8423223 DOI: 10.1101/2021.08.31.458247] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The successful development of several COVID-19 vaccines has substantially reduced morbidity and mortality in regions of the world where the vaccines have been deployed. However, in the wake of the emergence of viral variants, able to evade vaccine induced neutralizing antibodies, real world vaccine efficacy has begun to show differences across the mRNA platforms, suggesting that subtle variation in immune responses induced by the BNT162b2 and mRNA1273 vaccines may provide differential protection. Given our emerging appreciation for the importance of additional antibody functions, beyond neutralization, here we profiled the postboost binding and functional capacity of the humoral response induced by the BNT162b2 and mRNA-1273 in a cohort of hospital staff. Both vaccines induced robust humoral immune responses to WT SARS-CoV-2 and VOCs. However, differences emerged across epitopespecific responses, with higher RBD- and NTD-specific IgA, as well as functional antibodies (ADNP and ADNK) in mRNA-1273 vaccine recipients. Additionally, RBD-specific antibody depletion highlighted the different roles of non-RBD-specific antibody effector function induced across the mRNA vaccines, providing novel insights into potential differences in protective immunity generated across these vaccines in the setting of newly emerging VOCs.
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Affiliation(s)
| | - Deniz Cizmeci
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | | | - Ai-ris Collier
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | | | | | | | - Colin Mann
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Fatima Amanat
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Diana Dayal
- Space Exploration Technologies Corp, Hawthorne, CA, USA
| | - Justin Rhee
- Space Exploration Technologies Corp, Hawthorne, CA, USA
| | | | | | - Elon R. Musk
- Space Exploration Technologies Corp, Hawthorne, CA, USA
| | - Anil S. Menon
- Space Exploration Technologies Corp, Hawthorne, CA, USA
| | - Erica Ollmann Saphire
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Dan H. Barouch
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
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25
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Aljindan RY, Al-Subaie AM, Al-Ohali AI, Kumar D T, Doss C GP, Kamaraj B. Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Comput Biol Med 2021; 135:104654. [PMID: 34346317 PMCID: PMC8282961 DOI: 10.1016/j.compbiomed.2021.104654] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 12/22/2022]
Abstract
COVID-19 is an infectious and pathogenic viral disease caused by SARS-CoV-2 that leads to septic shock, coagulation dysfunction, and acute respiratory distress syndrome. The spreading rate of SARS-CoV-2 is higher than MERS-CoV and SARS-CoV. The receptor-binding domain (RBD) of the Spike-protein (S-protein) interacts with the human cells through the host angiotensin-converting enzyme 2 (ACE2) receptor. However, the molecular mechanism of pathological mutations of S-protein is still unclear. In this perspective, we investigated the impact of mutations in the S-protein and their interaction with the ACE2 receptor for SAR-CoV-2 viral infection. We examined the stability of pathological nonsynonymous mutations in the S-protein, and the binding behavior of the ACE2 receptor with the S-protein upon nonsynonymous mutations using the molecular docking and MM_GBSA approaches. Using the extensive bioinformatics pipeline, we screened the destabilizing (L8V, L8W, L18F, Y145H, M153T, F157S, G476S, L611F, A879S, C1247F, and C1254F) and stabilizing (H49Y, S50L, N501Y, D614G, A845V, and P1143L) nonsynonymous mutations in the S-protein. The docking and binding free energy (ddG) scores revealed that the stabilizing nonsynonymous mutations show increased interaction between the S-protein and the ACE2 receptor compared to native and destabilizing S-proteins and that they may have been responsible for the virulent high level. Further, the molecular dynamics simulation (MDS) approach reveals the structural transition of mutants (N501Y and D614G) S-protein. These insights might help researchers to understand the pathological mechanisms of the S-protein and provide clues regarding mutations in viral infection and disease propagation. Further, it helps researchers to develop an efficient treatment approach against this SARS-CoV-2 pandemic.
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Affiliation(s)
- Reem Y Aljindan
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
| | - Abeer M Al-Subaie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
| | - Ahoud I Al-Ohali
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
| | - Thirumal Kumar D
- Meenakshi Academy of Higher Education and Research, Chennai, Tamil Nadu, 600078, India.
| | - George Priya Doss C
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
| | - Balu Kamaraj
- Department of Neuroscience Technology, College of Applied Medical Sciences in Jubail, Imam Abdulrahman Bin Faisal University, Jubail, Saudi Arabia.
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