1
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Shum MHH, Lee Y, Tam L, Xia H, Chung OLW, Guo Z, Lam TTY. Binding affinity between coronavirus spike protein and human ACE2 receptor. Comput Struct Biotechnol J 2024; 23:759-770. [PMID: 38304547 PMCID: PMC10831124 DOI: 10.1016/j.csbj.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Coronaviruses (CoVs) pose a major risk to global public health due to their ability to infect diverse animal species and potential for emergence in humans. The CoV spike protein mediates viral entry into the cell and plays a crucial role in determining the binding affinity to host cell receptors. With particular emphasis on α- and β-coronaviruses that infect humans and domestic animals, current research on CoV receptor use suggests that the exploitation of the angiotensin-converting enzyme 2 (ACE2) receptor poses a significant threat for viral emergence with pandemic potential. This review summarizes the approaches used to study binding interactions between CoV spike proteins and the human ACE2 (hACE2) receptor. Solid-phase enzyme immunoassays and cell binding assays allow qualitative assessment of binding but lack quantitative evaluation of affinity. Surface plasmon resonance, Bio-layer interferometry, and Microscale Thermophoresis on the other hand, provide accurate affinity measurement through equilibrium dissociation constants (KD). In silico modeling predicts affinity through binding structure modeling, protein-protein docking simulations, and binding energy calculations but reveals inconsistent results due to the lack of a standardized approach. Machine learning and deep learning models utilize simulated and experimental protein-protein interaction data to elucidate the critical residues associated with CoV binding affinity to hACE2. Further optimization and standardization of existing approaches for studying binding affinity could aid pandemic preparedness. Specifically, prioritizing surveillance of CoVs that can bind to human receptors stands to mitigate the risk of zoonotic spillover.
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Affiliation(s)
- Marcus Ho-Hin Shum
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
| | - Yang Lee
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Centre for Immunology and Infection (C2i), Hong Kong Science Park, Hong Kong, China
| | - Leighton Tam
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
| | - Hui Xia
- Department of Chemistry, South University of Science and Technology of China, China
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Oscar Lung-Wa Chung
- Department of Chemistry, South University of Science and Technology of China, China
| | - Zhihong Guo
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
- Centre for Immunology and Infection (C2i), Hong Kong Science Park, Hong Kong, China
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2
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Banerjee T, Gosai A, Yousefi N, Garibay OO, Seal S, Balasubramanian G. Examining sialic acid derivatives as potential inhibitors of SARS-CoV-2 spike protein receptor binding domain. J Biomol Struct Dyn 2024; 42:6342-6358. [PMID: 37424217 DOI: 10.1080/07391102.2023.2234044] [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: 05/02/2023] [Accepted: 07/01/2023] [Indexed: 07/11/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) has been the primary reason behind the COVID-19 global pandemic which has affected millions of lives worldwide. The fundamental cause of the infection is the molecular binding of the viral spike protein receptor binding domain (SP-RBD) with the human cell angiotensin-converting enzyme 2 (ACE2) receptor. The infection can be prevented if the binding of RBD-ACE2 is resisted by utilizing certain inhibitors or drugs that demonstrate strong binding affinity towards the SP RBD. Sialic acid based glycans found widely in human cells and tissues have notable propensity of binding to viral proteins of the coronaviridae family. Recent experimental literature have used N-acetyl neuraminic acid (Sialic acid) to create diagnostic sensors for SARS-CoV-2, but a detailed interrogation of the underlying molecular mechanisms is warranted. Here, we perform all atom molecular dynamics (MD) simulations for the complexes of certain Sialic acid-based molecules with that of SP RBD of SARS CoV-2. Our results indicate that Sialic acid not only reproduces a binding affinity comparable to the RBD-ACE2 interactions, it also assumes the longest time to dissociate completely from the protein binding pocket of SP RBD. Our predictions corroborate that a combination of electrostatic and van der Waals energies as well the polar hydrogen bond interactions between the RBD residues and the inhibitors influence free energy of binding.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Tanumoy Banerjee
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, PA, USA
| | | | - Niloofar Yousefi
- Industrial Engineering and Management Systems, University of Central Florida, Orlando, FL, USA
| | - Ozlem Ozmen Garibay
- Industrial Engineering and Management Systems, University of Central Florida, Orlando, FL, USA
| | - Sudipta Seal
- College of Medicine, Bionix Cluster, University of Central Florida, Orlando, FL, USA
- Advanced Materials Processing and Analysis Center, Dept. of Materials Science and Engineering, University of Central Florida, Orlando, FL, USA
| | - Ganesh Balasubramanian
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, PA, USA
- Institute of Functional Materials & Devices and College of Health, Lehigh University, Bethlehem, PA, USA
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3
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Rasmussen L, Sanders S, Sosa M, McKellip S, Nebane NM, Martinez-Gzegozewska Y, Reece A, Ruiz P, Manuvakhova A, Zhai L, Warren B, Curry A, Zeng Q, Bostwick JR, Vinson PN. A high-throughput response to the SARS-CoV-2 pandemic. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100160. [PMID: 38761981 DOI: 10.1016/j.slasd.2024.100160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/24/2024] [Accepted: 05/06/2024] [Indexed: 05/20/2024]
Abstract
Four years after the beginning of the COVID-19 pandemic, it is important to reflect on the events that have occurred during that time and the knowledge that has been gained. The response to the pandemic was rapid and highly resourced; it was also built upon a foundation of decades of federally funded basic and applied research. Laboratories in government, pharmaceutical, academic, and non-profit institutions all played roles in advancing pre-2020 discoveries to produce clinical treatments. This perspective provides a summary of how the development of high-throughput screening methods in a biosafety level 3 (BSL-3) environment at Southern Research Institute (SR) contributed to pandemic response efforts. The challenges encountered are described, including those of a technical nature as well as those of working under the pressures of an unpredictable virus and pandemic.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Ling Zhai
- Southern Research, Birmingham, AL, USA
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4
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Peng C, Lv X, Zhang Z, Lin J, Li D. The Recognition Pathway of the SARS-CoV-2 Spike Receptor-Binding Domain to Human Angiotensin-Converting Enzyme 2. Molecules 2024; 29:1875. [PMID: 38675695 PMCID: PMC11054751 DOI: 10.3390/molecules29081875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
COVID-19 caused by SARS-CoV-2 has spread around the world. The receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 is a critical component that directly interacts with host ACE2. Here, we simulate the ACE2 recognition processes of RBD of the WT, Delta, and OmicronBA.2 variants using our recently developed supervised Gaussian accelerated molecular dynamics (Su-GaMD) approach. We show that RBD recognizes ACE2 through three contact regions (regions I, II, and III), which aligns well with the anchor-locker mechanism. The higher binding free energy in State d of the RBDOmicronBA.2-ACE2 system correlates well with the increased infectivity of OmicronBA.2 in comparison with other variants. For RBDDelta, the T478K mutation affects the first step of recognition, while the L452R mutation, through its nearby Y449, affects the RBDDelta-ACE2 binding in the last step of recognition. For RBDOmicronBA.2, the E484A mutation affects the first step of recognition, the Q493R, N501Y, and Y505H mutations affect the binding free energy in the last step of recognition, mutations in the contact regions affect the recognition directly, and other mutations indirectly affect recognition through dynamic correlations with the contact regions. These results provide theoretical insights for RBD-ACE2 recognition and may facilitate drug design against SARS-CoV-2.
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Affiliation(s)
- Can Peng
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300350, China; (C.P.); (X.L.)
| | - Xinyue Lv
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300350, China; (C.P.); (X.L.)
| | - Zhiqiang Zhang
- Xiongan Institute of Innovation, Xiong’an New Area 070001, China;
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300350, China; (C.P.); (X.L.)
| | - Dongmei Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300350, China; (C.P.); (X.L.)
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5
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Nguyen HL, Nguyen TQ, Li MS. SARS-CoV-2 Omicron Subvariants Do Not Differ Much in Binding Affinity to Human ACE2: A Molecular Dynamics Study. J Phys Chem B 2024; 128:3340-3349. [PMID: 38564480 PMCID: PMC11017248 DOI: 10.1021/acs.jpcb.3c06270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 03/12/2024] [Accepted: 03/12/2024] [Indexed: 04/04/2024]
Abstract
The emergence of the variant of concern Omicron (B.1.1.529) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exacerbates the COVID-19 pandemic due to its high contagious ability. Studies have shown that the Omicron binds human ACE2 more strongly than the wild type. The prevalence of Omicron in new cases of COVID-19 promotes novel lineages with improved receptor binding affinity and immune evasion. To shed light on this open problem, in this work, we investigated the binding free energy of the receptor binding domain of the Omicron lineages BA.2, BA.2.3.20, BA.3, BA4/BA5, BA.2.75, BA.2.75.2, BA.4.6, XBB.1, XBB.1.5, BJ.1, BN.1, BQ.1.1, and CH.1.1 to human ACE2 using all-atom molecular dynamics simulation and the molecular mechanics Poisson-Boltzmann surface area method. The results show that these lineages have increased binding affinity compared to the BA.1 lineage, and BA.2.75 and BA.2.75.2 subvariants bind ACE2 more strongly than others. However, in general, the binding affinities of the Omicron lineages do not differ significantly from each other. The electrostatic force dominates over the van der Waals force in the interaction between Omicron lineages and human cells. Based on our results, we argue that viral evolution does not further improve the affinity of SARS-CoV-2 for ACE2 but may increase immune evasion.
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Affiliation(s)
- 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
| | - Thai Quoc Nguyen
- Faculty
of Physics, VNU University of Science, Vietnam
National University, 334 Nguyen Trai, Hanoi 100000, Vietnam
- Dong
Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh
City, Dong Thap 81000, Vietnam
| | - Mai Suan Li
- Institute
of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, Warsaw 02-668, Poland
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6
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Qian J, Zhang S, Wang F, Li J, Zhang J. What makes SARS-CoV-2 unique? Focusing on the spike protein. Cell Biol Int 2024; 48:404-430. [PMID: 38263600 DOI: 10.1002/cbin.12130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/25/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024]
Abstract
Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) seriously threatens public health and safety. Genetic variants determine the expression of SARS-CoV-2 structural proteins, which are associated with enhanced transmissibility, enhanced virulence, and immune escape. Vaccination is encouraged as a public health intervention, and different types of vaccines are used worldwide. However, new variants continue to emerge, especially the Omicron complex, and the neutralizing antibody responses are diminished significantly. In this review, we outlined the uniqueness of SARS-CoV-2 from three perspectives. First, we described the detailed structure of the spike (S) protein, which is highly susceptible to mutations and contributes to the distinct infection cycle of the virus. Second, we systematically summarized the immunoglobulin G epitopes of SARS-CoV-2 and highlighted the central role of the nonconserved regions of the S protein in adaptive immune escape. Third, we provided an overview of the vaccines targeting the S protein and discussed the impact of the nonconserved regions on vaccine effectiveness. The characterization and identification of the structure and genomic organization of SARS-CoV-2 will help elucidate its mechanisms of viral mutation and infection and provide a basis for the selection of optimal treatments. The leaps in advancements regarding improved diagnosis, targeted vaccines and therapeutic remedies provide sound evidence showing that scientific understanding, research, and technology evolved at the pace of the pandemic.
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Affiliation(s)
- Jingbo Qian
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Shichang Zhang
- Department of Clinical Laboratory Medicine, Shenzhen Hospital of Southern Medical University, Shenzhen, China
| | - Fang Wang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jiexin Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
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7
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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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Maity S, Acharya A. Many Roles of Carbohydrates: A Computational Spotlight on the Coronavirus S Protein Binding. ACS APPLIED BIO MATERIALS 2024; 7:646-656. [PMID: 36947738 PMCID: PMC10880061 DOI: 10.1021/acsabm.2c01064] [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: 12/22/2022] [Accepted: 03/08/2023] [Indexed: 03/24/2023]
Abstract
Glycosylation is one of the post-translational modifications with more than 50% of human proteins being glycosylated. The exact nature and chemical composition of glycans are inaccessible to X-ray or cryo-electron microscopy imaging techniques. Therefore, computational modeling studies and molecular dynamics must be used as a "computational microscope". The spike (S) protein of SARS-CoV-2 is heavily glycosylated, and a few glycans play a more functional role "beyond shielding". In this mini-review, we discuss computational investigations of the roles of specific S-protein and ACE2 glycans in the overall ACE2-S protein binding. We highlight different functions of specific glycans demonstrated in myriad computational models and simulations in the context of the SARS-CoV-2 virus binding to the receptor. We also discuss interactions between glycocalyx and the S protein, which may be utilized to design prophylactic polysaccharide-based therapeutics targeting the S protein. In addition, we underline the recent emergence of coronavirus variants and their impact on the S protein and its glycans.
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Affiliation(s)
- Suman Maity
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Atanu Acharya
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
- BioInspired
Syracuse, Syracuse University, Syracuse, New York 13244, United States
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9
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Kim YJ, Min J. Advances in nanobiosensors during the COVID-19 pandemic and future perspectives for the post-COVID era. NANO CONVERGENCE 2024; 11:3. [PMID: 38206526 PMCID: PMC10784265 DOI: 10.1186/s40580-023-00410-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/07/2023] [Indexed: 01/12/2024]
Abstract
The unprecedented threat of the highly contagious virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes exponentially increased infections of coronavirus disease 2019 (COVID-19), highlights the weak spots of the current diagnostic toolbox. In the midst of catastrophe, nanobiosensors offer a new opportunity as an alternative tool to fill a gap among molecular tests, rapid antigen tests, and serological tests. Nanobiosensors surpass the potential of antigen tests because of their enhanced sensitivity, thus enabling us to see antigens as stable and easy-to-access targets. During the first three years of the COVID-19 pandemic, a substantial number of studies have reported nanobiosensors for the detection of SARS-CoV-2 antigens. The number of articles on nanobiosensors and SARS-CoV-2 exceeds the amount of nanobiosensor research on detecting previous infectious diseases, from influenza to SARS-CoV and MERS-CoV. This unprecedented publishing pace also implies the significance of SARS-CoV-2 and the present pandemic. In this review, 158 studies reporting nanobiosensors for detecting SARS-CoV-2 antigens are collected to discuss the current challenges of nanobiosensors using the criteria of point-of-care (POC) diagnostics along with COVID-specific issues. These advances and lessons during the pandemic pave the way for preparing for the post-COVID era and potential upcoming infectious diseases.
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Affiliation(s)
- Young Jun Kim
- School of Integrative Engineering, Chung-Ang University, Heukseok-Dong, Dongjak-Gu, Seoul, 06974, Republic of Korea
| | - Junhong Min
- School of Integrative Engineering, Chung-Ang University, Heukseok-Dong, Dongjak-Gu, Seoul, 06974, Republic of Korea.
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Chinnadurai RK, Ponne S, Chitra L, Kumar R, Thayumanavan P, Subramanian B. Pharmacoinformatic approach to identify potential phytochemicals against SARS-CoV-2 spike receptor-binding domain in native and variants of concern. Mol Divers 2023; 27:2741-2766. [PMID: 36547813 PMCID: PMC9773690 DOI: 10.1007/s11030-022-10580-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 11/24/2022] [Indexed: 12/24/2022]
Abstract
Severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) pathogenesis is initiated by the binding of SARS-CoV-2 spike (S) protein with the angiotensin-converting enzyme 2 receptor (ACE2R) on the host cell surface. The receptor-binding domain (RBD) of the S protein mediates the binding and is more prone to mutations resulting in the generation of different variants. Recently, molecules with the potential to inhibit the interaction of S protein with ACE2R have been of interest due to their therapeutic value. In this context, the present work was performed to identify potential RBD binders from the Indian medicinal plant's phytochemical database through virtual screening, molecular docking, and molecular dynamic simulation. Briefly, 1578 compounds filtered from 9596 phytochemicals were chosen for screening against the RBD of the native SARS-CoV-2 S protein. Based on the binding energy, the top 30 compounds were selected and re-docked individually against the native and five variants of concern (VOCs: alpha, beta, gamma, delta, and omicron) of SARS-CoV-2. Four phytochemicals, namely withanolide F, serotobenine, orobanchol, and gibberellin A51, were found to be potential RBD binders in native and all SARS-CoV-2 VOCs. Among the four, withanolide F exhibited lower binding energy (- 10.84 to - 8.56 kcal/mol) and better ligand efficiency (- 0.3 to - 0.25) against all forms of RBD and hence was subjected to a 100 ns MD simulation which confirmed its stringent binding to the RBDs in native and VOCs. The study prioritizes withanolide F as a prospective COVID-19 (Coronavirus disease) therapeutic agent based on the observations. It warrants deeper investigations into the four promising leads for understanding their precise therapeutic value.
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Affiliation(s)
- Raj Kumar Chinnadurai
- Mahatma Gandhi Medical Advanced Research Institute, Sri Balaji Vidhyapeeth (Deemed to be University), Pondicherry, 607402, India.
| | - Saravanaraman Ponne
- Department of Biotechnology, Pondicherry University, Pondicherry, 605014, India
| | - Loganathan Chitra
- Department of Biochemistry, Periyar University, Salem, Tamil Nadu, 636011, India
| | - Rajender Kumar
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, 106 91, Stockholm, Sweden
| | | | - Balanehru Subramanian
- School of Biological Sciences, Sri Balaji Vidhyapeeth (Deemed to be University), Pondicherry, 607402, India
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11
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Wei L, Chen Y, Feng X, Yao J, Zhang L, Zhou X, Yan G, Qiu H, Wang C, Lu H. Elucidation of N-/ O-glycosylation and site-specific mapping of sialic acid linkage isomers of SARS-CoV-2 human receptor angiotensin-converting enzyme 2. Analyst 2023; 148:5002-5011. [PMID: 37728433 DOI: 10.1039/d3an01079a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
Human angiotensin-converting enzyme 2 (hACE2) is the primary receptor for cellular entry of SARS-CoV-2 into human host cells. hACE2 is heavily glycosylated and glycans on the receptor may play a role in viral binding. Thus, comprehensive characterization of hACE2 glycosylation could aid our understanding of interactions between the receptor and SARS-CoV-2 spike (S) protein, as well as provide a basis for the development of therapeutic drugs targeting this crucial interaction. Herein, 138 N-glycan compositions were identified, most of which are complex-type N-glycans, from seven N-glycosites of hACE2. Among them, 67% contain at least one sialic acid residue. At the level of glycopeptides, the overall quantification of sialylated glycan isomers observed on the sites N322 and N546 have a higher degree of NeuAc (α2-3)Gal (over 80.3%) than that of other N-glycosites (35.6-71.0%). In terms of O-glycans, 69 glycan compositions from 12 O-glycosites were identified, and especially, the C-terminus of hACE2 is heavily O-glycosylated. The terminal sialic acid linkage type of H1N1S1 and H1N1S2 are covered highly with α2,3-sialic acid. These findings could aid the investigation of the interaction between SARS-CoV-2 and human host cells.
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Affiliation(s)
- Liming Wei
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, 131 Dongan Road, 20032 Shanghai, China.
| | - Yuning Chen
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences Department, 555 Zuchongzhi Road, 201203 Shanghai, China.
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, 100049 Beijing, China
| | - Xiaoxiao Feng
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, 131 Dongan Road, 20032 Shanghai, China.
| | - Jun Yao
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, 131 Dongan Road, 20032 Shanghai, China.
| | - Lei Zhang
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, 131 Dongan Road, 20032 Shanghai, China.
| | - Xinwen Zhou
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, 131 Dongan Road, 20032 Shanghai, China.
| | - Guoquan Yan
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, 131 Dongan Road, 20032 Shanghai, China.
| | - Hong Qiu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences Department, 555 Zuchongzhi Road, 201203 Shanghai, China.
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, 100049 Beijing, China
| | - Chunhe Wang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences Department, 555 Zuchongzhi Road, 201203 Shanghai, China.
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, 100049 Beijing, China
| | - Haojie Lu
- Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, 131 Dongan Road, 20032 Shanghai, China.
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12
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Hou D, Cao W, Kim S, Cui X, Ziarnik M, Im W, Zhang XF. Biophysical investigation of interactions between SARS-CoV-2 spike protein and neuropilin-1. Protein Sci 2023; 32:e4773. [PMID: 37656811 PMCID: PMC10510470 DOI: 10.1002/pro.4773] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 08/19/2023] [Accepted: 08/29/2023] [Indexed: 09/03/2023]
Abstract
Recent studies have suggested that neuropilin-1 (NRP1) may serve as a potential receptor in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. However, the biophysical characteristics of interactions between NRP1 and SARS-CoV-2 remain unclear. In this study, we examined the interactions between NRP1 and various SARS-CoV-2 spike (S) fragments, including the receptor-binding domain (RBD) and the S protein trimer in a soluble form or expressed on pseudovirions, using atomic force microscopy and structural modeling. Our measurements shows that NRP1 interacts with the RBD and trimer at a higher binding frequency (BF) compared to ACE2. This NRP1-RBD interaction has also been predicted and simulated via AlphaFold2 and molecular dynamics simulations, and the results indicate that their binding patterns are very similar to RBD-ACE2 interactions. Additionally, under similar loading rates, the most probable unbinding forces between NRP1 and S trimer (both soluble form and on pseudovirions) are larger than the forces between NRP1 and RBD and between trimer and ACE2. Further analysis indicates that NRP1 has a stronger binding affinity to the SARS-CoV-2 S trimer with a dissociation rate of 0.87 s-1 , four times lower than the dissociation rate of 3.65 s-1 between NRP1 and RBD. Moreover, additional experiments show that RBD-neutralizing antibodies can significantly reduce the BF for both ACE2 and NRP1. Together, the study suggests that NRP1 can be an alternative receptor for SARS-CoV-2 attachment to human cells, and the neutralizing antibodies targeting SARS-CoV-2 RBD can reduce the binding between SARS-CoV-2 and NRP1.
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Affiliation(s)
- Decheng Hou
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
- Department of Biomedical EngineeringUniversity of Massachusetts AmherstAmherstMassachusettsUSA
| | - Wenpeng Cao
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
| | - Seonghan Kim
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
| | - Xinyu Cui
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
- Department of Biomedical EngineeringUniversity of Massachusetts AmherstAmherstMassachusettsUSA
| | - Matthew Ziarnik
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
| | - Wonpil Im
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
- Departments of Biological Sciences, Chemistry, and Computer Science and EngineeringLehigh UniversityBethlehemUSA
| | - X. Frank Zhang
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
- Department of Biomedical EngineeringUniversity of Massachusetts AmherstAmherstMassachusettsUSA
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13
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Li B, Zhao Y, Wu X, Wu H, Tang W, Yu X, Mou J, Tan W, Jin M, Li W, Zhang Q, Liu M. Abiotic Synthetic Antibody Inhibitor with Broad-Spectrum Neutralization and Antiviral Efficacy against Escaping SARS-CoV-2 Variants. ACS NANO 2023; 17:7017-7034. [PMID: 36971310 PMCID: PMC10074723 DOI: 10.1021/acsnano.3c02050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 03/23/2023] [Indexed: 06/18/2023]
Abstract
The rapid emergence and spread of vaccine/antibody-escaping variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed serious challenges to our efforts in combating corona virus disease 2019 (COVID-19) pandemic. A potent and broad-spectrum neutralizing reagent against these escaping mutants is extremely important for the development of strategies for the prevention and treatment of SARS-CoV-2 infection. We herein report an abiotic synthetic antibody inhibitor as a potential anti-SARS-CoV-2 therapeutic agent. The inhibitor, Aphe-NP14, was selected from a synthetic hydrogel polymer nanoparticle library created by incorporating monomers with functionalities complementary to key residues of the SARS-CoV-2 spike glycoprotein receptor binding domain (RBD) involved in human angiotensin-converting enzyme 2 (ACE2) binding. It has high capacity, fast adsorption kinetics, strong affinity, and broad specificity in biologically relevant conditions to both the wild type and the current variants of concern, including Beta, Delta, and Omicron spike RBD. The Aphe-NP14 uptake of spike RBD results in strong blockage of spike RBD-ACE2 interaction and thus potent neutralization efficacy against these escaping spike protein variant pseudotyped viruses. It also inhibits live SARS-CoV-2 virus recognition, entry, replication, and infection in vitro and in vivo. The Aphe-NP14 intranasal administration is found to be safe due to its low in vitro and in vivo toxicity. These results establish a potential application of abiotic synthetic antibody inhibitors in the prevention and treatment of the infection of emerging or possibly future SARS-CoV-2 variants.
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Affiliation(s)
- Bingxue Li
- Key Laboratory of Arable Land Conservation (Middle and
Lower Reaches of Yangtse River), Ministry of Agriculture and Rural Affairs, Hubei Key
Laboratory of Soil Environment and Pollution Remediation, State Environmental Protection
Key Laboratory of Soil Health and Green Remediation, College of Resources and Environment,
Huazhong Agricultural University, Wuhan 430070,
China
| | - Ya Zhao
- National Key Laboratory of Agricultural Microbiology,
Huazhong Agricultural University, Wuhan 430070,
China
| | - Xuefan Wu
- State Key Laboratory of Virology, Wuhan
Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of
Sciences, Wuhan 430071, China
- University of Chinese Academy of
Sciences, Beijing 100049, China
| | - Haiyan Wu
- Key Laboratory of Arable Land Conservation (Middle and
Lower Reaches of Yangtse River), Ministry of Agriculture and Rural Affairs, Hubei Key
Laboratory of Soil Environment and Pollution Remediation, State Environmental Protection
Key Laboratory of Soil Health and Green Remediation, College of Resources and Environment,
Huazhong Agricultural University, Wuhan 430070,
China
| | - Weicheng Tang
- Key Laboratory of Arable Land Conservation (Middle and
Lower Reaches of Yangtse River), Ministry of Agriculture and Rural Affairs, Hubei Key
Laboratory of Soil Environment and Pollution Remediation, State Environmental Protection
Key Laboratory of Soil Health and Green Remediation, College of Resources and Environment,
Huazhong Agricultural University, Wuhan 430070,
China
| | - Xiaoyang Yu
- Key Laboratory of Arable Land Conservation (Middle and
Lower Reaches of Yangtse River), Ministry of Agriculture and Rural Affairs, Hubei Key
Laboratory of Soil Environment and Pollution Remediation, State Environmental Protection
Key Laboratory of Soil Health and Green Remediation, College of Resources and Environment,
Huazhong Agricultural University, Wuhan 430070,
China
| | - Jianqiong Mou
- Key Laboratory of Arable Land Conservation (Middle and
Lower Reaches of Yangtse River), Ministry of Agriculture and Rural Affairs, Hubei Key
Laboratory of Soil Environment and Pollution Remediation, State Environmental Protection
Key Laboratory of Soil Health and Green Remediation, College of Resources and Environment,
Huazhong Agricultural University, Wuhan 430070,
China
| | - Wenfeng Tan
- Key Laboratory of Arable Land Conservation (Middle and
Lower Reaches of Yangtse River), Ministry of Agriculture and Rural Affairs, Hubei Key
Laboratory of Soil Environment and Pollution Remediation, State Environmental Protection
Key Laboratory of Soil Health and Green Remediation, College of Resources and Environment,
Huazhong Agricultural University, Wuhan 430070,
China
| | - Meilin Jin
- National Key Laboratory of Agricultural Microbiology,
Huazhong Agricultural University, Wuhan 430070,
China
- College of Veterinary Medicine, Huazhong
Agricultural University, Wuhan 430070, China
- Key Laboratory of Development of Veterinary Diagnostic
Products, Ministry of Agriculture, Wuhan 430070,
China
| | - Wei Li
- State Key Laboratory of Virology, Wuhan
Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of
Sciences, Wuhan 430071, China
| | - Qiang Zhang
- National Key Laboratory of Agricultural Microbiology,
Huazhong Agricultural University, Wuhan 430070,
China
- College of Biomedicine and Health,
Huazhong Agricultural University, Wuhan 430070,
China
- Hubei Jiangxia Laboratory,
Wuhan 430200, China
| | - Mingming Liu
- Key Laboratory of Arable Land Conservation (Middle and
Lower Reaches of Yangtse River), Ministry of Agriculture and Rural Affairs, Hubei Key
Laboratory of Soil Environment and Pollution Remediation, State Environmental Protection
Key Laboratory of Soil Health and Green Remediation, College of Resources and Environment,
Huazhong Agricultural University, Wuhan 430070,
China
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14
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Feng S, Park S, Choi YK, Im W. CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications. J Chem Theory Comput 2023; 19:2161-2185. [PMID: 37014931 PMCID: PMC10174225 DOI: 10.1021/acs.jctc.2c01246] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
Molecular dynamics simulations of membranes and membrane proteins serve as computational microscopes, revealing coordinated events at the membrane interface. As G protein-coupled receptors, ion channels, transporters, and membrane-bound enzymes are important drug targets, understanding their drug binding and action mechanisms in a realistic membrane becomes critical. Advances in materials science and physical chemistry further demand an atomistic understanding of lipid domains and interactions between materials and membranes. Despite a wide range of membrane simulation studies, generating a complex membrane assembly remains challenging. Here, we review the capability of CHARMM-GUI Membrane Builder in the context of emerging research demands, as well as the application examples from the CHARMM-GUI user community, including membrane biophysics, membrane protein drug-binding and dynamics, protein-lipid interactions, and nano-bio interface. We also provide our perspective on future Membrane Builder development.
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Affiliation(s)
- Shasha Feng
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Soohyung Park
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Yeol Kyo Choi
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Wonpil Im
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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15
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da Costa HHM, Orts DJB, Moura AD, Duarte-Neto AN, Cirqueira CS, Réssio RA, Kanamura CT, Miguita K, Ferreira JE, Santos RTM, Adriani PP, Cunha-Junior JP, Astray RM, Catarino RM, Lancelotti M, Prudencio CR. RBD and Spike DNA-Based Immunization in Rabbits Elicited IgG Avidity Maturation and High Neutralizing Antibody Responses against SARS-CoV-2. Viruses 2023; 15:v15020555. [PMID: 36851769 PMCID: PMC9959588 DOI: 10.3390/v15020555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/23/2023] [Accepted: 02/11/2023] [Indexed: 02/19/2023] Open
Abstract
Neutralizing antibodies (nAbs) are a critical part of coronavirus disease 2019 (COVID-19) research as they are used to gain insight into the immune response to severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) infections. Among the technologies available for generating nAbs, DNA-based immunization methods are an alternative to conventional protocols. In this pilot study, we investigated whether DNA-based immunization by needle injection in rabbits was a viable approach to produce a functional antibody response. We demonstrated that three doses of DNA plasmid carrying the gene encoding the full-length spike protein (S) or the receptor binding domain (RBD) of SARS-CoV-2 induced a time-dependent increase in IgG antibody avidity maturation. Moreover, the IgG antibodies displayed high cross neutralization by live SARS-CoV-2 and pseudoviruses neutralization assays. Thus, we established a simple, low cost and feasible DNA-based immunization protocol in rabbits that elicited high IgG avidity maturation and nAbs production against SARS-CoV-2, highlighting the importance of DNA-based platforms for developing new immunization strategies against SARS-CoV-2 and future emerging epidemics.
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Affiliation(s)
- Hernan H. M. da Costa
- Immunology Center, Institute Adolfo Lutz, São Paulo 01246-902, Brazil
- Graduate Program Interunits in Biotechnology, University of São Paulo, São Paulo 05508-000, Brazil
| | - Diego J. B. Orts
- Immunology Center, Institute Adolfo Lutz, São Paulo 01246-902, Brazil
| | - Andrew D. Moura
- Immunology Center, Institute Adolfo Lutz, São Paulo 01246-902, Brazil
| | | | | | - Rodrigo A. Réssio
- Pathology Center, Institute Adolfo Lutz, São Paulo 01246-902, Brazil
| | | | - Karen Miguita
- Pathology Center, Institute Adolfo Lutz, São Paulo 01246-902, Brazil
| | | | | | - Patricia P. Adriani
- Skinzymes Biotechnology Ltd., São Paulo 05441-040, Brazil
- Laboratory of Nanopharmaceuticals and Delivery Systems, Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Jair P. Cunha-Junior
- Laboratory of Immunochemistry and Immunotechnology, Department of Immunology, Federal University of Uberlândia, Uberlândia 38405-317, Brazil
| | - Renato M. Astray
- Multi-Purpose Laboratory, Butantan Institute, São Paulo 05503-900, Brazil
| | | | - Marcelo Lancelotti
- Faculty of Pharmaceutical Sciences, Campinas State University, Campinas 13083-871, Brazil
| | - Carlos R. Prudencio
- Immunology Center, Institute Adolfo Lutz, São Paulo 01246-902, Brazil
- Graduate Program Interunits in Biotechnology, University of São Paulo, São Paulo 05508-000, Brazil
- Correspondence: ; Tel.: +55-11-3068-2886
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16
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Damin F, Galbiati S, Clementi N, Ferrarese R, Mancini N, Sola L, Chiari M. Dual-Domain Reporter Approach for Multiplex Identification of Major SARS-CoV-2 Variants of Concern in a Microarray-Based Assay. BIOSENSORS 2023; 13:269. [PMID: 36832035 PMCID: PMC9953785 DOI: 10.3390/bios13020269] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Since the emergence of the COVID-19 pandemic in December 2019, the SARS-CoV-2 virus continues to evolve into many variants emerging around the world. To enable regular surveillance and timely adjustments in public health interventions, it is of the utmost importance to accurately monitor and track the distribution of variants as rapidly as possible. Genome sequencing is the gold standard for monitoring the evolution of the virus, but it is not cost-effective, rapid and easily accessible. We have developed a microarray-based assay that can distinguish known viral variants present in clinical samples by simultaneously detecting mutations in the Spike protein gene. In this method, the viral nucleic acid, extracted from nasopharyngeal swabs, after RT-PCR, hybridizes in solution with specific dual-domain oligonucleotide reporters. The domains complementary to the Spike protein gene sequence encompassing the mutation form hybrids in solution that are directed by the second domain ("barcode" domain) at specific locations on coated silicon chips. The method utilizes characteristic fluorescence signatures to unequivocally differentiate, in a single assay, different known SARS-CoV-2 variants. In the nasopharyngeal swabs of patients, this multiplex system was able to genotype the variants which have caused waves of infections worldwide, reported by the WHO as being of concern (VOCs), namely Alpha, Beta, Gamma, Delta and Omicron variants.
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Affiliation(s)
- Francesco Damin
- National Research Council of Italy, Institute of Chemical Sciences and Technologies “G. Natta”, 20131 Milan, Italy
| | - Silvia Galbiati
- Complications of Diabetes Units, Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Nicola Clementi
- Laboratory of Medical Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, Italy
- Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Roberto Ferrarese
- Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Nicasio Mancini
- Laboratory of Medical Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, Italy
- Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Laura Sola
- National Research Council of Italy, Institute of Chemical Sciences and Technologies “G. Natta”, 20131 Milan, Italy
| | - Marcella Chiari
- National Research Council of Italy, Institute of Chemical Sciences and Technologies “G. Natta”, 20131 Milan, Italy
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17
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Kim S, Liu Y, Ziarnik M, Seo S, Cao Y, Zhang XF, Im W. Binding of human ACE2 and RBD of Omicron enhanced by unique interaction patterns among SARS-CoV-2 variants of concern. J Comput Chem 2023; 44:594-601. [PMID: 36398990 PMCID: PMC9825653 DOI: 10.1002/jcc.27025] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/11/2022] [Accepted: 10/11/2022] [Indexed: 11/20/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing COVID-19, has continued to mutate and spread worldwide despite global vaccination efforts. In particular, the Omicron variant, first identified in South Africa in late November 2021, has become the dominant strain worldwide. Compared to the original strain identified in Wuhan, Omicron features 50 genetic mutations, with 15 mutations in the receptor-binding domain (RBD) of the spike protein, which binds to the human angiotensin-converting enzyme 2 (ACE2) receptor for viral entry. However, it is not completely understood how these mutations alter the interaction and binding strength between the Omicron RBD and ACE2. In this study, we used a combined steered molecular dynamics (SMD) simulation and experimental microscale thermophoresis (MST) approach to quantify the interaction between Omicron RBD and ACE2. We report that the Omicron brings an enhanced RBD-ACE2 interface through N501Y, Q498R, and T478K mutations; the changes further lead to unique interaction patterns, reminiscing the features of previously dominated variants, Alpha (N501Y) and Delta (L452R and T478K). Among the Q493K and Q493R, we report that Q493R shows stronger binding to ACE2 than Q493K due to increased interactions. Our MST data confirmed that the Omicron mutations in RBD are associated with a five-fold higher binding affinity to ACE2 compared to the RBD of the original strain. In conclusion, our results could help explain the Omicron variant's prevalence in human populations, as higher interaction forces or affinity for ACE2 likely promote greater viral binding and internalization, leading to increased infectivity.
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Affiliation(s)
- Seonghan Kim
- Department of Bioengineering, Daejeon 34141, Republic of Korea
| | - Yi Liu
- Department of Bioengineering, Daejeon 34141, Republic of Korea
| | - Matthew Ziarnik
- Department of Bioengineering, Daejeon 34141, Republic of Korea
| | - Sangjae Seo
- Korean Institute of Science and Technology Information, Daejeon 34141, Republic of Korea
| | - Yiwei Cao
- Departments of Biological Sciences, Chemistry, and Computer Science and Engineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA
| | - X. Frank Zhang
- Department of Bioengineering, Daejeon 34141, Republic of Korea
- Current address: Department of Biomedical Engineering, University of Massachusetts Amherst, 240 Thatcher Road, Amherst, MA 01003, USA
| | - Wonpil Im
- Department of Bioengineering, Daejeon 34141, Republic of Korea
- Departments of Biological Sciences, Chemistry, and Computer Science and Engineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA
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18
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Neuropilin-1 Mediates SARS-CoV-2 Infection of Astrocytes in Brain Organoids, Inducing Inflammation Leading to Dysfunction and Death of Neurons. mBio 2022; 13:e0230822. [PMID: 36314791 PMCID: PMC9765283 DOI: 10.1128/mbio.02308-22] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is frequently associated with neurological deficits, but how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces these effects remains unclear. Here, we show that astrocytes are readily infected by SARS-CoV-2, but surprisingly, neuropilin-1, not angiotensin-converting enzyme 2 (ACE2), serves as the principal receptor mediating cell entry. Infection is further positively modulated by the two-pore segment channel 2 (TPC2) protein that regulates membrane trafficking and endocytosis. Astrocyte infection produces a pathological response closely resembling reactive astrogliosis characterized by elevated type I interferon (IFN) production, increased inflammation, and the decreased expression of transporters of water, ions, choline, and neurotransmitters. These combined events initiated within astrocytes produce a hostile microenvironment that promotes the dysfunction and death of uninfected bystander neurons. IMPORTANCE SARS-CoV-2 infection primarily targets the lung but may also damage other organs, including the brain, heart, kidney, and intestine. Central nervous system (CNS) pathologies include loss of smell and taste, headache, delirium, acute psychosis, seizures, and stroke. Pathological loss of gray matter occurs in SARS-CoV-2 infection, but it is unclear whether this is due to direct viral infection, indirect effects associated with systemic inflammation, or both. Here, we used induced pluripotent stem cell (iPSC)-derived brain organoids and primary human astrocytes from the cerebral cortex to study direct SARS-CoV-2 infection. Our findings support a model where SARS-CoV-2 infection of astrocytes produces a panoply of changes in the expression of genes regulating innate immune signaling and inflammatory responses. The deregulation of these genes in astrocytes produces a microenvironment within the CNS that ultimately disrupts normal neuron function, promoting neuronal cell death and CNS deficits.
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19
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An Analysis of the Capturing and Passing Ability of a DNA Origami Nanocarrier with the Aid of Molecular Dynamics Simulation. Mol Biotechnol 2022:10.1007/s12033-022-00636-4. [DOI: 10.1007/s12033-022-00636-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/01/2022] [Indexed: 12/14/2022]
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20
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Khater I, Nassar A. Potential antiviral peptides targeting the SARS-CoV-2 spike protein. BMC Pharmacol Toxicol 2022; 23:91. [PMID: 36461109 PMCID: PMC9716172 DOI: 10.1186/s40360-022-00627-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The coronavirus disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection became an international pandemic and created a public health crisis. The binding of the viral Spike glycoprotein to the human cell receptor angiotensin-converting enzyme 2 (ACE2) initiates viral infection. The development of efficient treatments to combat coronavirus disease is considered essential. METHODS An in silico approach was employed to design amino acid peptide inhibitor against the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein. The designed inhibitor (SARS-CoV-2 PEP 49) consists of amino acids with the α1 helix and the β4 - β5 sheets of ACE2. The PEP-FOLD3 web tool was used to create the 3D structures of the peptide amino acids. Analyzing the interaction between ACE2 and the RBD of the Spike protein for three protein data bank entries (6M0J, 7C8D, and 7A95) indicated that the interacting amino acids were contained inside two regions of ACE2: the α1 helical protease domain (PD) and the β4 - β5 sheets. RESULTS Molecular docking analysis of the designed inhibitor demonstrated that SARS-CoV-2 PEP 49 attaches directly to the ACE2 binding site of the Spike protein with a binding affinity greater than the ACE2, implying that the SARS-CoV-2 PEP 49 model may be useful as a potential RBD binding blocker.
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Affiliation(s)
- Ibrahim Khater
- grid.7776.10000 0004 0639 9286Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Aaya Nassar
- grid.7776.10000 0004 0639 9286Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt ,grid.253615.60000 0004 1936 9510Department of Clinical Research and Leadership, School of Medicine and Health Sciences, George Washington University, Washington DC, USA
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21
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Suh D, Feng S, Lee H, Zhang H, Park S, Kim S, Lee J, Choi S, Im W. CHARMM-GUI Enhanced Sampler for various collective variables and enhanced sampling methods. Protein Sci 2022; 31:e4446. [PMID: 36124940 PMCID: PMC9601830 DOI: 10.1002/pro.4446] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 11/08/2022]
Abstract
Enhanced sampling methodologies modifying underlying Hamiltonians can be used for the systems with a rugged potential energy surface that makes it hard to observe convergence using conventional unbiased molecular dynamics (MD) simulations. We present CHARMM-GUI Enhanced Sampler, a web-based tool to prepare various enhanced sampling simulations inputs with user-selected collective variables (CVs). Enhanced Sampler provides inputs for the following nine methods: accelerated MD, Gaussian accelerated MD, conformational flooding, metadynamics, adaptive biasing force, steered MD, temperature replica exchange MD, replica exchange solute tempering 2, and replica exchange umbrella sampling for the method-implemented MD packages including AMBER, CHARMM, GENESIS, GROMACS, NAMD, and OpenMM. Users only need to select a group of atoms via intuitive web-implementation in order to define commonly used nine CVs of interest: center of mass based distance, angle, dihedral, root-mean-square-distance, radius of gyration, distance projected on axis, two types of angles projected on axis, and coordination numbers. The enhanced sampling methods are tested with several biological systems to illustrate their efficiency over conventional MD. Enhanced Sampler with carefully optimized system-dependent parameters will help users to get meaningful results from their enhanced sampling simulations.
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Affiliation(s)
- Donghyuk Suh
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and EngineeringLehigh UniversityBethlehemPennsylvaniaUSA
- Research Institute for Pharmaceutical Sciences, College of Pharmacy and Graduate School of Pharmaceutical SciencesEwha Womans UniversitySeoulRepublic of Korea
| | - Shasha Feng
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and EngineeringLehigh UniversityBethlehemPennsylvaniaUSA
| | - Hwayoung Lee
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and EngineeringLehigh UniversityBethlehemPennsylvaniaUSA
| | - Han Zhang
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and EngineeringLehigh UniversityBethlehemPennsylvaniaUSA
| | - Sang‐Jun Park
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and EngineeringLehigh UniversityBethlehemPennsylvaniaUSA
| | - Seonghan Kim
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and EngineeringLehigh UniversityBethlehemPennsylvaniaUSA
| | - Jumin Lee
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and EngineeringLehigh UniversityBethlehemPennsylvaniaUSA
| | - Sun Choi
- Research Institute for Pharmaceutical Sciences, College of Pharmacy and Graduate School of Pharmaceutical SciencesEwha Womans UniversitySeoulRepublic of Korea
| | - Wonpil Im
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and EngineeringLehigh UniversityBethlehemPennsylvaniaUSA
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22
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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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23
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Lv N, Cao Z. RBD spatial orientation of the spike protein and its binding to ACE2: insight into the high infectivity of the SARS-CoV-2 Delta variant from MD simulations. Phys Chem Chem Phys 2022; 24:24155-24165. [PMID: 36168828 DOI: 10.1039/d2cp03425e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The spike glycoprotein on the surface of the SARS-CoV-2 envelope plays an important role in its invasion into host cells. The binding of the spike glycoprotein RBD to the angiotensin-converting enzyme 2 (ACE2) receptor as a critical step in the spread of the virus has been explored intensively since the outbreak of COVID-19, but the high transmissibility of the virus such as the Delta variant is still not fully understood. Here, molecular simulations on the binding interactions of the wild-type spike protein and its four variants (Beta, Kappa, Delta, and Mu) with ACE2 and the antibody were performed, and the present results reveal that the residue mutations will not strengthen the binding affinity of the variant for ACE2, but remarkably influences the spatial orientation of the spike protein. Only the up-right conformational receptor binding domain (RBD) can bind ACE2, which is stabilized by the nearby RBDs in the down state, revealing that the RBD bears dual functional characteristics. The present results provide new insights into plausible mechanisms for high infectivity of the virus variants and their immune escape.
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Affiliation(s)
- Nan Lv
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, P. R. China.
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, P. R. China.
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24
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Singh J, Vashishtha S, Rahman SA, Ehtesham NZ, Alam A, Kundu B, Dobrindt U. Energetics of Spike Protein Opening of SARS-CoV-1 and SARS-CoV-2 and Its Variants of Concern: Implications in Host Receptor Scanning and Transmission. Biochemistry 2022; 61:2188-2197. [PMID: 36166360 DOI: 10.1021/acs.biochem.2c00301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The receptor binding domain(s) (RBD) of spike (S) proteins of SARS-CoV-1 and SARS-CoV-2 (severe acute respiratory syndrome coronavirus) undergoes closed to open transition to engage with host ACE2 receptors. In this study, using multi atomistic (equilibrium) and targeted (non-equilibrium) molecular dynamics simulations, we have compared energetics of RBD opening pathways in full-length (modeled from cryo-EM structures) S proteins of SARS-CoV-1 and SARS-CoV-2. Our data indicate that amino acid variations at the RBD interaction interface can culminate into distinct free energy landscapes of RBD opening in these S proteins. We further report that mutations in the S protein of SARS-CoV-2 variants of concern can reduce the protein-protein interaction affinity of RBD(s) with its neighboring domains and could favor its opening to access ACE2 receptors. The findings can also aid in predicting the impact of future mutations on the rate of S protein opening for rapid host receptor scanning.
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Affiliation(s)
- Jasdeep Singh
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology-Delhi, Hauz Khas, New Delhi 110016, India
| | - Shubham Vashishtha
- Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, Hauz Khas, New Delhi 110016, India
| | - Syed Asad Rahman
- BioInception Pvt. Ltd., Future Business Centre, Kings Hedges Road, Cambridge CB4 2HY, U.K
| | - Nasreen Zafar Ehtesham
- ICMR National Institute of Pathology, Safdarjung Hospital Campus, New Delhi 110029, India
| | - Anwar Alam
- ICMR National Institute of Pathology, Safdarjung Hospital Campus, New Delhi 110029, India
| | - Bishwajit Kundu
- Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, Hauz Khas, New Delhi 110016, India
| | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Münster 48149, Germany
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25
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Kayabolen A, Akcan U, Özturan D, Ulbegi‐Polat H, Sahin GN, Pinarbasi‐Degirmenci N, Bayraktar C, Soyler G, Sarayloo E, Nurtop E, Ozer B, Guney‐Esken G, Barlas T, Yildirim IS, Dogan O, Karahuseyinoglu S, Lack NA, Kaya M, Albayrak C, Can F, Solaroglu I, Bagci‐Onder T. Protein Scaffold-Based Multimerization of Soluble ACE2 Efficiently Blocks SARS-CoV-2 Infection In Vitro and In Vivo. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2201294. [PMID: 35896894 PMCID: PMC9353362 DOI: 10.1002/advs.202201294] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Soluble ACE2 (sACE2) decoys are promising agents to inhibit SARS-CoV-2, as their efficiency is unlikely to be affected by escape mutations. However, their success is limited by their relatively poor potency. To address this challenge, multimeric sACE2 consisting of SunTag or MoonTag systems is developed. These systems are extremely effective in neutralizing SARS-CoV-2 in pseudoviral systems and in clinical isolates, perform better than the dimeric or trimeric sACE2, and exhibit greater than 100-fold neutralization efficiency, compared to monomeric sACE2. SunTag or MoonTag fused to a more potent sACE2 (v1) achieves a sub-nanomolar IC50 , comparable with clinical monoclonal antibodies. Pseudoviruses bearing mutations for variants of concern, including delta and omicron, are also neutralized efficiently with multimeric sACE2. Finally, therapeutic treatment of sACE2(v1)-MoonTag provides protection against SARS-CoV-2 infection in an in vivo mouse model. Therefore, highly potent multimeric sACE2 may offer a promising treatment approach against SARS-CoV-2 infections.
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Affiliation(s)
- Alisan Kayabolen
- Koç University Research Center for Translational Medicine (KUTTAM)Koç UniversityIstanbul34450Turkey
| | - Ugur Akcan
- Koç University Research Center for Translational Medicine (KUTTAM)Koç UniversityIstanbul34450Turkey
| | - Doğancan Özturan
- Koç University Research Center for Translational Medicine (KUTTAM)Koç UniversityIstanbul34450Turkey
| | - Hivda Ulbegi‐Polat
- Genetic Engineering and Biotechnology InstituteTUBITAK Marmara Research CenterKocaeli41470Turkey
| | - Gizem Nur Sahin
- Koç University Research Center for Translational Medicine (KUTTAM)Koç UniversityIstanbul34450Turkey
| | | | - Canan Bayraktar
- Koç University Research Center for Translational Medicine (KUTTAM)Koç UniversityIstanbul34450Turkey
| | - Gizem Soyler
- Koç University Research Center for Translational Medicine (KUTTAM)Koç UniversityIstanbul34450Turkey
| | - Ehsan Sarayloo
- Koç University Research Center for Translational Medicine (KUTTAM)Koç UniversityIstanbul34450Turkey
- Department of BiotechnologyBeykoz Institute of Life Sciences and Biotechnology (BILSAB)Bezmialem Vakif UniversityIstanbul34820Turkey
| | - Elif Nurtop
- Koç University Isbank Center for Infectious Diseases (KUISCID)Istanbul34010Turkey
| | - Berna Ozer
- Koç University Isbank Center for Infectious Diseases (KUISCID)Istanbul34010Turkey
| | - Gulen Guney‐Esken
- Koç University Isbank Center for Infectious Diseases (KUISCID)Istanbul34010Turkey
| | - Tayfun Barlas
- Koç University Isbank Center for Infectious Diseases (KUISCID)Istanbul34010Turkey
| | - Ismail Selim Yildirim
- Genetic Engineering and Biotechnology InstituteTUBITAK Marmara Research CenterKocaeli41470Turkey
| | - Ozlem Dogan
- Koç University Isbank Center for Infectious Diseases (KUISCID)Istanbul34010Turkey
- Koç University School of MedicineDepartment of Medical MicrobiologyIstanbul34010Turkey
| | - Sercin Karahuseyinoglu
- Koç University Research Center for Translational Medicine (KUTTAM)Koç UniversityIstanbul34450Turkey
- Koç University School of Medicine, Department of Histology and EmbryologyIstanbul34450Türkiye
| | - Nathan A. Lack
- Koç University Research Center for Translational Medicine (KUTTAM)Koç UniversityIstanbul34450Turkey
- Vancouver Prostate CentreUniversity of British ColumbiaVancouverBC V6H 3Z6Canada
| | - Mehmet Kaya
- Koç University Research Center for Translational Medicine (KUTTAM)Koç UniversityIstanbul34450Turkey
| | - Cem Albayrak
- Koç University Research Center for Translational Medicine (KUTTAM)Koç UniversityIstanbul34450Turkey
- Department of BiotechnologyBeykoz Institute of Life Sciences and Biotechnology (BILSAB)Bezmialem Vakif UniversityIstanbul34820Turkey
| | - Fusun Can
- Koç University Isbank Center for Infectious Diseases (KUISCID)Istanbul34010Turkey
- Koç University School of MedicineDepartment of Medical MicrobiologyIstanbul34010Turkey
| | - Ihsan Solaroglu
- Koç University Research Center for Translational Medicine (KUTTAM)Koç UniversityIstanbul34450Turkey
- Department of Basic SciencesLoma Linda UniversityLoma LindaCA92354USA
| | - Tugba Bagci‐Onder
- Koç University Research Center for Translational Medicine (KUTTAM)Koç UniversityIstanbul34450Turkey
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26
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Monteil V, Eaton B, Postnikova E, Murphy M, Braunsfeld B, Crozier I, Kricek F, Niederhöfer J, Schwarzböck A, Breid H, Devignot S, Klingström J, Thålin C, Kellner MJ, Christ W, Havervall S, Mereiter S, Knapp S, Sanchez Jimenez A, Bugajska‐Schretter A, Dohnal A, Ruf C, Gugenberger R, Hagelkruys A, Montserrat N, Kozieradzki I, Hasan Ali O, Stadlmann J, Holbrook MR, Schmaljohn C, Oostenbrink C, Shoemaker RH, Mirazimi A, Wirnsberger G, Penninger JM. Clinical grade ACE2 as a universal agent to block SARS-CoV-2 variants. EMBO Mol Med 2022; 14:e15230. [PMID: 35781796 PMCID: PMC9350269 DOI: 10.15252/emmm.202115230] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 06/03/2022] [Accepted: 06/03/2022] [Indexed: 12/29/2022] Open
Abstract
The recent emergence of multiple SARS-CoV-2 variants has caused considerable concern due to both reduced vaccine efficacy and escape from neutralizing antibody therapeutics. It is, therefore, paramount to develop therapeutic strategies that inhibit all known and future SARS-CoV-2 variants. Here, we report that all SARS-CoV-2 variants analyzed, including variants of concern (VOC) Alpha, Beta, Gamma, Delta, and Omicron, exhibit enhanced binding affinity to clinical grade and phase 2 tested recombinant human soluble ACE2 (APN01). Importantly, soluble ACE2 neutralized infection of VeroE6 cells and human lung epithelial cells by all current VOC strains with markedly enhanced potency when compared to reference SARS-CoV-2 isolates. Effective inhibition of infections with SARS-CoV-2 variants was validated and confirmed in two independent laboratories. These data show that SARS-CoV-2 variants that have emerged around the world, including current VOC and several variants of interest, can be inhibited by soluble ACE2, providing proof of principle of a pan-SARS-CoV-2 therapeutic.
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Affiliation(s)
- Vanessa Monteil
- Unit of Clinical MicrobiologyKarolinska Institutet and Karolinska University HospitalStockholmSweden
| | - Brett Eaton
- NIAID Integrated Research Facility at Fort Detrick (IRF‐Frederick)FrederickMarylandUSA
| | - Elena Postnikova
- NIAID Integrated Research Facility at Fort Detrick (IRF‐Frederick)FrederickMarylandUSA
| | - Michael Murphy
- NIAID Integrated Research Facility at Fort Detrick (IRF‐Frederick)FrederickMarylandUSA
| | - Benedict Braunsfeld
- Institute for Molecular Modeling and SimulationUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
| | - Ian Crozier
- Clinical Research Monitoring Program DirectorateFrederick National Laboratory for Cancer ResearchFrederickMarylandUSA
| | | | | | | | | | - Stephanie Devignot
- Unit of Clinical MicrobiologyKarolinska Institutet and Karolinska University HospitalStockholmSweden
| | - Jonas Klingström
- Center for Infectious MedicineDepartment of Medicine HuddingeKarolinska InstitutetStockholmSweden
| | - Charlotte Thålin
- Department of Clinical SciencesKarolinska Institute Danderyd HospitalStockholmSweden
| | - Max J Kellner
- Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University at Vienna and MedicalUniversity of ViennaViennaAustria
| | - Wanda Christ
- Center for Infectious MedicineDepartment of Medicine HuddingeKarolinska InstitutetStockholmSweden
| | - Sebastian Havervall
- Department of Clinical SciencesKarolinska Institute Danderyd HospitalStockholmSweden
| | - Stefan Mereiter
- Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
| | - Sylvia Knapp
- Department of Medicine 1, Laboratory of Infection BiologyMedical University of ViennaViennaAustria
| | | | | | | | | | | | - Astrid Hagelkruys
- Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
| | - Nuria Montserrat
- Pluripotency for Organ RegenerationInstitute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
- Catalan Institution for Research and Advanced Studies (ICREA)BarcelonaSpain
| | - Ivona Kozieradzki
- Department of Medical Genetics, Life Sciences InstituteUniversity of British ColumbiaVancouverCanada
| | - Omar Hasan Ali
- Department of Medical Genetics, Life Sciences InstituteUniversity of British ColumbiaVancouverCanada
| | - Johannes Stadlmann
- Institute of Biochemistry, Department of ChemistryUniversity of Natural resources and Life, Sciences (BOKU)ViennaAustria
| | - Michael R Holbrook
- NIAID Integrated Research Facility at Fort Detrick (IRF‐Frederick)FrederickMarylandUSA
| | - Connie Schmaljohn
- NIAID Integrated Research Facility at Fort Detrick (IRF‐Frederick)FrederickMarylandUSA
| | - Chris Oostenbrink
- Institute for Molecular Modeling and SimulationUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
| | - Robert H Shoemaker
- Chemopreventive Agent Development Research Group, Division of Cancer PreventionNational Cancer Institute, National Institutes of HealthBethesdaMarylandUSA
| | - Ali Mirazimi
- Unit of Clinical MicrobiologyKarolinska Institutet and Karolinska University HospitalStockholmSweden
| | | | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
- Department of Medical Genetics, Life Sciences InstituteUniversity of British ColumbiaVancouverCanada
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27
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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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28
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The importance of effect sizes when comparing cycle threshold values of SARS-CoV-2 variants. PLoS One 2022; 17:e0271808. [PMID: 35862414 PMCID: PMC9302753 DOI: 10.1371/journal.pone.0271808] [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: 03/18/2022] [Accepted: 07/07/2022] [Indexed: 12/02/2022] Open
Abstract
Purpose We aimed to elaborate whether cycle threshold (Ct) values differ significantly between wild type SARS-CoV-2 (wtV) and certain viral variants and how strong or weak a potential significant effect might be. Methods In a retrospective study, we investigated 1873 SARS-CoV-2 positive samples for the occurrence of viral marker mutations. Age, gender, clinical setting, days after onset of symptoms, and Ct values were recorded. Statistical analysis was carried out with special consideration of effect sizes. Results During the study period wtV was detected in 1013 samples (54%), while 845 (45%) patients carried the Alpha variant of concern (VOC), and 15 (1%) the Beta VOC. For further analysis, only wtV and the Alpha VOC were included. In a multi-factor ANOVA and post-hoc test with Bonferroni-correction for the age groups we found significant main-effects for Ct values of the viral variant (wtV mean 26.4 (SD 4.27); Alpha VOC mean 25.0 (SD 3.84); F (1,1850) = 55.841; p < .001) and the clinical setting (outpatients: mean 25.7 (SD 4.1); inpatients: mean 27.0 (SD 4.2); F (1,1850) = 8.520, p = .004). However, since the effect sizes were very small (eta squared for the Alpha VOC = .029 and the clinical setting = .004), there was only a slight trend towards higher viral loads of the Alpha VOC compared to wtV. Conclusions In order to compare different variants of SARS-CoV-2 the calculation of effect sizes seems to be necessary. A combination of p-values as estimates of the existance of an effect and effect sizes as estimates of the magnitude of a potential effect may allow a better insight into transmission mechanisms of SARS-CoV-2.
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29
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Impact of the temperature on the interactions between common variants of the SARS-CoV-2 receptor binding domain and the human ACE2. Sci Rep 2022; 12:11520. [PMID: 35798770 PMCID: PMC9261887 DOI: 10.1038/s41598-022-15215-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/21/2022] [Indexed: 11/28/2022] Open
Abstract
Several key mutations in the Spike protein receptor binding domain (RBD) have been identified to influence its affinity for the human Angiotensin-Converting Enzyme 2 (ACE2). Here, we perform a comparative study of the ACE2 binding to the wild type (Wuhan) RBD and some of its variants: Alpha B.1.1.7, Beta B.1.351, Delta B.1.617.2, Kappa B.1.617.1, B.1.1.7 + L452R and Omicron B.1.1.529. Using a coiled-coil mediated tethering approach of ACE2 in a novel surface plasmon resonance (SPR)-based assay, we measured interactions at different temperatures. Binding experiments at 10 °C enhanced the kinetic dissimilarities between the RBD variants and allowed a proper fit to a Langmuir 1:1 model with high accuracy and reproducibility, thus unraveling subtle differences within RBD mutants and ACE2 glycovariants. Our study emphasizes the importance of SPR-based assay parameters in the acquisition of biologically relevant data and offers a powerful tool to deepen our understanding of the role of the various RBD mutations in ACE2 interaction binding parameters.
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30
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Basavarajappa SC, Liu AR, Bruchez A, Li Z, Suzart VG, Liu Z, Chen Y, Xiao TS, Buck M, Ramakrishnan P. Trimeric Receptor Binding Domain of SARS-CoV-2 Acts as a Potent Inhibitor of ACE2 Receptor-Mediated Viral Entry. iScience 2022; 25:104716. [PMID: 35813876 PMCID: PMC9251894 DOI: 10.1016/j.isci.2022.104716] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 05/12/2022] [Accepted: 06/29/2022] [Indexed: 11/26/2022] Open
Abstract
The COVID-19 pandemic has caused over four million deaths and effective methods to control CoV-2 infection, in addition to vaccines, are needed. The CoV-2 binds to the ACE2 on human cells through the receptor-binding domain (RBD) of the trimeric spike protein. Our modeling studies show that a modified trimeric RBD (tRBD) can interact with three ACE2 receptors, unlike the native spike protein, which binds to only one ACE2. We found that tRBD binds to the ACE2 with 58-fold higher affinity than monomeric RBD (mRBD) and blocks spike-dependent pseudoviral infection over 4-fold more effectively compared to the mRBD. Although mRBD failed to block CoV-2 USA-WA1/2020 infection, tRBD efficiently blocked the true virus infection in plaque assays. We show that tRBD is a potent inhibitor of CoV-2 through both competitive binding to the ACE2 and steric hindrance, and has the potential to emerge as a first-line therapeutic method to control COVID-19. tRBD binds multiple ACE2 receptors, while mRBD and spike bind one ACE2 receptor tRBD shows 4-fold higher inhibition of CoV-2 pseudovirus infection than mRBD tRBD, yet not mRBD, prevents CoV-2 USA-WA1/2020 from infecting Vero cells Use of tRBD is a potential therapeutic method to block CoV-2 infection
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31
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Nguyen H, Thai NQ, Nguyen PH, Li MS. SARS-CoV-2 Omicron Variant Binds to Human Cells More Strongly than the Wild Type: Evidence from Molecular Dynamics Simulation. J Phys Chem B 2022; 126:4669-4678. [PMID: 35723978 PMCID: PMC9235043 DOI: 10.1021/acs.jpcb.2c01048] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 06/06/2022] [Indexed: 12/12/2022]
Abstract
The emergence of the variant of concern Omicron (B.1.1.529) of the severe acute respiratory syndrome coronavirus 2 has aggravated the Covid-19 pandemic due to its very contagious ability. The high infection rate may be due to the high binding affinity of Omicron to human cells, but both experimental and computational studies have yielded conflicting results on this issue. Some studies have shown that the Omicron variant binds to human angiotensin-converting enzyme 2 (hACE2) more strongly than the wild type (WT), but other studies have reported comparable binding affinities. To shed light on this open problem, in this work, we calculated the binding free energy of the receptor binding domain (RBD) of the WT and Omicron spike protein to hACE2 using all-atom molecular dynamics simulation and the molecular mechanics Poisson-Boltzmann surface area method. We showed that Omicron binds to human cells more strongly than the WT due to increased RBD charge, which enhances electrostatic interaction with negatively charged hACE2. N440K, T478K, E484A, Q493R, and Q498R mutations in the RBD have been found to play a critical role in the stability of the RBD-hACE2 complex. The effect of homogeneous and heterogeneous models of glycans coating the viral RBD and the peptidyl domain of hACE2 was examined. Although the total binding free energy is not sensitive to the glycan model, the distribution of per-residue interaction energies depends on it. In addition, glycans have a little effect on the binding affinity of the WT RBD to hACE2.
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Affiliation(s)
- Hoang
Linh Nguyen
- Life
Science Lab, Institute for Computational
Science and Technology, Quang Trung
Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh
City 700000, Vietnam
- Ho
Chi Minh City University of Technology (HCMUT), Ho Chi Minh City 700000, Vietnam
- Vietnam
National University, Ho Chi Minh
City 700000, Vietnam
| | - Nguyen Quoc Thai
- Life
Science Lab, Institute for Computational
Science and Technology, Quang Trung
Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh
City 700000, Vietnam
- Dong
Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh
City, Dong Thap 8100, Vietnam
| | - Phuong H. Nguyen
- CNRS,
Universit́e de Paris, UPR9080, Laboratoire de Biochimie Th́eorique,
Paris, France; Institut de Biologie Physico-Chimique, FondationEdmond
de Rothschild, PSL Research University, Paris 75006, France
| | - Mai Suan Li
- Institute
of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, Warsaw 02-668, Poland
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Increased Risk of COVID-19 in Patients with Diabetes Mellitus-Current Challenges in Pathophysiology, Treatment and Prevention. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19116555. [PMID: 35682137 PMCID: PMC9180541 DOI: 10.3390/ijerph19116555] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/10/2022] [Accepted: 05/25/2022] [Indexed: 01/08/2023]
Abstract
Coronavirus disease-COVID-19 (coronavirus disease 2019) has become the cause of the global pandemic in the last three years. Its etiological factor is SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus type 2). Patients with diabetes (DM-diabetes mellitus), in contrast to healthy people not suffering from chronic diseases, are characterised by higher morbidity and mortality due to COVID-19. Patients who test positive for SARCoV-2 are at higher risk of developing hyperglycaemia. In this paper, we present, analyse and summarize the data on possible mechanisms underlying the increased susceptibility and mortality of patients with diabetes mellitus in the case of SARS-CoV-2 infection. However, further research is required to determine the optimal therapeutic management of patients with diabetes and COVID-19.
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Golcuk M, Hacisuleyman A, Yilmaz SZ, Taka E, Yildiz A, Gur M. SARS-CoV-2 Delta Variant Decreases Nanobody Binding and ACE2 Blocking Effectivity. J Chem Inf Model 2022; 62:2490-2498. [PMID: 35533364 PMCID: PMC9113008 DOI: 10.1021/acs.jcim.1c01523] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The Delta variant spreads more rapidly than previous variants of SARS-CoV-2. This variant comprises several mutations on the receptor-binding domain (RBDDelta) of its spike glycoprotein, which binds to the peptidase domain (PD) of angiotensin-converting enzyme 2 (ACE2) receptors in host cells. The RBD-PD interaction has been targeted by antibodies and nanobodies to prevent viral infection, but their effectiveness against the Delta variant remains unclear. Here, we investigated RBDDelta-PD interactions in the presence and absence of nanobodies H11-H4, H11-D4, and Ty1 by performing 21.8 μs of all-atom molecular dynamics simulations. Unbiased simulations revealed that Delta variant mutations strengthen RBD binding to ACE2 by increasing the hydrophobic interactions and salt bridge formation, but weaken interactions with H11-H4, H11-D4, and Ty1. Among these nanobodies H11-H4 and H11-D4 bind RBD without overlapping ACE2. They were unable to dislocate ACE2 from RBDDelta when bound side by side with ACE2 on RBD. Steered molecular dynamics simulations at comparable loading rates to high-speed atomic force microscopy (AFM) experiments estimated lower rupture forces of the nanobodies from RBDDelta compared to ACE2. Our results suggest that existing nanobodies are less effective to inhibit RBDDelta-PD interactions and a new generation of nanobodies is needed to neutralize the Delta variant.
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Affiliation(s)
- Mert Golcuk
- Department of Mechanical Engineering, Istanbul Technical University (ITU), 34437 Istanbul, Turkey
| | - Aysima Hacisuleyman
- Institute of Bioengineering, Swiss Federal Institute of Technology (EPFL), 1015 Lausanne, Switzerland
| | - Sema Zeynep Yilmaz
- Department of Mechanical Engineering, Istanbul Technical University (ITU), 34437 Istanbul, Turkey
| | - Elhan Taka
- Department of Mechanical Engineering, Istanbul Technical University (ITU), 34437 Istanbul, Turkey
| | - Ahmet Yildiz
- Physics Department, University of California, Berkeley, California 94720, United States.,Department of Molecular and Cellular Biology, University of California, Berkeley, California 94720, United States
| | - Mert Gur
- Department of Mechanical Engineering, Istanbul Technical University (ITU), 34437 Istanbul, Turkey
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Feng W, Xiang Y, Wu L, Chen Z, Li Q, Chen J, Guo Y, Xia D, Chen N, Zhang L, Zhu S, Zhao K. Nucleocapsid protein of SARS‐CoV‐2 is a potential target for developing new generation of vaccine. J Clin Lab Anal 2022; 36:e24479. [PMID: 35527696 PMCID: PMC9169192 DOI: 10.1002/jcla.24479] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 03/28/2022] [Accepted: 04/23/2022] [Indexed: 11/11/2022] Open
Abstract
Background Methods Results Conclusion
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Affiliation(s)
- Weixu Feng
- School of Basic Medical Science Wenzhou Medical University Wenzhou China
| | - Yunru Xiang
- School of Basic Medical Science Wenzhou Medical University Wenzhou China
| | - Lianpeng Wu
- Department of Laboratory Medicine The Sixth People Hospital of Wenzhou Wenzhou China
| | - Zhuo Chen
- School of Basic Medical Science Wenzhou Medical University Wenzhou China
| | - Qingfeng Li
- School of Basic Medical Science Wenzhou Medical University Wenzhou China
| | - Jun Chen
- School of Basic Medical Science Wenzhou Medical University Wenzhou China
| | - Yanru Guo
- School of Basic Medical Science Wenzhou Medical University Wenzhou China
| | - Dandan Xia
- Department of Laboratory Medicine The Sixth People Hospital of Wenzhou Wenzhou China
| | - Na Chen
- Department of Laboratory Medicine The Sixth People Hospital of Wenzhou Wenzhou China
| | - Lifang Zhang
- School of Basic Medical Science Wenzhou Medical University Wenzhou China
| | - Shanli Zhu
- School of Basic Medical Science Wenzhou Medical University Wenzhou China
| | - Kong‐Nan Zhao
- School of Basic Medical Science Wenzhou Medical University Wenzhou China
- Department of Obstetrics and Gynaecology The Second Affiliated Hospital and Yuyin Children Hospital of Wenzhou Medical University Wenzhou China
- Australian Institute for Bioengineering and Nanotechnology The University of Queensland St Lucia Queensland Australia
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35
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Jawad B, Adhikari P, Podgornik R, Ching WY. Binding Interactions between Receptor-Binding Domain of Spike Protein and Human Angiotensin Converting Enzyme-2 in Omicron Variant. J Phys Chem Lett 2022; 13:3915-3921. [PMID: 35481766 PMCID: PMC9063111 DOI: 10.1021/acs.jpclett.2c00423] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The emergence of new SARS-CoV-2 Omicron variant of concern (OV) has exacerbated the COVID-19 pandemic because of a large number of mutations in the spike protein, particularly in the receptor-binding domain (RBD), resulting in highly contagious and/or vaccine-resistant strains. Herein, we present a systematic analysis based on detailed molecular dynamics (MD) simulations in order to understand how the OV RBD mutations affect the ACE2 binding. We show that the OV RBD binds to ACE2 more efficiently and tightly predominantly because of strong electrostatic interactions, thereby promoting increased infectivity and transmissibility compared to other strains. Some of the OV RBD mutations are predicted to affect the antibody neutralization either through their role in the S-protein conformational changes, such as S371L, S373P, and S375F, or through changing its surface charge distribution, such as G339D, N440K, T478K, and E484A. Other mutations, such as K417N, G446S, and Y505H, decrease the ACE2 binding, whereas S447N, Q493R, G496S, Q498R, and N501Y tend to increase it.
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Affiliation(s)
- Bahaa Jawad
- Department
of Physics and Astronomy, University of
Missouri—Kansas City, Kansas City, Missouri 64110, United States
- Department
of Applied Sciences, University of Technology, Baghdad 10066, Iraq
| | - Puja Adhikari
- Department
of Physics and Astronomy, University of
Missouri—Kansas City, Kansas City, Missouri 64110, United States
| | - Rudolf Podgornik
- Wenzhou
Institute of the University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
- School
of Physical Sciences and Kavli Institute of Theoretical Science, University of Chinese Academy of Sciences, Beijing 100049, China
- CAS
Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100090, China
- Department
of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Wai-Yim Ching
- Department
of Physics and Astronomy, University of
Missouri—Kansas City, Kansas City, Missouri 64110, United States
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Zhang R, Ghosh S, Pal R. Predicting binding affinities of emerging variants of SARS-CoV-2 using spike protein sequencing data: observations, caveats and recommendations. Brief Bioinform 2022; 23:6569542. [PMID: 35437577 DOI: 10.1093/bib/bbac128] [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: 12/23/2021] [Revised: 02/13/2022] [Accepted: 03/16/2022] [Indexed: 11/13/2022] Open
Abstract
Predicting protein properties from amino acid sequences is an important problem in biology and pharmacology. Protein-protein interactions among SARS-CoV-2 spike protein, human receptors and antibodies are key determinants of the potency of this virus and its ability to evade the human immune response. As a rapidly evolving virus, SARS-CoV-2 has already developed into many variants with considerable variation in virulence among these variants. Utilizing the proteomic data of SARS-CoV-2 to predict its viral characteristics will, therefore, greatly aid in disease control and prevention. In this paper, we review and compare recent successful prediction methods based on long short-term memory (LSTM), transformer, convolutional neural network (CNN) and a similarity-based topological regression (TR) model and offer recommendations about appropriate predictive methodology depending on the similarity between training and test datasets. We compare the effectiveness of these models in predicting the binding affinity and expression of SARS-CoV-2 spike protein sequences. We also explore how effective these predictive methods are when trained on laboratory-created data and are tasked with predicting the binding affinity of the in-the-wild SARS-CoV-2 spike protein sequences obtained from the GISAID datasets. We observe that TR is a better method when the sample size is small and test protein sequences are sufficiently similar to the training sequence. However, when the training sample size is sufficiently large and prediction requires extrapolation, LSTM embedding and CNN-based predictive model show superior performance.
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Affiliation(s)
- Ruibo Zhang
- Department of Electrical and Computer Engineering, Texas Tech University, TX, USA
| | - Souparno Ghosh
- Department of Statistics, University of Nebraska - Lincoln, NB, USA
| | - Ranadip Pal
- Department of Electrical and Computer Engineering, Texas Tech University, TX, USA
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de Souza AS, de Freitas Amorim VM, Guardia GDA, dos Santos FF, Ulrich H, Galante PAF, de Souza RF, Guzzo CR. Severe Acute Respiratory Syndrome Coronavirus 2 Variants of Concern: A Perspective for Emerging More Transmissible and Vaccine-Resistant Strains. Viruses 2022; 14:827. [PMID: 35458557 PMCID: PMC9029021 DOI: 10.3390/v14040827] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/29/2022] [Accepted: 04/01/2022] [Indexed: 02/06/2023] Open
Abstract
Novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) are constantly threatening global public health. With no end date, the pandemic persists with the emergence of novel variants that threaten the effectiveness of diagnostic tests and vaccines. Mutations in the Spike surface protein of the virus are regularly observed in the new variants, potentializing the emergence of novel viruses with different tropism from the current ones, which may change the severity and symptoms of the disease. Growing evidence has shown that mutations are being selected in favor of variants that are more capable of evading the action of neutralizing antibodies. In this context, the most important factor guiding the evolution of SARS-CoV-2 is its interaction with the host's immune system. Thus, as current vaccines cannot block the transmission of the virus, measures complementary to vaccination, such as the use of masks, hand hygiene, and keeping environments ventilated remain essential to delay the emergence of new variants. Importantly, in addition to the involvement of the immune system in the evolution of the virus, we highlight several chemical parameters that influence the molecular interactions between viruses and host cells during invasion and are also critical tools making novel variants more transmissible. In this review, we dissect the impacts of the Spike mutations on biological parameters such as (1) the increase in Spike binding affinity to hACE2; (2) bound time for the receptor to be cleaved by the proteases; (3) how mutations associate with the increase in RBD up-conformation state in the Spike ectodomain; (4) expansion of uncleaved Spike protein in the virion particles; (5) increment in Spike concentration per virion particles; and (6) evasion of the immune system. These factors play key roles in the fast spreading of SARS-CoV-2 variants of concern, including the Omicron.
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Affiliation(s)
- Anacleto Silva de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
| | - Vitor Martins de Freitas Amorim
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
| | - Gabriela D. A. Guardia
- Centro de Oncologia Molecular, Hospital Sírio Libanes, São Paulo 01308-060, Brazil; (G.D.A.G.); (F.F.d.S.); (P.A.F.G.)
| | - Filipe F. dos Santos
- Centro de Oncologia Molecular, Hospital Sírio Libanes, São Paulo 01308-060, Brazil; (G.D.A.G.); (F.F.d.S.); (P.A.F.G.)
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil;
| | - Henning Ulrich
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil;
| | - Pedro A. F. Galante
- Centro de Oncologia Molecular, Hospital Sírio Libanes, São Paulo 01308-060, Brazil; (G.D.A.G.); (F.F.d.S.); (P.A.F.G.)
| | - Robson Francisco de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
| | - Cristiane Rodrigues Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
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Molecular Dynamics and MM-PBSA Analysis of the SARS-CoV-2 Gamma Variant in Complex with the hACE-2 Receptor. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27072370. [PMID: 35408761 PMCID: PMC9000566 DOI: 10.3390/molecules27072370] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/11/2022] [Accepted: 03/16/2022] [Indexed: 01/04/2023]
Abstract
The SARS-CoV-2 virus, since its appearance in 2019, has caused millions of cases and deaths. To date, there is no effective treatment or a vaccine that is fully protective. Despite the efforts made by governments and health institutions around the globe to control its propagation, the evolution of the virus has accelerated, diverging into hundreds of variants. However, not all of them are variants of concern (VoC’s). VoC’s have appeared in different regions and throughout the two years of the pandemic they have spread around the world. Specifically, in South America, the gamma variant (previously known as P.1) appeared in early 2021, bringing with it a second wave of infections. This variant contains the N501Y, E484K and K417T mutations in the receptor binding domain (RBD) of the spike protein. Although these mutations have been described experimentally, there is still no clarity regarding their role in the stabilization of the complex with the human angiotensin converting enzyme 2 (hACE-2) receptor. In this article we dissect the influence of mutations on the interaction with the hACE-2 receptor using molecular dynamics and estimations of binding affinity through a screened version of the molecular mechanics Poisson Boltzmann surface area (MM-PBSA) and interaction entropy. Our results indicate that mutations E484K and K417T compensate each other in terms of binding affinity, while the mutation N501Y promotes a more convoluted effect. This effect consists in the adoption of a cis configuration in the backbone of residue Y495 within the RBD, which in turn promotes polar interactions with the hACE-2 receptor. These results not only correlate with experimental observations and complement previous knowledge, but also expose new features associated with the specific contribution of concerned mutations. Additionally, we propose a recipe to assess the residue-specific contribution to the interaction entropy.
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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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40
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Eslami N, Aghbash PS, Shamekh A, Entezari-Maleki T, Nahand JS, Sales AJ, Baghi HB. SARS-CoV-2: Receptor and Co-receptor Tropism Probability. Curr Microbiol 2022; 79:133. [PMID: 35292865 PMCID: PMC8923825 DOI: 10.1007/s00284-022-02807-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 02/09/2022] [Indexed: 02/07/2023]
Abstract
The recent pandemic which arose from China, is caused by a pathogenic virus named "severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2)". Its rapid global expansion has inflicted an extreme public health concern. The attachment of receptor-binding domains (RBD) of the spike proteins (S) to the host cell's membrane, with or without the help of other cellular components such as proteases and especially co-receptors, is required for the first stage of its pathogenesis. In addition to humans, angiotensin-converting enzyme 2 (ACE2) is found on a wide range of vertebrate host's cellular surface. SARS-CoV-2 has a broad spectrum of tropism; thus, it can infect a vast range of tissues, organs, and hosts; even though the surface amino acids of the spike protein conflict in the receptor-binding region. Due to the heterogeneous ACE2 distribution and the presence of different domains on the SARS-CoV-2 spike protein for binding, the virus entry into diverse host cell types may depend on the host cells' receptor presentation with or without co-receptors. This review investigates multiple current types of receptor and co-receptor tropisms, with other molecular factors alongside their respective mechanisms, which facilitate the binding and entry of SARS-CoV-2 into the cells, extending the severity of the coronavirus disease 2019 (COVID-19). Understanding the pathogenesis of COVID-19 from this perspective can effectively help prevent this disease and provide more potent treatment strategies, particularly in vulnerable people with various cellular-level susceptibilities.
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Affiliation(s)
- Narges Eslami
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, 5166/15731, Tabriz, Iran
| | - Parisa Shiri Aghbash
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Drug Applied Research Centre, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Shamekh
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Taher Entezari-Maleki
- Department of Clinical Pharmacy, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
- Cardiovascular Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Javid Sadri Nahand
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Abolfazl Jafari Sales
- Department of Microbiology School of Basic Sciences, Islamic Azad University, Kazerun BranchKazerun, Iran
| | - Hossein Bannazadeh Baghi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, 5166/15731, Tabriz, Iran.
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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41
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Ambrose JM, Kullappan M, Patil S, Alzahrani KJ, Banjer HJ, Qashqari FSI, Raj AT, Bhandi S, Veeraraghavan VP, Jayaraman S, Sekar D, Agarwal A, Swapnavahini K, Krishna Mohan S. Plant-Derived Antiviral Compounds as Potential Entry Inhibitors against Spike Protein of SARS-CoV-2 Wild-Type and Delta Variant: An Integrative in SilicoApproach. Molecules 2022; 27:1773. [PMID: 35335139 PMCID: PMC8949152 DOI: 10.3390/molecules27061773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/03/2022] [Accepted: 03/05/2022] [Indexed: 12/24/2022] Open
Abstract
The wild-type SARS-CoV-2 has continuously evolved into several variants with increased transmissibility and virulence. The Delta variant which was initially identified in India created a devastating impact throughout the country during the second wave. While the efficacy of the existing vaccines against the latest SARS-CoV-2 variants remains unclear, extensive research is being carried out to develop potential antiviral drugs through approaches like in silico screening and drug-repurposing. This study aimed to conduct the docking-based virtual screening of 50 potential phytochemical compounds against a Spike glycoprotein of the wild-type and the Delta SARS-CoV-2 variant. Subsequently, molecular docking was performed for the five best compounds, such as Lupeol, Betulin, Hypericin, Corilagin, and Geraniin, along with synthetic controls. From the results obtained, it was evident that Lupeol exhibited a remarkable binding affinity towards the wild-type Spike protein (-8.54 kcal/mol), while Betulin showed significant binding interactions with the mutated Spike protein (-8.83 kcal/mol), respectively. The binding energy values of the selected plant compounds were slightly higher than that of the controls. Key hydrogen bonding and hydrophobic interactions of the resulting complexes were visualized, which explained their greater binding affinity against the target proteins-the Delta S protein of SARS-CoV-2, in particular. The lower RMSD, the RMSF values of the complexes and the ligands, Rg, H-bonds, and the binding free energies of the complexes together revealed the stability of the complexes and significant binding affinities of the ligands towards the target proteins. Our study suggests that Lupeol and Betulin could be considered as potential ligands for SARS-CoV-2 spike antagonists. Further experimental validations might provide new insights for the possible antiviral therapeutic interventions of the identified lead compounds and their analogs against COVID-19 infection.
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Affiliation(s)
- Jenifer Mallavarpu Ambrose
- Department of Research, Panimalar Medical College Hospital & Research Institute, Chennai 600123, India; (J.M.A.); (M.K.)
| | - Malathi Kullappan
- Department of Research, Panimalar Medical College Hospital & Research Institute, Chennai 600123, India; (J.M.A.); (M.K.)
| | - Shankargouda Patil
- Department of Maxillofacial Surgery and Diagnostic Sciences, Division of Oral Pathology, College of Dentistry, Jazan University, Jazan 45412, Saudi Arabia;
| | - Khalid J. Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; (K.J.A.); (H.J.B.)
| | - Hamsa Jameel Banjer
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; (K.J.A.); (H.J.B.)
| | - Fadi S. I. Qashqari
- Department of Microbiology, College of Medicine, Umm Al-Qura University, Makkah 24381, Saudi Arabia;
| | - A. Thirumal Raj
- Department of Oral Pathology and Microbiology, Sri Venkateswara Dental College and Hospital, Chennai 600130, India;
| | - Shilpa Bhandi
- Department of Restorative Dental Science, Division of Operative Dentistry, College of Dentistry, Jazan University, Jazan 45142, Saudi Arabia;
| | - Vishnu Priya Veeraraghavan
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai 600077, India;
| | - Selvaraj Jayaraman
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai 600077, India;
| | - Durairaj Sekar
- Centre for Cellular and Molecular Research, Saveetha Dental College & Hospitals, Saveetha Institute of Medical & Technical Sciences (SIMATS), Saveetha University, Chennai 600077, India;
| | - Alok Agarwal
- Department of Chemistry, Chinmaya Degree College, BHEL Haridwar 249403, India;
| | - Korla Swapnavahini
- Department of Biotechnology, Dr B.R. Ambedkar University, Etcherla, Srikakulam 532410, India;
| | - Surapaneni Krishna Mohan
- Departments of Biochemistry, Molecular Virology, Research, and Clinical Skills & Simulation, Panimalar Medical College Hospital & Research Institute, Chennai 600123, India
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Kirtipal N, Kumar S, Dubey SK, Dwivedi VD, Gireesh Babu K, Malý P, Bharadwaj S. Understanding on the possible routes for SARS CoV-2 invasion via ACE2 in the host linked with multiple organs damage. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 99:105254. [PMID: 35217145 PMCID: PMC8863418 DOI: 10.1016/j.meegid.2022.105254] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/12/2022] [Accepted: 02/19/2022] [Indexed: 02/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), accountable for causing the coronavirus diseases 2019 (COVID-19), is already declared as a pandemic disease globally. Like previously reported SARS-CoV strain, the novel SARS-CoV-2 also initiates the viral pathogenesis via docking viral spike-protein with the membranal angiotensin-converting enzyme 2 (ACE2) - a receptor on variety of cells in the human body. Therefore, COVID-19 is broadly characterized as a disease that targets multiple organs, particularly causing acute complications via organ-specific pathogenesis accompanied by destruction of ACE2+ cells, including alveolus, cardiac microvasculature, endothelium, and glomerulus. Under such circumstances, the high expression of ACE2 in predisposing individuals associated with anomalous production of the renin-angiotensin system (RAS) may promote enhanced viral load in COVID-19, which comparatively triggers excessive apoptosis. Furthermore, multi-organ injuries were found linked to altered ACE2 expression and inequality between the ACE2/angiotensin-(1-7)/mitochondrial Ang system (MAS) and renin-angiotensin-system (RAS) in COVID-19 patients. However, the exact pathogenesis of multi-organ damage in COVID-19 is still obscure, but several perspectives have been postulated, involving altered ACE2 expression linked with direct/indirect damages by the virus-induced immune responses, such as cytokinin storm. Thus, insights into the invasion of a virus with respect to ACE2 expression site can be helpful to simulate or understand the possible complications in the targeted organ during viral infection. Hence, this review summarizes the multiple organs invasion by SARS CoV-2 linked with ACE2 expression and their consequences, which can be helpful in the management of the COVID-19 pathogenesis under life-threatening conditions.
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Affiliation(s)
- Nikhil Kirtipal
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Sanjay Kumar
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India; Centre for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | | | - Vivek Dhar Dwivedi
- Centre for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India.
| | - K Gireesh Babu
- Department of Life Sciences, Parul Institute of Applied Sciences, Parul University, Limda, Vadodara, India.
| | - Petr Malý
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences v.v.i., BIOCEV Research Center, Vestec, Czech Republic.
| | - Shiv Bharadwaj
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences v.v.i., BIOCEV Research Center, Vestec, Czech Republic.
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Sensitivity of SARS-CoV-2 Life Cycle to IFN Effects and ACE2 Binding Unveiled with a Stochastic Model. Viruses 2022; 14:v14020403. [PMID: 35215996 PMCID: PMC8875829 DOI: 10.3390/v14020403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/27/2022] [Accepted: 02/04/2022] [Indexed: 02/01/2023] Open
Abstract
Mathematical modelling of infection processes in cells is of fundamental interest. It helps to understand the SARS-CoV-2 dynamics in detail and can be useful to define the vulnerability steps targeted by antiviral treatments. We previously developed a deterministic mathematical model of the SARS-CoV-2 life cycle in a single cell. Despite answering many questions, it certainly cannot accurately account for the stochastic nature of an infection process caused by natural fluctuation in reaction kinetics and the small abundance of participating components in a single cell. In the present work, this deterministic model is transformed into a stochastic one based on a Markov Chain Monte Carlo (MCMC) method. This model is employed to compute statistical characteristics of the SARS-CoV-2 life cycle including the probability for a non-degenerate infection process. Varying parameters of the model enables us to unveil the inhibitory effects of IFN and the effects of the ACE2 binding affinity. The simulation results show that the type I IFN response has a very strong effect on inhibition of the total viral progeny whereas the effect of a 10-fold variation of the binding rate to ACE2 turns out to be negligible for the probability of infection and viral production.
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Kim S, Liu Y, Ziarnik M, Cao Y, Zhang XF, Im W. Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.01.24.477633. [PMID: 35118473 PMCID: PMC8811907 DOI: 10.1101/2022.01.24.477633] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The 2019 coronavirus disease (COVID-19) pandemic has had devastating impacts on our global health. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing COVID-19, has continued to mutate and spread worldwide despite global vaccination efforts. In particular, the Omicron variant, first identified in South Africa in late November 2021, has now overtaken the Delta variant and become the dominant strain worldwide. Compared to the original strain identified in Wuhan, Omicron features 50 genetic mutations, with 15 mutations in the receptor-binding domain (RBD) of the spike protein, which binds to the human angiotensin-converting enzyme 2 (ACE2) receptor for viral entry. However, it is not completely understood how these mutations alter the interaction and binding strength between the Omicron RBD and ACE2. In this study, we used a combined steered molecular dynamics (SMD) simulation and experimental microscale thermophoresis (MST) approach to quantify the interaction between Omicron RBD and ACE2. We report that the Omicron brings an enhanced RBD-ACE2 interface through N501Y, Q493K/R, and T478K mutations; the changes further lead to unique interaction patterns, reminiscing the features of previously dominated variants, Alpha (N501Y) and Delta (L452R and T478K). Our MST data confirmed that the Omicron mutations in RBD are associated with a five-fold higher binding affinity to ACE2 compared to the RBD of the original strain. In conclusion, our result could help explain the Omicron variant’s prevalence in human populations, as higher interaction forces or affinity for ACE2 likely promote greater viral binding and internalization, leading to increased infectivity. TOC GRAPHIC
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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
| | - Matthew Ziarnik
- Department of Bioengineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA
| | - Yiwei Cao
- Departments 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,Correspondence and requests for materials should be addressed to X.F.Z and W.I. ( and )
| | - Wonpil Im
- Department of Bioengineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA,Departments of Biological Sciences, Chemistry, and Computer Science and Engineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA,Correspondence and requests for materials should be addressed to X.F.Z and W.I. ( and )
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45
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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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46
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Jeong GU, Yoon GY, Moon HW, Lee W, Hwang I, Kim H, Kim KD, Kim C, Ahn DG, Kim BT, Kim SJ, Kwon YC. Comparison of Plaque Size, Thermal Stability, and Replication Rate among SARS-CoV-2 Variants of Concern. Viruses 2021; 14:v14010055. [PMID: 35062259 PMCID: PMC8781966 DOI: 10.3390/v14010055] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/23/2021] [Accepted: 12/28/2021] [Indexed: 12/22/2022] Open
Abstract
SARS-CoV-2, like other RNA viruses, has a propensity for genetic evolution owing to the low fidelity of its viral polymerase. Several recent reports have described a series of novel SARS-CoV-2 variants. Some of these have been identified as variants of concern (VOCs), including alpha (B.1.1.7, Clade GRY), beta (B.1.351, Clade GH), gamma (P.1, Clade GR), and delta (B.1.617.2, Clade G). VOCs are likely to have some effect on transmissibility, antibody evasion, and changes in therapeutic or vaccine effectiveness. However, the physiological and virological understanding of these variants remains poor. We demonstrated that these four VOCs exhibited differences in plaque size, thermal stability at physiological temperature, and replication rates. The mean plaque size of beta was the largest, followed by those of gamma, delta, and alpha. Thermal stability, evaluated by measuring infectivity and half-life after prolonged incubation at physiological temperature, was correlated with plaque size in all variants except alpha. However, despite its relatively high thermal stability, alpha’s small plaque size resulted in lower replication rates and fewer progeny viruses. Our findings may inform further virological studies of SARS-CoV-2 variant characteristics, VOCs, and variants of interest. These studies are important for the effective management of the COVID-19 pandemic.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Seong-Jun Kim
- Correspondence: (S.-J.K.); (Y.-C.K.); Tel.: +82-42-860-7477 (S.-J.K.); +82-42-860-7028 (Y.-C.K.)
| | - Young-Chan Kwon
- Correspondence: (S.-J.K.); (Y.-C.K.); Tel.: +82-42-860-7477 (S.-J.K.); +82-42-860-7028 (Y.-C.K.)
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