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Lei S, Chen X, Wu J, Duan X, Men K. Small molecules in the treatment of COVID-19. Signal Transduct Target Ther 2022; 7:387. [PMID: 36464706 PMCID: PMC9719906 DOI: 10.1038/s41392-022-01249-8] [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] [Received: 07/26/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 12/11/2022] Open
Abstract
The outbreak of COVID-19 has become a global crisis, and brought severe disruptions to societies and economies. Until now, effective therapeutics against COVID-19 are in high demand. Along with our improved understanding of the structure, function, and pathogenic process of SARS-CoV-2, many small molecules with potential anti-COVID-19 effects have been developed. So far, several antiviral strategies were explored. Besides directly inhibition of viral proteins such as RdRp and Mpro, interference of host enzymes including ACE2 and proteases, and blocking relevant immunoregulatory pathways represented by JAK/STAT, BTK, NF-κB, and NLRP3 pathways, are regarded feasible in drug development. The development of small molecules to treat COVID-19 has been achieved by several strategies, including computer-aided lead compound design and screening, natural product discovery, drug repurposing, and combination therapy. Several small molecules representative by remdesivir and paxlovid have been proved or authorized emergency use in many countries. And many candidates have entered clinical-trial stage. Nevertheless, due to the epidemiological features and variability issues of SARS-CoV-2, it is necessary to continue exploring novel strategies against COVID-19. This review discusses the current findings in the development of small molecules for COVID-19 treatment. Moreover, their detailed mechanism of action, chemical structures, and preclinical and clinical efficacies are discussed.
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Affiliation(s)
- Sibei Lei
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
| | - Xiaohua Chen
- grid.54549.390000 0004 0369 4060Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072 China
| | - Jieping Wu
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
| | - Xingmei Duan
- grid.54549.390000 0004 0369 4060Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072 China
| | - Ke Men
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
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Wu Q, Kumar N, Lafuse WP, Ahumada OS, Saljoughian N, Whetstone E, Zani A, Patton AK, El Refaey M, Webb A, Pietrzak M, Yu L, KC M, Peeples ME, Ganesan LP, Yount JS, Rajaram MV. Influenza A virus modulates ACE2 expression and SARS-CoV-2 infectivity in human cardiomyocytes. iScience 2022; 25:105701. [PMID: 36474635 PMCID: PMC9715453 DOI: 10.1016/j.isci.2022.105701] [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: 10/22/2021] [Revised: 09/22/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
Influenza A virus (IAV) and SARS-CoV-2 virus are both acute respiratory viruses currently circulating in the human population. This study aims to determine the impact of IAV infection on SARS-CoV-2 pathogenesis and cardiomyocyte function. Infection of human bronchial epithelial cells (HBEC), A549 cells, lung fibroblasts (HLF), monocyte derived macrophages (MDMs), cardiac fibroblasts (HCF) and hiPSC-derived cardiomyocytes with IAV enhanced the expression of ACE2, the SARS-CoV-2 receptor. Similarly, IAV infection increased levels of ACE2 in the lungs of mice and humans. Of interest, we detected heavily glycosylated form of ACE2 in hiPSC-CMs and poorly glycosylated ACE2 in other cell types. Also, prior IAV infection enhances SARS-CoV-2 spike protein binding and viral entry in all cell types. However, efficient SARS-CoV-2 replication was uniquely inhibited in cardiomyocytes. Glycosylation of ACE2 correlated with enzymatic conversion of its substrate Ang II, induction of eNOS and nitric oxide production, may provide a potential mechanism for the restricted SARS-CoV-2 replication in cardiomyocytes.
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Affiliation(s)
- Qian Wu
- Department of Microbial Infection and Immunity, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH 43209, USA
| | - Naresh Kumar
- Department of Microbial Infection and Immunity, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH 43209, USA
| | - William P. Lafuse
- Department of Microbial Infection and Immunity, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH 43209, USA
| | - Omar Santiagonunez Ahumada
- Department of Microbial Infection and Immunity, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH 43209, USA
| | - Noushin Saljoughian
- Department of Microbial Infection and Immunity, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH 43209, USA
| | - Elizabeth Whetstone
- Department of Microbial Infection and Immunity, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH 43209, USA
| | - Ashley Zani
- Department of Microbial Infection and Immunity, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH 43209, USA
| | - Ashley K. Patton
- Department of Pathology, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH 43209, USA
| | - Mona El Refaey
- Department of Surgery, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH 43209, USA
| | - Amy Webb
- Department of Biomedical Informatics, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH 43209, USA
| | - Maciej Pietrzak
- Department of Biomedical Informatics, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH 43209, USA
| | - Lianbo Yu
- Department of Biomedical Informatics, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH 43209, USA
| | - Mahesh KC
- Department of Pediatrics, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH 43209, USA,Center for Vaccines and Immunity, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH 43209, USA
| | - Mark E. Peeples
- Department of Pediatrics, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH 43209, USA,Center for Vaccines and Immunity, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH 43209, USA
| | - Latha P. Ganesan
- Department of Internal Medicine College of Medicine, The Ohio State University, Wexner Medical Center, Columbus, OH 43210, USA
| | - Jacob S. Yount
- Department of Microbial Infection and Immunity, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH 43209, USA
| | - Murugesan V.S. Rajaram
- Department of Microbial Infection and Immunity, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH 43209, USA,Corresponding author
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Wang B, Zhao J, Liu S, Feng J, Luo Y, He X, Wang Y, Ge F, Wang J, Ye B, Huang W, Bo X, Wang Y, Xi JJ. ACE2 decoy receptor generated by high-throughput saturation mutagenesis efficiently neutralizes SARS-CoV-2 and its prevalent variants. Emerg Microbes Infect 2022; 11:1488-1499. [PMID: 35587428 PMCID: PMC9176695 DOI: 10.1080/22221751.2022.2079426] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The recent global pandemic was a spillover from the SARS-CoV-2 virus. Viral entry involves the receptor binding domain (RBD) of the viral spike protein interacting with the protease domain (PD) of the cellular receptor, ACE2. We hereby present a comprehensive mutational landscape of the effects of ACE2-PD point mutations on RBD-ACE2 binding using a saturation mutagenesis approach based on microarray-based oligo synthesis and a single-cell screening assay. We observed that changes in glycosylation sites and directly interacting sites of ACE2-PD significantly influenced ACE2-RBD binding. We further engineered an ACE2 decoy receptor with critical point mutations, D30I, L79W, T92N, N322V, and K475F, named C4-1. C4-1 shows a 200-fold increase in neutralization for the SARS-CoV-2 D614G pseudotyped virus compared to wild-type soluble ACE2 and a sevenfold increase in binding affinity to wild-type spike compared to the C-terminal Ig-Fc fused wild-type soluble ACE2. Moreover, C4-1 efficiently neutralized prevalent variants, especially the omicron variant (EC50=16 ng/mL), and rescued monoclonal antibodies, vaccine, and convalescent sera neutralization from viral immune-escaping. We hope to next investigate translating the therapeutic potential of C4-1 for the treatment of SARS-CoV-2.
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Affiliation(s)
- Bolun Wang
- Department of Biomedical Engineering, Peking University, Beijing, People's Republic of China
| | - Junxuan Zhao
- Department of Biomedical Engineering, Peking University, Beijing, People's Republic of China
| | - Shuo Liu
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Jingyuan Feng
- College of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Yufeng Luo
- Department of Biomedical Engineering, Peking University, Beijing, People's Republic of China
| | - Xinyu He
- Department of Biomedical Engineering, Peking University, Beijing, People's Republic of China
| | - Yanmin Wang
- Department of Biomedical Engineering, Peking University, Beijing, People's Republic of China
| | - Feixiang Ge
- Department of Biomedical Engineering, Peking University, Beijing, People's Republic of China
| | - Junyi Wang
- Department of Biomedical Engineering, Peking University, Beijing, People's Republic of China
| | - Buqing Ye
- Department of Biomedical Engineering, Peking University, Beijing, People's Republic of China
| | - Weijin Huang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Xiaochen Bo
- Institute of Health Service and Transfusion Medicine, Beijing, People's Republic of China
| | - Youchun Wang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, People's Republic of China
| | - Jianzhong Jeff Xi
- Department of Biomedical Engineering, Peking University, Beijing, People's Republic of China
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Long Chain N3-PUFA Decreases ACE2 Protein Levels and Prevents SARS-CoV-2 Cell Entry. Int J Mol Sci 2022; 23:ijms232213825. [PMID: 36430303 PMCID: PMC9695276 DOI: 10.3390/ijms232213825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 10/28/2022] [Accepted: 11/07/2022] [Indexed: 11/12/2022] Open
Abstract
Angiotensin-converting enzyme 2 (ACE2) is a target of interest for both COVID-19 and cardiovascular disease management. Even though lower ACE2 levels may be beneficial in SARS-CoV-2 infectivity, maintaining the ACE1/ACE2 balance is also crucial for cardiovascular health. So far, reports describing conditions capable of altering ACE2 protein levels, especially via dietary components, are limited. In this study, the effects of omega-3 polyunsaturated fatty acids (n3-PUFA) on the protein levels of ACE1 and ACE2 in rodent tissues, human endothelial and kidney cell lines, and human plasma were examined. The ability of n3-PUFA to affect the entry of the SARS-CoV-2 pseudovirus into cells was also tested. Docosahexaenoic acid (DHA), and in some cases eicosapentaenoic acid (EPA), but not α-linoleic acid (ALA), reduced both ACE1 and ACE2 (non-glycosylated p100 and glycosylated p130 forms) in the heart, aorta, and kidneys of obese rats, as well as in human EA.hy926 endothelial and HEK293 kidney cells. Dietary supplementation with either DHA or ALA had no effect on plasma soluble ACE2 levels in humans. However, treatment of HEK293 cells with 80 and 125 µM DHA for 16 h inhibited the entry of the SARS-CoV-2 pseudovirus. These results strongly suggest that DHA treatment may reduce the ability of SARS-CoV-2 to infect cells via a mechanism involving a decrease in the absolute level of ACE2 protein as well as its glycosylation. Our findings warrant further evaluation of long-chain n3-PUFA supplements as a novel option for restricting SARS-CoV-2 infectivity in the general population.
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55
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Isobe A, Arai Y, Kuroda D, Okumura N, Ono T, Ushiba S, Nakakita SI, Daidoji T, Suzuki Y, Nakaya T, Matsumoto K, Watanabe Y. ACE2 N-glycosylation modulates interactions with SARS-CoV-2 spike protein in a site-specific manner. Commun Biol 2022; 5:1188. [PMID: 36335195 PMCID: PMC9637154 DOI: 10.1038/s42003-022-04170-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 10/25/2022] [Indexed: 11/08/2022] Open
Abstract
SARS-CoV-2 has evolved continuously and accumulated spike mutations with each variant having a different binding for the cellular ACE2 receptor. It is not known whether the interactions between such mutated spikes and ACE2 glycans are conserved among different variant lineages. Here, we focused on three ACE2 glycosylation sites (53, 90 and 322) that are geometrically close to spike binding sites and investigated the effect of their glycosylation pattern on spike affinity. These glycosylation deletions caused distinct site-specific changes in interactions with the spike and acted cooperatively. Of note, the particular interaction profiles were conserved between the SARS-CoV-2 parental virus and the variants of concern (VOCs) Delta and Omicron. Our study provides insights for a better understanding of the importance of ACE2 glycosylation on ACE2/SARS-CoV-2 spike interaction and guidance for further optimization of soluble ACE2 for therapeutic use.
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Affiliation(s)
- Ayana Isobe
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Yasuha Arai
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Daisuke Kuroda
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Nobuaki Okumura
- Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Takao Ono
- SANKEN, Osaka University, Osaka, 567-0047, Japan
| | - Shota Ushiba
- Murata Manufacturing Co., Ltd., Kyoto, 617-8555, Japan
| | - Shin-Ichi Nakakita
- Division of Functional Glycomics, Kagawa University, Kagawa, 761-0793, Japan
| | - Tomo Daidoji
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Yasuo Suzuki
- Department of Medical Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan
| | - Takaaki Nakaya
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | | | - Yohei Watanabe
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan.
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56
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Dehghani J, Movafeghi A, Mathieu-Rivet E, Mati-Baouche N, Calbo S, Lerouge P, Bardor M. Microalgae as an Efficient Vehicle for the Production and Targeted Delivery of Therapeutic Glycoproteins against SARS-CoV-2 Variants. Mar Drugs 2022; 20:md20110657. [PMID: 36354980 PMCID: PMC9698596 DOI: 10.3390/md20110657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/27/2022] Open
Abstract
Severe acute respiratory syndrome–Coronavirus 2 (SARS-CoV-2) can infect various human organs, including the respiratory, circulatory, nervous, and gastrointestinal ones. The virus is internalized into human cells by binding to the human angiotensin-converting enzyme 2 (ACE2) receptor through its spike protein (S-glycoprotein). As S-glycoprotein is required for the attachment and entry into the human target cells, it is the primary mediator of SARS-CoV-2 infectivity. Currently, this glycoprotein has received considerable attention as a key component for the development of antiviral vaccines or biologics against SARS-CoV-2. Moreover, since the ACE2 receptor constitutes the main entry route for the SARS-CoV-2 virus, its soluble form could be considered as a promising approach for the treatment of coronavirus disease 2019 infection (COVID-19). Both S-glycoprotein and ACE2 are highly glycosylated molecules containing 22 and 7 consensus N-glycosylation sites, respectively. The N-glycan structures attached to these specific sites are required for the folding, conformation, recycling, and biological activity of both glycoproteins. Thus far, recombinant S-glycoprotein and ACE2 have been produced primarily in mammalian cells, which is an expensive process. Therefore, benefiting from a cheaper cell-based biofactory would be a good value added to the development of cost-effective recombinant vaccines and biopharmaceuticals directed against COVID-19. To this end, efficient protein synthesis machinery and the ability to properly impose post-translational modifications make microalgae an eco-friendly platform for the production of pharmaceutical glycoproteins. Notably, several microalgae (e.g., Chlamydomonas reinhardtii, Dunaliella bardawil, and Chlorella species) are already approved by the U.S. Food and Drug Administration (FDA) as safe human food. Because microalgal cells contain a rigid cell wall that could act as a natural encapsulation to protect the recombinant proteins from the aggressive environment of the stomach, this feature could be used for the rapid production and edible targeted delivery of S-glycoprotein and soluble ACE2 for the treatment/inhibition of SARS-CoV-2. Herein, we have reviewed the pathogenesis mechanism of SARS-CoV-2 and then highlighted the potential of microalgae for the treatment/inhibition of COVID-19 infection.
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Affiliation(s)
- Jaber Dehghani
- Université de Rouen Normandie, Laboratoire GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, F-76000 Rouen, France
| | - Ali Movafeghi
- Department of Plant, Cell and Molecular Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz 5166616471, Iran
| | - Elodie Mathieu-Rivet
- Université de Rouen Normandie, Laboratoire GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, F-76000 Rouen, France
| | - Narimane Mati-Baouche
- Université de Rouen Normandie, Laboratoire GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, F-76000 Rouen, France
| | - Sébastien Calbo
- Université de Rouen Normandie, Inserm U1234, F-76000 Rouen, France
| | - Patrice Lerouge
- Université de Rouen Normandie, Laboratoire GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, F-76000 Rouen, France
| | - Muriel Bardor
- Université de Rouen Normandie, Laboratoire GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, F-76000 Rouen, France
- Correspondence: ; Tel.: +33-2-35-14-67-51
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Hou X, Gao J, Wang Y. Epistatic Variations in the Omicron Receptor Binding Domain Can Enhance Host Recognition: An In Silico Assessment and Prediction. J Phys Chem Lett 2022; 13:8808-8815. [PMID: 36106917 DOI: 10.1021/acs.jpclett.2c02209] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The hypermutated receptor binding domain (RBD) of the Omicron (B.1.1.529) lineage exhibits a different binding interface with human angiotensin-converting enzyme 2 (ACE2) relative to that of the wild-type Wuhan Hu-1, yet how the altered interaction will affect viral evolution is largely unknown. Here, we used molecular dynamics simulation to characterize the binding features of the Omicron BA.1/hACE2 complex and used free energy perturbation calculations to assess the ongoing and putative variations. The complex reveals a substantial rearrangement of the interfacial hydrogen-bond network: R493 of RBD forms a dynamic electrostatic interaction with both E35 and D38 of hACE2, which prohibits the hydrogen bonds of R498-D38 and Y449-D38. Whereas most circulating mutations minimally affect RBD binding to hACE2, the charge-altering mutation R493Q attenuates the affinity by abolishing the electrostatic interaction. However, the potential variants H505Y or N417K/R493Q could restore and gain even greater binding affinities than BA.1 as a result of their optimized interaction network and epistasis effects.
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Affiliation(s)
- Xudong Hou
- School of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, People's Republic of China
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518132, People's Republic of China
| | - Jiali Gao
- School of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, People's Republic of China
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518132, People's Republic of China
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Yingjie Wang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518132, People's Republic of China
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58
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Li Z, Yong H, Wang W, Gao Y, Wang P, Chen X, Lu J, Zheng J, Bai J. GSK3326595 is a promising drug to prevent SARS-CoV-2 Omicron and other variants infection by inhibiting ACE2-R671 di-methylation. J Med Virol 2022; 95:e28158. [PMID: 36114164 PMCID: PMC9537780 DOI: 10.1002/jmv.28158] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 08/18/2022] [Accepted: 09/14/2022] [Indexed: 01/11/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused COVID-19 epidemic is worsening. Binding of the Spike1 protein of SARS-CoV-2 with the angiotensin-converting enzyme 2 (ACE2) receptor mediates entry of the virus into host cells. Many reports show that protein arginine methylation by protein arginine methyltransferases (PRMTs) is important for the functions of these proteins, but it remains unclear whether ACE2 is methylated by PRMTs. Here, we show that PRMT5 catalyses ACE2 symmetric dimethylation at residue R671 (meR671-ACE2). We indicate that PRMT5-mediated meR671-ACE2 promotes SARS-CoV-2 receptor-binding domain (RBD) binding with ACE2 probably by enhancing ACE2 N-glycosylation modification. We also reveal that the PRMT5-specific inhibitor GSK3326595 is able to dramatically reduce ACE2 binding with RBD. Moreover, we discovered that meR671-ACE2 plays an important role in ACE2 binding with Spike1 of the SARS-CoV-2 Omicron, Delta, and Beta variants; and we found that GSK3326595 strongly attenuates ACE2 interaction with Spike1 of the SARS-CoV-2 Omicron, Delta, and Beta variants. Finally, SARS-CoV-2 pseudovirus infection assays uncovered that PRMT5-mediated meR671-ACE2 is essential for SARS-CoV-2 infection in human cells, and pseudovirus infection experiments confirmed that GSK3326595 can strongly suppress SARS-CoV-2 infection of host cells. Our findings suggest that as a clinical phase II drug for several kinds of cancers, GSK3326595 is a promising candidate to decrease SARS-CoV-2 infection by inhibiting ACE2 methylation and ACE2-Spike1 interaction.
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Affiliation(s)
- Zhongwei Li
- Cancer InstituteXuzhou Medical UniversityXuzhouJiangsuChina,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical UniversityXuzhouJiangsuChina
| | - Hongmei Yong
- Department of OncologyThe Affiliated Huai'an Hospital of Xuzhou Medical University and The Second People's Hospital of Huai'anHuaianJiangsuChina
| | - Wenwen Wang
- Cancer InstituteXuzhou Medical UniversityXuzhouJiangsuChina
| | - Yue Gao
- Cancer InstituteXuzhou Medical UniversityXuzhouJiangsuChina
| | - Pengfei Wang
- Cancer InstituteXuzhou Medical UniversityXuzhouJiangsuChina
| | - Xintian Chen
- Cancer InstituteXuzhou Medical UniversityXuzhouJiangsuChina
| | - Jun Lu
- The Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE)Northeast Normal UniversityChangchunChina
| | - Junnian Zheng
- Cancer InstituteXuzhou Medical UniversityXuzhouJiangsuChina,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical UniversityXuzhouJiangsuChina
| | - Jin Bai
- Cancer InstituteXuzhou Medical UniversityXuzhouJiangsuChina,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical UniversityXuzhouJiangsuChina
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59
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Badawi S, Mohamed FE, Alkhofash NR, John A, Ali A, Ali BR. Characterization of ACE2 naturally occurring missense variants: impact on subcellular localization and trafficking. Hum Genomics 2022; 16:35. [PMID: 36056420 PMCID: PMC9438391 DOI: 10.1186/s40246-022-00411-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 07/01/2022] [Indexed: 02/08/2023] Open
Abstract
Background Human angiotensin-converting enzyme 2 (ACE2), a type I transmembrane receptor physiologically acting as a carboxypeptidase enzyme within the renin-angiotensin system (RAS), is a critical mediator of infection by several severe acute respiratory syndrome (SARS) corona viruses. For instance, it has been demonstrated that ACE2 is the primary receptor for the SARS-CoV-2 entry to many human cells through binding to the viral spike S protein. Consequently, genetic variability in ACE2 gene has been suggested to contribute to the variable clinical manifestations in COVID-19. Many of those genetic variations result in missense variants within the amino acid sequence of ACE2. The potential effects of those variations on binding to the spike protein have been speculated and, in some cases, demonstrated experimentally. However, their effects on ACE2 protein folding, trafficking and subcellular targeting have not been established. Results In this study we aimed to examine the potential effects of 28 missense variants (V801G, D785N, R768W, I753T, L731F, L731I, I727V, N720D, R710H, R708W, S692P, E668K, V658I, N638S, A627V, F592L, G575V, A501T, I468V, M383I, G173S, N159S, N149S, D38E, N33D, K26R, I21T, and S19P) distributed across the ACE2 receptor domains on its subcellular trafficking and targeting through combinatorial approach involving in silico analysis and experimental subcellular localization analysis. Our data show that none of the studied missense variants (including 3 variants predicted to be deleterious R768W, G575V, and G173S) has a significant effect on ACE2 intracellular trafficking and subcellular targeting to the plasma membrane. Conclusion Although the selected missense variants display no significant change in ACE2 trafficking and subcellular localization, this does not rule out their effect on viral susceptibility and severity. Further studies are required to investigate the effect of ACE2 variants on its expression, binding, and internalization which might explain the variable clinical manifestations associated with the infection. Supplementary Information The online version contains supplementary material available at 10.1186/s40246-022-00411-1.
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Affiliation(s)
- Sally Badawi
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box: 15551, Al-Ain, United Arab Emirates
| | - Feda E Mohamed
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box: 15551, Al-Ain, United Arab Emirates
| | - Nesreen R Alkhofash
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box: 15551, Al-Ain, United Arab Emirates
| | - Anne John
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box: 15551, Al-Ain, United Arab Emirates
| | - Amanat Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box: 15551, Al-Ain, United Arab Emirates
| | - Bassam R Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box: 15551, Al-Ain, United Arab Emirates. .,Zayed Centre for Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.
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60
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Pipitò L, Rujan R, Reynolds CA, Deganutti G. Molecular dynamics studies reveal structural and functional features of the SARS-CoV-2 spike protein. Bioessays 2022; 44:e2200060. [PMID: 35843871 PMCID: PMC9350306 DOI: 10.1002/bies.202200060] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/21/2022] [Accepted: 07/01/2022] [Indexed: 12/23/2022]
Abstract
The SARS-CoV-2 virus is responsible for the COVID-19 pandemic the world experience since 2019. The protein responsible for the first steps of cell invasion, the spike protein, has probably received the most attention in light of its central role during infection. Computational approaches are among the tools employed by the scientific community in the enormous effort to study this new affliction. One of these methods, namely molecular dynamics (MD), has been used to characterize the function of the spike protein at the atomic level and unveil its structural features from a dynamic perspective. In this review, we focus on these main findings, including spike protein flexibility, rare S protein conformational changes, cryptic epitopes, the role of glycans, drug repurposing, and the effect of spike protein variants.
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Affiliation(s)
- Ludovico Pipitò
- Centre for Sport, Exercise and Life Sciences (CSELS)Faculty of Health and Life SciencesCoventry UniversityCoventryUK
| | - Roxana‐Maria Rujan
- Centre for Sport, Exercise and Life Sciences (CSELS)Faculty of Health and Life SciencesCoventry UniversityCoventryUK
| | - Christopher A. Reynolds
- Centre for Sport, Exercise and Life Sciences (CSELS)Faculty of Health and Life SciencesCoventry UniversityCoventryUK
| | - Giuseppe Deganutti
- Centre for Sport, Exercise and Life Sciences (CSELS)Faculty of Health and Life SciencesCoventry UniversityCoventryUK
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Hattori T, Saito T, Okuya K, Takahashi Y, Miyamoto H, Kajihara M, Igarashi M, Takada A. Human ACE2 Genetic Polymorphism Affecting SARS-CoV and SARS-CoV-2 Entry into Cells. Microbiol Spectr 2022; 10:e0087022. [PMID: 35862965 PMCID: PMC9430119 DOI: 10.1128/spectrum.00870-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/27/2022] [Indexed: 11/29/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 have a single envelope glycoprotein (S protein) that binds to human angiotensin-converting enzyme 2 (ACE2) on the host cell membrane. Previous mutational scanning studies have suggested that some substitutions corresponding to single nucleotide variants (SNVs) in human ACE2 affect the binding affinity to the receptor binding domain (RBD) of the SARS-CoV-2 S protein. However, the importance of these substitutions in actual virus infection is still unclear. In this study, we investigated the effects of the reported ACE2 SNV substitutions on the entry of SARS-CoV and SARS-CoV-2 into cells, using vesicular stomatitis Indiana virus (VSIV) pseudotyped with S proteins of these coronaviruses (CoVs). HEK293T cells transfected with plasmids expressing ACE2 having each SNV substitution were infected with the pseudotyped VSIVs and relative infectivities were determined compared to the cells expressing wild-type ACE2. We found that some of the SNV substitutions positively or negatively affected the infectivities of the pseudotyped viruses. Particularly, the H505R substitution significantly enhanced the infection with the pseudotyped VSIVs, including those having the substitutions found in the S protein RBD of SARS-CoV-2 variants of concern. Our findings suggest that human ACE2 SNVs may potentially affect cell susceptibilities to SARS-CoV and SARS-CoV-2. IMPORTANCE SARS-CoV and SARS-CoV-2 are known to cause severe pneumonia in humans. The S protein of these CoVs binds to the ACE2 molecule on the plasma membrane and mediates virus entry into cells. The interaction between the S protein and ACE2 is thought to be important for host susceptibility to these CoVs. Although previous studies suggested that some SNV substitutions in ACE2 might affect the binding to the S protein, it remains elusive whether these SNV substitutions actually alter the efficiency of the entry of SARS CoVs into cells. We analyzed the impact of the ACE2 SNVs on the cellular entry of SARS CoVs using pseudotyped VSIVs having the S protein on the viral surface. We found that some of the SNV substitutions positively or negatively affected the infectivities of the viruses. Our data support the notion that genetic polymorphisms of ACE2 may potentially influence cell susceptibilities to SARS CoVs.
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Affiliation(s)
- Takanari Hattori
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Takeshi Saito
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kosuke Okuya
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yuji Takahashi
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hiroko Miyamoto
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Masahiro Kajihara
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Manabu Igarashi
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Ayato Takada
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
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Abstract
Despite effective spike-based vaccines and monoclonal antibodies, the SARS-CoV-2 pandemic continues more than two and a half years post-onset. Relentless investigation has outlined a causative dynamic between host-derived antibodies and reciprocal viral subversion. Integration of this paradigm into the architecture of next generation antiviral strategies, predicated on a foundational understanding of the virology and immunology of SARS-CoV-2, will be critical for success. This review aims to serve as a primer on the immunity endowed by antibodies targeting SARS-CoV-2 spike protein through a structural perspective. We begin by introducing the structure and function of spike, polyclonal immunity to SARS-CoV-2 spike, and the emergence of major SARS-CoV-2 variants that evade immunity. The remainder of the article comprises an in-depth dissection of all major epitopes on SARS-CoV-2 spike in molecular detail, with emphasis on the origins, neutralizing potency, mechanisms of action, cross-reactivity, and variant resistance of representative monoclonal antibodies to each epitope.
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Affiliation(s)
- John M Errico
- Department of Pathology & Immunology, Washington University School of Medicine, St Louis, MO, United States
| | - Lucas J Adams
- Department of Pathology & Immunology, Washington University School of Medicine, St Louis, MO, United States
| | - Daved H Fremont
- Department of Pathology & Immunology, Washington University School of Medicine, St Louis, MO, United States; Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, United States; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, United States.
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63
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Fazekas Z, Menyhárd DK, Perczel A. Omicron Binding Mode: Contact Analysis and Dynamics of the Omicron Receptor-Binding Domain in Complex with ACE2. J Chem Inf Model 2022; 62:3844-3853. [PMID: 35849759 PMCID: PMC9331008 DOI: 10.1021/acs.jcim.2c00397] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Indexed: 12/12/2022]
Abstract
On 26 November 2021, the WHO classified the Omicron variant of the SARS-CoV-2 virus (B.1.1.529 lineage) as a variant of concern (VOC) (COVID-19 Variant Data, Department of Health, 2022). The Omicron variant contains as many as 26 unique mutations of effects not yet determined (Venkatakrishnan, A., Open Science Framework, 2021). Out of its total of 34 Spike protein mutations, 15 are located on the receptor-binding domain (S-RBD) (Stanford Coronavirus Antiviral & Resistance Database, 2022) that directly contacts the angiotensin-converting enzyme 2 (ACE2) host receptor and is also a primary target for antibodies. Here, we studied the binding mode of the S-RBD domain of the Spike protein carrying the Omicron mutations and the globular domain of human ACE2 using molecular dynamics (MD) simulations. We identified new and key Omicron-specific interactions such as R493 (of mutation Q493R), which forms salt bridges both with E35 and D38 of ACE2, Y501 (N501Y), which forms an edge-to-face aromatic interaction with Y41, and Y505 (Y505H), which makes an H-bond with E37 and K353. The glycan chains of ACE2 also bind differently in the WT and Omicron variants in response to different charge distributions on the surface of Spike proteins. However, while the Omicron mutations considerably improve the overall electrostatic fit of the two interfaces, the total number of specific and favorable interactions between the two does not increase. The dynamics of the complexes are highly affected too, making the Omicron S-RBD:ACE2 complex more rigid; the two main interaction sites, Patches I and II, isolated in the WT complex, become connected in the Omicron complex through the alternating interaction of R493 and R498 with E35 and D38.
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Affiliation(s)
- Zsolt Fazekas
- Laboratory of Structural Chemistry and Biology,
Institute of Chemistry, ELTE Eötvös Loránd
University, Budapest 1117, Hungary
- ELTE Hevesy György PhD School of Chemistry,
ELTE Eötvös Loránd University, Budapest
1117, Hungary
| | - Dóra K. Menyhárd
- Laboratory of Structural Chemistry and Biology,
Institute of Chemistry, ELTE Eötvös Loránd
University, Budapest 1117, Hungary
- MTA-ELTE Protein Modeling Research Group,
Eötvös Loránd Research Network (ELKH), ELTE
Eötvös Loránd University, Budapest 1117,
Hungary
| | - András Perczel
- Laboratory of Structural Chemistry and Biology,
Institute of Chemistry, ELTE Eötvös Loránd
University, Budapest 1117, Hungary
- MTA-ELTE Protein Modeling Research Group,
Eötvös Loránd Research Network (ELKH), ELTE
Eötvös Loránd University, Budapest 1117,
Hungary
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64
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Wozney AJ, Smith MA, Abdrabbo M, Birch CM, Cicigoi KA, Dolan CC, Gerzema AEL, Hansen A, Henseler EJ, LaBerge B, Leavens CM, Le CN, Lindquist AC, Ludwig RK, O'Reilly MG, Reynolds JH, Sherman BA, Sillman HW, Smith MA, Snortheim MJ, Svaren LM, Vanderpas EC, Voon A, Wackett MJ, Weiss MM, Hati S, Bhattacharyya S. Evolution of Stronger SARS-CoV-2 Variants as Revealed Through the Lens of Molecular Dynamics Simulations. Protein J 2022; 41:444-456. [PMID: 35913554 PMCID: PMC9340756 DOI: 10.1007/s10930-022-10065-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2022] [Indexed: 12/03/2022]
Abstract
Using molecular dynamics simulations, the protein–protein interactions of the receptor-binding domain of the wild-type and seven variants of the severe acute respiratory syndrome coronavirus 2 spike protein and the peptidase domain of human angiotensin-converting enzyme 2 were investigated. These variants are alpha, beta, gamma, delta, eta, kappa, and omicron. Using 100 ns simulation data, the residue interaction networks at the protein–protein interface were identified. Also, the impact of mutations on essential protein dynamics, backbone flexibility, and interaction energy of the simulated protein–protein complexes were studied. The protein–protein interface for the wild-type, delta, and omicron variants contained several stronger interactions, while the alpha, beta, gamma, eta, and kappa variants exhibited an opposite scenario as evident from the analysis of the inter-residue interaction distances and pair-wise interaction energies. The study reveals that two distinct residue networks at the central and right contact regions forge stronger binding affinity between the protein partners. The study provides a molecular-level insight into how enhanced transmissibility and infectivity by delta and omicron variants are most likely tied to a handful of interacting residues at the binding interface, which could potentially be utilized for future antibody constructs and structure-based antiviral drug design.
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Affiliation(s)
- Alec J Wozney
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Macey A Smith
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Mobeen Abdrabbo
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Cole M Birch
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Kelsey A Cicigoi
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Connor C Dolan
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Audrey E L Gerzema
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Abby Hansen
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Ethan J Henseler
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Ben LaBerge
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Caterra M Leavens
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Christine N Le
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Allison C Lindquist
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Rikaela K Ludwig
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Maggie G O'Reilly
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Jacob H Reynolds
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Brandon A Sherman
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Hunter W Sillman
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Michael A Smith
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Marissa J Snortheim
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Levi M Svaren
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Emily C Vanderpas
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Aidan Voon
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Miles J Wackett
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Moriah M Weiss
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Sanchita Hati
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA.
| | - Sudeep Bhattacharyya
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA.
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65
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Yusuf AP, Zhang JY, Li JQ, Muhammad A, Abubakar MB. Herbal medications and natural products for patients with covid-19 and diabetes mellitus: Potentials and challenges. PHYTOMEDICINE PLUS : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 2:100280. [PMID: 35463625 PMCID: PMC9014648 DOI: 10.1016/j.phyplu.2022.100280] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 03/25/2022] [Accepted: 04/12/2022] [Indexed: 04/21/2023]
Abstract
BACKGROUND The presence of diabetes mellitus (DM) among COVID-19 patients is associated with increased hospitalization, morbidity, and mortality. Evidence has shown that hyperglycemia potentiates SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) infection and plays a central role in severe COVID-19 and diabetes comorbidity. In this review, we explore the therapeutic potentials of herbal medications and natural products in the management of COVID-19 and DM comorbidity and the challenges associated with the preexisting or concurrent use of these substances. METHODS Research papers that were published from January 2016 to December 2021 were retrieved from PubMed, ScienceDirect, and Google Scholar databases. Papers reporting clinical evidence of antidiabetic activities and any available evidence of the anti-COVID-19 potential of ten selected natural products were retrieved and analyzed for discussion in this review. RESULTS A total of 548 papers (73 clinical trials on the antidiabetic activities of the selected natural products and 475 research and review articles on their anti-COVID-19 potential) were retrieved from the literature search for further analysis. A total of 517 articles (reviews and less relevant research papers) were excluded. A cumulative sum of thirty-one (31) research papers (20 clinical trials and 10 others) met the criteria and have been discussed in this review. CONCLUSION The findings of this review suggest that phenolic compounds are the most promising phytochemicals in the management of COVID-19 and DM comorbidity. Curcumin and propolis have shown substantial evidence against COVID-19 and DM in humans and are thus, considered the best potential therapeutic options.
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Key Words
- 8-OHDG, 8-hydroxy-2’-deoxyguanosine
- ACE2
- ACE2, Angiotensin-converting enzyme 2
- ADMA, asymmetric de-methyl-arginine
- ARDS, acute respiratory distress syndrome
- COVID-19
- Comorbidity
- DM, diabetes mellitus
- Diabetes
- FBS, fasting blood sugar
- GLUT-4, glucose transporter-4
- GSK-3β, glycogen synthase kinase-3β
- HDL, high-density lipoprotein
- HOMA, homeostasis model assessment
- Herbal medication
- IAPP, islet amyloid polypeptide
- IFN, interferon
- IFNAR2, interferon-alpha receptor 2
- IL-6, interleukin-6
- LDL, low-density lipoprotein
- MDA, malondialdehyde
- Mpro, main protease
- Natural products
- PLpro, papain-like protease
- PON1, paraoxonase-1
- RBD, receptor-binding domain
- RCT, randomized control trial
- RdRp, RNA-dependent RNA polymerase
- SARS-CoV-2, severe acute respiratory syndrome coronavirus-2
- SFJDC, Shufeng Jiedu Capsule
- T1D, type 1 diabetes
- T2D, type 2 diabetes
- TAC, total antioxidant capacity
- TMPRSS2, transmembrane protease serine 2
- hs-CRP, high-sensitivity C-reactive protein
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Affiliation(s)
- Abdurrahman Pharmacy Yusuf
- Department of Biochemistry, School of Life Sciences, Federal University of Technology, P.M.B 65, Minna, Niger State, Nigeria
| | - Jian-Ye Zhang
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, P.R. China
| | - Jing-Quan Li
- The first Affiliated Hospital, Hainan Medical University, Haikou, P.R. China
| | - Aliyu Muhammad
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University Zaria, 810107, Kaduna State, Nigeria
| | - Murtala Bello Abubakar
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria
- Department of Physiology, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, P.M.B. 2254, Sokoto, Nigeria
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66
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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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67
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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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68
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Hu P, Bauer VL, Sawyer SL, Diaz-Griffero F. Human ACE2 Polymorphisms from Different Human Populations Modulate SARS-CoV-2 Infection. Viruses 2022; 14:1451. [PMID: 35891433 PMCID: PMC9319759 DOI: 10.3390/v14071451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/28/2022] [Accepted: 06/28/2022] [Indexed: 01/08/2023] Open
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in over 6 million deaths worldwide. The high variability in COVID-19 symptoms remains one of the most interesting mysteries of the pandemic. Genetic and environmental factors are likely to be key determinants of COVID-19 symptomatology. Here, we explored ACE2 as a genetic determinant for SARS-CoV-2 infection and COVID-19 symptomatology. Each human genome encodes two alleles of ACE2, which encodes the cell entry receptor for SARS-CoV-2. Here, we determined whether naturally occurring human ACE2 (hACE2) polymorphisms in the human population affect SARS-CoV-2 infection and the severity of COVID-19 symptoms. ACE2 variants S19P, I21V, E23K, K26R, K31R, N33I, H34R, E35K, and T92I showed increased virus infection compared to wild-type ACE2; thus, these variants could increase the risk for COVID-19. In contrast, variants D38V, Y83H, I468V, and N638S showed reduced infection, indicating a potential protective effect. hACE2 variants K26R and T92I increased infection by three-fold without changing the levels of ACE2 on the surface of the cells, suggesting that these variants may increase the risk of severe COVID-19. On the contrary, hACE2 variants D38V and Y83H decreased SARS-CoV-2 infection by four- and ten-fold, respectively, without changing surface expression, suggesting that these variants may protect against severe COVID-19. Remarkably, all protective hACE2 Polymorphisms were found almost exclusively in Asian populations, which may provide a partial explanation for the low COVID-19 mortality rates in Asian countries. Thus, hACE2 polymorphisms may modulate susceptibility to SARS-CoV-2 in the host and partially account for the differences in severity of COVID-19 among different ethnic groups.
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Affiliation(s)
- Pan Hu
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA;
| | - Vanessa L. Bauer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA; (V.L.B.); (S.L.S.)
| | - Sara L. Sawyer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA; (V.L.B.); (S.L.S.)
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA;
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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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70
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Xiang Y, Huang W, Liu H, Sang Z, Nambulli S, Tubiana J, Williams KL, Duprex WP, Schneidman-Duhovny D, Wilson IA, Taylor DJ, Shi Y. Superimmunity by pan-sarbecovirus nanobodies. Cell Rep 2022; 39:111004. [PMID: 35738279 PMCID: PMC9174178 DOI: 10.1016/j.celrep.2022.111004] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/09/2022] [Accepted: 06/03/2022] [Indexed: 11/23/2022] Open
Abstract
Vaccine boosters and infection can facilitate the development of SARS-CoV-2 antibodies with improved potency and breadth. Here, we observe superimmunity in a camelid extensively immunized with the SARS-CoV-2 receptor-binding domain (RBD). We rapidly isolate a large repertoire of specific ultra-high-affinity nanobodies that bind strongly to all known sarbecovirus clades using integrative proteomics. These pan-sarbecovirus nanobodies (psNbs) are highly effective against SARS-CoV and SARS-CoV-2 variants, including Omicron, with the best median neutralization potency at single-digit nanograms per milliliter. A highly potent, inhalable, and bispecific psNb (PiN-31) is also developed. Structural determinations of 13 psNbs with the SARS-CoV-2 spike or RBD reveal five epitope classes, providing insights into the mechanisms and evolution of their broad activities. The highly evolved psNbs target small, flat, and flexible epitopes that contain over 75% of conserved RBD surface residues. Their potencies are strongly and negatively correlated with the distance of the epitopes from the receptor binding sites.
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Affiliation(s)
- Yufei Xiang
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Wei Huang
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
| | - Zhe Sang
- The University of Pittsburgh and Carnegie Mellon University Program for Computational Biology, Pittsburgh, PA 15213, USA
| | - Sham Nambulli
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jérôme Tubiana
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel; Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Kevin L Williams
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - W Paul Duprex
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, Scripps Research, La Jolla, CA 92037, USA
| | - Derek J Taylor
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA; Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Yi Shi
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA; The University of Pittsburgh and Carnegie Mellon University Program for Computational Biology, Pittsburgh, PA 15213, USA; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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71
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Wieczór M, Genna V, Aranda J, Badia RM, Gelpí JL, Gapsys V, de Groot BL, Lindahl E, Municoy M, Hospital A, Orozco M. Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2022; 13:e1622. [PMID: 35935573 PMCID: PMC9347456 DOI: 10.1002/wcms.1622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
Exascale computing has been a dream for ages and is close to becoming a reality that will impact how molecular simulations are being performed, as well as the quantity and quality of the information derived for them. We review how the biomolecular simulations field is anticipating these new architectures, making emphasis on recent work from groups in the BioExcel Center of Excellence for High Performance Computing. We exemplified the power of these simulation strategies with the work done by the HPC simulation community to fight Covid-19 pandemics. This article is categorized under:Data Science > Computer Algorithms and ProgrammingData Science > Databases and Expert SystemsMolecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods.
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Affiliation(s)
- Miłosz Wieczór
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Department of Physical ChemistryGdansk University of TechnologyGdańskPoland
| | - Vito Genna
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Juan Aranda
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | | | - Josep Lluís Gelpí
- Barcelona Supercomputing CenterBarcelonaSpain
- Department of Biochemistry and BiomedicineUniversity of BarcelonaBarcelonaSpain
| | - Vytautas Gapsys
- Max Planck Institute for Multidisciplinary SciencesComputational Biomolecular Dynamics GroupGoettingenGermany
| | - Bert L. de Groot
- Max Planck Institute for Multidisciplinary SciencesComputational Biomolecular Dynamics GroupGoettingenGermany
| | - Erik Lindahl
- Department of Applied PhysicsSwedish e‐Science Research Center, KTH Royal Institute of TechnologyStockholmSweden
- Department of Biochemistry and Biophysics, Science for Life LaboratoryStockholm UniversityStockholmSweden
| | | | - Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Department of Biochemistry and BiomedicineUniversity of BarcelonaBarcelonaSpain
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72
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Ung L, Chodosh J. COVID-19 and the eye: alternative facts The 2022 Bowman Club, David L. Easty lecture. BMJ Open Ophthalmol 2022; 7:bmjophth-2022-001042. [PMID: 35675203 PMCID: PMC9114314 DOI: 10.1136/bmjophth-2022-001042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 04/18/2022] [Indexed: 01/08/2023] Open
Abstract
In addition to catastrophic loss of life, and dramatic and unwanted alterations to the daily lives of those left behind, the COVID-19 pandemic has fostered the publication and dissemination of an unprecedented quantity of peer-reviewed medical and scientific publications on a single subject. In particular, the ophthalmic literature is now replete with clinical and laboratory studies on putative eye involvement by SARS-CoV-2, the aetiologic agent of COVID-19. In this review, we critically appraise the published literature on COVID-19, and suggest that the quality of scientific peer review and editorial decision-making also suffered during the COVID-19 pandemic.
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Affiliation(s)
- Lawson Ung
- Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Epidemiology, Harvard University T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - James Chodosh
- Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
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73
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Trozzi F, Karki N, Song Z, Verma N, Kraka E, Zoltowski BD, Tao P. Allosteric control of ACE2 peptidase domain dynamics. Org Biomol Chem 2022; 20:3605-3618. [PMID: 35420112 PMCID: PMC9205182 DOI: 10.1039/d2ob00606e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The Angiotensin Converting Enzyme 2 (ACE2) assists the regulation of blood pressure and is the main target of the coronaviruses responsible for SARS and COVID19. The catalytic function of ACE2 relies on the opening and closing motion of its peptidase domain (PD). In this study, we investigated the possibility of allosterically controlling the ACE2 PD functional dynamics. After confirming that ACE2 PD binding site opening-closing motion is dominant in characterizing its conformational landscape, we observed that few mutations in the viral receptor binding domain fragments were able to impart different effects on the binding site opening of ACE2 PD. This showed that binding to the solvent exposed area of ACE2 PD can effectively alter the conformational profile of the protein, and thus likely its catalytic function. Using a targeted machine learning model and relative entropy-based statistical analysis, we proposed the mechanism for the allosteric perturbation that regulates the ACE2 PD binding site dynamics at atomistic level. The key residues and the source of the allosteric regulation of ACE PD dynamics are also presented.
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Affiliation(s)
- Francesco Trozzi
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, USA.
| | - Nischal Karki
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, USA.
| | - Zilin Song
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, USA.
| | - Niraj Verma
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, USA.
| | - Elfi Kraka
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, USA.
| | - Brian D Zoltowski
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, USA.
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, USA.
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74
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Yanagisawa S, Oikawa Y, Takagi S, Horikoshi Y, Satomura A, Imai K, Sakai J, Ishibashi N, Tarumoto N, Iida S, Nakayama H, Haga Y, Maesaki S, Shimada A. HbA1c level may be a risk factor for oxygen therapy requirement in patients with coronavirus disease 2019. J Diabetes Investig 2022; 13:909-917. [PMID: 34958706 PMCID: PMC9077726 DOI: 10.1111/jdi.13743] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 12/17/2021] [Accepted: 12/26/2021] [Indexed: 11/26/2022] Open
Abstract
INTRODUCTION Many clinical studies have identified significant predictors or risk factors for the severity or mortality of coronavirus disease 2019 (COVID-19) cases. However, there are very limited reports on the risk factors for requiring oxygen therapy during hospitalization. In particular, we sought to investigate whether plasma glucose and HbA1c levels could be risk factors for oxygen therapy requirement. MATERIALS AND METHODS A single-center, retrospective study was conducted of 131 COVID-19 patients hospitalized at Saitama Medical University Hospital between March 2020 and November 2020. To identify the risk factors for oxygen therapy requirement during hospitalization, a stepwise multivariate binary logistic regression analysis was performed using several clinical parameters commonly obtained on admission, including plasma glucose and HbA1c levels. RESULTS Of the 131 patients with COVID-19, 33.6% (44/131) received oxygen therapy during hospitalization. According to the logistic regression analysis, male sex (odds ratio [OR]: 8.76, 95% confidence interval [CI]: 1.65-46.5, P < 0.05), age (OR: 1.07, 95% CI: 1.02-1.12, P < 0.01), HbA1c levels (OR: 1.94, 95% CI: 1.09-3.44, P < 0.05), and serum C-reactive protein (CRP) levels (OR: 2.22, 95% CI: 1.54-3.20, P < 0.01) emerged as independent variables associated with oxygen therapy requirement during hospitalization. CONCLUSIONS In addition to male sex, age, and serum CRP levels, HbA1c levels on admission may serve as a risk factor for oxygen therapy requirement during the clinical course of COVID-19, irrespective of diabetes history and status. This may contribute to the efficient delegation of limited numbers of hospital beds to patients at risk for oxygen therapy requirement.
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Affiliation(s)
| | - Yoichi Oikawa
- Department of Endocrinology and DiabetesSaitama Medical UniversitySaitamaJapan
| | - Sotaro Takagi
- Department of Endocrinology and DiabetesSaitama Medical UniversitySaitamaJapan
| | - Yuta Horikoshi
- Department of Endocrinology and DiabetesSaitama Medical UniversitySaitamaJapan
| | - Atsushi Satomura
- Department of Endocrinology and DiabetesSaitama Medical UniversitySaitamaJapan
| | - Kazuo Imai
- Department of Infectious Disease and Infection ControlSaitama Medical UniversitySaitamaJapan
| | - Jun Sakai
- Department of Infectious Disease and Infection ControlSaitama Medical UniversitySaitamaJapan
| | - Noriomi Ishibashi
- Department of Infectious Disease and Infection ControlSaitama Medical UniversitySaitamaJapan
| | - Norihito Tarumoto
- Department of Infectious Disease and Infection ControlSaitama Medical UniversitySaitamaJapan
| | - Shinichiro Iida
- Department of Cardiovascular MedicineSaitama Medical UniversitySaitamaJapan
| | - Hideto Nakayama
- Department of AnesthesiologySaitama Medical UniversitySaitamaJapan
| | - Yoshiyuki Haga
- Department of Intensive Care MedicineSaitama Medical UniversitySaitamaJapan
| | - Shigefumi Maesaki
- Department of Infectious Disease and Infection ControlSaitama Medical UniversitySaitamaJapan
| | - Akira Shimada
- Department of Endocrinology and DiabetesSaitama Medical UniversitySaitamaJapan
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75
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Soldevila B, Puig-Domingo M, Marazuela M. Basic mechanisms of SARS-CoV-2 infection. What endocrine systems could be implicated? Rev Endocr Metab Disord 2022; 23:137-150. [PMID: 34333732 PMCID: PMC8325622 DOI: 10.1007/s11154-021-09678-6] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/19/2021] [Indexed: 02/07/2023]
Abstract
Although SARS-CoV-2 viral attacks starts by the interaction of spike protein (S Protein) to ACE2 receptor located at the cell surface of respiratory tract and digestive system cells, different endocrine targets, endocrine organs and metabolic conditions are of fundamental relevance for understanding disease progression and special outcomes, in particular those of fatal consequences for the patient. During pandemic, moreover, a specific phenotype of COVID-19 metabolic patient has been described, characterized by being at particular risk of worse outcomes. In the present paper we describe the mechanism of viral interaction with endocrine organs, emphasizing the specific endocrine molecules of particular relevance explaining COVID-19 disease evolution and outcomes.
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Affiliation(s)
- Berta Soldevila
- Endocrinology and Nutrition Service, Department of Medicine, Germans Trias i Pujol Research Institute and Hospital, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Manel Puig-Domingo
- Endocrinology and Nutrition Service, Department of Medicine, Germans Trias i Pujol Research Institute and Hospital, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Mónica Marazuela
- Department of Endocrinology, Hospital Universitario de La Princesa, Instituto de Investigación de La Princesa, Universidad Autónoma de Madrid, Madrid, Spain.
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76
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Bakshi T, Pham D, Kaur R, Sun B. Hidden Relationships between N-Glycosylation and Disulfide Bonds in Individual Proteins. Int J Mol Sci 2022; 23:ijms23073742. [PMID: 35409101 PMCID: PMC8998389 DOI: 10.3390/ijms23073742] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 02/04/2023] Open
Abstract
N-Glycosylation (NG) and disulfide bonds (DBs) are two prevalent co/post-translational modifications (PTMs) that are often conserved and coexist in membrane and secreted proteins involved in a large number of diseases. Both in the past and in recent times, the enzymes and chaperones regulating these PTMs have been constantly discovered to directly interact with each other or colocalize in the ER. However, beyond a few model proteins, how such cooperation affects N-glycan modification and disulfide bonding at selective sites in individual proteins is largely unknown. Here, we reviewed the literature to discover the current status in understanding the relationships between NG and DBs in individual proteins. Our results showed that more than 2700 human proteins carry both PTMs, and fewer than 2% of them have been investigated in the associations between NG and DBs. We summarized both these proteins with the reported relationships in the two PTMs and the tools used to discover the relationships. We hope that, by exposing this largely understudied field, more investigations can be encouraged to unveil the hidden relationships of NG and DBs in the majority of membranes and secreted proteins for pathophysiological understanding and biotherapeutic development.
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Affiliation(s)
- Tania Bakshi
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada;
| | - David Pham
- Department of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada;
| | - Raminderjeet Kaur
- Faculty of Health Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada;
| | - Bingyun Sun
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada;
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- Correspondence:
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77
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Sheng Y, Vinjamuri A, Alvarez MRS, Xie Y, McGrath M, Chen S, Barboza M, Frieman M, Lebrilla CB. Host Cell Glycocalyx Remodeling Reveals SARS-CoV-2 Spike Protein Glycomic Binding Sites. Front Mol Biosci 2022; 9:799703. [PMID: 35372520 PMCID: PMC8964299 DOI: 10.3389/fmolb.2022.799703] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/31/2022] [Indexed: 12/12/2022] Open
Abstract
Glycans on the host cell membrane and viral proteins play critical roles in pathogenesis. Highly glycosylated epithelial cells represent the primary boundary separating embedded host tissues from pathogens within the respiratory and intestinal tracts. SARS-CoV-2, the causative agent for the COVID-19 pandemic, reaches into the respiratory tract. We found purified human milk oligosaccharides (HMOs) inhibited the viral binding on cells. Spike (S) protein receptor binding domain (RBD) binding to host cells were partly blocked by co-incubation with exogenous HMOs, most by 2-6-sialyl-lactose (6′SL), supporting the notion that HMOs can function as decoys in defense against SARS-Cov2. To investigate the effect of host cell glycocalyx on viral adherence, we metabolically modified and confirmed with glycomic methods the cell surface glycome to enrich specific N-glycan types including those containing sialic acids, fucose, mannose, and terminal galactose. Additionally, Immunofluorescence studies demonstrated that the S protein preferentially binds to terminal sialic acids with α-(2,6)-linkages. Furthermore, site-specific glycosylation of S protein RBD and its human receptor ACE2 were characterized using LC-MS/MS. We then performed molecular dynamics calculations on the interaction complex to further explore the interactive complex between ACE2 and the S protein. The results showed that hydrogen bonds mediated the interactions between ACE2 glycans and S protein with desialylated glycans forming significantly fewer hydrogen bonds. These results supported a mechanism where the virus binds initially to glycans on host cells preferring α-(2,6)-sialic acids and finds ACE2 and with the proper orientation infects the cell.
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Affiliation(s)
- Ying Sheng
- Department of Chemistry, University of California, Davis, Davis, CA, United States
- The Biochemistry, Molecular, Cellular and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, Davis, CA, United States
| | - Anita Vinjamuri
- Department of Chemistry, University of California, Davis, Davis, CA, United States
| | | | - Yixuan Xie
- Department of Chemistry, University of California, Davis, Davis, CA, United States
| | - Marisa McGrath
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Siyu Chen
- Department of Chemistry, University of California, Davis, Davis, CA, United States
| | - Mariana Barboza
- Department of Chemistry, University of California, Davis, Davis, CA, United States
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Matthew Frieman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California, Davis, Davis, CA, United States
- The Biochemistry, Molecular, Cellular and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, Davis, CA, United States
- *Correspondence: Carlito B. Lebrilla,
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78
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An insight into the mechanisms of COVID-19, SARS-CoV2 infection severity concerning β-cell survival and cardiovascular conditions in diabetic patients. Mol Cell Biochem 2022; 477:1681-1695. [PMID: 35235124 PMCID: PMC8889522 DOI: 10.1007/s11010-022-04396-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 02/16/2022] [Indexed: 01/08/2023]
Abstract
A significantly high percentage of hospitalized COVID-19 patients with diabetes mellitus (DM) had severe conditions and were admitted to ICU. In this review, we have delineated the plausible molecular mechanisms that could explain why there are increased clinical complications in patients with DM that become critically ill when infected with SARS-CoV2. RNA viruses have been classically implicated in manifestation of new onset diabetes. SARS-CoV2 infection through cytokine storm leads to elevated levels of pro-inflammatory cytokines creating an imbalance in the functioning of T helper cells affecting multiple organs. Inflammation and Th1/Th2 cell imbalance along with Th17 have been associated with DM, which can exacerbate SARS-CoV2 infection severity. ACE-2-Ang-(1-7)-Mas axis positively modulates β-cell and cardiac tissue function and survival. However, ACE-2 receptors dock SARS-CoV2, which internalize and deplete ACE-2 and activate Renin-angiotensin system (RAS) pathway. This induces inflammation promoting insulin resistance that has positive effect on RAS pathway, causes β-cell dysfunction, promotes inflammation and increases the risk of cardiovascular complications. Further, hyperglycemic state could upregulate ACE-2 receptors for viral infection thereby increasing the severity of the diabetic condition. SARS-CoV2 infection in diabetic patients with heart conditions are linked to worse outcomes. SARS-CoV2 can directly affect cardiac tissue or inflammatory response during diabetic condition and worsen the underlying heart conditions.
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79
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Head RJ, Lumbers ER, Jarrott B, Tretter F, Smith G, Pringle KG, Islam S, Martin JH. Systems analysis shows that thermodynamic physiological and pharmacological fundamentals drive COVID-19 and response to treatment. Pharmacol Res Perspect 2022; 10:e00922. [PMID: 35106955 PMCID: PMC8929328 DOI: 10.1002/prp2.922] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/05/2022] [Indexed: 12/12/2022] Open
Abstract
Why a systems analysis view of this pandemic? The current pandemic has inflicted almost unimaginable grief, sorrow, loss, and terror at a global scale. One of the great ironies with the COVID‐19 pandemic, particularly early on, is counter intuitive. The speed at which specialized basic and clinical sciences described the details of the damage to humans in COVID‐19 disease has been impressive. Equally, the development of vaccines in an amazingly short time interval has been extraordinary. However, what has been less well understood has been the fundamental elements that underpin the progression of COVID‐19 in an individual and in populations. We have used systems analysis approaches with human physiology and pharmacology to explore the fundamental underpinnings of COVID‐19 disease. Pharmacology powerfully captures the thermodynamic characteristics of molecular binding with an exogenous entity such as a virus and its consequences on the living processes well described by human physiology. Thus, we have documented the passage of SARS‐CoV‐2 from infection of a single cell to species jump, to tropism, variant emergence and widespread population infection. During the course of this review, the recurrent observation was the efficiency and simplicity of one critical function of this virus. The lethality of SARS‐CoV‐2 is due primarily to its ability to possess and use a variable surface for binding to a specific human target with high affinity. This binding liberates Gibbs free energy (GFE) such that it satisfies the criteria for thermodynamic spontaneity. Its binding is the prelude to human host cellular entry and replication by the appropriation of host cell constituent molecules that have been produced with a prior energy investment by the host cell. It is also a binding that permits viral tropism to lead to high levels of distribution across populations with newly formed virions. This thermodynamic spontaneity is repeated endlessly as infection of a single host cell spreads to bystander cells, to tissues, to humans in close proximity and then to global populations. The principal antagonism of this process comes from SARS‐CoV‐2 itself, with its relentless changing of its viral surface configuration, associated with the inevitable emergence of variants better configured to resist immune sequestration and importantly with a greater affinity for the host target and higher infectivity. The great value of this physiological and pharmacological perspective is that it reveals the fundamental thermodynamic underpinnings of SARS‐CoV‐2 infection.
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Affiliation(s)
- Richard J Head
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Eugenie R Lumbers
- School of Biomedical Sciences & Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia.,Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Bevyn Jarrott
- Florey Institute of Neuroscience & Mental Health, University of Melbourne, Parkville, Victoria, Australia
| | - Felix Tretter
- Bertalanffy Center for the Study of Systems Science, Vienna, Austria
| | - Gary Smith
- VP System Practice - International Society for System Sciences, Pontypool, UK
| | - Kirsty G Pringle
- School of Biomedical Sciences & Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia.,Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Saiful Islam
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Jennifer H Martin
- Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia.,Centre for Drug Repurposing and Medicines Research, Clinical Pharmacology, University of Newcastle, Newcastle, New South Wales, Australia
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80
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Chutipongtanate S, Morrow AL, Newburg DS. Human Milk Oligosaccharides: Potential Applications in COVID-19. Biomedicines 2022; 10:biomedicines10020346. [PMID: 35203555 PMCID: PMC8961778 DOI: 10.3390/biomedicines10020346] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 11/25/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has become a global health crisis with more than four million deaths worldwide. A substantial number of COVID-19 survivors continue suffering from long-COVID syndrome, a long-term complication exhibiting chronic inflammation and gut dysbiosis. Much effort is being expended to improve therapeutic outcomes. Human milk oligosaccharides (hMOS) are non-digestible carbohydrates known to exert health benefits in breastfed infants by preventing infection, maintaining immune homeostasis and nurturing healthy gut microbiota. These beneficial effects suggest the hypothesis that hMOS might have applications in COVID-19 as receptor decoys, immunomodulators, mucosal signaling agents, and prebiotics. This review summarizes hMOS biogenesis and classification, describes the possible mechanisms of action of hMOS upon different phases of SARS-CoV-2 infection, and discusses the challenges and opportunities of hMOS research for clinical applications in COVID-19.
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Affiliation(s)
- Somchai Chutipongtanate
- Pediatric Translational Research Unit, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
- Department of Clinical Epidemiology and Biostatistics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
- Faculty of Medicine Ramathibodi Hospital, Chakri Naruebodindra Medical Institute, Mahidol University, Samut Prakan 10540, Thailand
- Division of Epidemiology, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA;
| | - Ardythe L. Morrow
- Division of Epidemiology, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA;
- Division of Infectious Diseases, Department of Pediatrics, Cincinnati Children′s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - David S. Newburg
- Division of Epidemiology, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA;
- Correspondence: or
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81
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Fang P, Ji Y, Oellerich T, Urlaub H, Pan KT. Strategies for Proteome-Wide Quantification of Glycosylation Macro- and Micro-Heterogeneity. Int J Mol Sci 2022; 23:ijms23031609. [PMID: 35163546 PMCID: PMC8835892 DOI: 10.3390/ijms23031609] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/03/2022] Open
Abstract
Protein glycosylation governs key physiological and pathological processes in human cells. Aberrant glycosylation is thus closely associated with disease progression. Mass spectrometry (MS)-based glycoproteomics has emerged as an indispensable tool for investigating glycosylation changes in biological samples with high sensitivity. Following rapid improvements in methodologies for reliable intact glycopeptide identification, site-specific quantification of glycopeptide macro- and micro-heterogeneity at the proteome scale has become an urgent need for exploring glycosylation regulations. Here, we summarize recent advances in N- and O-linked glycoproteomic quantification strategies and discuss their limitations. We further describe a strategy to propagate MS data for multilayered glycopeptide quantification, enabling a more comprehensive examination of global and site-specific glycosylation changes. Altogether, we show how quantitative glycoproteomics methods explore glycosylation regulation in human diseases and promote the discovery of biomarkers and therapeutic targets.
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Affiliation(s)
- Pan Fang
- Department of Biochemistry and Molecular Biology, School of Biology & Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China;
| | - Yanlong Ji
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany;
- Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, 60590 Frankfurt am Main, Germany;
- Frankfurt Cancer Institute, Johann Wolfgang Goethe University, 60596 Frankfurt am Main, Germany
| | - Thomas Oellerich
- Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, 60590 Frankfurt am Main, Germany;
- Frankfurt Cancer Institute, Johann Wolfgang Goethe University, 60596 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany;
- Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
- Correspondence: (H.U.); (K.-T.P.)
| | - Kuan-Ting Pan
- Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, 60590 Frankfurt am Main, Germany;
- Frankfurt Cancer Institute, Johann Wolfgang Goethe University, 60596 Frankfurt am Main, Germany
- Correspondence: (H.U.); (K.-T.P.)
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82
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Nabel KG, Clark SA, Shankar S, Pan J, Clark LE, Yang P, Coscia A, McKay LGA, Varnum HH, Brusic V, Tolan NV, Zhou G, Desjardins M, Turbett SE, Kanjilal S, Sherman AC, Dighe A, LaRocque RC, Ryan ET, Tylek C, Cohen-Solal JF, Darcy AT, Tavella D, Clabbers A, Fan Y, Griffiths A, Correia IR, Seagal J, Baden LR, Charles RC, Abraham J. Structural basis for continued antibody evasion by the SARS-CoV-2 receptor binding domain. Science 2022; 375:eabl6251. [PMID: 34855508 PMCID: PMC9127715 DOI: 10.1126/science.abl6251] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 11/29/2021] [Indexed: 12/19/2022]
Abstract
Many studies have examined the impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants on neutralizing antibody activity after they have become dominant strains. Here, we evaluate the consequences of further viral evolution. We demonstrate mechanisms through which the SARS-CoV-2 receptor binding domain (RBD) can tolerate large numbers of simultaneous antibody escape mutations and show that pseudotypes containing up to seven mutations, as opposed to the one to three found in previously studied variants of concern, are more resistant to neutralization by therapeutic antibodies and serum from vaccine recipients. We identify an antibody that binds the RBD core to neutralize pseudotypes for all tested variants but show that the RBD can acquire an N-linked glycan to escape neutralization. Our findings portend continued emergence of escape variants as SARS-CoV-2 adapts to humans.
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MESH Headings
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/metabolism
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- BNT162 Vaccine/immunology
- Betacoronavirus/immunology
- COVID-19/immunology
- COVID-19/virology
- Cross Reactions
- Cryoelectron Microscopy
- Crystallography, X-Ray
- Epitopes
- Evolution, Molecular
- Humans
- Immune Evasion
- Models, Molecular
- Mutation
- Polysaccharides/analysis
- Protein Binding
- Protein Domains
- Receptors, Coronavirus/chemistry
- Receptors, Coronavirus/metabolism
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Viral Pseudotyping
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Affiliation(s)
- Katherine G. Nabel
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah A. Clark
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sundaresh Shankar
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Junhua Pan
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Lars E. Clark
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Pan Yang
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Adrian Coscia
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Lindsay G. A. McKay
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | - Haley H. Varnum
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Vesna Brusic
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nicole V. Tolan
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Guohai Zhou
- Center for Clinical Investigation, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Michaël Desjardins
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Division of Infectious Diseases, Department of Medicine, Centre Hospitalier de l’Université de Montréal, Montreal QC H2X 0C1, Canada
| | - Sarah E. Turbett
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sanjat Kanjilal
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Amy C. Sherman
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Anand Dighe
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Regina C. LaRocque
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Edward T. Ryan
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
| | - Casey Tylek
- AbbVie Bioresearch Center, Worcester, MA 01605, USA
| | | | | | | | | | - Yao Fan
- AbbVie Bioresearch Center, Worcester, MA 01605, USA
| | - Anthony Griffiths
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | | | - Jane Seagal
- AbbVie Bioresearch Center, Worcester, MA 01605, USA
| | - Lindsey R. Baden
- Center for Clinical Investigation, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
| | - Richelle C. Charles
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jonathan Abraham
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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83
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Zepeda-Cervantes J, Martínez-Flores D, Ramírez-Jarquín JO, Tecalco-Cruz ÁC, Alavez-Pérez NS, Vaca L, Sarmiento-Silva RE. Implications of the Immune Polymorphisms of the Host and the Genetic Variability of SARS-CoV-2 in the Development of COVID-19. Viruses 2022; 14:94. [PMID: 35062298 PMCID: PMC8778858 DOI: 10.3390/v14010094] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/22/2021] [Accepted: 12/28/2021] [Indexed: 01/08/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the current pandemic affecting almost all countries in the world. SARS-CoV-2 is the agent responsible for coronavirus disease 19 (COVID-19), which has claimed millions of lives around the world. In most patients, SARS-CoV-2 infection does not cause clinical signs. However, some infected people develop symptoms, which include loss of smell or taste, fever, dry cough, headache, severe pneumonia, as well as coagulation disorders. The aim of this work is to report genetic factors of SARS-CoV-2 and host-associated to severe COVID-19, placing special emphasis on the viral entry and molecules of the immune system involved with viral infection. Besides this, we analyze SARS-CoV-2 variants and their structural characteristics related to the binding to polymorphic angiotensin-converting enzyme type 2 (ACE2). Additionally, we also review other polymorphisms as well as some epigenetic factors involved in the immunopathogenesis of COVID-19. These factors and viral variability could explain the increment of infection rate and/or in the development of severe COVID-19.
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Affiliation(s)
- Jesús Zepeda-Cervantes
- Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Daniel Martínez-Flores
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Josué Orlando Ramírez-Jarquín
- Departamento de Neuropatología Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Ángeles C. Tecalco-Cruz
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México (UACM), Mexico City 06720, Mexico;
| | - Noé Santiago Alavez-Pérez
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Mexico City 07340, Mexico;
| | - Luis Vaca
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Rosa Elena Sarmiento-Silva
- Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
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84
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Alfaleh MA, Zawawi A, Al-Amri SS, Hashem AM. David versus goliath: ACE2-Fc receptor traps as potential SARS-CoV-2 inhibitors. MAbs 2022; 14:2057832. [PMID: 35380919 PMCID: PMC8986284 DOI: 10.1080/19420862.2022.2057832] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Anti-SARS-CoV-2 monoclonal antibodies and vaccines have shown improvement in lowering viral burden and hospitalization. However, emerging SARS-CoV-2 variants contain neutralizing antibody-escape mutations. Therefore, several reports have suggested the administration of recombinant angiotensin-converting enzyme 2 (rACE2) as a soluble receptor trap to block SARS-CoV-2 infection and limit viral escape potential. Several strategies have been implemented to enhance the efficacy of rACE2 as a therapeutic agent. Fc fusions have been used to improve pharmacokinetics and boost the affinity and avidity of ACE2 decoys for the virus spike protein. Furthermore, the intrinsic catalytic activity of ACE2 can be eliminated by introducing point mutations on the catalytic site of ACE2 to obtain an exclusive antiviral activity. This review summarizes different evolution platforms that have been used to enhance ACE2-Fc (i.e., immunoadhesins) as potential therapeutics for the current pandemic or future outbreaks of SARS-associated betacoronaviruses.
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Affiliation(s)
- Mohamed A Alfaleh
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah Saudi Arabia.,Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah Saudi Arabia
| | - Ayat Zawawi
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah Saudi Arabia.,Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah Saudi Arabia
| | - Sawsan S Al-Amri
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah Saudi Arabia
| | - Anwar M Hashem
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah Saudi Arabia.,Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah Saudi Arabia
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85
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Chan MC, Chan KK, Procko E, Shukla D. Machine learning guided design of high affinity ACE2 decoys for SARS-CoV-2 neutralization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.12.22.473902. [PMID: 34981064 PMCID: PMC8722601 DOI: 10.1101/2021.12.22.473902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A potential therapeutic candidate for neutralizing SARS-CoV-2 infection is engineering high-affinity soluble ACE2 decoy proteins to compete for binding of the viral spike (S) protein. Previously, a deep mutational scan of ACE2 was performed and has led to the identification of a triple mutant ACE2 variant, named ACE2 2 .v.2.4, that exhibits nanomolar affinity binding to the RBD domain of S. Using a recently developed transfer learning algorithm, TLmutation, we sought to identified other ACE2 variants, namely double mutants, that may exhibit similar binding affinity with decreased mutational load. Upon training a TLmutation model on the effects of single mutations, we identified several ACE2 double mutants that bind to RBD with tighter affinity as compared to the wild type, most notably, L79V;N90D that binds RBD with similar affinity to ACE2 2 .v.2.4. The successful experimental validation of the double mutants demonstrated the use transfer and supervised learning approaches for engineering protein-protein interactions and identifying high affinity ACE2 peptides for targeting SARS-CoV-2.
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Affiliation(s)
- Matthew C Chan
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL 61081
| | - Kui K Chan
- Cyrus Biotechnology, Inc., Seattle, WA, 98101
| | - Erik Procko
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61081
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL 61081
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86
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Capraz T, Kienzl NF, Laurent E, Perthold JW, Föderl-Höbenreich E, Grünwald-Gruber C, Maresch D, Monteil V, Niederhöfer J, Wirnsberger G, Mirazimi A, Zatloukal K, Mach L, Penninger JM, Oostenbrink C, Stadlmann J. Structure-guided glyco-engineering of ACE2 for improved potency as soluble SARS-CoV-2 decoy receptor. eLife 2021; 10:e73641. [PMID: 34927585 PMCID: PMC8730730 DOI: 10.7554/elife.73641] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/17/2021] [Indexed: 11/17/2022] Open
Abstract
Infection and viral entry of SARS-CoV-2 crucially depends on the binding of its Spike protein to angiotensin converting enzyme 2 (ACE2) presented on host cells. Glycosylation of both proteins is critical for this interaction. Recombinant soluble human ACE2 can neutralize SARS-CoV-2 and is currently undergoing clinical tests for the treatment of COVID-19. We used 3D structural models and molecular dynamics simulations to define the ACE2 N-glycans that critically influence Spike-ACE2 complex formation. Engineering of ACE2 N-glycosylation by site-directed mutagenesis or glycosidase treatment resulted in enhanced binding affinities and improved virus neutralization without notable deleterious effects on the structural stability and catalytic activity of the protein. Importantly, simultaneous removal of all accessible N-glycans from recombinant soluble human ACE2 yields a superior SARS-CoV-2 decoy receptor with promise as effective treatment for COVID-19 patients.
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Affiliation(s)
- Tümay Capraz
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU)ViennaAustria
| | - Nikolaus F Kienzl
- Institute of Plant Biotechnology and Cell Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU)ViennaAustria
| | - Elisabeth Laurent
- Institute of Molecular Biotechnology, Department of Biotechnology and Core Facility Biomolecular & Cellular Analysis, University of Natural Resources and Life Sciences (BOKU)ViennaAustria
| | - Jan W Perthold
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU)ViennaAustria
| | | | - Clemens Grünwald-Gruber
- Institute of Biochemistry, Department of Chemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Daniel Maresch
- Institute of Biochemistry, Department of Chemistry, University of Natural Resources and Life SciencesViennaAustria
| | - Vanessa Monteil
- Karolinska Institute, Department of Laboratory MedicineStockholmSweden
| | | | | | - Ali Mirazimi
- Karolinska Institute, Department of Laboratory MedicineStockholmSweden
- National Veterinary InstituteUppsalaSweden
| | - Kurt Zatloukal
- Diagnostic and Research Institute of Pathology, Medical University of GrazGrazAustria
| | - Lukas Mach
- Institute of Plant Biotechnology and Cell Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU)ViennaAustria
| | - Josef M Penninger
- IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. BohrViennaAustria
- Department of Medical Genetics, Life Sciences Institute, University of British ColumbiaVancouverCanada
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU)ViennaAustria
| | - Johannes Stadlmann
- Institute of Biochemistry, Department of Chemistry, University of Natural Resources and Life SciencesViennaAustria
- IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. BohrViennaAustria
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87
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Huang Y, Harris BS, Minami SA, Jung S, Shah PS, Nandi S, McDonald KA, Faller R. SARS-CoV-2 spike binding to ACE2 is stronger and longer ranged due to glycan interaction. Biophys J 2021; 121:79-90. [PMID: 34883069 PMCID: PMC8648368 DOI: 10.1016/j.bpj.2021.12.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 11/08/2021] [Accepted: 12/02/2021] [Indexed: 01/01/2023] Open
Abstract
Highly detailed steered molecular dynamics simulations are performed on differently glycosylated receptor binding domains of the severe acute respiratory syndrome coronavirus-2 spike protein. The binding strength and the binding range increase with glycosylation. The interaction energy rises very quickly when pulling the proteins apart and only slowly drops at larger distances. We see a catch-slip-type behavior whereby interactions during pulling break and are taken over by new interactions forming. The dominant interaction mode is hydrogen bonds, but Lennard-Jones and electrostatic interactions are relevant as well.
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Affiliation(s)
- Yihan Huang
- Department of Materials Science, UC Davis, Davis, California
| | | | - Shiaki A Minami
- Department of Chemical Engineering, UC Davis, Davis, California
| | - Seongwon Jung
- Department of Chemical Engineering, UC Davis, Davis, California
| | - Priya S Shah
- Department of Chemical Engineering, UC Davis, Davis, California; Department of Microbiology and Molecular Genetics, UC Davis, Davis, California
| | - Somen Nandi
- Department of Chemical Engineering, UC Davis, Davis, California; Global HealthShare Initiative, UC Davis, Davis, California
| | - Karen A McDonald
- Department of Chemical Engineering, UC Davis, Davis, California; Global HealthShare Initiative, UC Davis, Davis, California
| | - Roland Faller
- Department of Chemical Engineering, UC Davis, Davis, California.
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88
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Li R, Qin C. Expression pattern and function of SARS-CoV-2 receptor ACE2. BIOSAFETY AND HEALTH 2021; 3:312-318. [PMID: 34466800 PMCID: PMC8393493 DOI: 10.1016/j.bsheal.2021.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/12/2021] [Accepted: 08/25/2021] [Indexed: 02/05/2023] Open
Abstract
Since the outbreak at the end of 2019, SARS-CoV-2 has been spreading around the world for more than one year. Scientists have been intensely conducting research on this newly emerged coronavirus and the disease caused by it. Angiotensin-converting enzyme 2 (ACE2), as a receptor mediating the cellular entry of SARS-CoV-2, has become a hot spot for researchers. Here, we summarized the recent progresses on the function, expression and distribution characteristics of ACE2 in human body and among populations. We further discussed the interaction mechanism of ACE2 and SARS-CoV-2 S protein, focusing on key residues that effect interaction and binding ability of SARS-CoV-2 variants. This will facilitate researchers to better understand SARS-CoV-2 infection and transmission route, adaptation mechanism, and designing treatment strategies.
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Affiliation(s)
| | - Chengfeng Qin
- Corresponding author: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
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89
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Koehler M, Ray A, Moreira RA, Juniku B, Poma AB, Alsteens D. Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants. Nat Commun 2021; 12:6977. [PMID: 34848718 PMCID: PMC8633007 DOI: 10.1038/s41467-021-27325-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/15/2021] [Indexed: 12/13/2022] Open
Abstract
Despite an unprecedented global gain in knowledge since the emergence of SARS-CoV-2, almost all mechanistic knowledge related to the molecular and cellular details of viral replication, pathology and virulence has been generated using early prototypic isolates of SARS-CoV-2. Here, using atomic force microscopy and molecular dynamics, we investigated how these mutations quantitatively affected the kinetic, thermodynamic and structural properties of RBD-ACE2 complex formation. We observed for several variants of concern a significant increase in the RBD-ACE2 complex stability. While the N501Y and E484Q mutations are particularly important for the greater stability, the N501Y mutation is unlikely to significantly affect antibody neutralization. This work provides unprecedented atomistic detail on the binding of SARS-CoV-2 variants and provides insight into the impact of viral mutations on infection-induced immunity.
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Affiliation(s)
- Melanie Koehler
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Ankita Ray
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Rodrigo A Moreira
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Pawińskiego 5B, 02-106, Warsaw, Poland
| | - Blinera Juniku
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Adolfo B Poma
- International Center for Research on Innovative Biobased Materials (ICRI-BioM)-International Research Agenda, Lodz University of Technology, Żeromskiego 116, 90-924, Lodz, Poland.
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium.
- Walloon Excellence in Life sciences and Biotechnology (WELBIO), 1300, Wavre, Belgium.
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90
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Huang C, Tan Z, Zhao K, Zou W, Wang H, Gao H, Sun S, Bu D, Chai W, Li Y. The effect of N-glycosylation of SARS-CoV-2 spike protein on the virus interaction with the host cell ACE2 receptor. iScience 2021; 24:103272. [PMID: 34661088 PMCID: PMC8513389 DOI: 10.1016/j.isci.2021.103272] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/30/2021] [Accepted: 10/12/2021] [Indexed: 10/26/2022] Open
Abstract
The densely glycosylated spike (S) protein highly exposed on severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) surface mediates host cell entry by binding to the receptor angiotensin-converting enzyme 2 (ACE2). However, the role of glycosylation has not been fully understood. In this study, we investigated the effect of different N-glycosylation of S1 protein on its binding to ACE2. Using real-time surface plasmon resonance assay the negative effects were demonstrated by the considerable increase of binding affinities of de-N-glycosylated S1 proteins produced from three different expression systems including baculovirus-insect, Chinese hamster ovarian and two variants of human embryonic kidney 293 cells. Molecular dynamic simulations of the S1 protein-ACE2 receptor complex revealed the steric hindrance and Coulombic repulsion effects of different types of N-glycans on the S1 protein interaction with ACE2. The results should contribute to future pathological studies of SARS-CoV-2 and therapeutic development of Covid-19, particularly using recombinant S1 proteins as models.
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Affiliation(s)
- Chuncui Huang
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Zeshun Tan
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Keli Zhao
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Wenjun Zou
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Hui Wang
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6 Kexueyuan South Road, Beijing 100080, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Huanyu Gao
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Shiwei Sun
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6 Kexueyuan South Road, Beijing 100080, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Dongbo Bu
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, 6 Kexueyuan South Road, Beijing 100080, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Wengang Chai
- Glycosciences Laboratory, Faculty of Medicine, Imperial College London, London W12 0NN, UK
| | - Yan Li
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
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91
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Abstract
Methods for detecting and dissecting the interactions of virally encoded proteins are essential for probing basic viral biology and providing a foundation for therapeutic advances. The dearth of targeted therapeutics for the treatment of coronavirus disease 2019 (COVID-19), an ongoing global health crisis, underscores the importance of gaining a deeper understanding of the interactions of proteins encoded by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we describe the use of a convenient bacterial cell-based two-hybrid (B2H) system to analyze the SARS-CoV-2 proteome. We identified 16 distinct intraviral protein-protein interactions (PPIs), involving 16 proteins. We found that many of the identified proteins interact with more than one partner. Further, our system facilitates the genetic dissection of these interactions, enabling the identification of selectively disruptive mutations. We also describe a modified B2H system that permits the detection of disulfide bond-dependent PPIs in the normally reducing Escherichia coli cytoplasm, and we used this system to detect the interaction of the SARS-CoV-2 spike protein receptor-binding domain (RBD) with its cognate cell surface receptor ACE2. We then examined how the RBD-ACE2 interaction is perturbed by several RBD amino acid substitutions found in currently circulating SARS-CoV-2 variants. Our findings illustrate the utility of a genetically tractable bacterial system for probing the interactions of viral proteins and investigating the effects of emerging mutations. In principle, the system could also facilitate the identification of potential therapeutics that disrupt specific interactions of virally encoded proteins. More generally, our findings establish the feasibility of using a B2H system to detect and dissect disulfide bond-dependent interactions of eukaryotic proteins.
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92
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Gong Y, Qin S, Dai L, Tian Z. The glycosylation in SARS-CoV-2 and its receptor ACE2. Signal Transduct Target Ther 2021; 6:396. [PMID: 34782609 PMCID: PMC8591162 DOI: 10.1038/s41392-021-00809-8] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/10/2021] [Accepted: 10/24/2021] [Indexed: 02/05/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), a highly infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected more than 235 million individuals and led to more than 4.8 million deaths worldwide as of October 5 2021. Cryo-electron microscopy and topology show that the SARS-CoV-2 genome encodes lots of highly glycosylated proteins, such as spike (S), envelope (E), membrane (M), and ORF3a proteins, which are responsible for host recognition, penetration, binding, recycling and pathogenesis. Here we reviewed the detections, substrates, biological functions of the glycosylation in SARS-CoV-2 proteins as well as the human receptor ACE2, and also summarized the approved and undergoing SARS-CoV-2 therapeutics associated with glycosylation. This review may not only broad the understanding of viral glycobiology, but also provide key clues for the development of new preventive and therapeutic methodologies against SARS-CoV-2 and its variants.
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Affiliation(s)
- Yanqiu Gong
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China
| | - Suideng Qin
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China.
| | - Zhixin Tian
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China.
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93
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Schimmel L, Chew KY, Stocks CJ, Yordanov TE, Essebier P, Kulasinghe A, Monkman J, Dos Santos Miggiolaro AFR, Cooper C, de Noronha L, Schroder K, Lagendijk AK, Labzin LI, Short KR, Gordon EJ. Endothelial cells are not productively infected by SARS-CoV-2. Clin Transl Immunology 2021; 10:e1350. [PMID: 34721846 PMCID: PMC8542944 DOI: 10.1002/cti2.1350] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/24/2021] [Accepted: 10/03/2021] [Indexed: 12/16/2022] Open
Abstract
Objectives Thrombotic and microvascular complications are frequently seen in deceased COVID‐19 patients. However, whether this is caused by direct viral infection of the endothelium or inflammation‐induced endothelial activation remains highly contentious. Methods Here, we use patient autopsy samples, primary human endothelial cells and an in vitro model of the pulmonary epithelial–endothelial cell barrier. Results We show that primary human endothelial cells express very low levels of the SARS‐CoV‐2 receptor ACE2 and the protease TMPRSS2, which blocks their capacity for productive viral infection, and limits their capacity to produce infectious virus. Accordingly, endothelial cells can only be infected when they overexpress ACE2, or are exposed to very high concentrations of SARS‐CoV‐2. We also show that SARS‐CoV‐2 does not infect endothelial cells in 3D vessels under flow conditions. We further demonstrate that in a co‐culture model endothelial cells are not infected with SARS‐CoV‐2. Endothelial cells do however sense and respond to infection in the adjacent epithelial cells, increasing ICAM‐1 expression and releasing pro‐inflammatory cytokines. Conclusions Taken together, these data suggest that in vivo, endothelial cells are unlikely to be infected with SARS‐CoV‐2 and that infection may only occur if the adjacent pulmonary epithelium is denuded (basolateral infection) or a high viral load is present in the blood (apical infection). In such a scenario, whilst SARS‐CoV‐2 infection of the endothelium can occur, it does not contribute to viral amplification. However, endothelial cells may still play a key role in SARS‐CoV‐2 pathogenesis by sensing adjacent infection and mounting a pro‐inflammatory response to SARS‐CoV‐2.
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Affiliation(s)
- Lilian Schimmel
- Institute for Molecular Bioscience, Division of Cell and Developmental Biology The University of Queensland Brisbane QLD Australia
| | - Keng Yih Chew
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane QLD Australia
| | - Claudia J Stocks
- Institute for Molecular Bioscience, Division of Cell and Developmental Biology The University of Queensland Brisbane QLD Australia.,Institute for Molecular Bioscience, IMB Centre for Inflammation and Disease Research The University of Queensland Brisbane QLD Australia
| | - Teodor E Yordanov
- Institute for Molecular Bioscience, Division of Cell and Developmental Biology The University of Queensland Brisbane QLD Australia
| | - Patricia Essebier
- Institute for Molecular Bioscience, Division of Cell and Developmental Biology The University of Queensland Brisbane QLD Australia
| | - Arutha Kulasinghe
- The University of Queensland Diamantina Institute The University of Queensland Brisbane QLD Australia
| | - James Monkman
- School of Biomedical Science, Faculty of Health Queensland University of Technology Brisbane QLD Australia
| | | | - Caroline Cooper
- Pathology Queensland Princess Alexandra Hospital Brisbane QLD Australia.,Faculty of Medicine The University of Queensland Brisbane QLD Australia
| | - Lucia de Noronha
- School of Medicine & Center of Education, Research and Innovation Hospital Marcelino Champagnat - Pontifícia Universidade Católica do Paraná (PUCPR) Curitiba Brazil
| | - Kate Schroder
- Institute for Molecular Bioscience, Division of Cell and Developmental Biology The University of Queensland Brisbane QLD Australia.,Institute for Molecular Bioscience, IMB Centre for Inflammation and Disease Research The University of Queensland Brisbane QLD Australia
| | - Anne Karine Lagendijk
- Institute for Molecular Bioscience, Division of Cell and Developmental Biology The University of Queensland Brisbane QLD Australia
| | - Larisa I Labzin
- Institute for Molecular Bioscience, Division of Cell and Developmental Biology The University of Queensland Brisbane QLD Australia.,Institute for Molecular Bioscience, IMB Centre for Inflammation and Disease Research The University of Queensland Brisbane QLD Australia
| | - Kirsty R Short
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane QLD Australia
| | - Emma J Gordon
- Institute for Molecular Bioscience, Division of Cell and Developmental Biology The University of Queensland Brisbane QLD Australia.,School of Chemistry and Molecular Biosciences The University of Queensland Brisbane QLD Australia
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94
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Rowland R, Brandariz-Nuñez A. Analysis of the Role of N-Linked Glycosylation in Cell Surface Expression, Function, and Binding Properties of SARS-CoV-2 Receptor ACE2. Microbiol Spectr 2021; 9:e0119921. [PMID: 34494876 PMCID: PMC8557876 DOI: 10.1128/spectrum.01199-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/13/2021] [Indexed: 12/28/2022] Open
Abstract
Human angiotensin I-converting enzyme 2 (hACE2) is a type I transmembrane glycoprotein that serves as the major cell entry receptor for SARS-CoV and SARS-CoV-2. The viral spike (S) protein is required for the attachment to ACE2 and subsequent virus-host cell membrane fusion. Previous work has demonstrated the presence of N-linked glycans in ACE2. N-glycosylation is implicated in many biological activities, including protein folding, protein activity, and cell surface expression of biomolecules. However, the contribution of N-glycosylation to ACE2 function is poorly understood. Here, we examined the role of N-glycosylation in the activity and localization of two species with different susceptibility to SARS-CoV-2 infection, porcine ACE2 (pACE2) and hACE2. The elimination of N-glycosylation by tunicamycin (TM) treatment, or mutagenesis, showed that N-glycosylation is critical for the proper cell surface expression of ACE2 but not for its carboxiprotease activity. Furthermore, nonglycosylable ACE2 was localized predominantly in the endoplasmic reticulum (ER) and not at the cell surface. Our data also revealed that binding of SARS-CoV or SARS-CoV-2 S protein to porcine or human ACE2 was not affected by deglycosylation of ACE2 or S proteins, suggesting that N-glycosylation does not play a role in the interaction between SARS coronaviruses and the ACE2 receptor. Impairment of hACE2 N-glycosylation decreased cell-to-cell fusion mediated by SARS-CoV S protein but not that mediated by SARS-CoV-2 S protein. Finally, we found that hACE2 N-glycosylation is required for an efficient viral entry of SARS-CoV/SARS-CoV-2 S pseudotyped viruses, which may be the result of low cell surface expression of the deglycosylated ACE2 receptor. IMPORTANCE Understanding the role of glycosylation in the virus-receptor interaction is important for developing approaches that disrupt infection. In this study, we showed that deglycosylation of both ACE2 and S had a minimal effect on the spike-ACE2 interaction. In addition, we found that the removal of N-glycans of ACE2 impaired its ability to support an efficient transduction of SARS-CoV and SARS-CoV-2 S pseudotyped viruses. Our data suggest that the role of deglycosylation of ACE2 on reducing infection is likely due to a reduced expression of the viral receptor on the cell surface. These findings offer insight into the glycan structure and function of ACE2 and potentially suggest that future antiviral therapies against coronaviruses and other coronavirus-related illnesses involving inhibition of ACE2 recruitment to the cell membrane could be developed.
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Affiliation(s)
- Raymond Rowland
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Alberto Brandariz-Nuñez
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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95
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Baker AN, Richards SJ, Pandey S, Guy CS, Ahmad A, Hasan M, Biggs CI, Georgiou PG, Zwetsloot AJ, Straube A, Dedola S, Field RA, Anderson NR, Walker M, Grammatopoulos D, Gibson MI. Glycan-Based Flow-Through Device for the Detection of SARS-COV-2. ACS Sens 2021; 6:3696-3705. [PMID: 34634204 PMCID: PMC8525701 DOI: 10.1021/acssensors.1c01470] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/23/2021] [Indexed: 12/12/2022]
Abstract
The COVID-19 pandemic, and future pandemics, require diagnostic tools to track disease spread and guide the isolation of (a)symptomatic individuals. Lateral-flow diagnostics (LFDs) are rapid and of lower cost than molecular (genetic) tests, with current LFDs using antibodies as their recognition units. Herein, we develop a prototype flow-through device (related, but distinct to LFDs), utilizing N-acetyl neuraminic acid-functionalized, polymer-coated, gold nanoparticles as the detection/capture unit for SARS-COV-2, by targeting the sialic acid-binding site of the spike protein. The prototype device can give rapid results, with higher viral loads being faster than lower viral loads. The prototype's effectiveness is demonstrated using spike protein, lentiviral models, and a panel of heat-inactivated primary patient nasal swabs. The device was also shown to retain detection capability toward recombinant spike proteins from several variants (mutants) of concern. This study provides the proof of principle that glyco-lateral-flow devices could be developed to be used in the tracking monitoring of infectious agents, to complement, or as alternatives to antibody-based systems.
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Affiliation(s)
| | | | - Sarojini Pandey
- Institute of Precision Diagnostics and Translational
Medicine, University Hospitals Coventry and Warwickshire NHS
Trust, Clifford Bridge Road, Coventry CV2 2DX,
U.K.
| | - Collette S. Guy
- Department of Chemistry, University of
Warwick, Coventry CV4 7AL, U.K.
- School of Life Sciences, University of
Warwick, Coventry CV4 7AL, U.K.
| | - Ashfaq Ahmad
- Department of Chemistry, University of
Warwick, Coventry CV4 7AL, U.K.
- Warwick Medical School, University of
Warwick, Coventry CV4 7AL, U.K.
| | - Muhammad Hasan
- Department of Chemistry, University of
Warwick, Coventry CV4 7AL, U.K.
- Warwick Medical School, University of
Warwick, Coventry CV4 7AL, U.K.
| | - Caroline I. Biggs
- Department of Chemistry, University of
Warwick, Coventry CV4 7AL, U.K.
| | | | | | - Anne Straube
- Warwick Medical School, University of
Warwick, Coventry CV4 7AL, U.K.
| | - Simone Dedola
- Iceni Diagnostics Ltd., Norwich
Research Park, Norwich NR4 7GJ, U.K.
| | - Robert A. Field
- Iceni Diagnostics Ltd., Norwich
Research Park, Norwich NR4 7GJ, U.K.
- Department of Chemistry and Manchester Institute of
Biotechnology, University of Manchester, Manchester M1 7DN,
U.K.
| | - Neil R. Anderson
- Institute of Precision Diagnostics and Translational
Medicine, University Hospitals Coventry and Warwickshire NHS
Trust, Clifford Bridge Road, Coventry CV2 2DX,
U.K.
| | - Marc Walker
- Department of Physics, University of
Warwick, Coventry CV4 7AL, U.K.
| | - Dimitris Grammatopoulos
- Warwick Medical School, University of
Warwick, Coventry CV4 7AL, U.K.
- Institute of Precision Diagnostics and Translational
Medicine, University Hospitals Coventry and Warwickshire NHS
Trust, Clifford Bridge Road, Coventry CV2 2DX,
U.K.
| | - Matthew I. Gibson
- Department of Chemistry, University of
Warwick, Coventry CV4 7AL, U.K.
- Warwick Medical School, University of
Warwick, Coventry CV4 7AL, U.K.
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96
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Chen C, Boorla VS, Banerjee D, Chowdhury R, Cavener VS, Nissly RH, Gontu A, Boyle NR, Vandegrift K, Nair MS, Kuchipudi SV, Maranas CD. Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2. Proc Natl Acad Sci U S A 2021; 118:e2106480118. [PMID: 34588290 PMCID: PMC8594574 DOI: 10.1073/pnas.2106480118] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 01/22/2023] Open
Abstract
The association of the receptor binding domain (RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein with human angiotensin-converting enzyme 2 (hACE2) represents the first required step for cellular entry. SARS-CoV-2 has continued to evolve with the emergence of several novel variants, and amino acid changes in the RBD have been implicated with increased fitness and potential for immune evasion. Reliably predicting the effect of amino acid changes on the ability of the RBD to interact more strongly with the hACE2 can help assess the implications for public health and the potential for spillover and adaptation into other animals. Here, we introduce a two-step framework that first relies on 48 independent 4-ns molecular dynamics (MD) trajectories of RBD-hACE2 variants to collect binding energy terms decomposed into Coulombic, covalent, van der Waals, lipophilic, generalized Born solvation, hydrogen bonding, π-π packing, and self-contact correction terms. The second step implements a neural network to classify and quantitatively predict binding affinity changes using the decomposed energy terms as descriptors. The computational base achieves a validation accuracy of 82.8% for classifying single-amino acid substitution variants of the RBD as worsening or improving binding affinity for hACE2 and a correlation coefficient of 0.73 between predicted and experimentally calculated changes in binding affinities. Both metrics are calculated using a fivefold cross-validation test. Our method thus sets up a framework for screening binding affinity changes caused by unknown single- and multiple-amino acid changes offering a valuable tool to predict host adaptation of SARS-CoV-2 variants toward tighter hACE2 binding.
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Affiliation(s)
- Chen Chen
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802
| | - Veda Sheersh Boorla
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802
| | - Deepro Banerjee
- The Bioinformatics and Genomics Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Ratul Chowdhury
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802
| | - Victoria S Cavener
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Ruth H Nissly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Abhinay Gontu
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Nina R Boyle
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Kurt Vandegrift
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802
| | - Meera Surendran Nair
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Suresh V Kuchipudi
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802;
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802;
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97
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Ngo VA, Jha RK. Identifying key determinants and dynamics of SARS-CoV-2/ACE2 tight interaction. PLoS One 2021; 16:e0257905. [PMID: 34582502 PMCID: PMC8478251 DOI: 10.1371/journal.pone.0257905] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 09/13/2021] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 virus, the causative agent of Covid-19, has fired up a global pandemic. The virus interacts with the human receptor angiotensin-converting enzyme 2 (ACE2) for an invasion via receptor binding domain (RBD) on its spike protein. To provide a deeper understanding of this interaction, we performed microsecond simulations of the RBD-ACE2 complex for SARS-CoV-2 and compared it with the closely related SARS-CoV discovered in 2003. We show residues in the RBD of SARS-CoV-2 that were mutated from SARS-CoV, collectively help make the RBD anchor much stronger to the N-terminal part of ACE2 than the corresponding residues on RBD of SARS-CoV. This would result in a reduced dissociation rate of SARS-CoV-2 from human receptor protein compared to SARS-CoV. The phenomenon was consistently observed in simulations beyond 500 ns and was reproducible across different force fields. Altogether, our study adds more insight into the critical dynamics of the key residues at the virus spike and human receptor binding interface and potentially aids the development of diagnostics and therapeutics to combat the pandemic efficiently.
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Affiliation(s)
- Van A. Ngo
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Ramesh K. Jha
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
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98
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Plavec Z, Pöhner I, Poso A, Butcher SJ. Virus structure and structure-based antivirals. Curr Opin Virol 2021; 51:16-24. [PMID: 34564030 PMCID: PMC8460353 DOI: 10.1016/j.coviro.2021.09.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/13/2021] [Accepted: 09/12/2021] [Indexed: 01/18/2023]
Abstract
Structure-based antiviral developments in the past two years have been dominated by the structure determination and inhibition of SARS-CoV-2 proteins and new lead molecules for picornaviruses. The SARS-CoV-2 spike protein has been targeted successfully with antibodies, nanobodies, and receptor protein mimics effectively blocking receptor binding or fusion. The two most promising non-structural proteins sharing strong structural and functional conservation across virus families are the main protease and the RNA-dependent RNA polymerase, for which design and reuse of broad range inhibitors already approved for use has been an attractive avenue. For picornaviruses, the increasing recognition of the transient expansion of the capsid as a critical transition towards RNA release has been targeted through a newly identified, apparently widely conserved, druggable, interprotomer pocket preventing viral entry. We summarize some of the key papers in these areas and ponder the practical uses and contributions of molecular modeling alongside empirical structure determination.
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Affiliation(s)
- Zlatka Plavec
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland; Helsinki Institute of Life Sciences-Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
| | - Ina Pöhner
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Antti Poso
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland; University Hospital Tübingen, Department of Internal Medicine VII, Tübingen, Germany
| | - Sarah J Butcher
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland; Helsinki Institute of Life Sciences-Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
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99
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Ealey KN, Phillips J, Sung HK. COVID-19 and obesity: fighting two pandemics with intermittent fasting. Trends Endocrinol Metab 2021; 32:706-720. [PMID: 34275726 PMCID: PMC8226104 DOI: 10.1016/j.tem.2021.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/27/2021] [Accepted: 06/17/2021] [Indexed: 01/08/2023]
Abstract
Obesity is strongly and independently associated with an increased risk of severe illness and death from coronavirus disease 2019 (COVID-19). The pathophysiological changes that result from elevated body weight lead to metabolic dysfunction, chronic inflammation, impaired immunological responses, and multisystem disorders, which increase vulnerability to severe illness from COVID-19. While vaccination strategies are under way across the world, the second and third waves of the pandemic, along with the emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains, continue to threaten the stability of medical systems worldwide. Furthermore, evidence from previous pandemics suggests that vaccines are less effective in obese individuals than in their healthy-weight counterparts over the long term. Therefore, a consideration of lifestyle changes that can boost metabolic health and immunity is critical to reduce the risk of complications and severe illness from viral infection. In this review, we discuss the potential mechanisms linking excess body weight with COVID-19 morbidity. We also present evidence that intermittent fasting (IF), a dietary program that has gained popularity in recent years, may be an effective strategy to improve metabolic health and immunity and thus reduce the impact of obesity on COVID-19 morbidity and mortality.
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Affiliation(s)
- Kafi N Ealey
- Translational Medicine Program, The Hospital for Sick Children, Toronto, ON, Canada.
| | - Joy Phillips
- Translational Medicine Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Hoon-Ki Sung
- Translational Medicine Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
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Uyar A, Dickson A. Perturbation of ACE2 Structural Ensembles by SARS-CoV-2 Spike Protein Binding. J Chem Theory Comput 2021; 17:5896-5906. [PMID: 34383488 PMCID: PMC8370119 DOI: 10.1021/acs.jctc.1c00325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The human ACE2 enzyme serves as a critical first recognition point of coronaviruses, including SARS-CoV-2. In particular, the extracellular domain of ACE2 interacts directly with the S1 tailspike protein of the SARS-CoV-2 virion through a broad protein-protein interface. Although this interaction has been characterized by X-ray crystallography, these structures do not reveal significant differences in the ACE2 structure upon S1 protein binding. In this work, using several all-atom molecular dynamics simulations, we show persistent differences in the ACE2 structure upon binding. These differences are determined with the linear discriminant analysis (LDA) machine learning method and validated using independent training and testing datasets, including long trajectories generated by D. E. Shaw Research on the Anton 2 supercomputer. In addition, long trajectories for 78 potent ACE2-binding compounds, also generated by D. E. Shaw Research, were projected onto the LDA classification vector in order to determine whether the ligand-bound ACE2 structures were compatible with S1 protein binding. This allows us to predict which compounds are "apo-like" versus "complex-like" and to pinpoint long-range ligand-induced allosteric changes in the ACE2 structure.
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Affiliation(s)
- Arzu Uyar
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing Michigan 48824, United States
| | - Alex Dickson
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing Michigan 48824, United States.,Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing Michigan 48824, United States
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