1
|
Zhang L, Yu R, Wang L, Zhang Z, Lu Y, Zhou P, Wang Y, Guo H, Pan L, Liu X. Serial cell culture passaging in vitro led to complete attenuation and changes in the characteristic features of a virulent porcine deltacoronavirus strain. J Virol 2024; 98:e0064524. [PMID: 39012141 PMCID: PMC11334472 DOI: 10.1128/jvi.00645-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 06/22/2024] [Indexed: 07/17/2024] Open
Abstract
Porcine deltacoronavirus (PDCoV) is an important enteric coronavirus that has caused enormous economic losses in the pig industry worldwide. However, no commercial vaccine is currently available. Therefore, developing a safe and efficacious live-attenuated vaccine candidate is urgently needed. In this study, the PDCoV strain CH/XJYN/2016 was continuously passaged in LLC-PK cells until passage 240, and the virus growth kinetics in cell culture, pathogenicity in neonatal piglets, transcriptome differences after LLC-PK infection, changes in the functional characteristics of the spike (S) protein in the high- and low-passage strains, genetic variation of the virus genome, resistance to pepsin and acid, and protective effects of this strain when used as a live-attenuated vaccine were examined. The results of animal experiments demonstrated that the virulent PDCoV strain CH/XJYN/2016 was completely attenuated and not pathogenic in piglets following serial cell passage. Genome sequence analysis showed that amino acid mutations in nonstructural proteins were mainly concentrated in Nsp3, structural protein mutations were mainly concentrated in the S protein, and the N, M, and E genes were conserved. Transcriptome comparison revealed that compared with negative control cells, P10-infected LLC-PK cells had the most differentially expressed genes (DEGs), while P0 and P240 had the least number of DEGs. Analysis of trypsin dependence and related structural differences revealed that the P10 S protein interacted more strongly with trypsin and that the P120 S protein interacted more strongly with the APN receptor. Moreover, the infectivity of P240 was not affected by pepsin but was significantly decreased after exposure to low pH. Furthermore, the P240-based live-attenuated vaccine provided complete protection to piglets against the challenge of virulent PDCoV. In conclusion, we showed that a PDCoV strain was completely attenuated through serial passaging in vitro. These results provide insights into the potential molecular mechanisms of PDCoV attenuation and the development of a promising live-attenuated PDCoV vaccine.IMPORTANCEPorcine deltacoronavirus (PDCoV) is one of the most important enteropathogenic pathogens that cause diarrhea in pigs of various ages, especially in suckling piglets, and causes enormous economic losses in the global commercial pork industry. There are currently no effective measures to prevent and control PDCoV. As reported in previous porcine epidemic diarrhea virus (PEDV) and transmissible gastroenteritis virus studies, inactivated vaccines usually elicit less robust protective immune responses than live-attenuated vaccines in native sows. Therefore, identifying potential attenuation mechanisms, gene evolution, pathogenicity differences during PDCoV passaging, and immunogenicity as live-attenuated vaccines is important for elucidating the mechanism of attenuation and developing safe and effective vaccines for virulent PDCoV strains. In this study, we demonstrated that the virulence of the PDCoV strain CH/XJYN/2016 was completely attenuated following serial cell passaging in vitro, and changes in the biological characteristics and protection efficacy of the strain were evaluated. Our results help elucidate the mechanism of PDCoV attenuation and support the development of appropriate designs for the study of live PDCoV vaccines.
Collapse
Affiliation(s)
- Liping Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Department of Disease and Biosafety Control, National Center of Technology Innovation for Pigs, Lanzhou, China
| | - Ruiming Yu
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Department of Disease and Biosafety Control, National Center of Technology Innovation for Pigs, Lanzhou, China
| | - Lianshun Wang
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Department of Disease and Biosafety Control, National Center of Technology Innovation for Pigs, Lanzhou, China
| | - Zhongwang Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Department of Disease and Biosafety Control, National Center of Technology Innovation for Pigs, Lanzhou, China
| | - Yanzhen Lu
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Department of Disease and Biosafety Control, National Center of Technology Innovation for Pigs, Lanzhou, China
| | - Peng Zhou
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Department of Disease and Biosafety Control, National Center of Technology Innovation for Pigs, Lanzhou, China
| | - Yonglu Wang
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Department of Disease and Biosafety Control, National Center of Technology Innovation for Pigs, Lanzhou, China
| | - Huichen Guo
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Department of Disease and Biosafety Control, National Center of Technology Innovation for Pigs, Lanzhou, China
| | - Li Pan
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Department of Disease and Biosafety Control, National Center of Technology Innovation for Pigs, Lanzhou, China
| | - Xinsheng Liu
- State Key Laboratory for Animal Disease Control and Prevention, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Department of Disease and Biosafety Control, National Center of Technology Innovation for Pigs, Lanzhou, China
| |
Collapse
|
2
|
Zhang W, Shi K, Hsueh FC, Mendoza A, Ye G, Huang L, Perlman S, Aihara H, Li F. Structural basis for mouse receptor recognition by bat SARS2-like coronaviruses. Proc Natl Acad Sci U S A 2024; 121:e2322600121. [PMID: 39083418 PMCID: PMC11317568 DOI: 10.1073/pnas.2322600121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 06/11/2024] [Indexed: 08/02/2024] Open
Abstract
The animal origin of SARS-CoV-2 remains elusive, lacking a plausible evolutionary narrative that may account for its emergence. Its spike protein resembles certain segments of BANAL-236 and RaTG13, two bat coronaviruses considered possible progenitors of SARS-CoV-2. Additionally, its spike contains a furin motif, a common feature of rodent coronaviruses. To explore the possible involvement of rodents in the emergence of SARS-CoV-2 spike, we examined the crystal structures of the spike receptor-binding domains (RBDs) of BANAL-236 and RaTG13 each complexed with mouse receptor ACE2. Both RBDs have residues at positions 493 and 498 that align well with two virus-binding hotspots on mouse ACE2. Our biochemical evidence supports that both BANAL-236 and RaTG13 spikes can use mouse ACE2 as their entry receptor. These findings point to a scenario in which these bat coronaviruses may have coinfected rodents, leading to a recombination of their spike genes and a subsequent acquisition of a furin motif in rodents, culminating in the emergence of SARS-CoV-2.
Collapse
Affiliation(s)
- Wei Zhang
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN55455
- Center for Emerging Viruses, University of Minnesota, Minneapolis, MN55455
| | - Ke Shi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN55455
| | - Fu-Chun Hsueh
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN55455
- Center for Emerging Viruses, University of Minnesota, Minneapolis, MN55455
| | - Alise Mendoza
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN55455
- Center for Emerging Viruses, University of Minnesota, Minneapolis, MN55455
| | - Gang Ye
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN55455
- Center for Emerging Viruses, University of Minnesota, Minneapolis, MN55455
| | - Linfen Huang
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN55455
- Center for Emerging Viruses, University of Minnesota, Minneapolis, MN55455
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA52242
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN55455
| | - Fang Li
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN55455
- Center for Emerging Viruses, University of Minnesota, Minneapolis, MN55455
| |
Collapse
|
3
|
Kober DL, Caballero Van Dyke MC, Eitson JL, Boys IN, McDougal MB, Rosenbaum DM, Schoggins JW. Development of a mutant aerosolized ACE2 that neutralizes SARS-CoV-2 in vivo. mBio 2024; 15:e0076824. [PMID: 38771062 PMCID: PMC11237572 DOI: 10.1128/mbio.00768-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 04/17/2024] [Indexed: 05/22/2024] Open
Abstract
The rapid evolution of SARS-CoV-2 variants highlights the need for new therapies to prevent disease spread. SARS-CoV-2, like SARS-CoV-1, uses the human cell surface protein angiotensin-converting enzyme 2 (ACE2) as its native receptor. Here, we design and characterize a mutant ACE2 that enables rapid affinity purification of a dimeric protein by altering the active site to prevent autoproteolytic digestion of a C-terminal His10 epitope tag. In cultured cells, mutant ACE2 competitively inhibits lentiviral vectors pseudotyped with spikes from multiple SARS-CoV-2 variants and infectious SARS-CoV-2. Moreover, the protein can be nebulized and retains virus-binding properties. We developed a system for the delivery of aerosolized ACE2 to K18-hACE2 mice and demonstrated protection by our modified ACE2 when delivered as a prophylactic agent. These results show proof-of-concept for an aerosolized delivery method to evaluate anti-SARS-CoV-2 agents in vivo and suggest a new tool in the ongoing fight against SARS-CoV-2 and other ACE2-dependent viruses. IMPORTANCE The rapid evolution of SARS-CoV-2 variants poses a challenge for immune recognition and antibody therapies. However, the virus is constrained by the requirement that it recognizes a human host receptor protein. A recombinant ACE2 could protect against SARS-CoV-2 infection by functioning as a soluble decoy receptor. We designed a mutant version of ACE2 with impaired catalytic activity to enable the purification of the protein using a single affinity purification step. This protein can be nebulized and retains the ability to bind the relevant domains from SARS-CoV-1 and SARS-CoV-2. Moreover, this protein inhibits viral infection against a panel of coronaviruses in cells. Finally, we developed an aerosolized delivery system for animal studies and show the modified ACE2 offers protection in an animal model of COVID-19. These results show proof-of-concept for an aerosolized delivery method to evaluate anti-SARS-CoV-2 agents in vivo and suggest a new tool in the ongoing fight against SARS-CoV-2.
Collapse
Affiliation(s)
- Daniel L. Kober
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | | | - Jennifer L. Eitson
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Ian N. Boys
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Matthew B. McDougal
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Daniel M. Rosenbaum
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - John W. Schoggins
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| |
Collapse
|
4
|
Hsueh FC, Shi K, Mendoza A, Bu F, Zhang W, Aihara H, Li F. Structural basis for raccoon dog receptor recognition by SARS-CoV-2. PLoS Pathog 2024; 20:e1012204. [PMID: 38709834 PMCID: PMC11098500 DOI: 10.1371/journal.ppat.1012204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/16/2024] [Accepted: 04/17/2024] [Indexed: 05/08/2024] Open
Abstract
Since the COVID-19 outbreak, raccoon dogs have been suggested as a potential intermediary in transmitting SARS-CoV-2 to humans. To understand their role in the COVID-19 pandemic and the species barrier for SARS-CoV-2 transmission to humans, we analyzed how their ACE2 protein interacts with SARS-CoV-2 spike protein. Biochemical data showed that raccoon dog ACE2 is an effective receptor for SARS-CoV-2 spike protein, though not as effective as human ACE2. Structural comparisons highlighted differences in the virus-binding residues of raccoon dog ACE2 compared to human ACE2 (L24Q, Y34H, E38D, T82M, R353K), explaining their varied effectiveness as receptors for SARS-CoV-2. These variations contribute to the species barrier that exists between raccoon dogs and humans regarding SARS-CoV-2 transmission. Identifying these barriers can help assess the susceptibility of other mammals to SARS-CoV-2. Our research underscores the potential of raccoon dogs as SARS-CoV-2 carriers and identifies molecular barriers that affect the virus's ability to jump between species.
Collapse
Affiliation(s)
- Fu-Chun Hsueh
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
- Center for Emerging Viruses, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Ke Shi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Alise Mendoza
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
- Center for Emerging Viruses, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Fan Bu
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
- Center for Emerging Viruses, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Wei Zhang
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
- Center for Emerging Viruses, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Fang Li
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
- Center for Emerging Viruses, University of Minnesota, Minneapolis, Minnesota, United States of America
| |
Collapse
|
5
|
Fan Y, Hou Y, Li Q, Dian Z, Wang B, Xia X. RNA virus diversity in rodents. Arch Microbiol 2023; 206:9. [PMID: 38038743 DOI: 10.1007/s00203-023-03732-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 12/02/2023]
Abstract
Many zoonotic disease emergencies are associated with RNA viruses in rodents that substantially impact public health. With the widespread application of meta-genomics and meta-transcriptomics for virus discovery over the last decade, viral sequences deposited in public databases have expanded rapidly, and the number of novel viruses discovered in rodents has increased. As important reservoirs of zoonotic viruses, rodents have attracted increasing attention for the risk of potential spillover of rodent-borne viruses. However, knowledge of rodent viral diversity and the major factors contributing to the risk of zoonotic epidemic outbreaks remains limited. Therefore, this study analyzes the diversity and composition of rodent RNA viruses using virus records from the Database of Rodent-associated Viruses (DRodVir/ZOVER), which covers the published literatures and records in GenBank database, reviews the main rodent RNA virus-induced human infectious diseases, and discusses potential challenges in this field.
Collapse
Affiliation(s)
- Yayu Fan
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China
| | - Yutong Hou
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China
| | - Qian Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China
| | - Ziqin Dian
- Department of Clinical Laboratory, The First People's Hospital of Yunnan Province, Kunming, Yunnan, 650032, People's Republic of China
| | - Binghui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China.
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China.
| |
Collapse
|
6
|
Eleraky NE, El-Badry M, Omar MM, El-Koussi WM, Mohamed NG, Abdel-Lateef MA, Hassan AS. Curcumin Transferosome-Loaded Thermosensitive Intranasal in situ Gel as Prospective Antiviral Therapy for SARS-Cov-2. Int J Nanomedicine 2023; 18:5831-5869. [PMID: 37869062 PMCID: PMC10590117 DOI: 10.2147/ijn.s423251] [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: 06/18/2023] [Accepted: 09/23/2023] [Indexed: 10/24/2023] Open
Abstract
Purpose Immunomodulatory and broad-spectrum antiviral activities have motivated the evaluation of curcumin for Coronavirus infection 2019 (COVID-19) management. Inadequate bioavailability is the main impediment to the therapeutic effects of oral Cur. This study aimed to develop an optimal curcumin transferosome-loaded thermosensitive in situ gel to improve its delivery to the lungs. Methods Transferosomes were developed by using 33 screening layouts. The phospholipid concentration as well as the concentration and type of surfactant were considered independent variables. The entrapment efficiency (EE%), size, surface charge, and polydispersity index (PDI) were regarded as dependent factors. A cold technique was employed to develop thermosensitive in-situ gels. Optimized transferosomes were loaded onto the selected gels. The produced gel was assessed based on shape attributes, ex vivo permeability enhancement, and the safety of the nasal mucosa. The in vitro cytotoxicity, antiviral cytopathic effect, and plaque assay (CV/CPE/Plaque activity), and in vivo performance were evaluated after intranasal administration in experimental rabbits. Results The optimized preparation displayed a particle size of 664.3 ± 69.3 nm, EE% of 82.8 ± 0.02%, ZP of -11.23 ± 2.5 mV, and PDI of 0.6 ± 0.03. The in vitro curcumin release from the optimized transferosomal gel was markedly improved compared with that of the free drug-loaded gel. An ex vivo permeation study revealed a significant improvement (2.58-fold) in drug permeability across nasal tissues of sheep. Histopathological screening confirmed the safety of these preparations. This formulation showed high antiviral activity against SARS-CoV-2 at reduced concentrations. High relative bioavailability (226.45%) was attained after the formula intranasally administered to rabbits compared to the free drug in-situ gel. The curcumin transferosome gel displayed a relatively high lung accumulation after intranasal administration. Conclusion This study provides a promising formulation for the antiviral treatment of COVID-19 patients, which can be evaluated further in preclinical and clinical studies.
Collapse
Affiliation(s)
- Nermin E Eleraky
- Department of Pharmaceutics, Faculty of Pharmacy, Assiut University, Assiut, Egypt
| | - Mahmoud El-Badry
- Department of Pharmaceutics, Faculty of Pharmacy, Assiut University, Assiut, Egypt
| | - Mahmoud M Omar
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Deraya University, Minia, Egypt
- Department of Pharmaceutics and Clinical Pharmacy, Faculty of Pharmacy, Sohag University, Sohag, Egypt
| | - Wesam M El-Koussi
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Sohag University, Sohag, Egypt
| | - Noha G Mohamed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Sphinx University, Assiut, Egypt
| | - Mohamed A Abdel-Lateef
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut Branch, Assiut, Egypt
| | - Abeer S Hassan
- Department of Pharmaceutics, Faculty of Pharmacy, South Valley University, Qena, Egypt
| |
Collapse
|
7
|
Kober DL, Caballero Van Dyke MC, Eitson JL, Boys IN, McDougal MB, Rosenbaum DM, Schoggins JW. Development of a mutant aerosolized ACE2 that neutralizes SARS-CoV-2 in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.559550. [PMID: 37808801 PMCID: PMC10557691 DOI: 10.1101/2023.09.26.559550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The rapid evolution of SARS-CoV-2 variants highlights the need for new therapies to prevent disease spread. SARS-CoV-2, like SARS-CoV-1, uses the human cell surface protein angiotensin-converting enzyme 2 (ACE2) as its native receptor. Here, we design and characterize a mutant ACE2 that enables rapid affinity purification of a dimeric protein by altering the active site to prevent autoproteolytic digestion of a C-terminal His10 epitope tag. In cultured cells, mutant ACE2 competitively inhibits lentiviral vectors pseudotyped with spike from multiple SARS-CoV-2 variants, and infectious SARS-CoV-2. Moreover, the protein can be nebulized and retains virus-binding properties. We developed a system for delivery of aerosolized ACE2 to K18-hACE2 mice and demonstrate protection by our modified ACE2 when delivered as a prophylactic agent. These results show proof-of-concept for an aerosolized delivery method to evaluate anti-SARS-CoV-2 agents in vivo and suggest a new tool in the ongoing fight against SARS-CoV-2 and other ACE2-dependent viruses.
Collapse
Affiliation(s)
- Daniel L. Kober
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | - Jennifer L. Eitson
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ian N. Boys
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Matthew B. McDougal
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Daniel M. Rosenbaum
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - John W. Schoggins
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| |
Collapse
|
8
|
Shakibay Senobari Z, Masoumian Hosseini M, Teimouri MB, Rezayan AH, Samarghandian S, Hekmat A. Chromone-embedded peptidomimetics and furopyrimidines as highly potent SARS-CoV-2 infection inhibitors: docking and MD simulation study. BMC Res Notes 2023; 16:224. [PMID: 37735703 PMCID: PMC10515067 DOI: 10.1186/s13104-023-06508-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 09/14/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND COVID-19 is a respiratory illness caused by SARS-CoV-2. Pharmaceutical companies aim to control virus spread through effective drugs. This study investigates chromone compound derivatives' ability to inhibit viral entry and prevent replication. METHOD This study investigated the inhibitory effect of chromone-embedded peptidomimetics and furopyrimidines on 7BZ5 from Severe Acute Respiratory Syndrome CoV-2, Homo sapiens, and 6LU7 from Bat SARS-like CoV using molecular docking. The crystal structure of these proteins was obtained from the Protein Data Bank, and the inhibition site was determined using ligand binding interaction options. The 3D structure was protonated and energetically minimised using MOE software. Chromone derivatives were designed in three dimensions, and their energy was minimised using MOE 2019. The molecular drug-likeness was calculated using SwissADME, Lipinski and Benigni-Bossa's rule, and toxicity was calculated using Toxtree v3.1.0 software. Compounds with pharmacological properties were selected for molecular docking, and interactions were assessed using MOE 2019. MD simulations of Mpro-ch-p complexes were performed to evaluate root mean square fluctuations (RMSF) and measure protein stability. RESULT The pharmacokinetic tests revealed that chromone derivatives of the peptidomimetic family have acceptable pharmacokinetic activity in the human body. Some compounds, such as Ch-p1, Ch-p2, Ch-p6, Ch-p7, Ch-p12, and Ch-p13, have pronounced medicinal properties. Molecular docking revealed high affinity for binding to SARS-CoV-2 protease. Ch-p7 had the highest binding energy, likely due to its inhibitory property. A 10 ns molecular dynamics study confirmed the stability of the protein-ligand complex, resulting in minimal fluctuations in the system's backbone. The MM-GBSA analysis revealed free energies of binding of - 19.54 kcal/mol. CONCLUSIONS The study investigated the inhibition of viral replication using chromone derivatives, finding high inhibitory effects in the peptidomimetic family compared to other studies.
Collapse
Affiliation(s)
| | - Mohsen Masoumian Hosseini
- Department of Biochemistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Department of E-Learning in Medical Science, Tehran University of Medical Sciences, Tehran, Iran.
| | | | - Ali Hossein Rezayan
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, 1417466191, Iran
| | - Saeed Samarghandian
- Department of Basic Medical Sciences, Neyshabur University of Medical Sciences, Neyshabur, Iran
| | - Azadeh Hekmat
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| |
Collapse
|
9
|
Zhang W, Shi K, Geng Q, Herbst M, Wang M, Huang L, Bu F, Liu B, Aihara H, Li F. Structural evolution of SARS-CoV-2 omicron in human receptor recognition. J Virol 2023; 97:e0082223. [PMID: 37578233 PMCID: PMC10506476 DOI: 10.1128/jvi.00822-23] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/28/2023] [Indexed: 08/15/2023] Open
Abstract
Understanding the evolutionary strategies of the SARS-CoV-2 omicron variant is crucial for comprehending the COVID-19 pandemic and preventing future coronavirus pandemics. In this study, we determined the crystal structures of the receptor-binding domains (RBDs) from currently circulating omicron subvariants XBB.1 and XBB.1.5 (also the emerging XBB.1.9.1), each complexed with human ACE2. We studied how individual RBD residues evolved structurally in omicron subvariants, specifically how they adapted to human ACE2. Our findings revealed that residues 493 and 496, which exhibited good human ACE2 adaptation in pre-omicron variants, evolved to poor adaptation in early omicron subvariants (but with good adaption to mouse ACE2) and then reverted to good adaptation in recent omicron subvariants. This result is consistent with the hypothesis that non-human animals facilitated the evolution of early omicron subvariants. Additionally, residue 486, which exhibited good human ACE2 adaptation in early omicron subvariants, evolved to poor adaptation in later omicron subvariants and then returned to good adaptation in recent omicron subvariants. This result is consistent with the hypothesis that immune evasion facilitated the evolution of later omicron subvariants. Thus, our study suggests that both non-human animals and immune evasion may have contributed to driving omicron evolution at different stages of the pandemic. IMPORTANCE The sudden emergence and continued evolution of the SARS-CoV-2 omicron variant have left many mysteries unanswered, such as the origin of early omicron subvariants and the factors driving omicron evolution. To address these questions, we studied the crystal structures of human ACE2-bound receptor-binding domains (RBDs) from omicron subvariants XBB.1 and XBB.1.5 (XBB.1.9.1). Our in-depth structural analysis sheds light on how specific RBD mutations adapt to either human or mouse ACE2 and suggests non-human animals and immune evasion may have influenced omicron evolution during different stages of the pandemic. These findings provide valuable insights into the mechanisms underlying omicron evolution, deepen our understanding of the COVID-19 pandemic, and have significant implications for preventing future coronavirus pandemics.
Collapse
Affiliation(s)
- Wei Zhang
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
- Center for Coronavirus Research, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ke Shi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Qibin Geng
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
- Center for Coronavirus Research, University of Minnesota, Minneapolis, Minnesota, USA
| | - Morgan Herbst
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
- Center for Coronavirus Research, University of Minnesota, Minneapolis, Minnesota, USA
| | - Michael Wang
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
- Center for Coronavirus Research, University of Minnesota, Minneapolis, Minnesota, USA
| | - Linfen Huang
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
- Center for Coronavirus Research, University of Minnesota, Minneapolis, Minnesota, USA
| | - Fan Bu
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
- Center for Coronavirus Research, University of Minnesota, Minneapolis, Minnesota, USA
| | - Bin Liu
- Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Fang Li
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
- Center for Coronavirus Research, University of Minnesota, Minneapolis, Minnesota, USA
| |
Collapse
|
10
|
Mulgaonkar N, Wang H, Zhang J, Roundy CM, Tang W, Chaki SP, Pauvolid-Corrêa A, Hamer GL, Fernando S. Montelukast and Telmisartan as Inhibitors of SARS-CoV-2 Omicron Variant. Pharmaceutics 2023; 15:1891. [PMID: 37514075 PMCID: PMC10385313 DOI: 10.3390/pharmaceutics15071891] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023] Open
Abstract
Earlier studies with montelukast (M) and telmisartan (T) have revealed their potential antiviral properties against SARS-CoV-2 wild-type (WT) but have not assessed their efficacy against emerging Variants of Concern (VOCs) such as Omicron. Our research fills this gap by investigating these drugs' impact on VOCs, a topic that current scientific literature has largely overlooked. We employed computational methodologies, including molecular mechanics and machine learning tools, to identify drugs that could potentially disrupt the SARS-CoV-2 spike RBD-ACE2 protein interaction. This led to the identification of two FDA-approved small molecule drugs, M and T, conventionally used for treating asthma and hypertension, respectively. Our study presents an additional potential use for these drugs as antivirals. Our results show that both M and T can inhibit not only the WT SARS-CoV-2 but also, in the case of M, the Omicron variant, without reaching cytotoxic concentrations. This novel finding fills an existing gap in the literature and introduces the possibility of repurposing these drugs for SARS-CoV-2 VOCs, an essential step in responding to the evolving global pandemic.
Collapse
Affiliation(s)
- Nirmitee Mulgaonkar
- Biological and Agricultural Engineering Department, Texas A&M University, College Station, TX 77843, USA
| | - Haoqi Wang
- Biological and Agricultural Engineering Department, Texas A&M University, College Station, TX 77843, USA
| | - Junrui Zhang
- Biological and Agricultural Engineering Department, Texas A&M University, College Station, TX 77843, USA
| | | | - Wendy Tang
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Sankar Prasad Chaki
- Texas A&M Global Health Research Complex, Division of Research, Texas A&M University, College Station, TX 77843, USA
| | - Alex Pauvolid-Corrêa
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Gabriel L Hamer
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Sandun Fernando
- Biological and Agricultural Engineering Department, Texas A&M University, College Station, TX 77843, USA
| |
Collapse
|
11
|
Ma C, Liu C, Xiong Q, Gu M, Shi L, Wang C, Si J, Tong F, Liu P, Huang M, Yan H. Broad host tropism of ACE2-using MERS-related coronaviruses and determinants restricting viral recognition. Cell Discov 2023; 9:57. [PMID: 37321999 DOI: 10.1038/s41421-023-00566-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 05/14/2023] [Indexed: 06/17/2023] Open
Abstract
Recently, two Middle East respiratory syndrome coronavirus (MERS-CoV) closely related to bat merbecoviruses, NeoCoV and PDF-2180, were discovered to use angiotensin-converting enzyme 2 (ACE2) for entry. The two viruses cannot use human ACE2 efficiently, and their host range and cross-species transmissibility across a wide range of mammalian species remain unclear. Herein, we characterized the species-specific receptor preference of these viruses by testing ACE2 orthologues from 49 bats and 53 non-bat mammals through receptor-binding domain (RBD)-binding and pseudovirus entry assays. Results based on bat ACE2 orthologues revealed that the two viruses were unable to use most, but not all, ACE2 from Yinpterochiropteran bats (Yin-bats), which is distinct from NL63 and SARS-CoV-2. Besides, both viruses exhibited broad receptor recognition spectra across non-bat mammals. Genetic and structural analyses of bat ACE2 orthologues highlighted four crucial host range determinants, all confirmed by subsequent functional assays in human and bat cells. Notably, residue 305, participating in a critical viral receptor interaction, plays a crucial role in host tropism determination, particularly in non-bat mammals. Furthermore, NeoCoV and PDF-2180 mutants with enhanced human ACE2 recognition expanded the potential host range, especially by enhancing their interaction with an evolutionarily conserved hydrophobic pocket. Our results elucidate the molecular basis for the species-specific ACE2 usage of MERS-related viruses and shed light on their zoonotic risks.
Collapse
Affiliation(s)
- Chengbao Ma
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Chen Liu
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Qing Xiong
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Mengxue Gu
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Lulu Shi
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Chunli Wang
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Junyu Si
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Fei Tong
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Peng Liu
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Meiling Huang
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Huan Yan
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China.
| |
Collapse
|
12
|
Pelucelli A, Peana M, Orzeł B, Piasta K, Gumienna-Kontecka E, Medici S, Zoroddu MA. Zn 2+ and Cu 2+ Interaction with the Recognition Interface of ACE2 for SARS-CoV-2 Spike Protein. Int J Mol Sci 2023; 24:ijms24119202. [PMID: 37298154 DOI: 10.3390/ijms24119202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
The spike protein (S) of SARS-CoV-2 is able to bind to the human angiotensin-converting enzyme 2 (ACE2) receptor with a much higher affinity compared to other coronaviruses. The binding interface between the ACE2 receptor and the spike protein plays a critical role in the entry mechanism of the SARS-CoV-2 virus. There are specific amino acids involved in the interaction between the S protein and the ACE2 receptor. This specificity is critical for the virus to establish a systemic infection and cause COVID-19 disease. In the ACE2 receptor, the largest number of amino acids playing a crucial role in the mechanism of interaction and recognition with the S protein is located in the C-terminal part, which represents the main binding region between ACE2 and S. This fragment is abundant in coordination residues such as aspartates, glutamates, and histidine that could be targeted by metal ions. Zn2+ ions bind to the ACE2 receptor in its catalytic site and modulate its activity, but it could also contribute to the structural stability of the entire protein. The ability of the human ACE2 receptor to coordinate metal ions, such as Zn2+, in the same region where it binds to the S protein could have a crucial impact on the mechanism of recognition and interaction of ACE2-S, with consequences on their binding affinity that deserve to be investigated. To test this possibility, this study aims to characterize the coordination ability of Zn2+, and also Cu2+ for comparison, with selected peptide models of the ACE2 binding interface using spectroscopic and potentiometric techniques.
Collapse
Affiliation(s)
- Alessio Pelucelli
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, 07100 Sassari, Italy
| | - Massimiliano Peana
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, 07100 Sassari, Italy
| | - Bartosz Orzeł
- Faculty of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Karolina Piasta
- Faculty of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland
| | | | - Serenella Medici
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, 07100 Sassari, Italy
| | - Maria Antonietta Zoroddu
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, 07100 Sassari, Italy
| |
Collapse
|
13
|
Sharfin Rahman M, De Alwis Watuthanthrige N, Chandrarathne BM, Page RC, Konkolewicz D. Polymer modification of SARS-CoV-2 spike protein impacts its ability to bind key receptor. Eur Polym J 2023; 184:111767. [PMID: 36531158 PMCID: PMC9749382 DOI: 10.1016/j.eurpolymj.2022.111767] [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: 10/20/2022] [Revised: 12/09/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022]
Abstract
The global spread of SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) has caused the loss of many human lives and severe economic losses. SARS-CoV-2 mediates its infection in humans via the spike glycoprotein. The receptor binding domain of the SARS-CoV-2 spike protein binds to its cognate receptor, angiotensin converting enzyme-2 (ACE2) to initiate viral entry. In this study, we examine how polymer modification of the spike protein receptor binding domain impacts binding to ACE2. The horseradish peroxidase conjugated receptor binding domain was modified with a range of polymers including hydrophilic N,N-dimethylacrylamide, hydrophobic N-isopropylacrylamide, cationic 3-(N,N-dimethylamino)propylacrylamide, and anionic 2-acrylamido-2-methylpropane sulfonic acid polymers. The effect of polymer chain length was observed using N,N-dimethylacrylamide polymers with degrees of polymerization of 5, 10 and 25. Polymer conjugation of the receptor binding domain significantly reduced the interaction with ACE2 protein, as determined by an enzyme-linked immunosorbent assay. Stability analysis showed that these conjugates remained highly stable even after seven days incubation at physiological temperature. Hence, this study provides a detailed view of the effect specific type of modification using a library of polymers with different functionalities in interrupting RBD-ACE2 interaction.
Collapse
Affiliation(s)
| | | | | | - Richard C. Page
- Corresponding authors at: Department of Chemistry and Biochemistry, 651 East High Street, Miami University, Oxford, OH 45056, USA
| | - Dominik Konkolewicz
- Corresponding authors at: Department of Chemistry and Biochemistry, 651 East High Street, Miami University, Oxford, OH 45056, USA
| |
Collapse
|
14
|
Kumar A, Asghar A, Singh HN, Faiq MA, Kumar S, Narayan RK, Kumar G, Dwivedi P, Sahni C, Jha RK, Kulandhasamy M, Prasoon P, Sesham K, Kant K, Pandey SN. SARS-CoV-2 Omicron Variant Genomic Sequences and Their Epidemiological Correlates Regarding the End of the Pandemic: In Silico Analysis. JMIR BIOINFORMATICS AND BIOTECHNOLOGY 2023; 4:e42700. [PMID: 36688013 PMCID: PMC9843602 DOI: 10.2196/42700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/29/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Background Emergence of the new SARS-CoV-2 variant B.1.1.529 worried health policy makers worldwide due to a large number of mutations in its genomic sequence, especially in the spike protein region. The World Health Organization (WHO) designated this variant as a global variant of concern (VOC), which was named "Omicron." Following Omicron's emergence, a surge of new COVID-19 cases was reported globally, primarily in South Africa. Objective The aim of this study was to understand whether Omicron had an epidemiological advantage over existing variants. Methods We performed an in silico analysis of the complete genomic sequences of Omicron available on the Global Initiative on Sharing Avian Influenza Data (GISAID) database to analyze the functional impact of the mutations present in this variant on virus-host interactions in terms of viral transmissibility, virulence/lethality, and immune escape. In addition, we performed a correlation analysis of the relative proportion of the genomic sequences of specific SARS-CoV-2 variants (in the period from October 1 to November 29, 2021) with matched epidemiological data (new COVID-19 cases and deaths) from South Africa. Results Compared with the current list of global VOCs/variants of interest (VOIs), as per the WHO, Omicron bears more sequence variation, specifically in the spike protein and host receptor-binding motif (RBM). Omicron showed the closest nucleotide and protein sequence homology with the Alpha variant for the complete sequence and the RBM. The mutations were found to be primarily condensed in the spike region (n=28-48) of the virus. Further mutational analysis showed enrichment for the mutations decreasing binding affinity to angiotensin-converting enzyme 2 receptor and receptor-binding domain protein expression, and for increasing the propensity of immune escape. An inverse correlation of Omicron with the Delta variant was noted (r=-0.99, P<.001; 95% CI -0.99 to -0.97) in the sequences reported from South Africa postemergence of the new variant, subsequently showing a decrease. There was a steep rise in new COVID-19 cases in parallel with the increase in the proportion of Omicron isolates since the report of the first case (74%-100%). By contrast, the incidence of new deaths did not increase (r=-0.04, P>.05; 95% CI -0.52 to 0.58). Conclusions In silico analysis of viral genomic sequences suggests that the Omicron variant has more remarkable immune-escape ability than existing VOCs/VOIs, including Delta, but reduced virulence/lethality than other reported variants. The higher power for immune escape for Omicron was a likely reason for the resurgence in COVID-19 cases and its rapid rise as the globally dominant strain. Being more infectious but less lethal than the existing variants, Omicron could have plausibly led to widespread unnoticed new, repeated, and vaccine breakthrough infections, raising the population-level immunity barrier against the emergence of new lethal variants. The Omicron variant could have thus paved the way for the end of the pandemic.
Collapse
Affiliation(s)
- Ashutosh Kumar
- Department of Anatomy All India Institute of Medical Sciences-Patna Patna India
- Etiologically Elusive Disorders Research Network New Delhi India
| | - Adil Asghar
- Department of Anatomy All India Institute of Medical Sciences-Patna Patna India
- Etiologically Elusive Disorders Research Network New Delhi India
| | - Himanshu N Singh
- Etiologically Elusive Disorders Research Network New Delhi India
- Department of Systems Biology Columbia University Irving Medical Center New York, NY United States
| | - Muneeb A Faiq
- Etiologically Elusive Disorders Research Network New Delhi India
- New York University Langone Health Center Robert I Grossman School of Medicine New York University New York, NY United States
| | - Sujeet Kumar
- Etiologically Elusive Disorders Research Network New Delhi India
- Center for Proteomics and Drug Discovery Amity Institute of Biotechnology Amity University, Maharashtra Mumbai India
| | - Ravi K Narayan
- Etiologically Elusive Disorders Research Network New Delhi India
- Dr BC Roy Multi-speciality Medical Research Centre Indian Institute of Technology Kharagpur India
| | - Gopichand Kumar
- Department of Anatomy All India Institute of Medical Sciences-Patna Patna India
- Etiologically Elusive Disorders Research Network New Delhi India
| | - Prakhar Dwivedi
- Department of Anatomy All India Institute of Medical Sciences-Patna Patna India
- Etiologically Elusive Disorders Research Network New Delhi India
| | - Chetan Sahni
- Etiologically Elusive Disorders Research Network New Delhi India
- Department of Anatomy Institute of Medical Sciences Banaras Hindu University Varanasi India
| | - Rakesh K Jha
- Department of Anatomy All India Institute of Medical Sciences-Patna Patna India
- Etiologically Elusive Disorders Research Network New Delhi India
| | - Maheswari Kulandhasamy
- Etiologically Elusive Disorders Research Network New Delhi India
- Department of Biochemistry Maulana Azad Medical College New Delhi India
| | - Pranav Prasoon
- Etiologically Elusive Disorders Research Network New Delhi India
- School of Medicine University of Pittsburgh Pittsburgh, PA United States
| | - Kishore Sesham
- Etiologically Elusive Disorders Research Network New Delhi India
- Department of Anatomy All India Institute of Medical Sciences-Mangalagiri Mangalagiri India
| | - Kamla Kant
- Etiologically Elusive Disorders Research Network New Delhi India
- Department of Microbiology All India Institute of Medical Sciences-Bathinda Bathinda India
| | - Sada N Pandey
- Etiologically Elusive Disorders Research Network New Delhi India
- Department of Zoology Banaras Hindu University Varanasi India
| |
Collapse
|
15
|
Piplani S, Winkler D, Honda-Okubo Y, Khanna V, Petrovsky N. In Silico Structure-Based Vaccine Design. Methods Mol Biol 2023; 2673:371-399. [PMID: 37258928 DOI: 10.1007/978-1-0716-3239-0_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Structure-based vaccine design (SBVD) is an important technique in computational vaccine design that uses structural information on a targeted protein to design novel vaccine candidates. This increasing ability to rapidly model structural information on proteins and antibodies has provided the scientific community with many new vaccine targets and novel opportunities for future vaccine discovery. This chapter provides a comprehensive overview of the status of in silico SBVD and discusses the current challenges and limitations. Key strategies in the field of SBVD are exemplified by a case study on design of COVID-19 vaccines targeting SARS-CoV-2 spike protein.
Collapse
Affiliation(s)
| | - David Winkler
- School of Pharmacy, University of Nottingham, Nottingham, UK
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
| | | | | | | |
Collapse
|
16
|
Juthi RT, Sazed SA, Sarmin M, Haque R, Alam MS. COVID-19 and diarrhea: putative mechanisms and management. Int J Infect Dis 2023; 126:125-131. [PMID: 36403817 PMCID: PMC9672967 DOI: 10.1016/j.ijid.2022.11.018] [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: 09/16/2022] [Revised: 11/08/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19), has recently posed a threat to global health by spreading at a high rate and taking millions of lives worldwide. Along with the respiratory symptoms, there are gastrointestinal manifestations and one of the most common gastrointestinal symptoms is diarrhea which is seen in a significant percentage of COVID-19 patients. LITERATURE REVIEW Several studies have shown the plausible correlation between overexpressed angiotensin converting enzyme 2 (ACE2) in enterocytes and SARS-CoV-2, as ACE2 is the only known receptor for the virus entry. Along with the dysregulated ACE2, there are other contributing factors such as gut microbiome dysbiosis, adverse effects of antiviral and antibiotics for treating infections and inflammatory response to SARS-CoV-2 which bring about increased permeability of gut cells and subsequent occurrence of diarrhea. Few studies found that the SARS-CoV-2 is capable of damaging liver cells too. No single effective treatment option is available. LIMITATIONS Confirmed pathophysiology is still unavailable. Studies regarding global population are also insufficient. CONCLUSION In this review, based on the previous works and literature, we summarized the putative molecular pathophysiology of COVID-19 associated diarrhea, concomitant complications and the standard practices of management of diarrhea and hepatic manifestations in international setups.
Collapse
Affiliation(s)
- Rifat Tasnim Juthi
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Saiful Arefeen Sazed
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Monira Sarmin
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Rashidul Haque
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mohammad Shafiul Alam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh,Corresponding author. Mohammad Shafiul Alam, Scientist, Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka-1212, Bangladesh. Tel: +8801711-469232
| |
Collapse
|
17
|
Wang Y, Ma J, Jiang Y. Transcription factor Nrf2 as a potential therapeutic target for COVID-19. Cell Stress Chaperones 2023; 28:11-20. [PMID: 36417098 PMCID: PMC9685020 DOI: 10.1007/s12192-022-01296-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 08/08/2022] [Accepted: 09/09/2022] [Indexed: 11/24/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) is caused by a novel severe acute respiratory syndrome (SARS)-like coronavirus (SARS-CoV-2). Critically ill patients with SARS-COV-2 infection frequently exhibit signs of high oxidative stress and systemic inflammation, which accounts for most of the mortality. Antiviral strategies to inhibit the pathogenic consequences of COVID-19 are urgently required. The nuclear factor erythroid 2-related transcription factor (Nrf2) is a transcription factor that is involved in antioxidant and anti-inflammatory defense in several tissues and cells. This review tries to present an overview of the role of Nrf2 in the treatment of COVID-19.
Collapse
Affiliation(s)
- Yifan Wang
- Department of Infectious Diseases, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Jing Ma
- Department of Infectious Diseases, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Yongfang Jiang
- Department of Infectious Diseases, The Second Xiangya Hospital, Central South University, Changsha, 410011, China.
| |
Collapse
|
18
|
Carvalho PPD, Alves NA. Featuring ACE2 binding SARS-CoV and SARS-CoV-2 through a conserved evolutionary pattern of amino acid residues. J Biomol Struct Dyn 2022; 40:11719-11728. [PMID: 34486937 PMCID: PMC8425439 DOI: 10.1080/07391102.2021.1965028] [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: 12/24/2022]
Abstract
Spike (S) glycoproteins mediate the coronavirus entry into the host cell. The S1 subunit of S-proteins contains the receptor-binding domain (RBD) that is able to recognize different host receptors, highlighting its remarkable capacity to adapt to their hosts along the viral evolution. While RBD in spike proteins is determinant for the virus-receptor interaction, the active residues lie at the receptor-binding motif (RBM), a region located in RBD that plays a fundamental role binding the outer surface of their receptors. Here, we address the hypothesis that SARS-CoV and SARS-CoV-2 strains able to use angiotensin-converting enzyme 2 (ACE2) proteins have adapted their RBM along the viral evolution to explore specific conformational topology driven by the residues YGF to infect host cells. We also speculate that this YGF-based mechanism can act as a protein signature located at the RBM to distinguish coronaviruses able to use ACE2 as a cell entry receptor.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Patrícia P. D. Carvalho
- Departamento de Física, FFCLRP, Universidade de São Paulo, Ribeirão Preto, SP, Brazil,CONTACT Patrícia P. D. Carvalho ;
| | - Nelson A. Alves
- Departamento de Física, FFCLRP, Universidade de São Paulo, Ribeirão Preto, SP, Brazil,Nelson Alves
| |
Collapse
|
19
|
Acosta‐Gutiérrez S, Buckley J, Battaglia G. The Role of Host Cell Glycans on Virus Infectivity: The SARS-CoV-2 Case. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 10:e2201853. [PMID: 36417571 PMCID: PMC9811451 DOI: 10.1002/advs.202201853] [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: 03/30/2022] [Revised: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Glycans are ubiquitously expressed sugars, coating the cell and protein surfaces. They are found on many proteins as either short and branched chains or long chains sticking out from special membrane proteins, known as proteoglycans. This sugar cushion, the glycocalyx, modulates specific interactions and protects the cell. Here it is shown that both the expression of proteoglycans and the glycans expressed on the surface of both the host and virus proteins have a critical role in modulating viral attachment to the cell. A mathematical model using SARS-Cov-2 as an archetypical virus to study the glycan role during infection is proposed. It is shown that this occurs via a tug-of-war of forces. On one side, the multivalent molecular recognition that viral proteins have toward specific host glycans and receptors. On the other side, the glycan steric repulsion that a virus must overcome to approach such specific receptors. By balancing both interactions, viral tropism can be predicted. In other words, the authors can map out the cells susceptible to virus infection in terms of receptors and proteoglycans compositions.
Collapse
Affiliation(s)
- Silvia Acosta‐Gutiérrez
- Institute for the Physics of Living SystemsUniversity College LondonLondonCentral LondonUK
- Institute of Structural and Molecular BiologyUniversity College LondonLondonCentral LondonUK
- Department of ChemistryUniversity College London20 Gordon StLondonCentral LondonWC1H 0AJUK
| | - Joseph Buckley
- Institute for the Physics of Living SystemsUniversity College LondonLondonCentral LondonUK
- Institute of Structural and Molecular BiologyUniversity College LondonLondonCentral LondonUK
- Department of ChemistryUniversity College London20 Gordon StLondonCentral LondonWC1H 0AJUK
| | - Giuseppe Battaglia
- Institute for the Physics of Living SystemsUniversity College LondonLondonCentral LondonUK
- Institute of Structural and Molecular BiologyUniversity College LondonLondonCentral LondonUK
- Department of ChemistryUniversity College London20 Gordon StLondonCentral LondonWC1H 0AJUK
- Institute for Bioengineering of Catalunya (IBEC)The Barcelona Institute of Science and TechnologyBarcelonaBarcelona08028Spain
- Catalan Institution for Research and Advances Studies (ICREA)BarcelonaSpain
| |
Collapse
|
20
|
Kodchakorn K, Kongtawelert P. Molecular dynamics study on the strengthening behavior of Delta and Omicron SARS-CoV-2 spike RBD improved receptor-binding affinity. PLoS One 2022; 17:e0277745. [PMID: 36395151 PMCID: PMC9671323 DOI: 10.1371/journal.pone.0277745] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 11/02/2022] [Indexed: 11/19/2022] Open
Abstract
The COVID-19 pandemic caused by a virus that can be transmitted from human to human via air droplets has changed the quality of life and economic systems all over the world. The viral DNA has mutated naturally over time leading to the diversity of coronavirus victims which has posed a serious threat to human security on a massive scale. The current variants have developed in a dominant way and are considered "Variants of Concern" by the World Health Organization (WHO). In this work, Kappa (B.1.617.1), Delta (B.1.617.2), and Omicron (B.1.1.529) variants were obtained to evaluate whether naturally occurring mutations have strengthened viral infectivity. We apply reliable in silico structural dynamics and energetic frameworks of the mutated S-RBD protein for ACE2-binding to analyze and compare the structural information related to the wild-type. In particular, the hotspot residues at Q493, Q498, and N501 on the S-RBD protein were determined as contributing factors to the employment stability of the relevant binding interface. The L452R mutation induces an increment of the hydrogen bonds formed by changing the Q493 environment for ACE2 binding. Moreover, the Q493K exchange in Omicron enables the formation of two additional salt bridges, leading to a strong binding affinity by increased electrostatic interaction energy. These results could be used in proposing concrete informative data for a structure-based design engaged in finding better therapeutics against novel variants.
Collapse
Affiliation(s)
- Kanchanok Kodchakorn
- Thailand Excellence Center for Tissue Engineering and Stem Cells, Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Prachya Kongtawelert
- Thailand Excellence Center for Tissue Engineering and Stem Cells, Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- * E-mail:
| |
Collapse
|
21
|
Zhang W, Shi K, Geng Q, Ye G, Aihara H, Li F. Structural basis for mouse receptor recognition by SARS-CoV-2 omicron variant. Proc Natl Acad Sci U S A 2022; 119:e2206509119. [PMID: 36256797 PMCID: PMC9636943 DOI: 10.1073/pnas.2206509119] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 09/22/2022] [Indexed: 11/25/2022] Open
Abstract
The sudden emergence and rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) omicron variant has raised questions about its animal reservoir. Here, we investigated receptor recognition of the omicron's receptor-binding domain (RBD), focusing on four of its mutations (Q493R, Q498R, N501Y, and Y505H) surrounding two mutational hotspots. These mutations have variable effects on the RBD's affinity for human angiotensin-converting enzyme 2 (ACE2), but they all enhance the RBD's affinity for mouse ACE2. We further determined the crystal structure of omicron RBD complexed with mouse ACE2. The structure showed that all four mutations are viral adaptations to mouse ACE2: three of them (Q493R, Q498R, and Y505H) are uniquely adapted to mouse ACE2, whereas the other one (N501Y) is adapted to both human ACE2 and mouse ACE2. These data reveal that the omicron RBD was well adapted to mouse ACE2 before omicron started to infect humans, providing insight into the potential evolutionary origin of the omicron variant.
Collapse
Affiliation(s)
- Wei Zhang
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN 55455
- Center for Coronavirus Research, University of Minnesota, Minneapolis, MN 55455
| | - Ke Shi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455
| | - Qibin Geng
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN 55455
- Center for Coronavirus Research, University of Minnesota, Minneapolis, MN 55455
| | - Gang Ye
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN 55455
- Center for Coronavirus Research, University of Minnesota, Minneapolis, MN 55455
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455
| | - Fang Li
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN 55455
- Center for Coronavirus Research, University of Minnesota, Minneapolis, MN 55455
| |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
Goyal R, Gautam RK, Chopra H, Dubey AK, Singla RK, Rayan RA, Kamal MA. Comparative highlights on MERS-CoV, SARS-CoV-1, SARS-CoV-2, and NEO-CoV. EXCLI JOURNAL 2022; 21:1245-1272. [PMID: 36483910 PMCID: PMC9727256 DOI: 10.17179/excli2022-5355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 09/23/2022] [Indexed: 01/25/2023]
Abstract
The severe acute respiratory syndrome (SARS-CoV, now SARS-CoV-1), middle east respiratory syndrome (MERS-CoV), Neo-CoV, and 2019 novel coronavirus (SARS-CoV-2/COVID-19) are the most notable coronaviruses, infecting the number of people worldwide by targeting the respiratory system. All these viruses are of zoonotic origin, predominantly from bats which are one of the natural reservoir hosts for coronaviruses. Thus, the major goal of our review article is to compare and contrast the characteristics and attributes of these coronaviruses. The SARS-CoV-1, MERS-CoV, and COVID-19 have many viral similarities due to their classification, they are not genetically related. COVID-19 shares approximately 79 % of its genome with SARS-CoV-1 and about 50 % with MERS-CoV. The shared receptor protein, ACE2 exhibit the most striking genetic similarities between SARS-CoV-1 and SARS-CoV-2. SARS-CoV primarily replicates in the epithelial cells of the respiratory system, but it may also affect macrophages, monocytes, activated T cells, and dendritic cells. MERS-CoV not only infects and replicates inside the epithelial and immune cells, but it may lyse them too, which is one of the common reasons for MERS's higher mortality rate. The details of infections caused by SARS-CoV-2 and lytic replication mechanisms in host cells are currently mysterious. In this review article, we will discuss the comparative highlights of SARS-CoV-1, MERS-CoV, SARS-CoV-2, and Neo-CoV, concerning their structural features, morphological characteristics, sources of virus origin and their evolutionary transitions, infection mechanism, computational study approaches, pathogenesis and their severity towards several diseases, possible therapeutic approaches, and preventive measures.
Collapse
Affiliation(s)
- Rajat Goyal
- MM College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, Haryana, India,MM School of Pharmacy, Maharishi Markandeshwar University, Sadopur-Ambala, India
| | - Rupesh K. Gautam
- Department of Pharmacology, Indore Institute of Pharmacy, Rau, Indore, India-453331,*To whom correspondence should be addressed: Rupesh K. Gautam, Department of Pharmacology, Indore Institute of Pharmacy, IIST Campus, Opposite IIM Indore, Rau-Pithampur Road, Indore – 453331 (M.P.), India; Tel.: +91 9413654324, E-mail:
| | - Hitesh Chopra
- Chitkara College of Pharmacy, Chitkara University, Punjab, India-140401
| | | | - Rajeev K. Singla
- Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China,School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab-144411, India
| | - Rehab A. Rayan
- Department of Epidemiology, High Institute of Public Health, Alexandria University, 5422031, Egypt
| | - Mohammad Amjad Kamal
- Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China,King Fahd Medical Research Center, King Abdulaziz University, Saudi Arabia,Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Bangladesh,Enzymoics, 7 Peterlee Place, Hebersham NSW 2770; Novel Global Community Educational Foundation, Australia
| |
Collapse
|
24
|
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is transmitted between humans and minks, and some mutations in the spike (S) protein, especially in the receptor-binding domain (RBD), have been identified in mink-derived viruses. Here, we examined binding of the mink angiotensin-converting enzyme 2 (ACE2) receptor to mink-derived and important human-originating variants, and we demonstrated that most of the RBD variants increased the binding affinities to mink ACE2 (mkACE2). Cryo-electron microscopy structures of the mkACE2-RBD Y453F (with a Y-to-F change at position 453) and mkACE2-RBD F486L complexes helped identify the key residues that facilitate changes in mkACE2 binding affinity. Additionally, the data indicated that the Y453F and F486L mutations reduced the binding affinities to some human monoclonal antibodies, and human vaccinated sera efficiently prevented infection of human cells by pseudoviruses expressing Y453F, F486L, or N501T RBD. Our findings provide an important molecular mechanism for the rapid adaptation of SARS-CoV-2 in minks and highlight the potential influence of the main mink-originating variants for humans. IMPORTANCE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a broad range of hosts. Mink-derived SARS-CoV-2 can transmit back to humans. There is an urgent need to understand the binding mechanism of mink-derived SARS-CoV-2 variants to mink receptor. In this study, we identified all mutations in the receptor-binding domain (RBD) of spike (S) protein from mink-derived SARS-CoV-2, and we demonstrated the enhanced binding affinity of mink angiotensin-converting enzyme 2 (ACE2) to most of the mink-derived RBD variants as well as important human-originating RBD variants. Cryo-electron microscopy structures revealed that the Y453F and F486L mutations enhanced the binding forces in the interaction interface. In addition, Y453F and F486L mutations reduced the binding affinities to some human monoclonal antibodies, and the SARS-CoV-2 pseudoviruses with Y453F, F486L, or N501T mutations were neutralized by human vaccinated sera. Therefore, our results provide valuable information for understanding the cross-species transmission mechanism of SARS-CoV-2.
Collapse
|
25
|
Beeraka NM, Sukocheva OA, Lukina E, Liu J, Fan R. Development of antibody resistance in emerging mutant strains of SARS CoV-2: Impediment for COVID-19 vaccines. Rev Med Virol 2022; 32:e2346. [PMID: 35416390 PMCID: PMC9111059 DOI: 10.1002/rmv.2346] [Citation(s) in RCA: 10] [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: 08/27/2021] [Revised: 01/28/2022] [Accepted: 03/06/2022] [Indexed: 02/05/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a highly infectious agent associated with unprecedented morbidity and mortality. A failure to stop growth of COVID-19-linked morbidity rates is caused by SARS-CoV-2 mutations and the emergence of new highly virulent SARS-CoV-2 strains. Several acquired SARS-CoV-2 mutations reflect viral adaptations to host immune defence. Mutations in the virus Spike-protein were associated with the lowered effectiveness of current preventive therapies, including vaccines. Recent in vitro studies detected diminished neutralisation capacity of vaccine-induced antibodies, which are targeted to bind Spike receptor-binding and N-terminal domains in the emerging strains. Lower than expected inhibitory activity of antibodies was reported against viruses with E484K Spike mutation, including B.1.1.7 (UK), P.1 (Brazil), B.1.351 (South African), and new Omicron variant (B.1.1.529) with E484A mutation. The vaccine effectiveness is yet to be examined against new mutant strains of SARS-CoV-2 originating in Europe, Nigeria, Brazil, South Africa, and India. To prevent the loss of anti-viral protection in vivo, often defined as antibody resistance, it is required to target highly conserved viral sequences (including Spike protein) and enhance the potency of antibody cocktails. In this review, we assess the reported mutation-acquiring potential of coronaviruses and compare efficacies of current COVID-19 vaccines against 'parent' and 'mutant' strains of SARS-CoV-2 (Kappa (B.1.617.1), Delta (B.1.617.2), and Omicron (B.1.1.529)).
Collapse
Affiliation(s)
- Narasimha M. Beeraka
- Department of Radiation OncologyCancer CenterThe First Affiliated Hospital of ZhengzhouZhengzhouChina
- Department of Human AnatomyI.M. Sechenov First Moscow State Medical University (Sechenov University)MoscowRussian Federation
| | - Olga A. Sukocheva
- Discipline of Health SciencesCollege of Nursing and Health SciencesFlinders University of South AustraliaBedford ParkAustralia
| | - Elena Lukina
- Discipline of BiologyCollege of SciencesFlinders University of South AustraliaBedford ParkAustralia
| | - Junqi Liu
- Department of Radiation OncologyCancer CenterThe First Affiliated Hospital of ZhengzhouZhengzhouChina
| | - Ruitai Fan
- Department of Radiation OncologyCancer CenterThe First Affiliated Hospital of ZhengzhouZhengzhouChina
| |
Collapse
|
26
|
Rodríguez Y, Cardoze SM, Obineche OW, Melo C, Persaud A, Fernández Romero JA. Small Molecules Targeting SARS-CoV-2 Spike Glycoprotein Receptor-Binding Domain. ACS OMEGA 2022; 7:28779-28789. [PMID: 35991504 PMCID: PMC9380817 DOI: 10.1021/acsomega.2c00844] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the coronavirus disease 2019 (COVID-19) pandemic. Several variants of SARS-CoV-2 have emerged worldwide. These variants show different transmissibility infectivity due to mutations in the viral spike (S) glycoprotein that interacts with the human angiotensin-converting enzyme 2 (hACE2) receptor and facilitates viral entry into target cells. Despite the effective SARS-CoV-2 vaccines, we still need to identify selective antivirals, and the S glycoprotein is a key target to neutralize the virus. We hypothesize that small molecules could disrupt the interaction of S glycoprotein with hACE2 and inhibit viral entry. We analyzed the S glycoprotein-hACE2 complex structure (PDB: 7DF4) and created models for different viral variants using visual molecular dynamics (VMD) and molecular operating environment (MOE) programs. Moreover, we started the hits search by performing structure-based molecular docking virtual screening of commercially available small molecules against S glycoprotein models using OEDocking FRED-4.0.0.0 software. The FRED-4.0.0.0 Chemguass4 scoring function was used to rank the small molecules based on their affinities. The best candidate compounds were purchased and tested using a standard SARS-CoV-2 pseudotyped cell-based bioassay to investigate their antiviral activity. Three of these compounds, alone or in combination, showed antiviral selectivity. These small molecules may lead to an effective antiviral treatment or serve as probes to better understand the biology of SARS-CoV-2.
Collapse
Affiliation(s)
- Yoel Rodríguez
- Department
of Natural Sciences, Hostos Community College
of The City University of New York, 500 Grand Concourse, Bronx, New York, New York 10451, United States
- Department
of Pharmacological Sciences, Icahn School
of Medicine at Mount Sinai, 1425 Madison Avenue, New York, New York 10029, United
States
| | - Scarlet Martínez Cardoze
- Department
of Natural Sciences, Hostos Community College
of The City University of New York, 500 Grand Concourse, Bronx, New York, New York 10451, United States
| | - Onyinyechi W. Obineche
- Department
of Natural Sciences, Hostos Community College
of The City University of New York, 500 Grand Concourse, Bronx, New York, New York 10451, United States
| | - Claudia Melo
- Department
of Science, Borough of Manhattan Community
College of The City University of New York, 199 Chambers St, New York, New York 10007, United States
- Brooklyn
College of The City University of New York, 2900 Bedford Avenue, New
York, New York 11210, United States
| | - Ashanna Persaud
- Department
of Science, Borough of Manhattan Community
College of The City University of New York, 199 Chambers St, New York, New York 10007, United States
| | - José A. Fernández Romero
- Department
of Science, Borough of Manhattan Community
College of The City University of New York, 199 Chambers St, New York, New York 10007, United States
- Center
for Biomedical Research, The Population
Council, 1230 York Avenue, New York, New York 10065, United States
| |
Collapse
|
27
|
Tai JH, Sun HY, Tseng YC, Li G, Chang SY, Yeh SH, Chen PJ, Chaw SM, Wang HY. Contrasting patterns in the early stage of SARS-CoV-2 evolution between humans and minks. Mol Biol Evol 2022; 39:6658056. [PMID: 35934827 PMCID: PMC9384665 DOI: 10.1093/molbev/msac156] [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] [Indexed: 11/13/2022] Open
Abstract
One of the unique features of SARS-CoV-2 is its apparent neutral evolution during the early pandemic (before February 2020). This contrasts with the preceding SARS-CoV epidemics, where viruses evolved adaptively. SARS-CoV-2 may exhibit a unique or adaptive feature which deviates from other coronaviruses. Alternatively, the virus may have been cryptically circulating in humans for a sufficient time to have acquired adaptive changes before the onset of the current pandemic. To test the scenarios above, we analyzed the SARS-CoV-2 sequences from minks (Neovision vision) and parental humans. In the early phase of the mink epidemic (April to May 2020), nonsynonymous to synonymous mutation ratio per site in the spike protein is 2.93, indicating a selection process favoring adaptive amino acid changes. Mutations in the spike protein were concentrated within its receptor binding domain and receptor binding motif. An excess of high frequency derived variants produced by genetic hitchhiking was found during the middle (June to July 2020) and late phase I (August to September 2020) of the mink epidemic. In contrast, the site frequency spectra of early SARS-CoV-2 in humans only show an excess of low frequency mutations, consistent with the recent outbreak of the virus. Strong positive selection in the mink SARS-CoV-2 implies the virus may not be pre-adapted to a wide range of hosts and illustrates how a virus evolves to establish a continuous infection in a new host. Therefore, the lack of positive selection signal during the early pandemic in humans deserves further investigation.
Collapse
Affiliation(s)
- Jui Hung Tai
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - Hsiao Yu Sun
- Taipei Municipal Zhongshan Girls High School, Taipei 10490, Taiwan
| | - Yi Cheng Tseng
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Guanghao Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Sui Yuan Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
| | - Shiou Hwei Yeh
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei 10617, Taiwan
| | - Pei Jer Chen
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan.,Department of Microbiology, College of Medicine, National Taiwan University, Taipei 10617, Taiwan.,Hepatitis Research Center, National Taiwan University College of Medicine and National Taiwan University Hospital, Taipei 10002, Taiwan.,Department of Internal Medicine, National Taiwan University College of Medicine and National Taiwan University Hospital, Taipei 10002, Taiwan.,Department of Medical Research, National Taiwan University College of Medicine and National Taiwan University Hospital, Taipei 10002, Taiwan
| | - Shu Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Hurng Yi Wang
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan.,Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 10617, Taiwan.,Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei 10002, Taiwan
| |
Collapse
|
28
|
Li Y, Zheng P, Liu T, Shi C, Wang B, Xu Y, Jin T. Structural Requirements and Plasticity of Receptor-Binding Domain in Human Coronavirus Spike. Front Mol Biosci 2022; 9:930931. [PMID: 35903152 PMCID: PMC9315343 DOI: 10.3389/fmolb.2022.930931] [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: 04/28/2022] [Accepted: 06/06/2022] [Indexed: 11/22/2022] Open
Abstract
The most recent human coronaviruses including severe acute respiratory syndrome coronavirus-2 causing severe respiratory tract infection and high pathogenicity bring significant global public health concerns. Infections are initiated by recognizing host cell receptors by coronavirus spike protein S1 subunit, and then S2 mediates membrane fusion. However, human coronavirus spikes undergo frequent mutation, which may result in diverse pathogenesis and infectivity. In this review, we summarize some of these recent structural and mutational characteristics of RBD of human coronavirus spike protein and their interaction with specific human cell receptors and analyze the structural requirements and plasticity of RBD. Stability of spike protein, affinity toward receptor, virus fitness, and infectivity are the factors controlling the viral tropisms. Thus, understanding the molecular details of RBDs and their mutations is critical in deciphering virus evolution. Structural information of spike and receptors of human coronaviruses not only reveals the molecular mechanism of host–microbe interaction and pathogenesis but also helps develop effective drug to control these infectious pathogens and cope with the future emerging coronavirus outbreaks.
Collapse
Affiliation(s)
- Yajuan Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Peiyi Zheng
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Tingting Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Cuixiao Shi
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Bo Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yuanhong Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Tengchuan Jin
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| |
Collapse
|
29
|
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.
Collapse
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
| |
Collapse
|
30
|
Roelle SM, Shukla N, Pham AT, Bruchez AM, Matreyek KA. Expanded ACE2 dependencies of diverse SARS-like coronavirus receptor binding domains. PLoS Biol 2022; 20:e3001738. [PMID: 35895696 PMCID: PMC9359572 DOI: 10.1371/journal.pbio.3001738] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 08/08/2022] [Accepted: 07/01/2022] [Indexed: 11/18/2022] Open
Abstract
Viral spillover from animal reservoirs can trigger public health crises and cripple the world economy. Knowing which viruses are primed for zoonotic transmission can focus surveillance efforts and mitigation strategies for future pandemics. Successful engagement of receptor protein orthologs is necessary during cross-species transmission. The clade 1 sarbecoviruses including Severe Acute Respiratory Syndrome-related Coronavirus (SARS-CoV) and SARS-CoV-2 enter cells via engagement of angiotensin converting enzyme-2 (ACE2), while the receptor for clade 2 and clade 3 remains largely uncharacterized. We developed a mixed cell pseudotyped virus infection assay to determine whether various clades 2 and 3 sarbecovirus spike proteins can enter HEK 293T cells expressing human or Rhinolophus horseshoe bat ACE2 proteins. The receptor binding domains from BtKY72 and Khosta-2 used human ACE2 for entry, while BtKY72 and Khosta-1 exhibited widespread use of diverse rhinolophid ACE2s. A lysine at ACE2 position 31 appeared to be a major determinant of the inability of these RBDs to use a certain ACE2 sequence. The ACE2 protein from Rhinolophus alcyone engaged all known clade 3 and clade 1 receptor binding domains. We observed little use of Rhinolophus ACE2 orthologs by the clade 2 viruses, supporting the likely use of a separate, unknown receptor. Our results suggest that clade 3 sarbecoviruses from Africa and Europe use Rhinolophus ACE2 for entry, and their spike proteins appear primed to contribute to zoonosis under the right conditions. Knowing which viruses are primed for zoonotic transmission can focus surveillance efforts and mitigation strategies for future pandemics. This study shows that SARS-like coronaviruses identified in bats from Europe and Africa can use a range of horseshoe bat ACE2s for entry. In addition, viruses found in Russia and Kenya also have the ability to at least weakly use human ACE2.
Collapse
Affiliation(s)
- Sarah M. Roelle
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Nidhi Shukla
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Anh T. Pham
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Anna M. Bruchez
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Kenneth A. Matreyek
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
- * E-mail:
| |
Collapse
|
31
|
Albohy A, Zahran EM, Abdelmohsen UR, Salem MA, Al-Warhi T, Al-Sanea MM, Abelyan N, Khalil HE, Desoukey SY, Fouad MA, Kamel MS. Multitarget in silico studies of Ocimum menthiifolium, family Lamiaceae against SARS-CoV-2 supported by molecular dynamics simulation. J Biomol Struct Dyn 2022; 40:4062-4072. [PMID: 33317409 PMCID: PMC7784784 DOI: 10.1080/07391102.2020.1852964] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 11/15/2020] [Indexed: 12/19/2022]
Abstract
The novel strain of human coronavirus, emerged in December 2019, which has been designated as SARS-CoV-2, causes a severe acute respiratory syndrome. Since then, it has arisen as a serious threat to the world public health. Since no approved vaccines or drugs has been found to efficiently stop the virulent spread of the virus, progressive inquiries targeting these viruses are urgently needed, especially those from plant sources. Metabolic profiling using LC-HR-ESI-MS of the butanol extract of Ocimum menthiifolium (Lamiaceae) aerial parts yielded 10 compounds including flavonoids, iridoids and phenolics. As it has been previously reported that some flavonoids can be used as anti-SARS drugs by targeting SARS-CoV-1 3CLpro, we chose to examine 14 flavonoids (detected by metabolomics and other compounds isolated via several chromatographic techniques). We investigated their potential binding interactions with the 4 main SARS-CoV-2 targets: Mpro, nsp16/nsp10 complex, ACE2-PD and RBD-S-protein via molecular docking. Docking results indicated that the nsp16/nsp10 complex has the best binding affinities where the strongest binding was detected with apigenin-7-O-rutinoside, prunin and acaciin with -9.4, -9.3 and -9.3 kcal/mol binding energy, respectively, compared to the control (SAM) with -8.2 kcal/mol. Furthermore, the stability of these complexes was studied using molecular dynamics of 150 ns, which were then compared to their complexes in the other three targets. MM-PBSA calculations suggested the high stability of acaciin-nsp16 complex with binding energy of -110 kJ/mol. This study sheds light on the structure-based design of natural flavonoids as anti-SARS-CoV-2 drugs targeting the nsp16/10 complex.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Amgad Albohy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt
| | - Eman Maher Zahran
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, New Minia City, Egypt
| | - Usama Ramadan Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, New Minia City, Egypt
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, Egypt
| | - M. Alaraby Salem
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, October University of Modern Sciences and Arts (MSA), Giza, Egypt
| | - Tarfah Al-Warhi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Mohammad M. Al-Sanea
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Aljouf, Saudi Arabia
| | - Narek Abelyan
- Institute of Biomedicine and Pharmacy, Russian-Armenian University, Yerevan, Armenia
| | - Hany Ezzat Khalil
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Hofuf, Saudi Arabia
| | - Samar Yehia Desoukey
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, Egypt
| | - Mostafa Ahmed Fouad
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, Egypt
| | - Mohamed Salah Kamel
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, New Minia City, Egypt
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, Egypt
| |
Collapse
|
32
|
Abduljaleel Z, Shahzad N, Aziz SA, Malik SM. Monoclonal antibody designed for SARS-nCoV-2 spike protein of receptor binding domain on antigenic targeted epitopes for inhibition to prevent viral entry. Mol Divers 2022; 27:695-708. [PMID: 35616802 PMCID: PMC9133318 DOI: 10.1007/s11030-022-10449-x] [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: 02/12/2022] [Accepted: 04/19/2022] [Indexed: 11/25/2022]
Abstract
SARS, or severe acute respiratory syndrome, is caused by a novel coronavirus (COVID-19). This situation has compelled many pharmaceutical R&D companies and public health research sectors to focus their efforts on developing effective therapeutics. SARS-nCoV-2 was chosen as a protein spike to targeted monoclonal antibodies and therapeutics for prevention and treatment. Deep mutational scanning created a monoclonal antibody to characterize the effects of mutations in a variable antibody fragment based on its expression levels, specificity, stability, and affinity for specific antigenic conserved epitopes to the Spike-S-Receptor Binding Domain (RBD). Improved contacts between Fv light and heavy chains and the targeted antigens of RBD could result in a highly potent neutralizing antibody (NAbs) response as well as cross-protection against other SARS-nCoV-2 strains. It undergoes multipoint core mutations that combine enhancing mutations, resulting in increased binding affinity and significantly increased stability between RBD and antibody. In addition, we improved. Structures of variable fragment (Fv) complexed with the RBD of Spike protein were subjected to our established in-silico antibody-engineering platform to obtain enhanced binding affinity to SARS-nCoV-2 and develop ability profiling. We found that the size and three-dimensional shape of epitopes significantly impacted the activity of antibodies produced against the RBD of Spike protein. Overall, because of the conformational changes between RBD and hACE2, it prevents viral entry. As a result of this in-silico study, the designed antibody can be used as a promising therapeutic strategy to treat COVID-19.
Collapse
Affiliation(s)
- Zainularifeen Abduljaleel
- Science and Technology Unit, Umm Al-Qura University, P.O. Box 715, Mecca, 21955, Kingdom of Saudi Arabia.
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O. Box 715, Mecca, 21955, Kingdom of Saudi Arabia.
- The Regional Laboratory, Molecular Diagnostics Unit, Department of Molecular Biology, Ministry of Health (MOH), P.O. Box 6251, Mecca, Saudi Arabia.
| | - Naiyer Shahzad
- Department of Pharmacology and Toxicology, Faculty of Medicine, Umm Al-Qura University, Mecca, Saudi Arabia
| | - Syed A Aziz
- Department of Pathology and Lab Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
| | - Shaheer M Malik
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, Mecca, Saudi Arabia
| |
Collapse
|
33
|
Cantoni D, Mayora-Neto M, Thakur N, Elrefaey AME, Newman J, Vishwanath S, Nadesalingam A, Chan A, Smith P, Castillo-Olivares J, Baxendale H, Charleston B, Heeney J, Bailey D, Temperton N. Pseudotyped Bat Coronavirus RaTG13 is efficiently neutralised by convalescent sera from SARS-CoV-2 infected patients. Commun Biol 2022; 5:409. [PMID: 35505237 PMCID: PMC9065041 DOI: 10.1038/s42003-022-03325-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 03/28/2022] [Indexed: 12/24/2022] Open
Abstract
RaTG13 is a close relative of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, sharing 96% sequence similarity at the genome-wide level. The spike receptor binding domain (RBD) of RaTG13 contains a number of amino acid substitutions when compared to SARS-CoV-2, likely impacting affinity for the ACE2 receptor. Antigenic differences between the viruses are less well understood, especially whether RaTG13 spike can be efficiently neutralised by antibodies generated from infection with, or vaccination against, SARS-CoV-2. Using RaTG13 and SARS-CoV-2 pseudotypes we compared neutralisation using convalescent sera from previously infected patients or vaccinated healthcare workers. Surprisingly, our results revealed that RaTG13 was more efficiently neutralised than SARS-CoV-2. In addition, neutralisation assays using spike mutants harbouring single and combinatorial amino acid substitutions within the RBD demonstrated that both spike proteins can tolerate multiple changes without dramatically reducing neutralisation. Moreover, introducing the 484 K mutation into RaTG13 resulted in increased neutralisation, in contrast to the same mutation in SARS-CoV-2 (E484K). This is despite E484K having a well-documented role in immune evasion in variants of concern (VOC) such as B.1.351 (Beta). These results indicate that the future spill-over of RaTG13 and/or related sarbecoviruses could be mitigated using current SARS-CoV-2-based vaccination strategies.
Collapse
Affiliation(s)
- Diego Cantoni
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent & Greenwich, Chatham, UK
| | - Martin Mayora-Neto
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent & Greenwich, Chatham, UK
| | - Nazia Thakur
- The Pirbright Institute, Guildford, Surrey, GU24 0NF, UK
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Joseph Newman
- The Pirbright Institute, Guildford, Surrey, GU24 0NF, UK
| | - Sneha Vishwanath
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Andrew Chan
- DIOSynVax, University of Cambridge, Madingley Road, CB3-0ES, Cambridge, UK
| | - Peter Smith
- DIOSynVax, University of Cambridge, Madingley Road, CB3-0ES, Cambridge, UK
| | | | | | | | - Jonathan Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- DIOSynVax, University of Cambridge, Madingley Road, CB3-0ES, Cambridge, UK
| | - Dalan Bailey
- The Pirbright Institute, Guildford, Surrey, GU24 0NF, UK.
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent & Greenwich, Chatham, UK.
| |
Collapse
|
34
|
Ruiz-Aravena M, McKee C, Gamble A, Lunn T, Morris A, Snedden CE, Yinda CK, Port JR, Buchholz DW, Yeo YY, Faust C, Jax E, Dee L, Jones DN, Kessler MK, Falvo C, Crowley D, Bharti N, Brook CE, Aguilar HC, Peel AJ, Restif O, Schountz T, Parrish CR, Gurley ES, Lloyd-Smith JO, Hudson PJ, Munster VJ, Plowright RK. Ecology, evolution and spillover of coronaviruses from bats. Nat Rev Microbiol 2022; 20:299-314. [PMID: 34799704 PMCID: PMC8603903 DOI: 10.1038/s41579-021-00652-2] [Citation(s) in RCA: 89] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2021] [Indexed: 12/24/2022]
Abstract
In the past two decades, three coronaviruses with ancestral origins in bats have emerged and caused widespread outbreaks in humans, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since the first SARS epidemic in 2002-2003, the appreciation of bats as key hosts of zoonotic coronaviruses has advanced rapidly. More than 4,000 coronavirus sequences from 14 bat families have been identified, yet the true diversity of bat coronaviruses is probably much greater. Given that bats are the likely evolutionary source for several human coronaviruses, including strains that cause mild upper respiratory tract disease, their role in historic and future pandemics requires ongoing investigation. We review and integrate information on bat-coronavirus interactions at the molecular, tissue, host and population levels. We identify critical gaps in knowledge of bat coronaviruses, which relate to spillover and pandemic risk, including the pathways to zoonotic spillover, the infection dynamics within bat reservoir hosts, the role of prior adaptation in intermediate hosts for zoonotic transmission and the viral genotypes or traits that predict zoonotic capacity and pandemic potential. Filling these knowledge gaps may help prevent the next pandemic.
Collapse
Affiliation(s)
- Manuel Ruiz-Aravena
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Clifton McKee
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Amandine Gamble
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Tamika Lunn
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD, Australia
| | - Aaron Morris
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Celine E Snedden
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Claude Kwe Yinda
- National Institute of Allergy and Infectious Diseases, Hamilton, MT, USA
| | - Julia R Port
- National Institute of Allergy and Infectious Diseases, Hamilton, MT, USA
| | - David W Buchholz
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Yao Yu Yeo
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Christina Faust
- Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Elinor Jax
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Lauren Dee
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Devin N Jones
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Maureen K Kessler
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
- Department of Ecology, Montana State University, Bozeman, MT, USA
| | - Caylee Falvo
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Daniel Crowley
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Nita Bharti
- Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Cara E Brook
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Hector C Aguilar
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Alison J Peel
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD, Australia
| | - Olivier Restif
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Tony Schountz
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Colin R Parrish
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Emily S Gurley
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - James O Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Peter J Hudson
- Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Vincent J Munster
- National Institute of Allergy and Infectious Diseases, Hamilton, MT, USA
| | - Raina K Plowright
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA.
| |
Collapse
|
35
|
Geng Q, Shi K, Ye G, Zhang W, Aihara H, Li F. Structural Basis for Human Receptor Recognition by SARS-CoV-2 Omicron Variant BA.1. J Virol 2022; 96:e0024922. [PMID: 35343765 PMCID: PMC9044962 DOI: 10.1128/jvi.00249-22] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 02/25/2022] [Indexed: 12/12/2022] Open
Abstract
The highly contagious and fast-spreading omicron variant of SARS-CoV-2 infects the respiratory tracts efficiently. The receptor-binding domain (RBD) of the omicron spike protein recognizes human angiotensin-converting enzyme 2 (ACE2) as its receptor and plays a critical role in the tissue tropism of SARS-CoV-2. Here, we showed that the omicron RBD (strain BA.1) binds to ACE2 more strongly than does the prototypic RBD from the original Wuhan strain. We also measured how individual omicron mutations affect ACE2 binding. We further determined the crystal structure of the omicron RBD (engineered to facilitate crystallization) complexed with ACE2 at 2.6 Å. The structure shows that omicron mutations caused significant structural rearrangements of two mutational hot spots at the RBD/ACE2 interface, elucidating how each omicron mutation affects ACE2 binding. The enhanced ACE2 binding by the omicron RBD may facilitate the omicron variant's infection of the respiratory tracts where ACE2 expression level is low. Our study provides insights into the receptor recognition and tissue tropism of the omicron variant. IMPORTANCE Despite the scarcity of the SARS-CoV-2 receptor-human angiotensin-converting enzyme 2 (ACE2)-in the respiratory tract, the omicron variant efficiently infects the respiratory tract, causing rapid and widespread infections of COVID-19. The omicron variant contains extensive mutations in the receptor-binding domain (RBD) of its spike protein that recognizes human ACE2. Here, using a combination of biochemical and X-ray crystallographic approaches, we showed that the omicron RBD binds to ACE2 with enhanced affinity and also elucidated the role of each of the omicron mutations in ACE2 binding. The enhanced ACE2 binding by the omicron RBD may contribute to the omicron variant's new viral tropism in the respiratory tract despite the low level of ACE2 expression in the tissue. These findings help us to understand tissue tropism of the omicron variant and shed light on the molecular evolution of SARS-CoV-2.
Collapse
Affiliation(s)
- Qibin Geng
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA
- Center for Coronavirus Research, University of Minnesota, Saint Paul, Minnesota, USA
| | - Ke Shi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Gang Ye
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA
- Center for Coronavirus Research, University of Minnesota, Saint Paul, Minnesota, USA
| | - Wei Zhang
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA
- Center for Coronavirus Research, University of Minnesota, Saint Paul, Minnesota, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Fang Li
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA
- Center for Coronavirus Research, University of Minnesota, Saint Paul, Minnesota, USA
| |
Collapse
|
36
|
Govind Kumar V, Ogden DS, Isu UH, Polasa A, Losey J, Moradi M. Prefusion spike protein conformational changes are slower in SARS-CoV-2 than in SARS-CoV-1. J Biol Chem 2022; 298:101814. [PMID: 35278433 PMCID: PMC8907130 DOI: 10.1016/j.jbc.2022.101814] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 03/04/2022] [Accepted: 03/06/2022] [Indexed: 01/01/2023] Open
Abstract
Within the last 2 decades, severe acute respiratory syndrome coronaviruses 1 and 2 (SARS-CoV-1 and SARS-CoV-2) have caused two major outbreaks; yet, for reasons not fully understood, the coronavirus disease 2019 pandemic caused by SARS-CoV-2 has been significantly more widespread than the 2003 SARS epidemic caused by SARS-CoV-1, despite striking similarities between these two viruses. The SARS-CoV-1 and SARS-CoV-2 spike proteins, both of which bind to host cell angiotensin-converting enzyme 2, have been implied to be a potential source of their differential transmissibility. However, the mechanistic details of prefusion spike protein binding to angiotensin-converting enzyme 2 remain elusive at the molecular level. Here, we performed an extensive set of equilibrium and nonequilibrium microsecond-level all-atom molecular dynamics simulations of SARS-CoV-1 and SARS-CoV-2 prefusion spike proteins to determine their differential dynamic behavior. Our results indicate that the active form of the SARS-CoV-2 spike protein is more stable than that of SARS-CoV-1 and the energy barrier associated with the activation is higher in SARS-CoV-2. These results suggest that not only the receptor-binding domain but also other domains such as the N-terminal domain could play a crucial role in the differential binding behavior of SARS-CoV-1 and SARS-CoV-2 spike proteins.
Collapse
Affiliation(s)
- Vivek Govind Kumar
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | - Dylan S Ogden
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | - Ugochi H Isu
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | - Adithya Polasa
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | - James Losey
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | - Mahmoud Moradi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA.
| |
Collapse
|
37
|
Gyebi GA, Adegunloye AP, Ibrahim IM, Ogunyemi OM, Afolabi SO, Ogunro OB. Prevention of SARS-CoV-2 cell entry: insight from in silico interaction of drug-like alkaloids with spike glycoprotein, human ACE2, and TMPRSS2. J Biomol Struct Dyn 2022; 40:2121-2145. [PMID: 33089728 PMCID: PMC7594191 DOI: 10.1080/07391102.2020.1835726] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 10/07/2020] [Indexed: 12/28/2022]
Abstract
COVID-19 is a respiratory disease caused by SARS-CoV-2, an enveloped positive sense RNA virus. The SARS-CoV-2 spike glycoprotein, human angiotensin-converting enzyme 2 (ACE2) and human transmembrane protease serine 2 (TMPRSS2) are essential for the host cell-mediated viral entry. Targeting these proteins represent viable options to stop the first stage of infection and transmission. Hence, 97 alkaloids from African medicinal plants with reported antiviral activity were evaluated for this purpose via in silico studies. These alkaloids were docked for their interactions with SARS-CoV-2 spike glycoprotein, ACE2, and TMPRSS2. Top 20 alkaloids with highest binding affinities were further screened for their interactions with spike glycoprotein of SARS-CoV and MERS-CoV, and with ACE2-SARS-CoV-2 receptor-binding domain complex (ACE2-RBD). The energy profiling, molecular dynamics simulation (MDS), binding free energy base on Molecular Mechanics/Generalized Born Surface Area (MMGBSA), clustering of MDS trajectories, and virtual physicochemical and pharmacokinetic screening of the best docked alkaloids were performed. Results revealed that more than 15 alkaloids interacted better than the reference compounds. 10-Hydroxyusambarensine and Cryptospirolepine were docked in a similar binding pattern to the S1-specificy pocket of TMPRSS2 as camostat (reference inhibitor). The strong binding affinities, stability of the alkaloid-protein complexes and amino acid interactions displayed by cryptospirolepine, 10-hydroxyusambarensine, and cryptoquindoline with important binding hotspots of the proteins suggest these alkaloids have the potential of altering the capacity of SARS-CoV-2 membrane mediated host cell entry. Further in vitro and in vivo evaluation of these "drug-like" alkaloids as potential inhibitors of coronavirus cell entry is proposed.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Gideon A. Gyebi
- Department of Biological Sciences, Salem University, Lokoja, Nigeria
| | | | - Ibrahim M. Ibrahim
- Faculty of Sciences, Department of Biophysics, Cairo University, Giza, Egypt
| | | | - Saheed O. Afolabi
- Faculty of Basic Medical Sciences, Department of Pharmacology and Therapeutics, University of Ilorin, Ilorin, Nigeria
| | - Olalekan B. Ogunro
- Department of Biological Sciences, KolaDaisi University, Ibadan, Nigeria
| |
Collapse
|
38
|
Guo Y, Hu K, Li Y, Lu C, Ling K, Cai C, Wang W, Ye D. Targeting TNF-α for COVID-19: Recent Advanced and Controversies. Front Public Health 2022; 10:833967. [PMID: 35223745 PMCID: PMC8873570 DOI: 10.3389/fpubh.2022.833967] [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: 12/12/2021] [Accepted: 01/17/2022] [Indexed: 12/14/2022] Open
Abstract
Recent advances in the pathophysiologic understanding of coronavirus disease 2019 (COVID-19) suggests that cytokine release syndrome (CRS) has an association with the severity of disease, which is characterized by increased tumor necrosis factor α (TNF-α), interleukin (IL)-6, IL-2, IL-7, and IL-10. Hence, managing CRS has been recommended for rescuing severe COVID-19 patients. TNF-α, one of the pro-inflammatory cytokines commonly upregulated in acute lung injury, triggers CRS and facilitates SARS-CoV-2 interaction with angiotensin-converting enzyme 2 (ACE2). TNF-α inhibitors, therefore, may serve as an effective therapeutic strategy for attenuating disease progression in severe SARS-CoV-2 infection. Below, we review the possibilities and challenges of targeting the TNF-α pathway in COVID-19 treatment.
Collapse
Affiliation(s)
- Yi Guo
- Department of Vascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ke Hu
- Department of Vascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuxuan Li
- Department of Vascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chanjun Lu
- Department of Vascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ken Ling
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chuanqi Cai
- Department of Vascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weici Wang
- Department of Vascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Weici Wang
| | - Dawei Ye
- Department of Pancreatic-Biliary Surgery, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
- Department of Cancer Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Dawei Ye
| |
Collapse
|
39
|
Shehata AA, Attia YA, Rahman MT, Basiouni S, El-Seedi HR, Azhar EI, Khafaga AF, Hafez HM. Diversity of Coronaviruses with Particular Attention to the Interspecies Transmission of SARS-CoV-2. Animals (Basel) 2022; 12:ani12030378. [PMID: 35158701 PMCID: PMC8833600 DOI: 10.3390/ani12030378] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 01/30/2022] [Accepted: 02/01/2022] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Coronaviruses are a broad group of viruses that may infect a wide range of animals, including humans. Despite the fact that each coronavirus has a limited host range, frequent interspecies transmission of coronaviruses across diverse hosts has resulted in a complex ecology. The recently discovered SARS-CoV-2 virus is the clearest evidence of the danger of a global pandemic spreading. Natural infection with SARS-CoV-2 has been reported in a variety of domestic and wild animals, which may complicate the virus’s epidemiology and influence its development. In this review, we discussed the potential determinants of SARS-CoV-2 interspecies transmission. Additionally, despite the efforts that have been made to control this pandemic and to implement the One Health policy, several problems, such as the role of animals in SARS-CoV-2 evolution and the dynamics of interspecies transmission, are still unanswered. Abstract In December 2019, the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in China with serious impacts on global health and economy that is still ongoing. Although interspecies transmission of coronaviruses is common and well documented, each coronavirus has a narrowly restricted host range. Coronaviruses utilize different receptors to mediate membrane fusion and replication in the cell cytoplasm. The interplay between the receptor-binding domain (RBD) of coronaviruses and their coevolution are determinants for host susceptibility. The recently emerged SARS-CoV-2 caused the coronavirus disease 2019 (COVID-19) pandemic and has also been reported in domestic and wild animals, raising the question about the responsibility of animals in virus evolution. Additionally, the COVID-19 pandemic might also substantially have an impact on animal production for a long time. In the present review, we discussed the diversity of coronaviruses in animals and thus the diversity of their receptors. Moreover, the determinants of the susceptibility of SARS-CoV-2 in several animals, with special reference to the current evidence of SARS-CoV-2 in animals, were highlighted. Finally, we shed light on the urgent demand for the implementation of the One Health concept as a collaborative global approach to mitigate the threat for both humans and animals.
Collapse
Affiliation(s)
- Awad A. Shehata
- Birds and Rabbit Medicine Department, Faculty of Veterinary Medicine, University of Sadat City, Sadat City 32897, Egypt;
- Research and Development Section, PerNaturam GmbH, 56290 Gödenroth, Germany
| | - Youssef A. Attia
- Department of Agriculture, Faculty of Environmental Sciences, King Abdulaziz University, P.O. Box 80208, Jeddah 21589, Saudi Arabia;
- The Strategic Center to Kingdom Vision Realization, King Abdulaziz University, P.O. Box 80200, Jeddah 21589, Saudi Arabia
- Animal and Poultry Production Department, Faculty of Agriculture, Damanhour University, Damanhour 22516, Egypt
| | - Md. Tanvir Rahman
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh;
| | - Shereen Basiouni
- Clinical Pathology Department, Faculty of Veterinary Medicine, Benha University, Benha 13736, Egypt;
| | - Hesham R. El-Seedi
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China;
- Department of Chemistry, Faculty of Science, Menoufia University, Shebin El-Kom 32512, Egypt
| | - Esam I. Azhar
- Special Infectious Agents Unit—BSL3, King Fahd Medical Research Center and Department of Medical Laboratory Science, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia;
| | - Asmaa F. Khafaga
- Department of Pathology, Faculty of Veterinary Medicine, Alexandria University, Edfina 22758, Egypt;
| | - Hafez M. Hafez
- Institute of Poultry Diseases, Faculty of Veterinary Medicine, Free University of Berlin, 14163 Berlin, Germany
- Correspondence:
| |
Collapse
|
40
|
Mutational landscape and in silico structure models of SARS-CoV-2 spike receptor binding domain reveal key molecular determinants for virus-host interaction. BMC Mol Cell Biol 2022; 23:2. [PMID: 34991443 PMCID: PMC8736301 DOI: 10.1186/s12860-021-00403-4] [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] [Received: 03/03/2021] [Accepted: 12/23/2021] [Indexed: 12/15/2022] Open
Abstract
Background SARS-CoV-2, the causative agent of COVID-19 pandemic is a RNA virus prone to mutations. Formation of a stable binding interface between the Receptor Binding Domain (RBD) of SARS-CoV-2 Spike (S) protein and Angiotensin-Converting Enzyme 2 (ACE2) of host is pivotal for viral entry. RBD has been shown to mutate frequently during pandemic. Although, a few mutations in RBD exhibit enhanced transmission rates leading to rise of new variants of concern, most RBD mutations show sustained ACE2 binding and virus infectivity. Yet, how all these mutations make the binding interface constantly favourable for virus remain enigmatic. This study aims to delineate molecular rearrangements in the binding interface of SARS-CoV-2 RBD mutants. Results Here, we have generated a mutational and structural landscape of SARS-CoV-2 RBD in first six months of the pandemic. We analyzed 31,403 SARS-CoV-2 genomes randomly across the globe, and identified 444 non-synonymous mutations in RBD that cause 49 distinct amino acid substitutions in contact and non-contact amino acid residues. Molecular phylogenetic analysis suggested independent emergence of RBD mutants. Structural mapping of these mutations on the SARS-CoV-2 Wuhan reference strain RBD and structural comparison with RBDs from bat-CoV, SARS-CoV, and pangolin-CoV, all bound to human or mouse ACE2, revealed several changes in the interfacial interactions in all three binding clusters. Interestingly, interactions mediated via N487 residue in cluster-I and Y449, G496, T500, G502 residues in cluster-III remained largely unchanged in all RBD mutants. Further analysis showed that these interactions are evolutionarily conserved in sarbecoviruses which use ACE2 for entry. Importantly, despite extensive changes in the interface, RBD-ACE2 stability and binding affinities were maintained in all the analyzed mutants. Taken together, these findings reveal how SARS-CoV-2 uses its RBD residues to constantly remodel the binding interface. Conclusion Our study broadly signifies understanding virus-host binding interfaces and their alterations during pandemic. Our findings propose a possible interface remodelling mechanism used by SARS-CoV-2 to escape deleterious mutations. Future investigations will focus on functional validation of in-silico findings and on investigating interface remodelling mechanisms across sarbecoviruses. Thus, in long run, this study may provide novel clues to therapeutically target RBD-ACE2 interface for pan-sarbecovirus infections. Supplementary Information The online version contains supplementary material available at 10.1186/s12860-021-00403-4.
Collapse
|
41
|
Buratto D, Saxena A, Ji Q, Yang G, Pantano S, Zonta F. Rapid Assessment of Binding Affinity of SARS-COV-2 Spike Protein to the Human Angiotensin-Converting Enzyme 2 Receptor and to Neutralizing Biomolecules Based on Computer Simulations. Front Immunol 2021; 12:730099. [PMID: 34858396 PMCID: PMC8632240 DOI: 10.3389/fimmu.2021.730099] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/25/2021] [Indexed: 12/17/2022] Open
Abstract
SARS-CoV-2 infects humans and causes Coronavirus disease 2019 (COVID-19). The S1 domain of the spike glycoprotein of SARS-CoV-2 binds to human angiotensin-converting enzyme 2 (hACE2) via its receptor-binding domain, while the S2 domain facilitates fusion between the virus and the host cell membrane for entry. The spike glycoprotein of circulating SARS-CoV-2 genomes is a mutation hotspot. Some mutations may affect the binding affinity for hACE2, while others may modulate S-glycoprotein expression, or they could result in a virus that can escape from antibodies generated by infection with the original variant or by vaccination. Since a large number of variants are emerging, it is of vital importance to be able to rapidly assess their characteristics: while changes of binding affinity alone do not always cause direct advantages for the virus, they still can provide important insights on where the evolutionary pressure is directed. Here, we propose a simple and cost-effective computational protocol based on Molecular Dynamics simulations to rapidly screen the ability of mutated spike protein to bind to the hACE2 receptor and selected neutralizing biomolecules. Our results show that it is possible to achieve rapid and reliable predictions of binding affinities. A similar approach can be used to perform preliminary screenings of the potential effects of S-RBD mutations, helping to prioritize the more time-consuming and expensive experimental work.
Collapse
Affiliation(s)
- Damiano Buratto
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Abhishek Saxena
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Qun Ji
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Sergio Pantano
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
- Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Francesco Zonta
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| |
Collapse
|
42
|
Zekri ARN, Bahnasy AA, Hafez MM, Hassan ZK, Ahmed OS, Soliman HK, El-Sisi ER, Dine MHSE, Solimane MS, Latife LSA, Seadawy MG, Elsafty AS, Abouelhoda M. Characterization of the SARS-CoV-2 genomes in Egypt in first and second waves of infection. Sci Rep 2021; 11:21632. [PMID: 34732835 PMCID: PMC8566477 DOI: 10.1038/s41598-021-99014-4] [Citation(s) in RCA: 6] [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: 04/10/2021] [Accepted: 08/05/2021] [Indexed: 12/26/2022] Open
Abstract
At Wuhan, in December 2019, the SRAS-CoV-2 outbreak was detected and it has been the pandemic worldwide. This study aims to investigate the mutations in sequence of the SARS-CoV-2 genome and characterize the mutation patterns in Egyptian COVID-19 patients during different waves of infection. The samples were collected from 250 COVID-19 patients and the whole genome sequencing was conducted using Next Generation Sequencing. The viral sequence analysis showed 1115 different genome from all Egyptian samples in the second wave mutations including 613 missense mutations, 431 synonymous mutations, 25 upstream gene mutations, 24 downstream gene mutations, 10 frame-shift deletions, and 6 stop gained mutation. The Egyptian genomic strains sequenced in second wave of infection are different to that of the first wave. We observe a shift of lineage prevalence from the strain B.1 to B.1.1.1. Only one case was of the new English B.1.1.7. Few samples have one or two mutations of interest from the Brazil and South Africa isolates. New clade 20B appear by March 2020 and 20D appear by May 2020 till January 2021.
Collapse
Affiliation(s)
- Abdel-Rahman N Zekri
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, 11796, Egypt.
| | - Abeer A Bahnasy
- Surgical Pathology Department, National Cancer Institute, Cairo University, Cairo, 11796, Egypt
| | - Mohamed M Hafez
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, 11796, Egypt
| | - Zeinab K Hassan
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, 11796, Egypt
| | - Ola S Ahmed
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, 11796, Egypt
| | - Hany K Soliman
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, 11796, Egypt
| | - Enas R El-Sisi
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, 11796, Egypt
| | - Mona H Salah El Dine
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - May S Solimane
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Lamyaa S Abdel Latife
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | | | | | - Mohamed Abouelhoda
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo, 12613, Egypt
| |
Collapse
|
43
|
Tran TX, Lien NTK, Thu HT, Duy ND, Duong BTT, Quyen DV. Changes in the spike and nucleocapsid protein of porcine epidemic diarrhea virus strain in Vietnam-a molecular potential for the vaccine development? PeerJ 2021; 9:e12329. [PMID: 34721997 PMCID: PMC8530102 DOI: 10.7717/peerj.12329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/27/2021] [Indexed: 11/20/2022] Open
Abstract
Background Porcine epidemic diarrhea virus (PEDV) is a dangerous virus causing large piglet losses. PEDV spread rapidly between pig farms and caused the death of up to 90% of infected piglets. Current vaccines are only partially effective in providing immunity to suckling due to the rapid dissemination and ongoing evolution of PEDV. Methods In this study, the complete genome of a PEDV strain in Vietnam 2018 (IBT/VN/2018 strain) has been sequenced. The nucleotide sequence of each fragment was assembled to build a continuous complete sequence using the DNASTAR program. The complete nucleotide sequences and amino acid sequences of S, N, and ORF3 genes were aligned and analyzed to detect the mutations. Results The full-length genome was determined with 28,031 nucleotides in length which consisted of the 5'UTR, ORF1ab, S protein, ORF3, E protein, M protein, N protein, and 3'UTR region. The phylogenetic analysis showed that the IBT/VN/2018 strain was highly virulent belonged to the G2b subgroup along with the Northern American and Asian S-INDEL strains. Multiple sequence alignment of deduced amino acids revealed numerous mutations in the S, N, and ORF3 regions including one substitution 766P > L766 in the epitope SS6; two in the S0subdomain (135DN136 > 135SI136 and N144> D144); two in subdomain SHR1 at aa 1009L > M1009 and 1089S > L1089; one at aa 1279P > S1279 in subdomain SHR2 of the S protein; two at aa 364N > I364 and 378N > S378 in the N protein; four at aa 25L > S25, 70I > V70, 107C > F107, and 168D > N168 in the ORF3 protein. We identified two insertions (at aa 59NQGV62 and aa 145N) and one deletion (at aa 168DI169) in S protein. Remarkable, eight amino acid substitutions (294I > M294, 318A > S318, 335V > I335, 361A > T361, 497R > T497, 501SH502 > 501IY502, 506I > T506, 682V > I682, and 777P > L777) were found in SA subdomain. Besides, N- and O-glycosylation analysis of S, N, and ORF3 protein reveals three known sites (25G+, 123N+, and 62V+) and three novel sites (144D+, 1009M+, and 1279L+) in the IBT/VN/2018 strain compared with the vaccine strains. Taken together, the results showed that mutations in the S, N, and ORF3 genes can affect receptor specificity, viral pathogenicity, and the ability to evade the host immune system of the IBT/VN/2018 strain. Our results highlight the importance of molecular characterization of field strains of PEDV for the development of an effective vaccine to control PEDV infections in Vietnam.
Collapse
Affiliation(s)
- Thach Xuan Tran
- Dept of Molecular Microbiology, Institute of Biotechnology, Hanoi, Vietnam
| | - Nguyen T K Lien
- Functional of Genomics Lab, Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ha T Thu
- Dept of Molecular Microbiology, Institute of Biotechnology, Hanoi, Vietnam
| | - Nguyen Dinh Duy
- Dept of Molecular Microbiology, Institute of Biotechnology, Hanoi, Vietnam
| | - Bui T T Duong
- Dept of Molecular Microbiology, Institute of Biotechnology, Hanoi, Vietnam
| | - Dong Van Quyen
- Dept of Molecular Microbiology, Institute of Biotechnology, Hanoi, Vietnam.,University of Science and Technology of Ha Noi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| |
Collapse
|
44
|
King SB, Singh M. Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections. PLoS Comput Biol 2021; 17:e1009560. [PMID: 34793437 PMCID: PMC8601562 DOI: 10.1371/journal.pcbi.1009560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 10/12/2021] [Indexed: 12/24/2022] Open
Abstract
Severe acute respiratory coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, is of zoonotic origin. Evolutionary analyses assessing whether coronaviruses similar to SARS-CoV-2 infected ancestral species of modern-day animal hosts could be useful in identifying additional reservoirs of potentially dangerous coronaviruses. We reasoned that if a clade of species has been repeatedly exposed to a virus, then their proteins relevant for viral entry may exhibit adaptations that affect host susceptibility or response. We perform comparative analyses across the mammalian phylogeny of angiotensin-converting enzyme 2 (ACE2), the cellular receptor for SARS-CoV-2, in order to uncover evidence for selection acting at its binding interface with the SARS-CoV-2 spike protein. We uncover that in rodents there is evidence for adaptive amino acid substitutions at positions comprising the ACE2-spike interaction interface, whereas the variation within ACE2 proteins in primates and some other mammalian clades is not consistent with evolutionary adaptations. We also analyze aminopeptidase N (APN), the receptor for the human coronavirus 229E, a virus that causes the common cold, and find evidence for adaptation in primates. Altogether, our results suggest that the rodent and primate lineages may have had ancient exposures to viruses similar to SARS-CoV-2 and HCoV-229E, respectively.
Collapse
Affiliation(s)
- Sean B. King
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Mona Singh
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America
| |
Collapse
|
45
|
Abdurrahman L, Fang X, Zhang Y. Molecular Insights of SARS-CoV-2 Infection and Molecular Treatments. Curr Mol Med 2021; 22:621-639. [PMID: 34645374 DOI: 10.2174/1566524021666211013121831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 06/15/2021] [Accepted: 07/23/2021] [Indexed: 01/18/2023]
Abstract
The coronavirus disease emerged in December 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome-related coronavirus 2 (SARS-CoV-2) and its rapid global spread has brought an international health emergency and urgent responses for seeking efficient prevention and therapeutic treatment. This has led to imperative needs for illustration of the molecular pathogenesis of SARS-CoV-2, identification of molecular targets or receptors, and development of antiviral drugs, antibodies, and vaccines. In this study, we investigated the current research progress in combating SARS-CoV-2 infection. Based on the published research findings, we first elucidated, at the molecular level, SARS-CoV-2 viral structures, potential viral host-cell-invasion and pathogenic mechanisms, main virus-induced immune responses, and emerging SARS-CoV-2 variants. We then focused on the main virus- and host-based potential targets, summarized and categorized effective inhibitory molecules based on drug development strategies for COVID-19, that can guide efforts for the identification of new drugs and treatment for this problematic disease. Current research and development of antibodies and vaccines were also introduced and discussed. We concluded that the main virus entry route- SARS-CoV-2 spike protein interaction with ACE2 receptors has played a key role in guiding the development of therapeutic treatments against COVID-19, four main therapeutic strategies may be considered in developing molecular therapeutics, and drug repurposing is likely to be an easy, fast and low-cost approach in such a short period of time with urgent need of antiviral drugs. Additionally, the quick development of antibody and vaccine candidates has yielded promising results, but the wide-scale deployment of safe and effective COVID-19 vaccines remains paramount in solving the pandemic crisis. As new variants of the virus begun to emerge, the efficacy of these vaccines and treatments must be closely evaluated. Finally, we discussed the possible challenges of developing molecular therapeutics for COVID-19 and suggested some potential future efforts. Despite the limited availability of literatures, our attempt in this work to provide a relatively comprehensive overview of current SARS-CoV-2 studies can be helpful for quickly acquiring the key information of COVID-19 and further promoting this important research to control and diminish the pandemic.
Collapse
Affiliation(s)
- Lama Abdurrahman
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539. United States
| | - Xiaoqian Fang
- Department of Molecular Science, School of Medicine, The University of Texas Rio Grande Valley, Edinburg, Texas 78539. United States
| | - Yonghong Zhang
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539. United States
| |
Collapse
|
46
|
Hu W, Zhang Y, Fei P, Zhang T, Yao D, Gao Y, Liu J, Chen H, Lu Q, Mudianto T, Zhang X, Xiao C, Ye Y, Sun Q, Zhang J, Xie Q, Wang PH, Wang J, Li Z, Lou J, Chen W. Mechanical activation of spike fosters SARS-CoV-2 viral infection. Cell Res 2021; 31:1047-1060. [PMID: 34465913 PMCID: PMC8406658 DOI: 10.1038/s41422-021-00558-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 08/06/2021] [Indexed: 02/07/2023] Open
Abstract
The outbreak of SARS-CoV-2 (SARS2) has caused a global COVID-19 pandemic. The spike protein of SARS2 (SARS2-S) recognizes host receptors, including ACE2, to initiate viral entry in a complex biomechanical environment. Here, we reveal that tensile force, generated by bending of the host cell membrane, strengthens spike recognition of ACE2 and accelerates the detachment of spike's S1 subunit from the S2 subunit to rapidly prime the viral fusion machinery. Mechanistically, such mechano-activation is fulfilled by force-induced opening and rotation of spike's receptor-binding domain to prolong the bond lifetime of spike/ACE2 binding, up to 4 times longer than that of SARS-S binding with ACE2 under 10 pN force application, and subsequently by force-accelerated S1/S2 detachment which is up to ~103 times faster than that in the no-force condition. Interestingly, the SARS2-S D614G mutant, a more infectious variant, shows 3-time stronger force-dependent ACE2 binding and 35-time faster force-induced S1/S2 detachment. We also reveal that an anti-S1/S2 non-RBD-blocking antibody that was derived from convalescent COVID-19 patients with potent neutralizing capability can reduce S1/S2 detachment by 3 × 106 times under force. Our study sheds light on the mechano-chemistry of spike activation and on developing a non-RBD-blocking but S1/S2-locking therapeutic strategy to prevent SARS2 invasion.
Collapse
Affiliation(s)
- Wei Hu
- grid.13402.340000 0004 1759 700XDepartment of Cardiology of the Second Affiliated Hospital and Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang China
| | - Yong Zhang
- grid.9227.e0000000119573309Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Panyu Fei
- grid.13402.340000 0004 1759 700XDepartment of Cardiology of the Second Affiliated Hospital and Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang China ,grid.13402.340000 0004 1759 700XSchool of Mechanical Engineering, Zhejiang University, Hangzhou, Zhejiang China
| | - Tongtong Zhang
- grid.13402.340000 0004 1759 700XDepartment of Cardiology of the Second Affiliated Hospital and Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang China ,grid.13402.340000 0004 1759 700XDepartment of Hepatobiliary and Pancreatic Surgery, The Center for Integrated Oncology and Precision Medicine, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang China
| | - Danmei Yao
- grid.13402.340000 0004 1759 700XDepartment of Cardiology of the Second Affiliated Hospital and Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang China
| | - Yufei Gao
- grid.13402.340000 0004 1759 700XDepartment of Cardiology of the Second Affiliated Hospital and Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang China ,grid.13402.340000 0004 1759 700XSchool of Mechanical Engineering, Zhejiang University, Hangzhou, Zhejiang China
| | - Jia Liu
- grid.240324.30000 0001 2109 4251Department of Pathology, New York University Grossman School of Medicine, New York, NY USA ,grid.137628.90000 0004 1936 8753The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY USA
| | - Hui Chen
- grid.9227.e0000000119573309Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Qiao Lu
- grid.240324.30000 0001 2109 4251Department of Pathology, New York University Grossman School of Medicine, New York, NY USA ,grid.137628.90000 0004 1936 8753The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY USA
| | - Tenny Mudianto
- grid.240324.30000 0001 2109 4251Department of Pathology, New York University Grossman School of Medicine, New York, NY USA
| | - Xinrui Zhang
- grid.13402.340000 0004 1759 700XDepartment of Cardiology of the Second Affiliated Hospital and Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang China
| | - Chuxuan Xiao
- grid.13402.340000 0004 1759 700XCollaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the MOE Frontier Science Center for Brain Science & Brain-machine Integration, State Key Laboratory for Modern Optical Instrumentation Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang China
| | - Yang Ye
- grid.9227.e0000000119573309Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Qiming Sun
- grid.13402.340000 0004 1759 700XDepartment of Cardiology of the Second Affiliated Hospital and Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang China
| | - Jing Zhang
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong China
| | - Qi Xie
- grid.494629.40000 0004 8008 9315Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, Zhejiang China
| | - Pei-Hui Wang
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong China
| | - Jun Wang
- grid.240324.30000 0001 2109 4251Department of Pathology, New York University Grossman School of Medicine, New York, NY USA ,grid.137628.90000 0004 1936 8753The Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY USA
| | - Zhenhai Li
- grid.39436.3b0000 0001 2323 5732Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Institute of Applied Mathematics and Mechanics, School of Mechanics and Engineering Science, Shanghai University, Shanghai, China
| | - Jizhong Lou
- grid.9227.e0000000119573309Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China ,grid.508040.9Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong China
| | - Wei Chen
- grid.13402.340000 0004 1759 700XDepartment of Cardiology of the Second Affiliated Hospital and Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang China ,grid.13402.340000 0004 1759 700XCollaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the MOE Frontier Science Center for Brain Science & Brain-machine Integration, State Key Laboratory for Modern Optical Instrumentation Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang China ,grid.13402.340000 0004 1759 700XZhejiang Laboratory for Systems and Precision Medicine, Zhejiang University Medical Center, Hangzhou, Zhejiang China
| |
Collapse
|
47
|
Zarei M, Rahimi K, Hassanzadeh K, Abdi M, Hosseini V, Fathi A, Kakaei K. From the environment to the cells: An overview on pivotal factors which affect spreading and infection in COVID-19 pandemic. ENVIRONMENTAL RESEARCH 2021; 201:111555. [PMID: 34197816 PMCID: PMC8236413 DOI: 10.1016/j.envres.2021.111555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 05/24/2021] [Accepted: 06/16/2021] [Indexed: 05/06/2023]
Abstract
Several factors ranging from environmental risks to the genetics of the virus and that of the hosts, affect the spread of COVID-19. The impact of physicochemical variables on virus vitality and spread should be taken into account in experimental and clinical studies. Another avenue to explore is the effect of diet and its interaction with the immune system on SARS-CoV-2 infection and mortality rate. Past year have witnessed extensive studies on virus and pathophysiology of the COVID-19 disease and the cellular mechanisms of virus spreading. However, our knowledge has not reached a level where we plan an efficient therapeutic approach to prevent the virus entry to the cells or decreasing the spreading and morbidity in severe cases of disease. The risk of infection directly correlates with the control of virus spreading via droplets and aerosol transmission, as well as patient immune system response. A key goal in virus restriction and transmission rate is to understand the physicochemical structure of aerosol and droplet formation, and the parameters that affect the droplet-borne and airborne in different environmental conditions. The lifetime of droplets on different surfaces is described based on the contact angle. Hereby, we recommend regular use of high-quality face masks in high temperature and low humidity conditions. However, in humid and cold weather conditions, wearing gloves and frequently hand washing, gain a higher priority. Additionally, social distancing rules should be respected in all aforementioned conditions. We will also discuss different routes of SARS-CoV-2 entry into the cells and how multiple genetic factors play a role in the spread of the virus. Given the role of environmental and nutritional factors, we discuss and recommend some strategies to prevent the disease and protect the population against COVID-19. Since an effective vaccine can prevent the transmission of communicable diseases and abolish pandemics, we added a brief review of candidate SARS-CoV-2 vaccines.
Collapse
Affiliation(s)
- Mohammad Zarei
- Department of Food Science and Technology, School of Industrial Technology, Faculty of Applied Sciences, Universiti Teknologi MARA, 40450, Shah Alam, Selangor, Malaysia
| | - Karim Rahimi
- Department of Molecular Biology and Genetics, Gene Expression and Gene Medicine, Aarhus University, Aarhus, Denmark
| | - Kambiz Hassanzadeh
- Laboratory of Neuronal Cell Signaling, EBRI Rita Levi-Montalcini Foundation, Rome, 00161, Italy; Department of Biotechnology and Applied Clinical Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Mohammad Abdi
- Department of Clinical Biochemistry, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Vahedeh Hosseini
- Department of Molecular Medicine and Genetics, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Ali Fathi
- FUJIFILM Cellular Dynamics, Inc., Madison, WI, USA.
| | - Karim Kakaei
- Department of Chemistry, Faculty of Science, University of Maragheh, Maragheh, Iran.
| |
Collapse
|
48
|
Li L, Honda-Okubo Y, Huang Y, Jang H, Carlock MA, Baldwin J, Piplani S, Bebin-Blackwell AG, Forgacs D, Sakamoto K, Stella A, Turville S, Chataway T, Colella A, Triccas J, Ross TM, Petrovsky N. Immunisation of ferrets and mice with recombinant SARS-CoV-2 spike protein formulated with Advax-SM adjuvant protects against COVID-19 infection. Vaccine 2021; 39:5940-5953. [PMID: 34420786 PMCID: PMC8328570 DOI: 10.1016/j.vaccine.2021.07.087] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/24/2021] [Accepted: 07/29/2021] [Indexed: 12/12/2022]
Abstract
The development of a safe and effective vaccine is a key requirement to overcoming the COVID-19 pandemic. Recombinant proteins represent the most reliable and safe vaccine approach but generally require a suitable adjuvant for robust and durable immunity. We used the SARS-CoV-2 genomic sequence and in silico structural modelling to design a recombinant spike protein vaccine (Covax-19™). A synthetic gene encoding the spike extracellular domain (ECD) was inserted into a baculovirus backbone to express the protein in insect cell cultures. The spike ECD was formulated with Advax-SM adjuvant and first tested for immunogenicity in C57BL/6 and BALB/c mice. Covax-19 vaccine induced high spike protein binding antibody levels that neutralised the original lineage B.1.319 virus from which the vaccine spike protein was derived, as well as the variant B.1.1.7 lineage virus. Covax-19 vaccine also induced a high frequency of spike-specific CD4 + and CD8 + memory T-cells with a dominant Th1 phenotype associated with the ability to kill spike-labelled target cells in vivo. Ferrets immunised with Covax-19 vaccine intramuscularly twice 2 weeks apart made spike receptor binding domain (RBD) IgG and were protected against an intranasal challenge with SARS-CoV-2 virus given two weeks after the last immunisation. Notably, ferrets that received the two higher doses of Covax-19 vaccine had no detectable virus in their lungs or in nasal washes at day 3 post-challenge, suggesting that in addition to lung protection, Covax-19 vaccine may have the potential to reduce virus transmission. This data supports advancement of Covax-19 vaccine into human clinical trials.
Collapse
Affiliation(s)
- Lei Li
- Vaxine Pty Ltd., Bedford Park, Adelaide 5042, SA, Australia; College of Medicine and Public Health, Flinders University, Adelaide 5042, SA, Australia
| | - Yoshikazu Honda-Okubo
- Vaxine Pty Ltd., Bedford Park, Adelaide 5042, SA, Australia; College of Medicine and Public Health, Flinders University, Adelaide 5042, SA, Australia
| | - Ying Huang
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA
| | - Hyesun Jang
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA
| | - Michael A Carlock
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA
| | - Jeremy Baldwin
- Vaxine Pty Ltd., Bedford Park, Adelaide 5042, SA, Australia
| | - Sakshi Piplani
- Vaxine Pty Ltd., Bedford Park, Adelaide 5042, SA, Australia; College of Medicine and Public Health, Flinders University, Adelaide 5042, SA, Australia
| | | | - David Forgacs
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA
| | - Kaori Sakamoto
- Department of Pathology, University of Georgia, Athens, GA, USA
| | - Alberto Stella
- Centre for Virus Research, Westmead Millennium Institute, Westmead Hospital and University of Sydney, Sydney 2145, NSW, Australia
| | - Stuart Turville
- Centre for Virus Research, Westmead Millennium Institute, Westmead Hospital and University of Sydney, Sydney 2145, NSW, Australia
| | - Tim Chataway
- College of Medicine and Public Health, Flinders University, Adelaide 5042, SA, Australia
| | - Alex Colella
- College of Medicine and Public Health, Flinders University, Adelaide 5042, SA, Australia
| | - Jamie Triccas
- School of Medical Sciences and Marie Bashir Institute, University of Sydney, Sydney, NSW 2006, Australia
| | - Ted M Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA; Department of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Nikolai Petrovsky
- Vaxine Pty Ltd., Bedford Park, Adelaide 5042, SA, Australia; College of Medicine and Public Health, Flinders University, Adelaide 5042, SA, Australia.
| |
Collapse
|
49
|
Andújar SA, Gutiérrez LJ, Enriz RD, Baldoni HA. Structure, interface stability and hot-spots identification for RBD(SARS-CoV-2):hACE2 complex formation. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1979229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Sebastián A. Andújar
- Faculty of Chemistry, Biochemistry and Pharmacy, Multidisciplinary Institute of Biological Research (IMIBIO-SL. CONICET), National University of San Luis, San Luis, Argentina
| | - Lucas J. Gutiérrez
- Faculty of Chemistry, Biochemistry and Pharmacy, Multidisciplinary Institute of Biological Research (IMIBIO-SL. CONICET), National University of San Luis, San Luis, Argentina
| | - Ricardo D. Enriz
- Faculty of Chemistry, Biochemistry and Pharmacy, Multidisciplinary Institute of Biological Research (IMIBIO-SL. CONICET), National University of San Luis, San Luis, Argentina
| | - Héctor A. Baldoni
- Faculty of Chemistry, Biochemistry and Pharmacy, Institute of Applied Mathematics of San Luis (IMASL. CONICET), National University of San Luis, San Luis, Argentina
| |
Collapse
|
50
|
Vázquez-Valadez VH, Hernández-Serda A, Jiménez-Cabiedes MF, Aguirre-Vidal P, González-Tapia I, Carreño-Vargas L, Alarcón-López YA, Espejel-Fuentes A, Martínez-Soriano P, Lugo Álvarez M, Velázquez-Sánchez AM, Markarian NM, Angeles E, Abrahamyan L. Evaluation of Inhibitory Activity In Silico of In-House Thiomorpholine Compounds between the ACE2 Receptor and S1 Subunit of SARS-CoV-2 Spike. Pathogens 2021; 10:1208. [PMID: 34578240 PMCID: PMC8468748 DOI: 10.3390/pathogens10091208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/11/2021] [Accepted: 09/13/2021] [Indexed: 11/22/2022] Open
Abstract
At the end of 2019, the world was struck by the COVID-19 pandemic, which resulted in dire repercussions of unimaginable proportions. From the beginning, the international scientific community employed several strategies to tackle the spread of this disease. Most notably, these consisted of the development of a COVID-19 vaccine and the discovery of antiviral agents through the repositioning of already known drugs with methods such as de novo design. Previously, methylthiomorphic compounds, designed by our group as antihypertensive agents, have been shown to display an affinity with the ACE2 (angiotensin converting enzyme) receptor, a key mechanism required for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) entry into target cells. Therefore, the objective of this work consists of evaluating, in silico, the inhibitory activity of these compounds between the ACE2 receptor and the S1 subunit of the SARS-CoV-2 spike protein. Supported by the advances of different research groups on the structure of the coronavirus spike and the interaction of the latter with its receptor, ACE2, we carried out a computational study that examined the effect of in-house designed compounds on the inhibition of said interaction. Our results indicate that the polyphenol LQM322 is one of the candidates that should be considered as a possible anti-COVID-19 agent.
Collapse
Affiliation(s)
- Victor H. Vázquez-Valadez
- Departamento de Ciencias Biológicas FES Cuautitlán, Universidad Nacional Autónoma de México (UNAM), Av. 1 de Mayo SN Cuautitlán Izcalli, Estado de México, México CP 54750, Mexico;
| | - Alejandro Hernández-Serda
- Departamento de Ciencias Químicas FES Cuautitlán, Universidad Nacional Autónoma de México (UNAM), Av. 1 de Mayo SN Cuautitlán Izcalli, Estado de México, México CP 54750, Mexico; (A.H.-S.); (P.M.-S.); (A.M.V.-S.); (E.A.)
| | - Ma. Fernanda Jiménez-Cabiedes
- Laboratorio de Química Medicinal y Teórica FESC, Universidad Nacional Autónoma de México (UNAM), Av. 1 de Mayo SN Cuautitlán Izcalli, Estado de México, México CP 54750, Mexico; (M.F.J.-C.); (P.A.-V.); (I.G.-T.); (L.C.-V.); (Y.A.A.-L.); (A.E.-F.); (M.L.Á.)
| | - Pablo Aguirre-Vidal
- Laboratorio de Química Medicinal y Teórica FESC, Universidad Nacional Autónoma de México (UNAM), Av. 1 de Mayo SN Cuautitlán Izcalli, Estado de México, México CP 54750, Mexico; (M.F.J.-C.); (P.A.-V.); (I.G.-T.); (L.C.-V.); (Y.A.A.-L.); (A.E.-F.); (M.L.Á.)
| | - Ingrid González-Tapia
- Laboratorio de Química Medicinal y Teórica FESC, Universidad Nacional Autónoma de México (UNAM), Av. 1 de Mayo SN Cuautitlán Izcalli, Estado de México, México CP 54750, Mexico; (M.F.J.-C.); (P.A.-V.); (I.G.-T.); (L.C.-V.); (Y.A.A.-L.); (A.E.-F.); (M.L.Á.)
| | - Laura Carreño-Vargas
- Laboratorio de Química Medicinal y Teórica FESC, Universidad Nacional Autónoma de México (UNAM), Av. 1 de Mayo SN Cuautitlán Izcalli, Estado de México, México CP 54750, Mexico; (M.F.J.-C.); (P.A.-V.); (I.G.-T.); (L.C.-V.); (Y.A.A.-L.); (A.E.-F.); (M.L.Á.)
| | - Yoshio A. Alarcón-López
- Laboratorio de Química Medicinal y Teórica FESC, Universidad Nacional Autónoma de México (UNAM), Av. 1 de Mayo SN Cuautitlán Izcalli, Estado de México, México CP 54750, Mexico; (M.F.J.-C.); (P.A.-V.); (I.G.-T.); (L.C.-V.); (Y.A.A.-L.); (A.E.-F.); (M.L.Á.)
| | - Andrea Espejel-Fuentes
- Laboratorio de Química Medicinal y Teórica FESC, Universidad Nacional Autónoma de México (UNAM), Av. 1 de Mayo SN Cuautitlán Izcalli, Estado de México, México CP 54750, Mexico; (M.F.J.-C.); (P.A.-V.); (I.G.-T.); (L.C.-V.); (Y.A.A.-L.); (A.E.-F.); (M.L.Á.)
| | - Pablo Martínez-Soriano
- Departamento de Ciencias Químicas FES Cuautitlán, Universidad Nacional Autónoma de México (UNAM), Av. 1 de Mayo SN Cuautitlán Izcalli, Estado de México, México CP 54750, Mexico; (A.H.-S.); (P.M.-S.); (A.M.V.-S.); (E.A.)
| | - Miguel Lugo Álvarez
- Laboratorio de Química Medicinal y Teórica FESC, Universidad Nacional Autónoma de México (UNAM), Av. 1 de Mayo SN Cuautitlán Izcalli, Estado de México, México CP 54750, Mexico; (M.F.J.-C.); (P.A.-V.); (I.G.-T.); (L.C.-V.); (Y.A.A.-L.); (A.E.-F.); (M.L.Á.)
| | - Ana María Velázquez-Sánchez
- Departamento de Ciencias Químicas FES Cuautitlán, Universidad Nacional Autónoma de México (UNAM), Av. 1 de Mayo SN Cuautitlán Izcalli, Estado de México, México CP 54750, Mexico; (A.H.-S.); (P.M.-S.); (A.M.V.-S.); (E.A.)
| | - Nathan Marko Markarian
- Swine and Poultry Infectious Diseases Research Center (CRIPA) and Research Group on Infectious Diseases in Production Animals (GREMIP), Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC J2S 2M2, Canada;
| | - Enrique Angeles
- Departamento de Ciencias Químicas FES Cuautitlán, Universidad Nacional Autónoma de México (UNAM), Av. 1 de Mayo SN Cuautitlán Izcalli, Estado de México, México CP 54750, Mexico; (A.H.-S.); (P.M.-S.); (A.M.V.-S.); (E.A.)
| | - Levon Abrahamyan
- Swine and Poultry Infectious Diseases Research Center (CRIPA) and Research Group on Infectious Diseases in Production Animals (GREMIP), Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC J2S 2M2, Canada;
| |
Collapse
|