SARS CoV-2 Spike protein in silico interaction with ACE2 receptors from wild and domestic species
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been declared a pandemic by the World Health Organization (WHO) and since its first report it has become a major public health concern. SARS-CoV-2 is closely related to SARS-CoV and SARS-related bat coronaviruses and it has been de...
- Autores:
-
Rendón Marín, Santiago
Martínez Gutiérrez, Marlén
Whittaker, Gary
Jaimes, Javier Andres
Ruiz Sáenz, Julián
- Tipo de recurso:
- Article of investigation
- Fecha de publicación:
- 2021
- Institución:
- Universidad Cooperativa de Colombia
- Repositorio:
- Repositorio UCC
- Idioma:
- OAI Identifier:
- oai:repository.ucc.edu.co:20.500.12494/32931
- Acceso en línea:
- https://hdl.handle.net/20.500.12494/32931
- Palabra clave:
- SARS-CoV-2
COVID-19
Homology modeling
Molecular docking
Spike protein
- Rights
- openAccess
- License
- Atribución – No comercial – Compartir igual
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dc.title.spa.fl_str_mv |
SARS CoV-2 Spike protein in silico interaction with ACE2 receptors from wild and domestic species |
title |
SARS CoV-2 Spike protein in silico interaction with ACE2 receptors from wild and domestic species |
spellingShingle |
SARS CoV-2 Spike protein in silico interaction with ACE2 receptors from wild and domestic species SARS-CoV-2 COVID-19 Homology modeling Molecular docking Spike protein |
title_short |
SARS CoV-2 Spike protein in silico interaction with ACE2 receptors from wild and domestic species |
title_full |
SARS CoV-2 Spike protein in silico interaction with ACE2 receptors from wild and domestic species |
title_fullStr |
SARS CoV-2 Spike protein in silico interaction with ACE2 receptors from wild and domestic species |
title_full_unstemmed |
SARS CoV-2 Spike protein in silico interaction with ACE2 receptors from wild and domestic species |
title_sort |
SARS CoV-2 Spike protein in silico interaction with ACE2 receptors from wild and domestic species |
dc.creator.fl_str_mv |
Rendón Marín, Santiago Martínez Gutiérrez, Marlén Whittaker, Gary Jaimes, Javier Andres Ruiz Sáenz, Julián |
dc.contributor.author.none.fl_str_mv |
Rendón Marín, Santiago Martínez Gutiérrez, Marlén Whittaker, Gary Jaimes, Javier Andres Ruiz Sáenz, Julián |
dc.subject.spa.fl_str_mv |
SARS-CoV-2 COVID-19 Homology modeling Molecular docking Spike protein |
topic |
SARS-CoV-2 COVID-19 Homology modeling Molecular docking Spike protein |
description |
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been declared a pandemic by the World Health Organization (WHO) and since its first report it has become a major public health concern. SARS-CoV-2 is closely related to SARS-CoV and SARS-related bat coronaviruses and it has been described to use angiotensin converting enzyme 2 (ACE2) as a receptor. Natural SARS-CoV-2 infection in domestic and wildlife animals, measured by RT-qPCR, has been confirmed in different countries, especially from the Felidae family. In silico analysis of the interaction between the SARS-CoV-2 spike protein and the cellular receptor ACE2 in various animal species have suggested that wild felids and domestic cats could be susceptible to SARS-CoV-2 based on this interaction. Here, we performed a protein-protein molecular docking analysis of SARS-CoV-2 spike protein with the ACE2 receptor from different animals to elucidate the potential of those species as intermediate hosts or susceptible animals for SARS-CoV-2 infection. Compared to human ACE2, we found that ACE2 receptors from domestic cats and tigers could efficiently interact with RBD of SARS CoV-2 Spike protein. However, dog, ferret, and hamster ACE2 receptor interaction with SARS-CoV-2 S protein RBD was not predicted as favorable, demonstrating a potential differentiated susceptibility in the evaluated species. |
publishDate |
2021 |
dc.date.accessioned.none.fl_str_mv |
2021-01-28T16:56:46Z |
dc.date.available.none.fl_str_mv |
2021-01-28T16:56:46Z |
dc.date.issued.none.fl_str_mv |
2021-01 |
dc.type.none.fl_str_mv |
Artículos Científicos |
dc.type.coar.none.fl_str_mv |
http://purl.org/coar/resource_type/c_2df8fbb1 |
dc.type.coarversion.none.fl_str_mv |
http://purl.org/coar/version/c_970fb48d4fbd8a85 |
dc.type.driver.none.fl_str_mv |
info:eu-repo/semantics/article |
dc.type.version.none.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
format |
http://purl.org/coar/resource_type/c_2df8fbb1 |
status_str |
publishedVersion |
dc.identifier.issn.spa.fl_str_mv |
1664-8021 |
dc.identifier.uri.spa.fl_str_mv |
doi: 10.3389/fgene.2021.571707 |
dc.identifier.uri.none.fl_str_mv |
https://hdl.handle.net/20.500.12494/32931 |
dc.identifier.bibliographicCitation.spa.fl_str_mv |
Rendon-Marin, S., Martínez-Gutiérrez, M., Whittaker, G.R., Jaimes, JA., Ruiz-Saenz, J. (2021). SARS CoV-2 Spike Protein in Silico Interaction With ACE2 Receptors From Wild and Domestic Species. Front. Genet. 12:571707. doi: 10.3389/fgene.2021.571707 |
identifier_str_mv |
1664-8021 doi: 10.3389/fgene.2021.571707 Rendon-Marin, S., Martínez-Gutiérrez, M., Whittaker, G.R., Jaimes, JA., Ruiz-Saenz, J. (2021). SARS CoV-2 Spike Protein in Silico Interaction With ACE2 Receptors From Wild and Domestic Species. Front. Genet. 12:571707. doi: 10.3389/fgene.2021.571707 |
url |
https://hdl.handle.net/20.500.12494/32931 |
dc.relation.ispartofjournal.spa.fl_str_mv |
Front genetics |
dc.relation.references.spa.fl_str_mv |
Al-Tawfiq, J. A., Zumla, A., and Memish, Z. A. (2014). Travel implications of emerging coronaviruses: SARS and MERS-CoV. Travel Med. Infect. Dis. 12, 422–428. doi: 10.1016/j.tmaid.2014.06.007 Benkert, P., Biasini, M., and Schwede, T. (2011). Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics 27, 343–350. doi: 10.1093/bioinformatics/btq662 Bonilla-Aldana, D. K., Ruiz-Saenz, J., Martinez-Gutierrez, M., Tiwari, R., Dhama, K., Jaimes, J. A., et al. (2020). Concerns on the emerging research of SARS-CoV-2 on felines: could they be significant hosts/reservoirs. J. Pure Appl. Microbiol. 14, 1–6. doi: 10.22207/JPAM.14.SPL1.04 Bonilla-Aldana, D. K., Ruiz-Saenz, J., Martinez-Gutierrez, M., Tiwari, R., Dhama, K., Jaimes, J. A., et al. (2020). Concerns on the emerging research of SARS-CoV-2 on felines: could they be significant hosts/reservoirs. J. Pure Appl. Microbiol. 14, 1–6. doi: 10.22207/JPAM.14.SPL1.04 Brooke, G. N., and Prischi, F. (2020). Structural and functional modelling of SARS-CoV-2 entry in animal models. Sci. Rep. 10:15917. doi: 10.1038/ s41598-020-72528-z Cao, Y., Li, L., Feng, Z., Wan, S., Huang, P., Sun, X., et al. (2020). Comparative genetic analysis of the novel coronavirus (2019-nCoV/SARS-CoV-2) receptor ACE2 in different populations. Cell Discov. 6:11. doi: 10.1038/s41421-020- 0147-1 CDC (2020). "Confirmation of COVID-19 in Two Pet Cats in New York", (ed.) U.S.C.F.D.C.A.P. (Cdc). Chan, J. F. -W., Yuan, S., Kok, K. -H., Toi, K. K. -W., Chu, H., Yang, J., et al. (2020a). A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. Lancet 395, 514–523. doi: 10.1016/S0140-6736(20)30154-9 Chan, J. F. -W., Zhang, A. J., Yuan, S., Poon, V. K. -M., Chan, C. C. -S., Lee, A. C. -Y., et al. (2020b). Simulation of the clinical and pathological manifestations of Coronavirus disease 2019 (COVID-19) in golden Syrian hamster model: implications for disease pathogenesis and transmissibility. Clin. Infect. Dis. 71, 2428–2446. doi: 10.1093/cid/ciaa325 Chen, N., Zhou, M., Dong, X., Qu, J., Gong, F., Han, Y., et al. (2020). Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet 395, 507–513. doi: 10.1016/S0140-6736(20)30211-7 Cleary, S. J., Pitchford, S. C., Amison, R. T., Carrington, R., Robaina Cabrera, C. L., Magnen, M., et al. (2020). Animal models of mechanisms of SARS-CoV-2 infection and COVID-19 pathology. Br. J. Pharmacol. 177, 4851–4865. doi: 10.1111/bph.15143 Conceicao, C., Thakur, N., Human, S., Kelly, J. T., Logan, L., Bialy, D., et al. (2020). The SARS-CoV-2 spike protein has a broad tropism for mammalian ACE2 proteins. PLoS Biol. 18:e3001016. doi: 10.1371/journal.pbio.3001016 Cui, J., Li, F., and Shi, Z. L. (2019). Origin and evolution of pathogenic coronaviruses. Nat. Rev. Microbiol. 17, 181–192. doi: 10.1038/s41579-018-0118-9 Li, W., Zhang, C., Sui, J., Kuhn, J. H., Moore, M. J., Luo, S., et al. (2005). Receptor and viral determinants of SARS-coronavirus adaptation to human ACE2. EMBO J. 24, 1634–1643. doi: 10.1038/sj.emboj.7600640 Luan, J., Lu, Y., Jin, X., and Zhang, L. (2020). Spike protein recognition of mammalian ACE2 predicts the host range and an optimized ACE2 for SARS-CoV-2 infection. Biochem. Biophys. Res. Commun. 526, 165–169. doi: 10.1016/j.bbrc.2020.03.047 Martina, B. E., Haagmans, B. L., Kuiken, T., Fouchier, R. A., Rimmelzwaan, G. F., van Amerongen, G., et al. (2003). Virology: SARS virus infection of cats and ferrets. Nature 425:915. doi: 10.1038/425915a Millet, J. K., Jaimes, J. A., and Whittaker, G. R. (2020). Molecular diversity of coronavirus host cell entry receptors. FEMS Microbiol. Rev. fuaa057. doi: 10.1093/femsre/fuaa057 OIE (2020). Questions and Answers on the COVID-19. Available at: https:// www.oie.int/en/scientific-expertise/specific-information-and-recommendations/ questions-and-answers-on-2019novel-coronavirus/ [Online] Ortiz, M. E., Thurman, A., Pezzulo, A. A., Leidinger, M. R., Klesney-Tait, J. A., Karp, P. H., et al. (2020). Heterogeneous expression of the SARS-Coronavirus-2 receptor ACE2 in the human respiratory tract. EBioMedicine 60:102976. doi: 10.1016/j.ebiom.2020.102976 Richard, M., Kok, A., de Meulder, D., Bestebroer, T. M., Lamers, M. M., Okba, N. M., et al. (2020). SARS-CoV-2 is transmitted via contact and via the air between ferrets. bioRxiv. doi: 10.1101/2020.04.16.044503 [Preprint]x Zhai, X., Sun, J., Yan, Z., Zhang, J., Zhao, J., Zhao, Z., et al. (2020). Comparison of severe acute respiratory syndrome coronavirus 2 spike protein binding to ACE2 receptors from Human, pets, farm animals, and putative intermediate hosts. J. Virol. 94, e00831-20. doi: 10.1128/JVI.00831-20 Zhang, Q., Zhang, H., Huang, K., Yang, Y., Hui, X., Gao, J., et al. (2020). SARS-CoV-2 neutralizing serum antibodies in cats: a serological investigation. bioRxiv. doi: 10.1101/2020.04.01.021196 [Preprint]. Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., et al. (2020). A Novel Coronavirus from patients with pneumonia in China, 2019. N. Engl. J. Med. 382, 727–733. doi: 10.1056/NEJMoa2001017 |
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Frontier media Universidad Cooperativa de Colombia, Facultad de Ciencias de la Salud, Medicina Veterinaría y Zootecnia, Bucaramanga |
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Rendón Marín, SantiagoMartínez Gutiérrez, MarlénWhittaker, GaryJaimes, Javier AndresRuiz Sáenz, Julián122021-01-28T16:56:46Z2021-01-28T16:56:46Z2021-011664-8021doi: 10.3389/fgene.2021.571707https://hdl.handle.net/20.500.12494/32931Rendon-Marin, S., Martínez-Gutiérrez, M., Whittaker, G.R., Jaimes, JA., Ruiz-Saenz, J. (2021). SARS CoV-2 Spike Protein in Silico Interaction With ACE2 Receptors From Wild and Domestic Species. Front. Genet. 12:571707. doi: 10.3389/fgene.2021.571707The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been declared a pandemic by the World Health Organization (WHO) and since its first report it has become a major public health concern. SARS-CoV-2 is closely related to SARS-CoV and SARS-related bat coronaviruses and it has been described to use angiotensin converting enzyme 2 (ACE2) as a receptor. Natural SARS-CoV-2 infection in domestic and wildlife animals, measured by RT-qPCR, has been confirmed in different countries, especially from the Felidae family. In silico analysis of the interaction between the SARS-CoV-2 spike protein and the cellular receptor ACE2 in various animal species have suggested that wild felids and domestic cats could be susceptible to SARS-CoV-2 based on this interaction. Here, we performed a protein-protein molecular docking analysis of SARS-CoV-2 spike protein with the ACE2 receptor from different animals to elucidate the potential of those species as intermediate hosts or susceptible animals for SARS-CoV-2 infection. Compared to human ACE2, we found that ACE2 receptors from domestic cats and tigers could efficiently interact with RBD of SARS CoV-2 Spike protein. However, dog, ferret, and hamster ACE2 receptor interaction with SARS-CoV-2 S protein RBD was not predicted as favorable, demonstrating a potential differentiated susceptibility in the evaluated species.http://scienti.colciencias.gov.co:8081/cvlac/visualizador/generarCurriculoCv.do?cod_rh=0000153095https://scienti.minciencias.gov.co/cvlac/visualizador/generarCurriculoCv.do?cod_rh=0000213748https://orcid.org/0000-0002-1447-1458https://orcid.org/0000-0002-9429-0058https://scienti.minciencias.gov.co/gruplac/jsp/visualiza/visualizagr.jsp?nro=00000000000695julian.ruizs@campusucc.edu.comarlen.martinezg@campusucc.edu.cohttps://scholar.google.com/citations?user=o3Y7mZwAAAAJ&hl=eshttps://scholar.google.es/citations?user=flSrsSIAAAAJ&hl=es571707Frontier mediaUniversidad Cooperativa de Colombia, Facultad de Ciencias de la Salud, Medicina Veterinaría y Zootecnia, BucaramangaMedicina veterinaria y zootecniaBucaramangaSARS-CoV-2COVID-19Homology modelingMolecular dockingSpike proteinSARS CoV-2 Spike protein in silico interaction with ACE2 receptors from wild and domestic speciesArtículos Científicoshttp://purl.org/coar/resource_type/c_2df8fbb1http://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionAtribución – No comercial – Compartir igualinfo:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2Front geneticsAl-Tawfiq, J. A., Zumla, A., and Memish, Z. A. (2014). Travel implications of emerging coronaviruses: SARS and MERS-CoV. Travel Med. Infect. Dis. 12, 422–428. doi: 10.1016/j.tmaid.2014.06.007Benkert, P., Biasini, M., and Schwede, T. (2011). Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics 27, 343–350. doi: 10.1093/bioinformatics/btq662Bonilla-Aldana, D. K., Ruiz-Saenz, J., Martinez-Gutierrez, M., Tiwari, R., Dhama, K., Jaimes, J. A., et al. (2020). Concerns on the emerging research of SARS-CoV-2 on felines: could they be significant hosts/reservoirs. J. Pure Appl. Microbiol. 14, 1–6. doi: 10.22207/JPAM.14.SPL1.04Bonilla-Aldana, D. K., Ruiz-Saenz, J., Martinez-Gutierrez, M., Tiwari, R., Dhama, K., Jaimes, J. A., et al. (2020). Concerns on the emerging research of SARS-CoV-2 on felines: could they be significant hosts/reservoirs. J. Pure Appl. Microbiol. 14, 1–6. doi: 10.22207/JPAM.14.SPL1.04Brooke, G. N., and Prischi, F. (2020). Structural and functional modelling of SARS-CoV-2 entry in animal models. Sci. Rep. 10:15917. doi: 10.1038/ s41598-020-72528-zCao, Y., Li, L., Feng, Z., Wan, S., Huang, P., Sun, X., et al. (2020). Comparative genetic analysis of the novel coronavirus (2019-nCoV/SARS-CoV-2) receptor ACE2 in different populations. Cell Discov. 6:11. doi: 10.1038/s41421-020- 0147-1CDC (2020). "Confirmation of COVID-19 in Two Pet Cats in New York", (ed.) U.S.C.F.D.C.A.P. (Cdc).Chan, J. F. -W., Yuan, S., Kok, K. -H., Toi, K. K. -W., Chu, H., Yang, J., et al. (2020a). A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. Lancet 395, 514–523. doi: 10.1016/S0140-6736(20)30154-9Chan, J. F. -W., Zhang, A. J., Yuan, S., Poon, V. K. -M., Chan, C. C. -S., Lee, A. C. -Y., et al. (2020b). Simulation of the clinical and pathological manifestations of Coronavirus disease 2019 (COVID-19) in golden Syrian hamster model: implications for disease pathogenesis and transmissibility. Clin. Infect. Dis. 71, 2428–2446. doi: 10.1093/cid/ciaa325Chen, N., Zhou, M., Dong, X., Qu, J., Gong, F., Han, Y., et al. (2020). Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet 395, 507–513. doi: 10.1016/S0140-6736(20)30211-7Cleary, S. J., Pitchford, S. C., Amison, R. T., Carrington, R., Robaina Cabrera, C. L., Magnen, M., et al. (2020). Animal models of mechanisms of SARS-CoV-2 infection and COVID-19 pathology. Br. J. Pharmacol. 177, 4851–4865. doi: 10.1111/bph.15143Conceicao, C., Thakur, N., Human, S., Kelly, J. T., Logan, L., Bialy, D., et al. (2020). The SARS-CoV-2 spike protein has a broad tropism for mammalian ACE2 proteins. PLoS Biol. 18:e3001016. doi: 10.1371/journal.pbio.3001016Cui, J., Li, F., and Shi, Z. L. (2019). Origin and evolution of pathogenic coronaviruses. Nat. Rev. Microbiol. 17, 181–192. doi: 10.1038/s41579-018-0118-9Li, W., Zhang, C., Sui, J., Kuhn, J. H., Moore, M. J., Luo, S., et al. (2005). Receptor and viral determinants of SARS-coronavirus adaptation to human ACE2. EMBO J. 24, 1634–1643. doi: 10.1038/sj.emboj.7600640Luan, J., Lu, Y., Jin, X., and Zhang, L. (2020). Spike protein recognition of mammalian ACE2 predicts the host range and an optimized ACE2 for SARS-CoV-2 infection. Biochem. Biophys. Res. Commun. 526, 165–169. doi: 10.1016/j.bbrc.2020.03.047Martina, B. E., Haagmans, B. L., Kuiken, T., Fouchier, R. A., Rimmelzwaan, G. F., van Amerongen, G., et al. (2003). Virology: SARS virus infection of cats and ferrets. Nature 425:915. doi: 10.1038/425915aMillet, J. K., Jaimes, J. A., and Whittaker, G. R. (2020). Molecular diversity of coronavirus host cell entry receptors. FEMS Microbiol. Rev. fuaa057. doi: 10.1093/femsre/fuaa057OIE (2020). Questions and Answers on the COVID-19. Available at: https:// www.oie.int/en/scientific-expertise/specific-information-and-recommendations/ questions-and-answers-on-2019novel-coronavirus/ [Online]Ortiz, M. E., Thurman, A., Pezzulo, A. A., Leidinger, M. R., Klesney-Tait, J. A., Karp, P. H., et al. (2020). Heterogeneous expression of the SARS-Coronavirus-2 receptor ACE2 in the human respiratory tract. EBioMedicine 60:102976. doi: 10.1016/j.ebiom.2020.102976Richard, M., Kok, A., de Meulder, D., Bestebroer, T. M., Lamers, M. M., Okba, N. M., et al. (2020). SARS-CoV-2 is transmitted via contact and via the air between ferrets. bioRxiv. doi: 10.1101/2020.04.16.044503 [Preprint]xZhai, X., Sun, J., Yan, Z., Zhang, J., Zhao, J., Zhao, Z., et al. (2020). Comparison of severe acute respiratory syndrome coronavirus 2 spike protein binding to ACE2 receptors from Human, pets, farm animals, and putative intermediate hosts. J. Virol. 94, e00831-20. doi: 10.1128/JVI.00831-20Zhang, Q., Zhang, H., Huang, K., Yang, Y., Hui, X., Gao, J., et al. (2020). SARS-CoV-2 neutralizing serum antibodies in cats: a serological investigation. bioRxiv. doi: 10.1101/2020.04.01.021196 [Preprint].Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., et al. (2020). A Novel Coronavirus from patients with pneumonia in China, 2019. N. Engl. J. 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