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...

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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
id COOPER2_569f677e9b84bc0054ab5ce9b9d00f18
oai_identifier_str oai:repository.ucc.edu.co:20.500.12494/32931
network_acronym_str COOPER2
network_name_str Repositorio UCC
repository_id_str
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
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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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spelling 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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