In silico comparison of SARS-CoV-2 spike protein-ACE2 binding affinities across species and implications for virus origin.

Scientific Reports
Sakshi PiplaniNikolai Petrovsky

Abstract

The devastating impact of the COVID-19 pandemic caused by SARS-coronavirus 2 (SARS-CoV-2) has raised important questions about its origins and the mechanism of its transfer to humans. A further question was whether companion or commercial animals could act as SARS-CoV-2 vectors, with early data suggesting susceptibility is species specific. To better understand SARS-CoV-2 species susceptibility, we undertook an in silico structural homology modelling, protein-protein docking, and molecular dynamics simulation study of SARS-CoV-2 spike protein's ability to bind angiotensin converting enzyme 2 (ACE2) from relevant species. Spike protein exhibited the highest binding to human (h)ACE2 of all the species tested, forming the highest number of hydrogen bonds with hACE2. Interestingly, pangolin ACE2 showed the next highest binding affinity despite having a relatively low sequence homology, whereas the affinity of monkey ACE2 was much lower despite its high sequence similarity to hACE2. These differences highlight the power of a structural versus a sequence-based approach to cross-species analyses. ACE2 species in the upper half of the predicted affinity range (monkey, hamster, dog, ferret, cat) have been shown to be permissive to SARS-...Continue Reading

References

Dec 5, 1993·Journal of Molecular Biology·A Sali, T L Blundell
Aug 23, 2001·Proceedings of the National Academy of Sciences of the United States of America·N A BakerJ A McCammon
Jul 21, 2004·Journal of Computational Chemistry·Eric F PettersenThomas E Ferrin
Nov 1, 2006·Protein Science : a Publication of the Protein Society·Min-Yi Shen, Andrej Sali
Jan 9, 2010·Acta Crystallographica. Section D, Biological Crystallography·Vincent B ChenDavid C Richardson
Dec 8, 2010·Bioinformatics·Pascal BenkertTorsten Schwede
May 23, 2014·Journal of Chemical Information and Modeling·Rashmi KumariAndrew Lynn
May 19, 2017·Nucleic Acids Research·Yumeng YanSheng-You Huang
Mar 1, 2020·Travel Medicine and Infectious Disease·Tauseef AhmadAlfonso J Rodriguez-Morales
Mar 1, 2020·International Journal of Surgery·Catrin SohrabiRiaz Agha
Mar 11, 2020·Cell·Alexandra C WallsDavid Veesler
Mar 21, 2020·Current Biology : CB·Tao ZhangZhigang Zhang
Mar 24, 2020·Biochemical and Biophysical Research Communications·Junwen LuanLeiliang Zhang
Mar 28, 2020·Science·Seth Berkley
Mar 28, 2020·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Jasper Fuk-Woo ChanKwok-Yung Yuen
Mar 29, 2020·Nature·Tommy Tsan-Yuk LamWu-Chun Cao
Mar 30, 2020·The Veterinary Record·Angel Almendros
Apr 1, 2020·Nature·Jian ShangFang Li
Apr 3, 2020·Journal of Medical Virology·Junwen LuanLeiliang Zhang
Apr 5, 2020·The Veterinary Record·Angel Almendros, Emily Gascoigne
Apr 8, 2020·Cell Host & Microbe·Young-Il KimYoung Ki Choi
Apr 10, 2020·Nature Protocols·Yumeng YanSheng-You Huang
Apr 11, 2020·Nature Reviews. Drug Discovery·Tung Thanh LeStephen Mayhew
Apr 14, 2020·JAMA : the Journal of the American Medical Association·James M SandersJames B Cutrell
Apr 23, 2020·Animal Models and Experimental Medicine·Pin YuChuan Qin
May 8, 2020·Nature·Kangpeng XiaoYongyi Shen
May 8, 2020·Nature·Linlin BaoChuan Qin
May 15, 2020·Nature·Thomas H C SitMalik Peiris
May 29, 2020·The Journal of Physical Chemistry Letters·Angelo SpinelloAlessandra Magistrato
May 31, 2020·International Journal of Molecular Sciences·Aleix GimenoSantiago Garcia-Vallvé
Jun 7, 2020·Proceedings of the National Academy of Sciences of the United States of America·Yingjie WangJiali Gao
Jun 20, 2020·Xenotransplantation·Tanja Opriessnig, Yao-Wei Huang
Jul 8, 2020·Pathogens·Ahmed S Abdel-Moneim, Elsayed M Abdelwhab
Jul 11, 2020·Nature Structural & Molecular Biology·Antoni G WrobelSteven J Gamblin
Jul 18, 2020·BioRxiv : the Preprint Server for Biology·M R AlexanderM S Madhur

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Citations

Apr 1, 2021·Environmental Chemistry Letters·Rossana SegretoDaoyu Zhang
Aug 28, 2021·Journal of Personalized Medicine·Maged N Kamel Boulos, Peng Zhang

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Software Mentioned

gromacs
HDOCK
UCSF Chimera package
MMPBSA
Modeller
tleap
HADDOCK
BLAST
UCSF Chimera
PSI

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