ArticleJournal of computer-aided molecular design2006
Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors.
Article in Journal of computer-aided molecular design, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 14 citations in OpenAlex.
- Review
- Modelling the active SARS-CoV-2 helicase complex as a basis for structure-based inhibitor design.Chemical science · 2021Article
- The Nonstructural Proteins Directing Coronavirus RNA Synthesis and Processing.Advances in virus research · 2016Review
- What we know but do not understand about nidovirus helicases.Virus research · 2015Review
- Development of chemical inhibitors of the SARS coronavirus: viral helicase as a potential target.Biochemical pharmacology · 2012Review
- Cooperative translocation enhances the unwinding of duplex DNA by SARS coronavirus helicase nsP13.Nucleic acids research · 2010Article
- The interactome: predicting the protein-protein interactions in cells.Cellular & molecular biology letters · 2009Review
- Interaction between SARS-CoV helicase and a multifunctional cellular protein (Ddx5) revealed by yeast and mammalian cell two-hybrid systems.Archives of virology · 2009Article
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The modeling of the severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain was performed using the protein structure prediction Meta Server and the 3D Jury method for model selection, which resulted in the identification of 1JPR, 1UAA and 1W36 PDB structures as suitable templates for creating a full atom 3D model. This model was further utilized to design small molecules that are expected to block an ATPase catalytic pocket thus inhibit the enzymatic activity. Binding sites for various functional groups were identified in a series of molecular dynamics calculation. Their positions in the catalytic pocket were used as constraints in the Cambridge structural database search for molecules having the pharmacophores that interacted most strongly with the enzyme in a desired position. The subsequent MD simulations followed by calculations of binding energies of the designed molecules were compared to ATP identifying the most successful candidates, for likely inhibitors - molecules possessing two phosphonic acid moieties at distal ends of the molecule.
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