RESUMEN
The novel coronavirus whose outbreak took place in December 2019 continues to spread at a rapid rate worldwide. In the absence of an effective vaccine, inhibitor repurposing or de novo drug design may offer a longer-term strategy to combat this and future infections due to similar viruses. Here, we report on detailed classical and mixed-solvent molecular dynamics simulations of the main protease (Mpro) enriched by evolutionary and stability analysis of the protein. The results were compared with those for a highly similar severe acute respiratory syndrome (SARS) Mpro protein. In spite of a high level of sequence similarity, the active sites in both proteins showed major differences in both shape and size, indicating that repurposing SARS drugs for COVID-19 may be futile. Furthermore, analysis of the binding site's conformational changes during the simulation time indicated its flexibility and plasticity, which dashes hopes for rapid and reliable drug design. Conversely, structural stability of the protein with respect to flexible loop mutations indicated that the virus' mutability will pose a further challenge to the rational design of small-molecule inhibitors. However, few residues contribute significantly to the protein stability and thus can be considered as key anchoring residues for Mpro inhibitor design.
Asunto(s)
Betacoronavirus/enzimología , Cisteína Endopeptidasas/química , Diseño de Fármacos , Inhibidores de Proteasas/farmacología , Bibliotecas de Moléculas Pequeñas , Proteínas no Estructurales Virales/antagonistas & inhibidores , Proteínas no Estructurales Virales/química , Antivirales/farmacología , Betacoronavirus/efectos de los fármacos , Betacoronavirus/genética , Sitios de Unión , COVID-19 , Dominio Catalítico , Proteasas 3C de Coronavirus , Infecciones por Coronavirus , Cristalografía por Rayos X , Cisteína Endopeptidasas/genética , Evaluación Preclínica de Medicamentos , Evolución Molecular , Modelos Moleculares , Simulación de Dinámica Molecular , Mutación , Pandemias , Neumonía Viral , Coronavirus Relacionado al Síndrome Respiratorio Agudo Severo/enzimología , SARS-CoV-2 , Solventes , Termodinámica , Proteínas no Estructurales Virales/genéticaRESUMEN
Several different approaches are used to describe the role of protein compartments and residues in catalysis and to identify key residues suitable for the modification of the activity or selectivity of the desired enzyme. In our research, we applied a combination of molecular dynamics simulations and a water tracking approach to describe the water accessible volume of Solanum tuberosum epoxide hydrolase. Using water as a molecular probe, we were able to identify small cavities linked with the active site: (i) one made up of conserved amino acids and indispensable for the proper positioning of catalytic water and (ii) two others in which modification can potentially contribute to enzyme selectivity and activity. Additionally, we identified regions suitable for de novo tunnel design that could also modify the catalytic properties of the enzyme. The identified hot-spots extend the list of the previously targeted residues used for modification of the regioselectivity of the enzyme. Finally, we have provided an example of a simple and elegant process for the detailed description of the network of cavities and tunnels, which can be used in the planning of enzyme modifications and can be easily adapted to the study of any other protein.