A highly effective medicine is urgently required to cure coronavirus disease 2019(COVID-19).For the purpose,we developed a molecular docking based webserver,namely D3 Targets-2019-nCoV,with two functions,one is for pr...A highly effective medicine is urgently required to cure coronavirus disease 2019(COVID-19).For the purpose,we developed a molecular docking based webserver,namely D3 Targets-2019-nCoV,with two functions,one is for predicting drug targets for drugs or active compounds observed from clinic or in vitro/in vivo studies,the other is for identifying lead compounds against potential drug targets via docking.This server has its unique features,(1)the potential target proteins and their different conformations involving in the whole process from virus infection to replication and release were included as many as possible;(2)all the potential ligand-binding sites with volume larger than 200 A^3 on a protein structure were identified for docking;(3)correlation information among some conformations or binding sites was annotated;(4)it is easy to be updated,and is accessible freely to public(https://www.d3 pharma.com/D3 Targets-2019-nCoV/index.php).Currently,the webserver contains 42 proteins[20 severe acute respiratory syndrome-related coronavirus 2(SARS-CoV-2)encoded proteins and 22 human proteins involved in virus infection,replication and release]with 69 different conformations/structures and 557 potential ligand-binding pockets in total.With 6 examples,we demonstrated that the webserver should be useful to medicinal chemists,pharmacologists and clinicians for efficiently discovering or developing effective drugs against the SARS-CoV-2 to cure COVID-19.展开更多
The conformational scan of anti-HIV peptide T22 ([Tyr5,12, Lys7]-polyphemusin II) backbone on a deformed potential energy surface (PES) was performed using the potential smoothing searching (PSS) protocol. All located...The conformational scan of anti-HIV peptide T22 ([Tyr5,12, Lys7]-polyphemusin II) backbone on a deformed potential energy surface (PES) was performed using the potential smoothing searching (PSS) protocol. All located minima were then transferred to the original PES using undeformed optimized potentials for liquid simulations (OPLS) potential function, and minimized by multi-con-former minimization (MCM). For solution-phase calculations, the GB/SA continuum model for water was used. This application of PSS integrated with MCM is proved a feasible method for solving the multiple-minimum problem in the conformational analysis of flexible molecules with cyclic structure.展开更多
基金supported by the National Key Research and Development Program of China(2017YFB0202601 and 2016YFA0502301)
文摘A highly effective medicine is urgently required to cure coronavirus disease 2019(COVID-19).For the purpose,we developed a molecular docking based webserver,namely D3 Targets-2019-nCoV,with two functions,one is for predicting drug targets for drugs or active compounds observed from clinic or in vitro/in vivo studies,the other is for identifying lead compounds against potential drug targets via docking.This server has its unique features,(1)the potential target proteins and their different conformations involving in the whole process from virus infection to replication and release were included as many as possible;(2)all the potential ligand-binding sites with volume larger than 200 A^3 on a protein structure were identified for docking;(3)correlation information among some conformations or binding sites was annotated;(4)it is easy to be updated,and is accessible freely to public(https://www.d3 pharma.com/D3 Targets-2019-nCoV/index.php).Currently,the webserver contains 42 proteins[20 severe acute respiratory syndrome-related coronavirus 2(SARS-CoV-2)encoded proteins and 22 human proteins involved in virus infection,replication and release]with 69 different conformations/structures and 557 potential ligand-binding pockets in total.With 6 examples,we demonstrated that the webserver should be useful to medicinal chemists,pharmacologists and clinicians for efficiently discovering or developing effective drugs against the SARS-CoV-2 to cure COVID-19.
基金Sun Ming thanks Prof. Ponder, J. W. and Prof. Nikiforovich, G. V. in Washington University for helpful discussions, and Prof. Garland Marshall and the Chinese State Scholarship Council for support.
文摘The conformational scan of anti-HIV peptide T22 ([Tyr5,12, Lys7]-polyphemusin II) backbone on a deformed potential energy surface (PES) was performed using the potential smoothing searching (PSS) protocol. All located minima were then transferred to the original PES using undeformed optimized potentials for liquid simulations (OPLS) potential function, and minimized by multi-con-former minimization (MCM). For solution-phase calculations, the GB/SA continuum model for water was used. This application of PSS integrated with MCM is proved a feasible method for solving the multiple-minimum problem in the conformational analysis of flexible molecules with cyclic structure.
