The Virtual Screening Of HNE Inhibitors And Conformational Space Search Of Peptide

Human Neutrophil Elastase(HNE)is related to many pulmonary inflammatory disorders.Even though the large number of HNE inhibitors described in the literature,and many of them were evaluated in clinical trials.However,because of some reasons,nowadays,only one inhibitor Sivelestat sodium hydrate(ONO-5046)was marketed,and it is limited to use in Japan and Korea for the treatment of acute lung injury,since its development in the USA was terminated in 2003.So,it is important to develop new HNE inhibitors to allow for more effective treatments for those pulmonary inflammatory disorders.In the paper,we used the method of computer aided drug design to obtain 4 new HNE inhibitors by virtual screening and study the binding modes between those inhibitors and HNE.On the basis of the information of the HNE crystal structures and the HNE inhibitors,we used the method combined ligand-based and structure-based to virtual screen.Then,after the screening of binding free energy calculation(MM/PBSA),the screening of ring systems and the analysis of the binding mode,the candidate compounds was chosen.Then we purchased some of those compounds and tested the biology activity,finally ensured 4 new HNE inhibitors with the inhibition activity to HNE in micromole.Next,we study the binding modes between the new inhibitors and HNE by docking,molecular dynamics simulation,binding free energy calculation(MM/PBSA).Compared to the biological activity,the calculated value of binding free energy of those inhibitors can get a good matching in the relative activity.It helps ensure the binding mode between the inhibitors and HNE is right.The virtual screening of the HNE inhibitors and the binding mode between the new HNE inhibitor with HNE can help develop additional potent HNE inhibitors.On the other hand,protein structure predictions are of paramount importance for understanding their function,as well as the interactions with other molecules.However,the use of molecular simulation techniques to directly predict the protein structure from the primary amino acid sequence is always hindered by the rough topology of the conformational space and the limited simulation time scale.We developed here a new strategy,named Multiple Simulated Annealing-Molecular Dynamics(MSA-MD)to identify the native states of a peptide and Trp-cage miniprotein.A cluster of structures folded to a CaRMSD below 2.0 A of the native structure can be obtained by performing MSA-MD simulation complexed with an empirical-based screening.In all the cases,the MSA-MD method turned out to be significantly more efficient in reaching the native structure compared to conventional Molecular Dynamics(cMD)and Simulated Annealing-Molecular Dynamics(SA-MD)simulation.