Computer-aided Rapid Identification And Biological Evaluation Of Bioactive Lead Compounds

In this paper,we employed advanced computer-aided drug design(CADD)technologies in the rapid identification of lead compounds in drug discovery.Based on the methodology investigations as well as the design of target-specific virtual screening strategies,we have successfully identified a number of bioactive lead compounds and carried out in-depth biological test.Compared with time-consuming and high-cost conventional experimental-based techniques,the proper integration of new CADD methods would effective accelerate drug development.Molecular docking,which is the indispensable emphasis in predicting binding conformations and energies of ligands to receptors,constructs the high-throughput virtual screening available.Considering the problems of low accuracy and high false positives within docking-based virtual screening,nine different charge-assigning methods were sufficiently explored for their molecular docking performance by using AutoDock4.2.It has heretofore been substantiated that the calculation of partial charge is very fundamental for the accurate conformation search and binding energy estimation.Our results clearly demonstrated that the empirical Gasteiger-Hiickel(GH)charge is the most applicable in virtual screening for large database;meanwhile,the semi-empirical AM1-BCC charge is practicable in lead compound optimization as well as accurate virtual screening for small databases.We further come to a conclusion that the different atomic charge assigned on atoms,in special function groups(such as phosphate groups),does contribute to the errors in total energy calculation.Additionally,we found that the current method used to calculate electrostatic interactions in AutoDock4.2 still needs to be improved.Lymphoid-specific tyrosine phosphatase(LYP),a critical signaling regulator of immune cells,is associated with various autoimmune diseases.Therefore,a specific LYP inhibitor has great therapeutic potential for treating autoimmune diseases.Herein,we applied a target-ligand interaction-based virtual screening method to identify novel LYP inhibitors.Nine LYP inhibitors with novel scaffolds were identified with eight reversible inhibitors(Ki values ranged from 2.87 to 28.03μM)and one covalent inhibitor.Interestingly,unlike traditional carboxylic acid type LYP inhibitors,the newly identified noncarboxylic acid compound A19 not only exhibits a good LYP selectivity,but also can effectively regulate the TCR signaling pathway.Thus,we carried out a second round of virtual screening towards noncarboxylic acid LYP inhibitors.Combining the use of three LYP crystal structures with different conformations of the WPD loop proved to be helpful to deal with protein flexibility and improve the performance of docking-based virtual screening.After a multistage virtual screening protocol,we identified eight micromolar(from 7.95 μM to 56.6 μM)LYP inhibitors with novel chemotypes.The above studies have not only successfully developed target-specific virtual screening strategies,but also provided a variety of novel scaffolds bearing LYP inhibitory activities.As key regulators of epigenetic regulation,human histone deacetylases(HDACs)have been identified as drug targets for the treatment of several cancers.However,in case of HDAC inhibitors,only a few virtual screening studies have been reported,likely because the current virtual screening methods cannot properly address the zinc-chelating interaction,which is essential for HDAC inhibition.Here,we developed a high-specificity ZBG-based pharmacophore model for HDAC8 inhibitors by incorporating customized ZBG features.Subsequently,pharmacophore-based virtual screening led to the discovery of three novel HDAC8 inhibitors with low micromole IC50 values(1.8-1.9μM).Further studies demonstrated that compound H8-A5 was selective for HDAC8 over HDAC 1/4 and showed anti-proliferation activity in MDA-MB-231 cancer cells.Molecular docking and molecular dynamic studies suggested a possible binding mode for H8-A5,which provides a good starting point for the development of HDAC 8 inhibitors in cancer treatment.SIRT1 a crucial member of the mammalian NAD+-dependent deacetylases,has emerged as an attractive therapeutic target for many aging related diseases.Resveratrol is a natural compound found in red wine and has been suggested to exert its potential health benefit through the activation of SIRT1.Up to now,the most widely accepted mechanism regarding SIRT1 activation is the allosteric mechanism,however,many molecular details regarding this allosteric mechanism remain unclear,and there are limitations to the current substrate-dependent allosteric mechanism of SIRT1 activation.In the current study,based on multiple extensive MD simulations as well as fragment-centric topographical mapping,we have proposed a detailed substrate-dependent mechanism for SIRT1 activation.Our newly proposed mechanism of SIRT1 activation is consistent with current experimental results and has significant implications for the rational design of new substrate-specific SIRT1 modulators.