Study On The Structure-Activity Relationship Of PDE4/PDE7 Dual Specific Inhibitors

Phosphodiesterase(PDEs) is a large family of enzymes that consists of 11 gene families(PDE1-11).PDE4 and PDE7 are medicinal target of anti-inflammation drugs.PDE4-specific inhibitors show in-vivo excellent anti-inflammation effect.However,these type of inhibitors generally bring side effect such as nausea and omit and thus their application as anti-inflammation drugs were greatly restricted.There is evidence that the inhibition of both PDE4 and PDE7 can overcome these side effect and keeping the pharmaceutical effects.As new generation of anti-inflammation drugs,PDE4 and PDE7 dual inhibitor attracts broad research interests.In chapter one,the sub-types,physiological function and in vivo distribution of PDE4 and PDE7 enzymes were introduced,followed by the systematic review on the structures and categories of PDE4/PDE7 dual-specific inhibitors.In chapter two,we reported the study on the structure-activity relationship of 59 dihydro-phthyridinediones derivative inhibitors by using Comparative Molecular Field Analysis(Co MFA)and Topomer Co MFA.The calculation results indicated that good structure-activity correlation could be obtained when rigid molecule scaffold fitting was applied.With respect to target enzyme PDE4,Co MFA predicted a correlation with q~2and r~2 respectively to be 0.535?0.946.With respect to target enzyme PDE7,Co MFA predicted a correlation with q~2and r~2respectively to be 0.655?0.924.Topomer Co MFA analysis reveal that when better inhibitory activity could be obtained,when a bulky electron withdrawn function groups were introduced to the para-position of the phenyl ring of the benzyl substituent(R1),or to the ortho,meta-position of the phenyl ring of alininoaceyl substituent(R2)of dihydro-phthyridinediones derivatives.In chapter three,we evaluated the binding free energies of PDE inhibitors predicted by two different methods,Auto Dock and MM-PBSA.By calculation the binding free energies of20 ligands with known experimental inhibitory activities against PDE,we found that the binding free energy predicted by Auto Dock or MM-PBSA correlated poorly with the negative logarithm IC50(p IC50)values of these inhibitors,and the resulted correlation coefficient are only 0.40 and 0.47,respectively.Dividing the predicted free energies of Auto Dock or MM-PBSA into their components such as electrostatic energy,Van de Waal interaction energy and desolvation energy,and correlating these components with p IC50 values by multiple regression analysis,better correlation coefficients could be obtained with values of 0.75 and0.67,respectively.The present calculation indicated the Auto Dock or MM-PBSA performed poorly in predicting the binding free energies of PDE inhibitors,and multiple regressions on the free energy components should be more hopeful in activity prediction.In chapter 4,we performed ligand-based virtually screening on the PDE4/PDE7 dual specific inhibitors.Firstly,three representative inhibitors were selected to study their binding modes with PDE4 or PDE7,by using Auto Dock program.Then the obtained binding modes were analyzed by Rocs module of Open Eye program in order to obtain geometrical and electron distribution characters.In the proceeding similarity search in the SPEC database,these character will be used as queries by Rocs to find out candidate molecules that fits well with the queries.These molecule structure will be further filtered by drug-like rules and those don't meet the rules were omitted.Finally,the rested molecule structures will be subject to docking studies in order to investigate the binding mode of these molecules with the targeted protein.Molecules with characteristic binding modes of PDE inhibitors and with predicted binding free energy lower than-8 kcal/mol were selected for wet experimental study.Through the above procedure,we finally obtained 78 molecules.These molecules were purchased and subjected to inhibitory activity tests against PDE4 and PDE7.27 molecules were found to have significant activities with inhibitory ratio greater than 50%under 10 u M concentration.In this study the hit ratio is as high as 35%,demonstrating that our virtual screening strategy is successful.In summary,we theoretically discussed multiple design strategies of PDE4/PDE7 dual specific inhibitors and similarity searching strategy was successful applied to obtain molecule structure with significant inhibitory activities.These molecule could be used as leading compounds for further re-design or optimization.Our molecule searching strategy could also be applied to other similar systems.