Study On The Mechanism Of Selectivity And Drug Resistance Of Protein-small Molecule System Based On Calculation Of Binding Free Energy

The nuclear protein poly(ADP-ribose)polymerase1(PARP1)inhibitors have been proven effective to potentiate both chemotherapeutic agents and radiotherapy.However,a major problem of most current PARP1 inhibitors is their lack of selectivity for PARP1 and its closest isoform PARP2.NMS-P118 is a highly selective PARP1 inhibitor which is in preclinical studies currently,and the results of studies showed that it binds PARP1 stronger than PARP2 and has many advantages such as excellent pharmacokinetic profiles.In this study,molecular dynamics(MD)simulation of NMS-P118 in complex with PARP1/2 is performed to understand the molecular mechanism of its selectivity.Alanine scanning together with free energy calculation using MM/GBSA and interaction entropy reveal key residues that are responsible for the selectivity.Although the conformation of the binding pockets and NMS-P118 are very similar in PARP1 and PARP2,most of the hot-spot residues in PARP1 have stronger binding free energy than the corresponding residues in PARP2.Detailed analysis of the binding energy shows that the 4’4-difluorocyclohexyl ring on NMS-P118 form favorable hydrophobic interaction with Y889 in PARP1.In addition,the H862 residue in PARP1 has stronger binding free energy than H428 in PARP2,which is due to shorter distance and stronger hydrogen bonds.Moreover,the negatively charged E763 residue in PARP1 forms stronger electrostatic interaction energy with the positively charged NMS-P118 than the Q332 residue in PARP2.These results rationalize the selectivity of NMS-P118 and may be useful for designing novel selective PARP inhibitors.In addition,the variation of protein-ligand binding affinity caused by protein mutation is the key reason to many genetic diseases and drug resistance.Therefore,it is very important to predict such mutation impacts on the binding free energy.In this paper,MD simulations were performed on some systems from the Platinum database,and MM/GBSA method is used to calculate the difference of binding free energy before and after the mutation.The correlation between the calculated result and the experimental value is 0.59,which provided some information for predicting the change of binding free energy before and after protein mutation.And it can be found that this method is more accurate for system in which residues on proteins are mutated to alanine,and the correlation is 0.65.In addition,statistical metrics are used to test the accuracy of this method for predicting key mutations.The results prove the calculated results are correlated with the experiment,but still need to be improved.For the key mutations,the energy change is mainly caused by van der Waals effect.Three examples are selected to analyze the interaction mechanism and explore the causes of energy change.