Study On The Binding Mechanism Of PD1 With PDL1/L2 And The Design Of PD1 Inhibitor

The signaling pathway regulated by programmed cell death protein 1(PD1)and its homologous ligand programmed death-ligands(PDL)has attracted great attention in the development of anticancer drugs.Most tumor cells can up-regulate PDL1 ligand and that inhibits the body’s immune system,preventing the immune system from killing tumor cells.One of the basic ideas for cancer antibody therapy is to block PD1/PDL protein-protein interaction(PPI).To date,several drugs for targeting PD1/PDL1 have been approved by the FDA(such as Nivolumab and Atezolizumab)and many else under(pre-)clinical research.Nevertheless,it is noteworthy that all these drugs(candidates)are monoclonal antibodies with the inherent disadvantages compared with small molecule drugs.Such as:(1)cannot be taken orally;(2)not easy to penetrate tumor tissue and physiological barrier;(3)high immunogenicity;(4)long half-life,pharmacokinetics not easy to control;(5)need cold chain transportation;(6)expensive.Undoubtedly,the development of small molecular inhibitors for PD1 pathway has great value.Unfortunately,the development of small molecule drugs is lagged far behind the monoclonal antibody drugs discovery in the field of tumor immunotherapy.Up to now,no small molecule inhibitors have been approved by FDA.There are two reasons why the design of small molecule inhibitors is so difficult.Firstly,is the poor mechanism understanding of PD1/PDL PPI,in spite of the atomic-detailed crystal structures of the apo-state PD1 and holo-state in PD1/PDL1 complex were reported recently.Another ligand named programmed death-ligand 2(PDL2)protein binds PD1 as well,however,the crystal structure of human did not solved yet.In recent years,several theoretical simulations on the study of conformational dynamics of PD1/PDL1 complex were carried out.Different from the widely-studied PD1/PDL1,the molecular modelling on PD1/PDL2 is even rare probed,due to the lack of crystal structure of human PDL2 protein.Understanding the mechanism of action between PD1/PDL1 and PD1/PDL2 is very important for small molecule targeting PD1 pathway,so it is necessary to study the interaction between PD1/PDL1 and PD1/PDL2 from the molecular level.Secondly,PD1/PDL interaction belongs to PPI,which has a large,hydrophobic and flat interaction interface,and lack of suitable docking sites.The traditional drug design method has bad effect.How to find a suitable docking site,and how to optimize the existing drug design methods to design a high affinity small molecule inhibitor for PD1 has important significance.This thesis consists of four chapters.The first chapter mainly describes the structure characteristics of PD1,PDL1,PDL2.In addition,the calculation methods,MD,MM/ GBSA,etc.used in this paper are also introduced.In chapter two,the binding mechanism of PD1 and PDL1\L2 ligands is clarified.We found the significantly different induce-fit binding mechanisms,and the hot-spot residues for PD1/PDL1(L2)complexes were detected,which is guidable for further designing small-molecular regulators to selectively break the PPI interfaces of PD1/ PD1/PDL1(L2).In chapter three,the rational design of high affinity small molecular inhibitors is presented.First of all,combined with the binding mechanism analysis and MD simulations,we found that PD1 C’D loop can form a stable pocket with C’ sheet,which has a good depth and space and is suitable for docking.Secondly,we modified the Fragment-based drug design method,taking 20 common amino acids as fragments,taking the target residence time,binding free energy and geometric matching degree as scores.Small molecule hit compounds with high affinity were designed.Chapter four summarizes the pros and cons of this thesis.