Insights into the mechanism of C5aR inhibition by PMX53 via implicit solvent molecular dynamics simulations and docking.

Phanourios Tamamis,Dimitrios Morikis,Georgios Archontis,Trent M Woodruff,Chris A Kieslich,Gregory V Nikiforovich

doi:10.1186/2046-1682-7-5

Abstract

BackgroundThe complement protein C5a acts by primarily binding and activating the G-protein coupled C5a receptor C5aR (CD88), and is implicated in many inflammatory diseases. The cyclic hexapeptide PMX53 (sequence Ace-Phe-[Orn-Pro-dCha-Trp-Arg]) is a full C5aR antagonist of nanomolar potency, and is widely used to study C5aR function in disease.ResultsWe construct for the first time molecular models for the C5aR:PMX53 complex without the a priori use of experimental constraints, via a computational framework of molecular dynamics (MD) simulations, docking, conformational clustering and free energy filtering. The models agree with experimental data, and are used to propose important intermolecular interactions contributing to binding, and to develop a hypothesis for the mechanism of PMX53 antagonism.ConclusionThis work forms the basis for the design of improved C5aR antagonists, as well as for atomic-detail mechanistic studies of complement activation and function. Our computational framework can be widely used to develop GPCR-ligand structural models in membrane environments, peptidomimetics and other chemical compounds with potential clinical use.

Highlights

The complement protein C5a acts by primarily binding and activating the G-protein coupled C5a receptor C5aR (CD88), and is implicated in many inflammatory diseases
Description of simulation systems C5aR receptor The human GPCR receptor C5aR consists of 350 amino acids, and has the typical GPCR topology, with an extracellular N-terminal fragment, seven trans-membrane (TM) helices interconnected by extracellular (EC) and intracellular (IC) loops, and an intracellular C-terminal fragment [26]
Earlier models of free C5aR, and the complex of C5aR with its natural activator, peptide C5a The C5aR protein has the typical GPCR topology, with an extracellular N-terminal fragment, seven trans-membrane (TM) helices interconnected by extracellular (EC) and intracellular (IC) loops, and an intracellular C-terminal fragment [55]

Summary

Introduction

The complement protein C5a acts by primarily binding and activating the G-protein coupled C5a receptor C5aR (CD88), and is implicated in many inflammatory diseases. We present the development of a structural model for the complex of membrane-embedded C5aR and its antagonist peptide PMX53. We accomplish this by an innovative and comprehensive computational framework that combines conformational sampling for both receptor and ligand with docking, and evaluates a large number (~300,000) of docked conformations by structural and free energy criteria. The complement system is a major and essential component of the innate immune response. It can be activated following infection or injury through four distinct pathways, which lead to opsonisation of pathogens, cell lysis, and the production of potent pro-inflammatory peptides. Given its potent inflammatory activity, prolonged or inappropriate activation of complement can generate unwanted C5a, which is implicated in many inflammatory diseases [2,3]

Objectives

Methods

Results

Conclusion