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Open Access Highly Accessed Research article

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

Phanourios Tamamis1, Chris A Kieslich2, Gregory V Nikiforovich3, Trent M Woodruff4, Dimitrios Morikis2* and Georgios Archontis1*

Author Affiliations

1 Department of Physics, University of Cyprus, PO 20537, CY1678 Nicosia, Cyprus

2 Department of Bioengineering, University of California, Riverside, CA 92521, USA

3 MolLife Design LLC, St. Louis 63141, USA

4 School of Biomedical Sciences, the University of Queensland, St Lucia 4072, Australia

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BMC Biophysics 2014, 7:5  doi:10.1186/2046-1682-7-5

Published: 12 August 2014

Abstract

Background

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. 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.

Results

We 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.

Conclusion

This 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.

Keywords:
Class A GPCR; C5aR; C5a; Complement system; Molecular dynamics; Docking; Implicit solvent; Membrane protein