Abstract 748: Development and application of novel <i>in silico</i> methods in the discovery and characterization of integrins antagonists
Authors: Andrea Spitaleri, Michela Ghitti, Silvia Mari, Claudio Bordignon, Gian-Paolo Rizzardi, Giovanna Musco
Journal: Cancer Research (2010)

Abstract Integrins play crucial roles in mediating tumour angiogenesis, therefore gaining increasing importance as drug targets in antiangiogenic cancer therapy. The peptide sequence Arg-Gly-Asp (RGD) is by far the most prominent ligand to promote specific cell adhesion through integrin stimulation and this sequence has been used as a lead for developing different integrin antagonists. Recent biochemical studies have shown that the deamidation of the NGR sequence gives rise to isoDGR, a new αvβ3-binding motif. To design low-molecular mass RGD or isoDGR-containing molecules, the determination of their biologically active conformation is a prerequisite. However, experimental measurements are usually insufficient to draw conclusions concerning the nature of all relevant conformers affecting binding affinity. As computational drug design becomes increasingly reliant on virtual screening and on high-throughput 3D modeling, the need for fast, robust, and reliable methods for sampling molecular conformations is warranted. We have successfully developed an innovative application of MetaDynamics (MtD), a fast computational method to efficiently sample the free energy of complex polyatomic systems in the space of a few course-grained quantities named collective variables (CVs). CVs allows to rapidly and exhaustively describe the whole conformational space accessible to these peptides. The method was applied to analyze a small library of RGD- and isoDGR-containing cyclopeptides to a) identify the highest populated conformations, b) predict their flexibility, and c) obtain reliable structural models that can be docked inside the receptor. Choosing the phi and psi angles of the central glycine as CV, we discriminated among αvβ3-binding and non-binding cyclopeptides. In addition, we demonstrated that the method is able to predict effect of chemical modifications, including metylation and acetylation, to affect flexibility and conformation of the peptides. To validate this approach and its prediction power, we search the whole protein data bank (PDB) using the RGD sequence, and then we mapped the phi and psi angle values of the central glycine for all RGD-containing structures. Remarkably, the natural distribution of glycine phi and psi angles reliably coincide with the one predicted by MtD. Furthermore, the distribution of phi and psi angles of the central glycine can be used as a descriptor to predict the receptor preference of αvβ3- and αIIbβ3-binding cyclopeptides and peptidomimetics. In conclusions, these findings may have an important impact on the discovery and characterization of new diagnostic and therapeutic agents based on the isoDGR motif, providing support for the rationale design and optimization of isoDGR peptidomimetics, for the fine-tuning of their conformations to increase receptor selectivity, and for selection of ligands for chemical synthesis. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 748.