Conformational analysis of peptides and proteins for drug design using molecular simulations

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Abstract

The intrinsic plasticity of biological systems provides opportunities for rational design of selective and potent ligands. Increasingly, computational methods are being applied to predict biomolecular flexibility. However, the motions involved in these processes can be large and occur on time scales generally difficult to achieve with standard simulation methods. In order to overcome the intrinsic limitations of classical molecular dynamics, this Ph.D project focuses on the application of advanced sampling computational techniques to capture the plasticity of diverse biological systems. The first of these applications involved the evaluation of the secondary structure of the N-terminal portion of p53 and its inverse, reverse and retro-inverso sequences by using replica exchange molecular dynamics simulations in implicit solvent. In this study, we also evaluated the effects of reversal of sequence and stereochemistry in mimicking an inhibitory pharmacophoric conformation. The results showed how the ability to mimic the parent peptide is severely compromised by backbone orientation (for D-amino acids) and side-chain orientation (for reversed sequences). Moreover, the structural information obtained from simulations showed good agreement with NMR and circular dichroism studies, confirming the validity of the combination of replica exchange molecular dynamics with the ff99SB force field and Generalized Born solvent model for computational modelling of D-peptide conformations.In a second work, we explored conformations of the DFG motif of the p38α mitogen-activated protein (MAP) kinase. To achieve this, we employed an advanced sampling simulation method that has been developed in-house, called swarm-enhanced sampling molecular dynamics (sesMD). In contrast to multiple independent MD simulations, swarm-coupled sesMD trajectories were able to sample a wide range of DFG conformations, some of which map onto existing crystal structures. Simulated structures intermediate between DFG-in and DFG-out conformations were predicted to have druggable pockets of interest for structure-based ligand design. Overall, sesMD shows promise as a useful tool for enhanced sampling of complex conformational landscapes. Finally, we used microsecond MD simulations to evaluate the molecular plasticity of R-spondins, a class of proteins involved in the activation of the Wnt pathway. The unbound R-spondin 1 is characterised by a closed conformation, while, when complexed to proteins LGR and RNF43/ZNRF3, assumes an open and more extended arrangement. This is true also for R-spondin 2, in both its unbound or bound forms. From our simulation, we find that the closed R-spondin 1 conformation is stable, whilst, R-spondin 1 and 2 from their open conformation explore several intermediate structures. In addition, we evaluated the druggability of a potential binding site located at the interface between the second and the third β-hairpin moiety of the first furin domain. The computational screening with small molecular fragments provided interesting insights about the druggability and the pharmacophoric features of the potential binding pockets identified, outlining promising future perspectives of structure-based design of Wnt pathway inhibitors.

Keyword(s)

Advanced sampling methods; Molecular dynamics simulations; Protein kinases; R-spondin proteins; Retro-inverso peptidomimetics

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