COMPUTATIONAL TECHNIQUES TO EVALUATE AT ATOMIC LEVEL THE MECHANISM OF MOLECULAR BINDING
Tesi di Dottorato
Data di Pubblicazione:
2017
Citazione:
COMPUTATIONAL TECHNIQUES TO EVALUATE AT ATOMIC LEVEL THE MECHANISM OF MOLECULAR BINDING / C. Paissoni ; tutor: L. Belvisi ; co-tutor: G. Musco ; coordinatore del corso di dottorato: M. Pizzotti. DIPARTIMENTO DI CHIMICA, 2017 Mar 28. 29. ciclo, Anno Accademico 2016. [10.13130/c-paissoni_phd2017-03-28].
Abstract:
Integrins are an important class of transmembrane receptors that relay signals bidirectionally across the plasma membrane, regulating several cell functions and playing a key role in diverse pathological processes. Specifically, integrin subtype αIIbβ3 is involved in thrombosis and stroke, while subtypes αvβ3 and α5β1 play an important role in angiogenesis and tumor progression. They therefore emerged as attractive pharmacological targets. In the past decades several peptides and peptidomimetics targeting these proteins and based on the integrin recognition motif RGD (Arg-Gly-Asp) have been developed, whereby their affinity and selectivity for a specific integrin subtype have been fine-tuned by modulation of RGD flanking residues, by cyclization or by introduction of chemical modifications. Thus far, the design and development of RGD-based cyclopeptides have been mainly based on empirical approaches, requiring expensive and time-consuming synthesis campaigns. In this field, the employment of computational tools, that could be valuable to accelerate the drug design and optimization process, has been limited by the inherent difficulties to predict in silico the three-dimensional structure and the inhibitory activity of cyclopeptides. However, recent improvements in both computational resources and in docking and modeling techniques are expected to open new perspectives in the development of cyclopeptides as modulators of protein-protein interactions and, particularly, as integrin inhibitors.
Within this PhD project, I have investigated the applicability of computational techniques in predicting and rationalizing how the environment of the recognition-motif in cyclopeptides (i.e. flanking residues and introduction of chemical modification) could influence their integrin affinity and selectivity. These features can regulate integrin affinity both by favoring direct interactions with the receptor and/or by modulating the three-dimensional conformation properties of the recognition motif. To take into account both these aspects, I have proposed and optimized a multi-stage computational protocol in which an exhaustive conformational sampling of the investigated cyclopeptides is followed by docking calculations and re-scoring techniques. Specifically: i) the exhaustive sampling could be achieved by using Metadynamics in its Bias Exchange variant (BE-META), an enhanced sampling technique which represents a valuable methodology for the acceleration of rare events, allowing to cross the high free energy barriers characteristic of cyclopeptides and providing reliable estimations of the populations of the accessible conformers. ii) The docking calculations, complemented with the re-scoring technique MM-GB/SA (Molecular Mechanics Generalized Born Surface Area) and the cluster analysis of the decoy poses, allow to evaluate the ability of each peptide to engage interactions with the receptors and to rank the docking poses according to their binding ability; iii) a joint analysis of the previous outcomes results in a reliable ranking of cyclopeptides based on their binding affinity and in the rationalization of their structure-activity relationship. This computational protocol has been exploited in two different applications, illustrated within the thesis.
In the first application the protocol has been applied to rationalize how the introduction of chemical modifications, specifically backbone N-methylation, impacts on the equilibrium conformation and consequently on the integrin affinity of five RGD containing cyclic hexapeptides, which were previously generated by the group of professor Kessler to modulate their selectivity for αIIbβ3 integrin. The study revealed that backbone N-methylation affects the preferences of the φ dihedral an
Tipologia IRIS:
Tesi di dottorato
Keywords:
Molecular Dynamics; Integrin; Docking; Computational Biology
Elenco autori:
C. Paissoni
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