The Importance of Detail: How Differences in Ligand Structures Determine Distinct Functional Responses in Integrin α_vβ₃

Abstract

Ligand‐based control of protein functional motions can provide novel opportunities in the study of fundamental biological mechanisms and in the development of novel therapeutics. In this work we addressed the ligand‐based modulation of integrin functions. Inhibitors of integrin αvβ3 are interesting anticancer agents but their molecular mechanisms are still unclear: Peptides and peptidomimetics characterized by the Arg‐Gly‐Asp (RGD) or isoAsp‐Gly‐Arg (isoDGR) binding motifs have shown controversial agonist/antagonist effects. We have investigated the differential mechanisms of integrin activation/deactivation by three distinct ligands (cyclo‐RGDf(NMe)V (Cilengitide), cyclo[DKP3‐RGD], cyclo[DKP3‐isoDGR]; DKP=diketopiperazine) through a comparative analysis of ligand‐controlled protein internal dynamics: Although RGD facilitates the onset of dynamic states leading to activation, isoDGR induces a diffuse rigidification of the complex consistent with antagonist activities. Computational predictions have been experimentally probed by showing that the antibody AP5, which is capable of recognizing the active form of integrin, binds specifically to the RGD complexes and not to the isoDGR complex, which supports opposite functional roles of the two motifs targeting the same binding site.

Nanogold Functionalized With Lipoamide-isoDGR: A Simple, Robust and Versatile Nanosystem for αvβ3-Integrin Targeting

“…This view is supported by the results of in vitro binding experiments showing that iso1, after coupling to nanogold via iso1-PEG 11 -LPA (herein called 1-Au), maintained its capability to bind purified αvβ3 and to recognize MRS melanoma cells, an αvβ3-expressing cell line previously used for the characterization of isoDGR-containing compounds (Nardelli et al, 2018;Paladino et al, 2019). Gold nanoparticles functionalized with iso1-PEG 11 -LPA can also be loaded with ∼11 molecules/NP of biologically active TNF, demonstrating that this strategy is also suitable for preparing bi-functional nanodrugs (called 1-Au/TNF) bearing both targeting and effector moieties.…”

Comparison of Linear vs. Cyclic RGD Pentapeptide Interactions with Integrin αvβ3 by Molecular Dynamics Simulations

“…Cyclic RGD had strong localization ability, and both the binding energy and binding efficiency with Mg 2+ were outstanding (Figures 5A and 7A). Thus, when considering the synthesis of RGD-targeting drugs, cyclic RGD peptides should be considered for their stability and effectiveness, and it is true that many drugs have been designed in recent years based on cyclic RGD, including Cilengitide [35,36].…”

Structural Model for Recruitment of RIT1 to the LZTR1 E3 Ligase: Evidences from an Integrated Computational Approach

“…Molecular recognition, binding phenomena, enzyme catalysis strongly rely on coupled conformational motions, and even small single changes are capable to induce large structural and functional switches. In this context, fine functional regulation can be achieved in the cell by allosteric mechanism by which an event/perturbation at a certain site can tune enzymatic activity or binding affinity in a distal region, leading to the activation of specific conformational states that meet functional requirements. − …”