Beyond MIDAS: An In Silico Study of a Putative Noncanonical C16 Binding Site in αvβ3 Integrin

TL;DR

This study uses computational methods to explore how a peptide called C16 interacts with a specific integrin receptor, revealing a new binding site that could help design better cancer therapies.

Contribution

The discovery of a putative noncanonical binding site in αvβ3 integrin that explains C16's specificity.

Findings

C16 interacts with αvβ3 integrin via a canonical MIDAS site and a novel noncanonical site (S2).

The S2 site in αvβ3 is stabilized by electrostatic and hydrophobic interactions, not present in α5β1.

MD simulations show αvβ3-C16 complexes are more stable than α5β1-C16 complexes.

Abstract

Integrins are essential
transmembrane receptors that mediate bidirectional
signaling between the extracellular matrix (ECM) and the cytoskeleton.
Among them, αvβ3 and α5β1 are key regulators
of angiogenesis, metastasis, and tumor progression. The laminin-1-derived
C16 peptide (KAFDITYVRLKF) interacts with both integrins, but the
molecular determinants governing its specificity remain unclear. Here,
we applied an integrative computational approach combining ADMET predictions,
molecular docking, and all-atom molecular dynamics (MD) simulations
to characterize C16 pharmacokinetics and its predicted binding modes
to αvβ3 and α5β1. In silico pharmacological profiling indicated that C16 displays low oral bioavailability
and limited permeability but possesses favorable binding properties
and moderate metabolic stability. Docking and MD analyses revealed
that C16 interacts with the canonical metal ion–dependent adhesion
site (MIDAS) in both integrins via conserved hydrogen bonds and hydrophobic
contacts. Strikingly, an additional putative noncanonical binding
pocket (S2) was identified in αvβ3 (not in α5β1),
located opposite the MIDAS. This site forms an amphiphilic interface
stabilized by complementary electrostatic and hydrophobic interactions,
providing a structural rationale for the preferential interaction
of C16 with αvβ3. MD simulations confirmed the stability
of both S1 and S2 complexes, with reduced conformational fluctuations
and lower binding free energies for αvβ3, particularly
at the S2 site. These computational findings propose a novel αvβ3
C16 recognition mode, offering computational insights into predicted
molecular determinants of integrin subtype selectivity and informing
the rational design of peptide-based therapeutics targeting angiogenesis
and tumor invasion.

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