A combined fragment-based virtual screening and STD-NMR approach for the identification of E-cadherin ligands

Cadherins promote cell-cell adhesion by forming homophilic interactions via their N-terminal extracellular domains. Hence, they have broad-ranging physiological effects on tissue organization and homeostasis. When dysregulated, cadherins contribute to different aspects of cancer progression and metastasis; therefore, targeting the cadherin adhesive interface with small-molecule antagonists is expected to have potential therapeutic and diagnostic value. Here, we used molecular docking simulations to evaluate the propensity of three different libraries of commercially available drug-like fragments (nearly 18,000 compounds) to accommodate into the Trp2 binding pocket of E-cadherin, a crucial site for the orchestration of the protein’s dimerization mechanism. Top-ranked fragments featuring five different aromatic chemotypes were expanded by means of a similarity search on the PubChem database (Tanimoto index >90%). Of this set, seven fragments containing an aromatic scaffold linked to an aliphatic chain bearing at least one amine group were finally selected for further analysis. Ligand-based NMR data (Saturation Transfer Difference, STD) and molecular dynamics simulations suggest that these fragments can bind E-cadherin mostly through their aromatic moiety, while their aliphatic portions may also diversely engage with the mobile regions of the binding site. A tetrahydro-β-carboline scaffold functionalized with an ethylamine emerged as the most promising fragment

Determination of the binding epitope of RGD-peptidomimetics to \u3b1v\u3b23 and \u3b1IIb\u3b23 integrin-rich intact cells by NMR and computational studies

NMR experiments (transferred NOE and Saturation Transfer Difference) were used to shed light on the binding epitope of RGD peptidomimetics 1-3 with integrins \u3b1v\u3b23 and \u3b1IIb\u3b23, expressed on the membrane of ECV304 bladder cancer cells and human platelets, respectively. The NMR results were supported by docking calculations in the active sites of \u3b1v\u3b23 and \u3b1IIb\u3b23 integrin receptors and were compared to the results of competitive \u3b1v\u3b23 receptor binding assays and competitive ECV304 cell adhesion experiments. While cis RGD ligand 1 interacts mainly with the \u3b1 integrin subunit through its basic guanidine group, trans RGD ligands 2 and 3 are able to interact with both the \u3b1 and \u3b2 integrin subunits via an electrostatic clam

“Don’t blame the shopkeeper!!” Food, drink and confectionery advertising and British Government market controls during the Second World War

A novel series of \u3b2-lactam derivatives that was designed and synthesized to target RGD-binding and leukocyte integrins is reported. The compound library was evaluated by investigating the effects on integrin-mediated cell adhesion and cell signaling in cell lines expressing \u3b1v\u3b23, \u3b1v\u3b25, \u3b1v\u3b26, \u3b15\u3b21, \u3b1IIb\u3b23, \u3b14\u3b21, and \u3b1L\u3b22 integrins. SAR analysis of the new series of azetidinones enabled the recognition of structural elements associated with integrin selectivity. We obtained selective and potent agonists that could induce cell adhesion and promote cell signaling mediated by \u3b1v\u3b23, \u3b1v\u3b25, \u3b15\u3b21, or \u3b14\u3b21 integrin, and antagonists for the integrins \u3b1v\u3b23 and \u3b15\u3b21, as well as \u3b14\u3b21 and \u3b1L\u3b22, preventing the effects elicited by the respective endogenous agonists

Synthesis and Biological Evaluation of RGD and isoDGR-Monomethyl Auristatin Conjugates Targeting Integrin (V3)

This work reports the synthesis of a series of small molecule-drug conjugates containing the \u3b1V\u3b23-integrin ligand cyclo[DKP-RGD] or cyclo[DKP-isoDGR], a lysosomally cleavable Val-Ala (VA) linker or an "uncleavable" version devoid of this sequence, and monomethyl Auristatin E (MMAE) or F (MMAF) as cytotoxic agent. The conjugates were obtained via a straightforward synthetic scheme taking advantage of a copper-catalyzed azide-alkyne cycloaddition as key-step. The conjugates were tested for their binding affinity to the isolated \u3b1v\u3b23 receptor, and shown to retain nanomolar IC50 values, in the same range of the free ligands. The cytotoxic activity of the conjugates was evaluated in cell viability assays with \u3b1v\u3b23 integrin over-expressing human glioblastoma (U87) and human melanoma (M21) cells. The conjugates possess a markedly lower cytotoxic activity compared to the free drugs, which is consistent with an inefficient integrin-mediated internalization. In almost all cases the conjugates featuring isoDGR as integrin ligand exhibited higher potency than their RGD counterparts. In particular, cyclo[DKP-isoDGR]-VA-MMAE conjugate has low nanomolar IC50 values in cell viability assays with both cancer cell lines tested (U87: 11.50 \ub1 0.13 nM; M21: 6.94 \ub1 0.09 nM) and is therefore a promising candidate for in vivo experiments.This work reports the synthesis of a series of small-molecule\u2013drug conjugates containing the \u3b1 V \u3b2 3 -integrin ligand cyclo[DKP-RGD] or cyclo[DKP-isoDGR], a lysosomally cleavable Val-Ala (VA) linker or an \u201cuncleavable\u201d version devoid of this sequence, and monomethyl auristatin E (MMAE) or F (MMAF) as the cytotoxic agent. The conjugates were obtained via a straightforward synthetic scheme taking advantage of a copper-catalyzed azide\u2013alkyne cycloaddition as the key step. The conjugates were tested for their binding affinity for the isolated \u3b1 v \u3b2 3 receptor and were shown to retain nanomolar IC 50 values, in the same range as those of the free ligands. The cytotoxic activity of the conjugates was evaluated in cell viability assays with \u3b1 v \u3b2 3 integrin overexpressing human glioblastoma (U87) and human melanoma (M21) cells. The conjugates possess markedly lower cytotoxic activity than the free drugs, which is consistent with inefficient integrin-mediated internalization. In almost all cases the conjugates featuring isoDGR as integrin ligand exhibited higher potency than their RGD counterparts. In particular, the cyclo[DKP-isoDGR]-VA-MMAE conjugate has low nanomolar IC 50 values in cell viability assays with both cancer cell lines tested (U87: 11.50\ub10.13 nm; M21: 6.94\ub10.09 nm) and is therefore a promising candidate for in vivo experiments

Rational Design of Antiangiogenic Helical Oligopeptides Targeting the Vascular Endothelial Growth Factor Receptors

Tumor angiogenesis, essential for cancer development, is regulated mainly by vascular endothelial growth factors (VEGFs) and their receptors (VEGFRs), which are overexpressed in cancer cells. Therefore, the VEGF/VEGFR interaction represents a promising pharmaceutical target to fight cancer progression. The VEGF surface interacting with VEGFRs comprises a short α-helix. In this work, helical oligopeptides mimicking the VEGF-C helix were rationally designed based on structural analyses and computational studies. The helical conformation was stabilized by optimizing intramolecular interactions and by introducing helix-inducing Cα,α-disubstituted amino acids. The conformational features of the synthetic peptides were characterized by circular dichroism and nuclear magnetic resonance, and their receptor binding properties and antiangiogenic activity were determined. The best hits exhibited antiangiogenic activity in vitro at nanomolar concentrations and were resistant to proteolytic degradation

Editorial: Peptides Targeting Protein-Protein Interactions: Methods and Applications

2 pagsPeer reviewe

High Affinity vs. Native Fibronectin in the Modulation of αvβ3 Integrin Conformational Dynamics: Insights from Computational Analyses and Implications for Molecular Design

<div><p>Understanding how binding events modulate functional motions of multidomain proteins is a major issue in chemical biology. We address several aspects of this problem by analyzing the differential dynamics of αvβ3 integrin bound to wild type (wtFN10, agonist) or high affinity (hFN10, antagonist) mutants of fibronectin. We compare the dynamics of complexes from large-scale domain motions to inter-residue coordinated fluctuations to characterize the distinctive traits of conformational evolution and shed light on the determinants of differential αvβ3 activation induced by different FN sequences. We propose an allosteric model for ligand-based integrin modulation: the conserved integrin binding pocket anchors the ligand, while different residues on the two FN10’s act as the drivers that reorganize relevant interaction networks, guiding the shift towards inactive (hFN10-bound) or active states (wtFN10-bound). We discuss the implications of results for the design of integrin inhibitors.</p></div

Close-up view of hFN10 complex.

<p>Important structural elements are indicated: α1 (green), α7 (red), strand β5 (blue). Mn²⁺ are displayed as transparent blue spheres. Ghost cartoons are used for αvβ3 (cyan and pink codes for αv and β3, respectively) and fibronectin (yellow). Ghost surface evidences W129_β3, Y122_β3, W1496_FN and Y1446_FN (from the right to the left). RGD-guanidinium and aspartic acids of the electrostatic clamp (namely D150_αv and D218_αv) are also indicated as sticks. Note that the solvent-exposed Y122_β3 belongs to β5 strand (blue) that spans the whole β3 subunit (see main text).</p

Glycomimetic antagonists of BC2L-C lectin: insights from molecular dynamics simulations

Opportunistic infections from multidrug-resistant pathogens such as Burkholderia cenocepacia are a threatening risk for hospital-bound patients suffering from immunocompromised conditions or cystic fibrosis. B. cenocepacia BC2L-C lectin has been linked to bacterial adhesion and biofilm formation, thus hindering its activity is seen as a promising strategy to reduce the severity of the infection. We recently described the first bifunctional ligands of the trimeric N-terminal domain of BC2L-C (BC2L-C-Nt), capable of simultaneously engaging its fucose-specific sugar binding site and a vicinal region at the interface between two monomers. Here, we report a computational workflow for the study of these glycomimetic bifunctional ligands in complex with BC2L-C-Nt, aimed at investigating the molecular basis of ligand binding and the dynamics of glycomimetic/lectin interactions. In particular, we evaluated the use of molecular docking in the protein trimer, followed by refinement using MM-GBSA re-scoring and MD simulations in explicit water. Computational results were compared to experimental data derived from X-ray crystallography and isothermal titration calorimetry. The computational protocol proved suitable to provide a reliable description of the interactions between the ligands and BC2L-C-Nt, highlighting the contribution of MD simulations in explicit solvent for a good fit with the experimental observations. The information achieved in the study and the whole workflow appear promising for the structure-based design of improved BC2L-C-Nt ligands as novel antimicrobials with antiadhesive properties