Residue-based pharmacophore approaches to study protein-protein interactions

Assessing the functional impact of protein binding site definition

Many biomedical applications, such as classification of binding specificities or bioengineering, depend on the accurate definition of protein binding interfaces. Depending on the choice of method used, substantially different sets of residues can be classified as belonging to the interface of a protein. A typical approach used to verify these definitions is to mutate residues and measure the impact of these changes on binding. Besides the lack of exhaustive data, this approach also suffers from the fundamental problem that a mutation introduces an unknown amount of alteration into an interface, which potentially alters the binding characteristics of the interface. In this study we explore the impact of alternative binding site definitions on the ability of a protein to recognize its cognate ligand using a pharmacophore approach, which does not affect the interface. The study also shows that methods for protein binding interface predictions should perform above approximately F-score = 0.7 accuracy level to capture the biological function of a protein.

Discovery of a Dual Tubulin and Neuropilin-1 (NRP1) Inhibitor with Potent In Vivo Anti-Tumor Activity via Pharmacophore-based Docking Screening, Structure Optimization, and Biological Evaluation

Dual inhibition of tubulin and neuropilin-1 (NRP1) may become an effective method for cancer treatment by simultaneously killing tumor cells and inhibiting tumor angiogenesis. Herein, we identified dual tubulin/NRP1-targeting inhibitor TN-2, which exhibited good inhibitory activity against both tubulin polymerization (IC50 = 0.71 ± 0.03 μM) and NRP1 (IC50 = 0.85 ± 0.04 μM). Importantly, it significantly inhibited the viability of several human prostate tumor cell lines. Further mechanism studies indicated that TN-2 could inhibit tubulin polymerization and cause G2/M arrest, thereby inducing cell apoptosis. It could also suppress cell tube formation, migration, and invasion. Moreover, TN-2 showed obvious antitumor effects on the PC-3 cell-derived xenograft model with negligible side effects and good pharmacokinetic profiles. These data demonstrate that TN-2 could be a promising dual-target chemotherapeutic agent for the treatment of prostate cancer.

Assessing the functional impact of protein binding site definition

Many biomedical applications, such as classification of binding specificities or bioengineering, depend on the accurate definition of protein binding interfaces. Depending on the choice of method used, substantially different sets of residues can be classified as belonging to the interface of a protein. A typical approach used to verify these definitions is to mutate residues and measure the impact of these changes on binding. Besides the lack of exhaustive data this approach generates, it also suffers from the fundamental problem that a mutation introduces an unknown amount of alteration into an interface, which potentially alters the binding characteristics of the interface. In this study we explore the impact of alternative binding site definitions on the ability of a protein to recognize its cognate ligand using a pharmacophore approach, which does not affect the interface. The study also provides guidance on the minimum expected accuracy of interface definition that is required to capture the biological function of a protein.

Allosteric regulation of binding specificity of HVEM for CD160 and BTLA ligands upon G89F mutation

Molecular interactions mediated by engagement of the Herpes virus entry mediator (HVEM) with members of TNF and Ig superfamily generate distinct signals in T cell activation pathways that modulate inflammatory and inhibitory responses. HVEM interacts with CD160 and B and T lymphocyte attenuator (BTLA), both members of the immunoglobulin (Ig) superfamily, which share a common binding site that is unique from that of LIGHT, a TNF ligand. BTLA or CD160 engagement with HVEM deliver inhibitory or stimulatory signals to the host immune response in a context dependent fashion, whereas HVEM engagement with LIGHT results in pro-inflammatory responses. We identified a mutation in human HVEM, G89F, which directly interferes with the human LIGHT interaction, but interestingly, also differentially modulates the binding of human BTLA and CD160 via an apparent allosteric mechanism involving recognition surfaces remote from the site of the mutation. Specifically, the G89F mutation enhances binding of CD160, while decreasing that of BTLA to HVEM in cell-based assays. Molecular dynamics simulations for wild-type and G89F mutant HVEM, bound to different sets of ligands, were performed to define the molecular basis of this unexpected allosteric effect. These results were leveraged to design additional human HVEM mutants with altered binding specificities.

Conformational changes of α-helical peptides with different hydrophobic residues induced by metal-ion binding

We designed peptides that formed helix bundle structures upon binding of the metal-ions to His residues to form a stable hydrophobic core, in order to analyze the effects of Ala, Val, Ile, and Leu residues, located in the hydrophobic core, together with His, on the conformational changes in respective peptides designated as HA, HV, HI, and HL, respectively. Circular dichroism measurements showed that HV and HI changed from random coil to helix bundle structures upon Zn2+ binding, similar to that observed for HA, while HL existed in the helix bundle structure even in the absence of Zn2+. Electron spin resonance measurements showed that Cu2+ coordination of HI and HL was quite different from that of HA and HV, indicating that HA and HV fluctuated to a greater extent in the solution, despite that their apparent α-helical contents being similar to those of HI and HL. This was also supported by the results obtained from the analyses of thermal stabilities. The change in the structural fluctuation for each peptide upon Zn2+ binding was evaluated based on binding thermodynamics using isothermal titration calorimetry. The structural flexibility in the metal-ion-bound state was found to be in the order HA > HV > HI, and that in the metal-ion-unbound state was found to be greater for HI than that for HL.