Rapid preparation of stable isotope labeled peptides that bind to target proteins by a phage library system

Targeting the cryptic sites: NMR-based strategy to improve protein druggability by controlling the conformational equilibrium

Cryptic ligand binding sites, which are not evident in the unligated structures, are beneficial in tackling with difficult but attractive drug targets, such as protein-protein interactions (PPIs). However, cryptic sites have thus far not been rationally pursued in the early stages of drug development. Here, we demonstrated by nuclear magnetic resonance that the cryptic site in Bcl-xL exists in a conformational equilibrium between the open and closed conformations under the unligated condition. While the fraction of the open conformation in the unligated wild-type Bcl-xL is estimated to be low, F143W mutation that is distal from the ligand binding site can substantially elevate the population. The F143W mutant showed a higher hit rate in a phage-display peptide screening, and the hit peptide bound to the cryptic site of the wild-type Bcl-xL. Therefore, by controlling the conformational equilibrium in the cryptic site, the opportunity to identify a PPI inhibitor could be improved.

Current NMR Techniques for Structure-Based Drug Discovery

A variety of nuclear magnetic resonance (NMR) applications have been developed for structure-based drug discovery (SBDD). NMR provides many advantages over other methods, such as the ability to directly observe chemical compounds and target biomolecules, and to be used for ligand-based and protein-based approaches. NMR can also provide important information about the interactions in a protein-ligand complex, such as structure, dynamics, and affinity, even when the interaction is too weak to be detected by ELISA or fluorescence resonance energy transfer (FRET)-based high-throughput screening (HTS) or to be crystalized. In this study, we reviewed current NMR techniques. We focused on recent progress in NMR measurement and sample preparation techniques that have expanded the potential of NMR-based SBDD, such as fluorine NMR (¹⁹F-NMR) screening, structure modeling of weak complexes, and site-specific isotope labeling of challenging targets.

Precise structural determination of weakly binding peptides by utilizing dihedral angle constraints

Structural determination of target-bound conformations of peptides is of primary importance for the optimization of peptide ligands and peptide-mimetic design. In the structural determination of weakly binding ligands, transferred nuclear Overhauser effect (TrNOE) methods have been widely used. However, not many distance constraints can be obtained from small peptide ligands by TrNOE, especially for peptides bound to a target molecule in an extended conformation. Therefore, for precise structural determination of weakly binding peptides, additional structural constraints are required. Here, we present a strategy to systematically introduce dihedral angle constraints obtained from multiple transferred cross-correlated relaxation experiments and demonstrate precise structures of weakly binding peptides. As a result, we could determine the bioactive conformations of phage-derived peptide ligands and define their core binding motifs.

Structural and interaction analysis of glycoprotein VI-binding peptide selected from a phage display library

Glycoprotein VI (GPVI) is a major collagen receptor on the platelet surface that recognizes the glycine-proline-hydroxyproline (GPO) sequence in the collagen molecule and plays a crucial role in thrombus formation. Inhibitors that block the interaction of GPVI with collagen have potential for use as antithrombotic drugs. For low molecular weight drug design for GPVI, it is essential to obtain precise structural and interaction information about GPVI-binding ligands. However, experimentally obtained structural and interaction information of small ligands, such as peptides, in the GPVI-bound state has not been reported. In this study, by screening a phage-displayed peptide library, we discovered a novel peptide ligand (pep-10L; YSDTDWLYFSTS) without any similarities to the sequence of collagen that inhibits GPVI-GPO binding. Systematic Ala scanning in surface plasmon resonance experiments and a saturation transfer difference NMR experiment revealed that Trp(6), Leu(7), Phe(9), and Ser(10) residues in the pep-10L peptide interacted with GPVI. Furthermore, the GPVI-bound conformation of the pep-10L peptide was determined using transferred nuclear Overhauser effect analysis. The obtained structure has revealed that the central part of pep-10L (Asp(5)-Phe(9)) has a helical conformation, the side chains of Trp(6), Leu(7), and Phe(9) form a hydrophobic side in the helix, and the Tyr(8) side chain faces the opposite direction from the hydrophobic side. Computational docking prediction has shown that the hydrophobic side of pep-10L sticks in the hydrophobic groove on the GPVI surface, which corresponds to the putative collagen-related peptide binding groove. These data could enable the structure-guided development of a small molecule GPVI antagonist.

NMR-Based Strategies to Elucidate Bioactive Conformations of Weakly Binding Ligands

Key processes in molecular biology are regulated by interactions between biomolecules. Protein-proteinand protein-ligand interactions, e.g., in signal transduction pathways, rely on the subtle interactionsbetween atoms at the binding interface of the involved molecules. Because biomolecules often havemany interacting partners, these interactions are not necessarily strong. The study of molecularrecognition gives insight into the complex network of signaling in life and is the basis of structure-baseddrug design.In the situation where the interaction is weak, one of the traditional methods that can be appliedto obtain structural information (internuclear distances) of the bound ligand is the so-called transferredNOE (trNOE) method. Recently, it became possible to use transferred cross-correlated relaxation (trCCR)to directly measure dihedral angles. The combined use of these two techniques significantly improvesthe precision of the structure determination of ligands weakly bound to macromolecules.The application of these techniques will be discussed in detail for a peptide derived fromIKKβ bound to the protein NEMO that plays an important rolein the NFκB pathway.