Novel approach of fragment-based lead discovery applied to renin inhibitors

Abstract

A novel approach was conducted for fragment-based lead discovery and applied to renin inhibitors. The biochemical screening of a fragment library against renin provided the hit fragment which showed a characteristic interaction pattern with the target protein. The hit fragment bound only to the S1, S3, and S3 (S3 subpocket) sites without any interactions with the catalytic aspartate residues (Asp32 and Asp215 (pepsin numbering)). Prior to making chemical modifications to the hit fragment, we first identified its essential binding sites by utilizing the hit fragment's substructures. Second, we created a new and smaller scaffold, which better occupied the identified essential S3 and S3 sites, by utilizing library synthesis with high-throughput chemistry. We then revisited the S1 site and efficiently explored a good building block attaching to the scaffold with library synthesis. In the library syntheses, the binding modes of each pivotal compound were determined and confirmed by X-ray crystallography and the library was strategically designed by structure-based computational approach not only to obtain a more active compound but also to obtain informative Structure Activity Relationship (SAR). As a result, we obtained a lead compound offering synthetic accessibility as well as the improved in vitro ADMET profiles. The fragments and compounds possessing a characteristic interaction pattern provided new structural insights into renin's active site and the potential to create a new generation of renin inhibitors. In addition, we demonstrated our FBDD strategy integrating highly sensitive biochemical assay, X-ray crystallography, and high-throughput synthesis and in silico library design aimed at fragment morphing at the initial stage was effective to elucidate a pocket profile and a promising lead compound.

Molecular Interactions of Pyrazine-Based Compounds to Proteins

“…In this particular case, neither halogen bond nor pyrazine ring was necessary for effective binding to the S3 pocket of renin. Next generation leads had isosteric exchange of pyrazine N-4 for carbon and exchange of chlorine for methyl, together yielding 6-methylpyridine fragment instead of the original 6-chloropyrazine . So, in this case we have observed a developmental switch of the chloro substituent (forming halogen bond with Phe) to methyl exerting less specific hydrophobic interactions to the binding subpocket.…”

“…Ligand 77O was a lead molecule in the fragment-based drug development of new renin inhibitors . In the crystallographic structure of ligand–renin complex (PDB ID 5T4S), the C–Cl bond of the chloropyrazine aims toward the plane of Phe119.…”

Structural and Thermodynamic Basis of the Enhanced Interaction between Kinesin Spindle Protein Eg5 and STLC-type Inhibitors

“…Detailed structural information on the interaction between a target protein and the hit compounds can help the rational design of small-molecule candidates with high affinity for the target in silico, which leads to structure-based drug design or fragment-based drug discovery. 1,3−5 Then, the biological activity of individual designed compounds is confirmed by molecular biology-based compound evaluation. There are reports showing the crystal structures of target biomolecules in complex with inhibitors that are well developed to have high inhibitory activity toward the targets.…”

“…Structure–activity relationship (SAR) studies using the structure-related molecules of initial hit compounds can lead to the identification of more potent compounds with high affinity for the target biomolecules. , Crystal structure analysis is a powerful tool for the development of molecular-targeted agents. Detailed structural information on the interaction between a target protein and the hit compounds can help the rational design of small-molecule candidates with high affinity for the target in silico, which leads to structure-based drug design or fragment-based drug discovery. ,− Then, the biological activity of individual designed compounds is confirmed by molecular biology-based compound evaluation. There are reports showing the crystal structures of target biomolecules in complex with inhibitors that are well developed to have high inhibitory activity toward the targets. − However, few articles focus on the structural differences of protein–inhibitor complexes by using a series of structure-related derivatives with different affinities.…”