title: Structure-based druggability assessment of the mammalian structural proteome with inclusion of light protein flexibility.
abstract: Advances reported over the last few years and the increasing availability of protein crystal structure data have greatly improved structure-based druggability approaches. However, in practice, nearly all druggability estimation methods are applied to protein crystal structures as rigid proteins, with protein flexibility often not directly addressed. The inclusion of protein flexibility is important in correctly identifying the druggability of pockets that would be missed by methods based solely on the rigid crystal structure. These include cryptic pockets and flexible pockets often found at protein-protein interaction interfaces. Here, we apply an approach that uses protein modeling in concert with druggability estimation to account for light protein backbone movement and protein side-chain flexibility in protein binding sites. We assess the advantages and limitations of this approach on widely-used protein druggability sets. Applying the approach to all mammalian protein crystal structures in the PDB results in identification of 69 proteins with potential druggable cryptic pockets.
authors: Schrödinger LLC, New York, New York, United States of America.
authors: Kathryn A
authors: KA
authors: Loving
authors: Amgen Inc., South San Francisco, California, United States of America.
authors: Andy
authors: A
authors: Lin
authors: Amgen Inc., South San Francisco, California, United States of America.
authors: Alan C
authors: AC
authors: Cheng
mesh_terms: D000818:Animals; D001665:Binding Sites; D015195:Drug Design; D008322:Mammals; D008958:Models, Molecular; D015233:Models, Statistical; D009281:Naphthalenes / Q000737:chemistry / Q000378:metabolism; D004364:Pharmaceutical Preparations / Q000737:chemistry / Q000378:metabolism*; D018583:Pliability; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D020543:Proteome / Q000737:chemistry* / Q000378:metabolism; D040901:Proteomics / Q000379:methods; D015203:Reproducibility of Results
chemical_list: D009281:Naphthalenes; D004364:Pharmaceutical Preparations; D011506:Proteins; D020543:Proteome; C031721:naphthalene