Comparative Modeling of CDK9 Inhibitors to Explore Selectivity and Structure-Activity Relationships

Abstract

Cyclin-dependent kinase 9 (CDK9) plays a key role in transcription elongation, and more recently it was also identified as the molecular target of a series of diaminothiazole compounds that reverse epigenetic silencing in a phenotypic assay. To better understand the structural basis underlying these compounds' activity and selectivity, we developed a comparative modeling approach that we describe herein. Briefly, this approach draws upon the strong structural conservation across the active conformation of all protein kinases, and their shared pattern of interactions with Type I inhibitors.Because of this, we hypothesized that the large collection of inhibitor/kinase structures available in the Protein Data Bank (PDB) would enable accurate modeling of this diaminothiazole series in complex with each CDK family member. We apply this new comparative modeling pipeline to build each of these structural models, and then demonstrate that these models provide retrospective rationale for the structure-activity relationships that ultimately guided optimization to the lead diaminothiazole compound MC180295 (14e). We then solved the crystal structure of the 14e/CDK9 complex, and found the resulting structure to be in excellent agreement with our corresponding comparative model. Finally, inspired by these models, we demonstrate how structural changes to 14e can be used to rationally tune this compound's selectivity profile. With the emergence of CDK9 as a promising target for therapeutic intervention in cancer, we anticipate that comparative modeling can provide a valuable tool to guide optimization of potency and selectivity of new inhibitors targeting this kinase.anti-tumoral activity coupled with immunosensitization [28]. With respect to selectivity, the preference of 14e for CDK9 over CDK2 and CDK7 was especially notable: due to their structural and functional similarities, most CDK9 inhibitors also inhibit CDK2 and CDK7 [29,30]. In our first study, we explored selectivity of 14e by developing a comparative modeling approach to build a model of the 14e/CDK9 complex, and then using this model to propose a structural basis for the observed selectivity [28].In the present study we expand our understanding of the structure-activity relationship (SAR) of the series and use these data to critically evaluate our comparative modeling approach. In particular, we present the SAR of 77 compounds related to 14e, and retrospectively assess the extent to which comparative modeling could have driven optimization. We also characterize 14e selectivity further, in light of a recent study demonstrating the surprising lack of selectivity in compounds ostensibly selective for other CDKs [6], and a report summarizing the broad selectivity profiles of CDK9 inhibitors that have advanced to clinical trials [22]. Finally, to definitively evaluate the accuracy of our comparative modeling for this application, we solve the crystal structure of 14e in complex with CDK9. Results and DiscussionOur previous study culminated with the identification and c...

Kincore: a web resource for structural classification of protein kinases and their inhibitors

“…al. have identified the catalytically primed structures (BLAminus) from the PDB to create a comparative modeling pipeline for the ligand bound structures of CDK kinases [28]. Paul and Srinivasan have done structural analyses of pseudokinases in Arabidopsis thaliana and compared with typical protein kinases by applying our conformational labels [14].…”

“…Several experimental and computational studies have reported applying the nomenclature from our previous work in structural analyses of kinases [11]. Lange and colleagues have solved the crystal structure of the pseudokinase IRAK3 (PDBID 6RUU) and identified its conformation as BLAminus, similar to the active state of a typical protein kinase [12] [28]. Paul and Srinivasan have done structural analyses of pseudokinases in Arabidopsis thaliana and compared with typical protein kinases by applying our conformational labels [14].…”

Rationalizing PROTAC-Mediated Ternary Complex Formation Using Rosetta

“…Because crystal structures were not available for foretinib bound to p38α or p38δ, these were generated via comparative modeling. The complete protocol for building these models is described in the context of a separate study [73].…”

Efficient Hit-to-Lead Searching of Kinase Inhibitor Chemical Space via Computational Fragment Merging

“…For clarity we will refer to each of these inhibitors by their names in PubChem. The five inhibitors are: 1) MC180295, a selective CDK9 inhibitor built on a diaminothiazole core [38,39] (PDB ID 6W9E)…”

“…Simply put, the chemical space available by enumerating these reactions is far larger than can be explored via "wet" medicinal chemistry. [39]. The rank of each analog in our screen is provided relative to the complete enumerated library (Figure 7).…”