Consensus Induced Fit Docking (cIFD): methodology, validation, and application to the discovery of novel Crm1 inhibitors.
We present the Consensus Induced Fit Docking (cIFD) approach for adapting a protein binding site to accommodate multiple diverse ligands for virtual screening. This novel approach results in a single binding site structure that can bind diverse chemotypes and is thus highly useful for efficient structure-based virtual screening. We first describe the cIFD method and its validation on three targets that were previously shown to be challenging for docking programs (COX-2, estrogen receptor, and HIV reverse transcriptase). We then demonstrate the application of cIFD to the challenging discovery of irreversible Crm1 inhibitors. We report the identification of 33 novel Crm1 inhibitors, which resulted from the testing of 402 purchased compounds selected from a screening set containing 261,680 compounds. This corresponds to a hit rate of 8.2 %. The novel Crm1 inhibitors reveal diverse chemical structures, validating the utility of the cIFD method in a real-world drug discovery project. This approach offers a pragmatic way to implicitly account for protein flexibility without the additional computational costs of ensemble docking or including full protein flexibility during virtual screening.
Karyopharm Therapeutics, 2 Mercer Road, Natick, MA 01760, USA. ori@karyopharm.com
Ori
O
Kalid
Dora
D
Toledo Warshaviak
Sharon
S
Shechter
Woody
W
Sherman
Sharon
S
Shacham
D051546:Cyclooxygenase 2 / Q000737:chemistry*; D016208:Databases, Factual; D015195:Drug Design; D055808:Drug Discovery; D004353:Drug Evaluation, Preclinical; D054303:HIV Reverse Transcriptase / Q000037:antagonists & inhibitors*; D006801:Humans; D028884:Karyopherins / Q000037:antagonists & inhibitors*; D004364:Pharmaceutical Preparations / Q000737:chemistry*; D011487:Protein Conformation; D018160:Receptors, Cytoplasmic and Nuclear / Q000037:antagonists & inhibitors*; D011960:Receptors, Estrogen / Q000037:antagonists & inhibitors*; D054852:Small Molecule Libraries; D054928:Validation Studies as Topic; D000097606:Exportin 1 Protein
D051546:Cyclooxygenase 2; D054303:HIV Reverse Transcriptase; D028884:Karyopherins; D004364:Pharmaceutical Preparations; D018160:Receptors, Cytoplasmic and Nuclear; D011960:Receptors, Estrogen; D054852:Small Molecule Libraries; D000097606:Exportin 1 Protein; C496540:PTGS2 protein, human