An efficient tool for identifying inhibitors based on 3D-QSAR and docking using feature-shape pharmacophore of biologically active conformation--a case study with CDK2/cyclinA.
This study proposes a fast and efficient approach for identifying novel inhibitors when the biologically active conformation of an inhibitor is known. The present study was carried out with CDK2/CyclinA inhibitors. The co-crystal structure of the most active ligand with CDK2/CyclinA was converted into a feature-shape query. This query served three purposes (i) alignment of molecules to generate 3D-QSAR model, (ii) rigid docking to the active site using GOLD, (iii) extracting hits from databases. A statistically valid 3D-QSAR (r(2)=0.867, q(2)=0.887) with good external set prediction (r(pred)(2)=0.890) was obtained. The docked poses were analyzed based on their interaction with hinge region (Glu81-Leu83) of CDK2. A reasonably good consensus score was generated using 11 scoring functions. The developed model was then successfully used to identify potential leads for CDK2/CyclinA inhibitors.
Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology (CSIR), 4 Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India. mailnahren@yahoo.com
Nahren Manuel
NM
Mascarenhas
Nanda
N
Ghoshal
D020134:Catalytic Domain; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D019925:Cyclin A / Q000037:antagonists & inhibitors* / Q000737:chemistry; D051357:Cyclin-Dependent Kinase 2 / Q000037:antagonists & inhibitors* / Q000737:chemistry; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology*; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D015394:Molecular Structure; D011720:Pyrazoles / Q000737:chemistry / Q000494:pharmacology*; D021281:Quantitative Structure-Activity Relationship; D013237:Stereoisomerism
D019925:Cyclin A; D004791:Enzyme Inhibitors; D011720:Pyrazoles; D051357:Cyclin-Dependent Kinase 2