Hylsova, Michaela published the artcileExplicit treatment of active-site waters enhances quantum mechanical/implicit solvent scoring: Inhibition of CDK2 by new pyrazolo[1,5-a]pyrimidines, Product Details of C11H11IO3, the main research area is pyrazolo pyrimidine derivative preparation CDK2 inhibitor structure solvent; ATP-competitive type I inhibitors; Cyclin-dependent kinase 2; Molecular dynamics; Protein-ligand binding; Pyrazolo[1,5-a]pyrimidine; Quantum mechanical scoring; Water thermodynamics; X-ray crystal structure.
We present comprehensive testing of solvent representation in quantum mechanics (QM)-based scoring of protein-ligand affinities. To this aim, we prepared 21 new inhibitors of cyclin-dependent kinase 2 (CDK2) with the pyrazolo[1,5-a]pyrimidine core, whose activities spanned three orders of magnitude. The crystal structure of a potent inhibitor bound to the active CDK2/cyclin A complex revealed that the biphenyl substituent at position 5 of the pyrazolo[1,5-a]pyrimidine scaffold was located in a previously unexplored pocket and that six water mols. resided in the active site. Using mol. dynamics, protein-ligand interactions and active-site water H-bond networks as well as thermodn. were probed. Thereafter, all the inhibitors were scored by the QM approach utilizing the COSMO implicit solvent model. Such a standard treatment failed to produce a correlation with the experiment (R2 = 0.49). However, the addition of the active-site waters resulted in significant improvement (R2 = 0.68). The activities of the compounds could thus be interpreted by taking into account their specific noncovalent interactions with CDK2 and the active-site waters. In summary, using a combination of several exptl. and theor. approaches we demonstrate that the inclusion of explicit solvent effects enhance QM/COSMO scoring to produce a reliable structure-activity relationship with phys. insights. More generally, this approach is envisioned to contribute to increased accuracy of the computational design of novel inhibitors.
European Journal of Medicinal Chemistry published new progress about Crystal structure. 63131-30-6 belongs to class iodides-buliding-blocks, name is Ethyl 3-(4-iodophenyl)-3-oxopropanoate, and the molecular formula is C11H11IO3, Product Details of C11H11IO3.
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Iodide – Wikipedia,
Iodide – an overview | ScienceDirect Topics – ScienceDirect.com