title: Explicit treatment of active-site waters enhances quantum mechanical/implicit solvent scoring: Inhibition of CDK2 by new pyrazolo[1,5-a]pyrimidines.
abstract: 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 molecules resided in the active site. Using molecular dynamics, protein-ligand interactions and active-site water H-bond networks as well as thermodynamics 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 experimental and theoretical approaches we demonstrate that the inclusion of explicit solvent effects enhance QM/COSMO scoring to produce a reliable structure-activity relationship with physical insights. More generally, this approach is envisioned to contribute to increased accuracy of the computational design of novel inhibitors.
authors.affiliation: Department of Chemistry, CZ Openscreen, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
authors.forename: Michaela
authors.initials: M
authors.lastname: Hylsová
authors.affiliation: Department of Chemistry, CZ Openscreen, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekařská 53, 656 91 Brno, Czech Republic.
authors.forename: Benoit
authors.initials: B
authors.lastname: Carbain
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic.
authors.forename: Jindřich
authors.initials: J
authors.lastname: Fanfrlík
authors.affiliation: Department of Chemistry, CZ Openscreen, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
authors.forename: Lenka
authors.initials: L
authors.lastname: Musilová
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic; Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University, 771 46 Olomouc, Czech Republic.
authors.forename: Susanta
authors.initials: S
authors.lastname: Haldar
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic; Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University, 771 46 Olomouc, Czech Republic.
authors.forename: Cemal
authors.initials: C
authors.lastname: Köprülüoğlu
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic; Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University, 771 46 Olomouc, Czech Republic.
authors.forename: Haresh
authors.initials: H
authors.lastname: Ajani
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic.
authors.forename: Pathik S
authors.initials: PS
authors.lastname: Brahmkshatriya
authors.affiliation: Laboratory of Growth Regulators, Faculty of Science, Palacký University, Institute of Experimental Botany, Šlechtitelů 27, 783 71 Olomouc, Czech Republic.
authors.forename: Radek
authors.initials: R
authors.lastname: Jorda
authors.affiliation: Laboratory of Growth Regulators, Faculty of Science, Palacký University, Institute of Experimental Botany, Šlechtitelů 27, 783 71 Olomouc, Czech Republic.
authors.forename: Vladimír
authors.initials: V
authors.lastname: Kryštof
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic; Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University, 771 46 Olomouc, Czech Republic.
authors.forename: Pavel
authors.initials: P
authors.lastname: Hobza
authors.affiliation: Centre de Biochimie Structurale, CNRS UMR 5048 - UM - INSERM U 1054, 29 rue de Navacelles, 34090 Montpellier, France.
authors.forename: Aude
authors.initials: A
authors.lastname: Echalier
authors.affiliation: Department of Chemistry, CZ Openscreen, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekařská 53, 656 91 Brno, Czech Republic. Electronic address: paruch@chemi.muni.cz.
authors.forename: Kamil
authors.initials: K
authors.lastname: Paruch
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic. Electronic address: lepsik@uochb.cas.cz.
authors.forename: Martin
authors.initials: M
authors.lastname: Lepšík
mesh_terms: D020134:Catalytic Domain; D019925:Cyclin A / Q000378:metabolism; D051357:Cyclin-Dependent Kinase 2 / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism; D015195:Drug Design; D006801:Humans; D056004:Molecular Dynamics Simulation; D047428:Protein Kinase Inhibitors / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology; D011743:Pyrimidines / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology*; D011789:Quantum Theory; D012997:Solvents / Q000737:chemistry*; D013329:Structure-Activity Relationship; D014867:Water / Q000737:chemistry*
chemical_list: D019925:Cyclin A; D047428:Protein Kinase Inhibitors; D011743:Pyrimidines; D012997:Solvents; D014867:Water; D051357:Cyclin-Dependent Kinase 2
keywords: 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