ReSCoSS: a flexible quantum chemistry workflow identifying relevant solution conformers of drug-like molecules

被引:22
作者
Udvarhelyi, Aniko [1 ]
Rodde, Stephane [2 ]
Wilcken, Rainer [2 ]
机构
[1] Novartis Pharma AG, Tech Res & Dev, CH-4002 Basel, Switzerland
[2] Novartis Inst BioMed Res, Global Discovery Chem, CH-4002 Basel, Switzerland
关键词
Conformations; Quantum chemistry; GFN-xTB; COSMO-RS; logP; ReSCoSS; COSMO-RS; ENERGY; APPROXIMATION; CONFORMATIONS; COEFFICIENTS; ANTAGONIST; PREDICTION; DISCOVERY; HYDRATION; SOLVENTS;
D O I
10.1007/s10822-020-00337-7
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Conformational equilibria are at the heart of drug design, yet their energetic description is often hampered by the insufficient accuracy of low-cost methods. Here we present a flexible and semi-automatic workflow based on quantum chemistry, ReSCoSS, designed to identify relevant conformers and predict their equilibria across different solvent environments in the Conductor-like Screening Model for Real Solvents (COSMO-RS) framework. We demonstrate the utility and accuracy of the workflow through conformational case studies on several drug-like molecules from literature where relevant conformations are known. We further show that including ReSCoSS conformers significantly improves COSMO-RS based predictions of physicochemical properties over single-conformation approaches. ReSCoSS has found broad adoption in the in-house drug discovery and development work streams and has contributed to establishing quantum-chemistry methods as a strategic pillar in ligand discovery. [GRAPHICS] .
引用
收藏
页码:399 / 415
页数:17
相关论文
共 63 条
[31]   A sobering assessment of small-molecule force field methods for low energy conformer predictions [J].
Kanal, Ilana Y. ;
Keith, John A. ;
Hutchison, Geoffrey R. .
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 2018, 118 (05)
[32]   CONDUCTOR-LIKE SCREENING MODEL FOR REAL SOLVENTS - A NEW APPROACH TO THE QUANTITATIVE CALCULATION OF SOLVATION PHENOMENA [J].
KLAMT, A .
JOURNAL OF PHYSICAL CHEMISTRY, 1995, 99 (07) :2224-2235
[33]   Refinement and parametrization of COSMO-RS [J].
Klamt, A ;
Jonas, V ;
Bürger, T ;
Lohrenz, JCW .
JOURNAL OF PHYSICAL CHEMISTRY A, 1998, 102 (26) :5074-5085
[34]   First principles calculations of aqueous pKa values for organic and inorganic acids using COSMO-RS reveal an inconsistency in the slope of the pKa scale [J].
Klamt, A ;
Eckert, F ;
Diedenhofen, M ;
Beck, ME .
JOURNAL OF PHYSICAL CHEMISTRY A, 2003, 107 (44) :9380-9386
[35]   COSMO - A NEW APPROACH TO DIELECTRIC SCREENING IN SOLVENTS WITH EXPLICIT EXPRESSIONS FOR THE SCREENING ENERGY AND ITS GRADIENT [J].
KLAMT, A ;
SCHUURMANN, G .
JOURNAL OF THE CHEMICAL SOCIETY-PERKIN TRANSACTIONS 2, 1993, (05) :799-805
[36]   The COSMO and COSMO-RS solvation models [J].
Klamt, Andreas .
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 2018, 8 (01)
[37]   Prediction of cyclohexane-water distribution coefficients with COSMO-RS on the SAMPL5 data set [J].
Klamt, Andreas ;
Eckert, Frank ;
Reinisch, Jens ;
Wichmann, Karin .
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 2016, 30 (11) :959-967
[38]   Prediction of the Free Energy of Hydration of a Challenging Set of Pesticide-Like Compounds [J].
Klamt, Andreas ;
Eckert, Frank ;
Diedenhofen, Michael .
JOURNAL OF PHYSICAL CHEMISTRY B, 2009, 113 (14) :4508-4510
[39]   A Real-World Perspective on Molecular Design [J].
Kuhn, Bernd ;
Guba, Wolfgang ;
Hert, Jerome ;
Banner, David ;
Bissantz, Caterina ;
Ceccarelli, Simona ;
Haap, Wolfgang ;
Koerner, Matthias ;
Kuglstatter, Andreas ;
Lerner, Christian ;
Mattei, Patrizio ;
Neidhart, Werner ;
Pinard, Emmanuel ;
Rudolph, Markus G. ;
Schulz-Gasch, Tanja ;
Wokering, Thomas ;
Stahl, Martin .
JOURNAL OF MEDICINAL CHEMISTRY, 2016, 59 (09) :4087-4102
[40]   LowModeMD-Implicit Low-Mode Velocity Filtering Applied to Conformational Search of Macrocycles and Protein Loops [J].
Labute, Paul .
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2010, 50 (05) :792-800