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Behara PK, Jang H, Horton JT, Gokey T, Dotson DL, Boothroyd S, Bayly CI, Cole DJ, Wang LP, Mobley DL. Benchmarking Quantum Mechanical Levels of Theory for Valence Parametrization in Force Fields. J Phys Chem B 2024; 128:7888-7902. [PMID: 39087913 PMCID: PMC11331531 DOI: 10.1021/acs.jpcb.4c03167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/09/2024] [Accepted: 07/15/2024] [Indexed: 08/02/2024]
Abstract
A wide range of density functional methods and basis sets are available to derive the electronic structure and properties of molecules. Quantum mechanical calculations are too computationally intensive for routine simulation of molecules in the condensed phase, prompting the development of computationally efficient force fields based on quantum mechanical data. Parametrizing general force fields, which cover a vast chemical space, necessitates the generation of sizable quantum mechanical data sets with optimized geometries and torsion scans. To achieve this efficiently, choosing a quantum mechanical method that balances computational cost and accuracy is crucial. In this study, we seek to assess the accuracy of quantum mechanical theory for specific properties such as conformer energies and torsion energetics. To comprehensively evaluate various methods, we focus on a representative set of 59 diverse small molecules, comparing approximately 25 combinations of functional and basis sets against the reference level coupled cluster calculations at the complete basis set limit.
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Affiliation(s)
- Pavan Kumar Behara
- Center
for Neurotherapeutics, University of California, Irvine, California 92697, United States
| | - Hyesu Jang
- Chemistry
Department, University of California at
Davis, Davis, California 95616, United States
- OpenEye
Scientific Software, Santa
Fe, New Mexico 87508, United States
| | - Joshua T. Horton
- School
of Natural and Environmental Sciences, Newcastle
University, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Trevor Gokey
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - David L. Dotson
- The
Open Force Field Initiative, Open Molecular Software Foundation, Davis, California 95616, United States
- Datryllic
LLC, Phoenix, Arizona 85003, United States
| | | | | | - Daniel J. Cole
- School
of Natural and Environmental Sciences, Newcastle
University, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Lee-Ping Wang
- Chemistry
Department, University of California at
Davis, Davis, California 95616, United States
| | - David L. Mobley
- Center
for Neurotherapeutics, University of California, Irvine, California 92697, United States
- Department
of Chemistry, University of California, Irvine, California 92697, United States
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2
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Kairys V, Baranauskiene L, Kazlauskiene M, Zubrienė A, Petrauskas V, Matulis D, Kazlauskas E. Recent advances in computational and experimental protein-ligand affinity determination techniques. Expert Opin Drug Discov 2024; 19:649-670. [PMID: 38715415 DOI: 10.1080/17460441.2024.2349169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024]
Abstract
INTRODUCTION Modern drug discovery revolves around designing ligands that target the chosen biomolecule, typically proteins. For this, the evaluation of affinities of putative ligands is crucial. This has given rise to a multitude of dedicated computational and experimental methods that are constantly being developed and improved. AREAS COVERED In this review, the authors reassess both the industry mainstays and the newest trends among the methods for protein - small-molecule affinity determination. They discuss both computational affinity predictions and experimental techniques, describing their basic principles, main limitations, and advantages. Together, this serves as initial guide to the currently most popular and cutting-edge ligand-binding assays employed in rational drug design. EXPERT OPINION The affinity determination methods continue to develop toward miniaturization, high-throughput, and in-cell application. Moreover, the availability of data analysis tools has been constantly increasing. Nevertheless, cross-verification of data using at least two different techniques and careful result interpretation remain of utmost importance.
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Affiliation(s)
- Visvaldas Kairys
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Lina Baranauskiene
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | | | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Vytautas Petrauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Egidijus Kazlauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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Szél V, Zsidó BZ, Jeszenői N, Hetényi C. Target-ligand binding affinity from single point enthalpy calculation and elemental composition. Phys Chem Chem Phys 2023; 25:31714-31725. [PMID: 37964670 DOI: 10.1039/d3cp04483a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Reliable target-ligand binding thermodynamics data are essential for successful drug design and molecular engineering projects. Besides experimental methods, a number of theoretical approaches have been introduced for the generation of binding thermodynamics data. However, available approaches often neglect electronic effects or explicit water molecules influencing target-ligand interactions. To handle electronic effects within a reasonable time frame, we introduce a fast calculator QMH-L using a single target-ligand complex structure pre-optimized at the molecular mechanics level. QMH-L is composed of the semi-empirical quantum mechanics calculation of binding enthalpy with predicted explicit water molecules at the complex interface, and a simple descriptor based on the elemental composition of the ligand. QMH-L estimates the target-ligand binding free energy with a root mean square error (RMSE) of 0.94 kcal mol-1. The calculations also provide binding enthalpy values and they were compared with experimental binding thermodynamics data collected from the most reliable isothermal titration calorimetry studies of systems including various protein targets and challenging, large peptide ligands with a molecular weight of up to 2-3 thousand. The single point enthalpy calculations of QMH-L require modest computational resources and are based on short runs with open source and/or free software like Gromacs, Mopac, MobyWat, and Fragmenter. QMH-L can be applied for fast, automated scoring of drug candidates during a virtual screen, enthalpic engineering of new ligands or thermodynamic explanation of complex interactions.
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Affiliation(s)
- Viktor Szél
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
| | - Balázs Zoltán Zsidó
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
| | - Norbert Jeszenői
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
| | - Csaba Hetényi
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
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4
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Vasile S, Roos K. Understanding the Structure-Activity Relationship through Density Functional Theory: A Simple Method Predicts Relative Binding Free Energies of Metalloenzyme Fragment-like Inhibitors. ACS OMEGA 2023; 8:21438-21449. [PMID: 37360476 PMCID: PMC10285960 DOI: 10.1021/acsomega.2c08156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/29/2023] [Indexed: 06/28/2023]
Abstract
Despite being involved in several human diseases, metalloenzymes are targeted by a small percentage of FDA-approved drugs. Development of novel and efficient inhibitors is required, as the chemical space of metal binding groups (MBGs) is currently limited to four main classes. The use of computational chemistry methods in drug discovery has gained momentum thanks to accurate estimates of binding modes and binding free energies of ligands to receptors. However, exact predictions of binding free energies in metalloenzymes are challenging due to the occurrence of nonclassical phenomena and interactions that common force field-based methods are unable to correctly describe. In this regard, we applied density functional theory (DFT) to predict the binding free energies and to understand the structure-activity relationship of metalloenzyme fragment-like inhibitors. We tested this method on a set of small-molecule inhibitors with different electronic properties and coordinating two Mn2+ ions in the binding site of the influenza RNA polymerase PAN endonuclease. We modeled the binding site using only atoms from the first coordination shell, hence reducing the computational cost. Thanks to the explicit treatment of electrons by DFT, we highlighted the main contributions to the binding free energies and the electronic features differentiating strong and weak inhibitors, achieving good qualitative correlation with the experimentally determined affinities. By introducing automated docking, we explored alternative ways to coordinate the metal centers and we identified 70% of the highest affinity inhibitors. This methodology provides a fast and predictive tool for the identification of key features of metalloenzyme MBGs, which can be useful for the design of new and efficient drugs targeting these ubiquitous proteins.
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5
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Vornweg JR, Wolter M, Jacob CR. A simple and consistent quantum-chemical fragmentation scheme for proteins that includes two-body contributions. J Comput Chem 2023; 44:1634-1644. [PMID: 37171574 DOI: 10.1002/jcc.27114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 05/13/2023]
Abstract
The Molecular Fractionation with Conjugate Caps (MFCC) method is a popular fragmentation method for the quantum-chemical treatment of proteins. However, it does not account for interactions between the amino acid fragments, such as intramolecular hydrogen bonding. Here, we present a combination of the MFCC fragmentation scheme with a second-order many-body expansion (MBE) that consistently accounts for all fragment-fragment, fragment-cap, and cap-cap interactions, while retaining the overall simplicity of the MFCC scheme with its chemically meaningful fragments. We show that with the resulting MFCC-MBE(2) scheme, the errors in the total energies of selected polypeptides and proteins can be reduced by up to one order of magnitude and relative energies of different protein conformers can be predicted accurately.
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Affiliation(s)
- Johannes R Vornweg
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Mario Wolter
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
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6
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White AF, Li C, Zhang X, Chan GKL. Quantum harmonic free energies for biomolecules and nanomaterials. NATURE COMPUTATIONAL SCIENCE 2023; 3:328-333. [PMID: 38177936 DOI: 10.1038/s43588-023-00432-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 03/13/2023] [Indexed: 01/06/2024]
Abstract
Obtaining the free energy of large molecules from quantum mechanical energy functions is a long-standing challenge. We describe a method that allows us to estimate, at the quantum mechanical level, the harmonic contributions to the thermodynamics of molecular systems of large size, with modest cost. Using this approach, we compute the vibrational thermodynamics of a series of diamond nanocrystals, and show that the error per atom decreases with system size in the limit of large systems. We further show that we can obtain the vibrational contributions to the binding free energies of prototypical protein-ligand complexes where exact computation is too expensive to be practical. Our work raises the possibility of routine quantum mechanical estimates of thermodynamic quantities in complex systems.
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Affiliation(s)
- Alec F White
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
- Quantum Simulation Technologies, Inc., Cambridge, MA, USA
| | - Chenghan Li
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Xing Zhang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Garnet Kin-Lic Chan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
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7
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Protein-ligand binding affinity prediction with edge awareness and supervised attention. iScience 2022; 26:105892. [PMID: 36691617 PMCID: PMC9860494 DOI: 10.1016/j.isci.2022.105892] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/12/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Accurate prediction of protein-ligand binding affinity is crucial in structure-based drug design but remains some challenges even with recent advances in deep learning: (1) Existing methods neglect the edge information in protein and ligand structure data; (2) current attention mechanisms struggle to capture true binding interactions in the small dataset. Herein, we proposed SEGSA_DTA, a SuperEdge Graph convolution-based and Supervised Attention-based Drug-Target Affinity prediction method, where the super edge graph convolution can comprehensively utilize node and edge information and the multi-supervised attention module can efficiently learn the attention distribution consistent with real protein-ligand interactions. Results on the multiple datasets show that SEGSA_DTA outperforms current state-of-the-art methods. We also applied SEGSA_DTA in repurposing FDA-approved drugs to identify potential coronavirus disease 2019 (COVID-19) treatments. Besides, by using SHapley Additive exPlanations (SHAP), we found that SEGSA_DTA is interpretable and further provides a new quantitative analytical solution for structure-based lead optimization.
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8
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Gorges J, Bädorf B, Hansen A, Grimme S. Efficient Computation of the Interaction Energies of Very Large Non-covalently Bound Complexes. Synlett 2022. [DOI: 10.1055/s-0042-1753141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
AbstractWe present a new benchmark set consisting of 16 large non-covalently bound systems (LNCI16) ranging from 380 up to 1988 atoms and featuring diverse interaction motives. Gas-phase interaction energies are calculated with various composite DFT, semi-empirical quantum mechanical (SQM), and force field (FF) methods and are evaluated using accurate DFT reference values. Of the employed QM methods, PBEh-3c proves to be the most robust for large systems with a relative mean absolute deviation (relMAD) of 8.5% with respect to the reference interaction energies. r2SCAN-3c yields an even smaller relMAD, at least for the subset of complexes for which the calculation could be converged, but is less robust for systems with smaller HOMO–LUMO gaps. The inclusion of Fock-exchange is therefore important for the description of very large non-covalent interaction (NCI) complexes in the gas phase. GFN2-xTB was found to be the best performer of the SQM methods with an excellent result of only 11.1% deviation. From the assessed force fields, GFN-FF and GAFF achieve the best accuracy. Considering their low computational costs, both can be recommended for routine calculations of very large NCI complexes, with GFN-FF being clearly superior in terms of general applicability. Hence, GFN-FF may be routinely applied in supramolecular synthesis planning.1 Introduction2 The LNCI16 Benchmark Set3 Computational Details4 Generation of Reference Values5 Results and Discussion6 Conclusions
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9
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Dutkiewicz Z. Computational methods for calculation of protein-ligand binding affinities in structure-based drug design. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2020-0034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Abstract
Drug design is an expensive and time-consuming process. Any method that allows reducing the time the costs of the drug development project can have great practical value for the pharmaceutical industry. In structure-based drug design, affinity prediction methods are of great importance. The majority of methods used to predict binding free energy in protein-ligand complexes use molecular mechanics methods. However, many limitations of these methods in describing interactions exist. An attempt to go beyond these limits is the application of quantum-mechanical description for all or only part of the analyzed system. However, the extensive use of quantum mechanical (QM) approaches in drug discovery is still a demanding challenge. This chapter briefly reviews selected methods used to calculate protein-ligand binding affinity applied in virtual screening (VS), rescoring of docked poses, and lead optimization stage, including QM methods based on molecular simulations.
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Affiliation(s)
- Zbigniew Dutkiewicz
- Department of Chemical Technology of Drugs , Poznan University of Medical Sciences , ul. Grunwaldzka 6 , 60-780 Poznań , Poznan , 60-780, Poland
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10
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Shakiba M, Stippell E, Li W, Akimov AV. Nonadiabatic Molecular Dynamics with Extended Density Functional Tight-Binding: Application to Nanocrystals and Periodic Solids. J Chem Theory Comput 2022; 18:5157-5180. [PMID: 35758936 DOI: 10.1021/acs.jctc.2c00297] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work, we report a new methodology for nonadiabatic molecular dynamics calculations within the extended tight-binding (xTB) framework. We demonstrate the applicability of the developed approach to finite and periodic systems with thousands of atoms by modeling "hot" electron relaxation dynamics in silicon nanocrystals and electron-hole recombination in both a graphitic carbon nitride monolayer and a titanium-based metal-organic framework (MOF). This work reports the nonadiabatic dynamic simulations in the largest Si nanocrystals studied so far by the xTB framework, with diameters up to 3.5 nm. For silicon nanocrystals, we find a non-monotonic dependence of "hot" electron relaxation rates on the nanocrystal size, in agreement with available experimental reports. We rationalize this relationship by a combination of decreasing nonadiabatic couplings related to system size and the increase of available coherent transfer pathways in systems with higher densities of states. We emphasize the importance of proper treatment of coherences for obtaining such non-monotonic dependences. We characterize the electron-hole recombination dynamics in the graphitic carbon nitride monolayer and the Ti-containing MOF. We demonstrate the importance of spin-adaptation and proper sampling of surface hopping trajectories in modeling such processes. We also assess several trajectory surface hopping schemes and highlight their distinct qualitative behavior in modeling the excited-state dynamics in superexchange-like models depending on how they handle coherences between nearly parallel states.
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Affiliation(s)
- Mohammad Shakiba
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Elizabeth Stippell
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Wei Li
- School of Chemistry and Materials Science, Hunan Agricultural University, Changsha 410128, China
| | - Alexey V Akimov
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
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12
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Rayka M, Karimi-Jafari MH, Firouzi R. ET-score: Improving Protein-ligand Binding Affinity Prediction Based on Distance-weighted Interatomic Contact Features Using Extremely Randomized Trees Algorithm. Mol Inform 2021; 40:e2060084. [PMID: 34021703 DOI: 10.1002/minf.202060084] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 04/20/2021] [Indexed: 12/15/2022]
Abstract
The molecular docking simulation is a key computational tool in modern drug discovery research that its predictive performance strongly depends on the employed scoring functions. Many recent studies have shown that the application of machine learning algorithms in the development of scoring functions has led to a significant improvement in docking performance. In this work, we introduce a new machine learning (ML) based scoring function called ET-Score, which employs the distance-weighted interatomic contacts between atom type pairs of the ligand and the protein for featurizing protein-ligand complexes and Extremely Randomized Trees algorithm for the training process. The performance of ET-Score is compared with some successful ML-based scoring functions and several popular classical scoring functions on the PDBbind 2016v core set. It is shown that our ET-Score model (with Pearson's correlation of 0.827 and RMSE of 1.332) achieves very good performance in comparison with most of the ML-based scoring functions and all classical scoring functions despite its extremely low computational cost. ET-Score's codes are freely available on the web at https://github.com/miladrayka/ET_Score.
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Affiliation(s)
- Milad Rayka
- Department of Physical Chemistry, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
| | | | - Rohoullah Firouzi
- Department of Physical Chemistry, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
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13
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Sulimov VB, Kutov DC, Taschilova AS, Ilin IS, Tyrtyshnikov EE, Sulimov AV. Docking Paradigm in Drug Design. Curr Top Med Chem 2021; 21:507-546. [PMID: 33292135 DOI: 10.2174/1568026620666201207095626] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/28/2020] [Accepted: 10/16/2020] [Indexed: 11/22/2022]
Abstract
Docking is in demand for the rational computer aided structure based drug design. A review of docking methods and programs is presented. Different types of docking programs are described. They include docking of non-covalent small ligands, protein-protein docking, supercomputer docking, quantum docking, the new generation of docking programs and the application of docking for covalent inhibitors discovery. Taking into account the threat of COVID-19, we present here a short review of docking applications to the discovery of inhibitors of SARS-CoV and SARS-CoV-2 target proteins, including our own result of the search for inhibitors of SARS-CoV-2 main protease using docking and quantum chemical post-processing. The conclusion is made that docking is extremely important in the fight against COVID-19 during the process of development of antivirus drugs having a direct action on SARS-CoV-2 target proteins.
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Affiliation(s)
- Vladimir B Sulimov
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
| | - Danil C Kutov
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
| | - Anna S Taschilova
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
| | - Ivan S Ilin
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
| | - Eugene E Tyrtyshnikov
- Institute of Numerical Mathematics of Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexey V Sulimov
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
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Spicher S, Grimme S. Single-Point Hessian Calculations for Improved Vibrational Frequencies and Rigid-Rotor-Harmonic-Oscillator Thermodynamics. J Chem Theory Comput 2021; 17:1701-1714. [DOI: 10.1021/acs.jctc.0c01306] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Sebastian Spicher
- Mulliken Center for Theoretical Chemistry, Institute of Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute of Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
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15
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Salthammer T, Monegel F, Schulz N, Uhde E, Grimme S, Seibert J, Hohm U, Palm W. Sensory Perception of Non-Deuterated and Deuterated Organic Compounds. Chemistry 2021; 27:1046-1056. [PMID: 33058253 PMCID: PMC7839723 DOI: 10.1002/chem.202003754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/10/2020] [Indexed: 11/24/2022]
Abstract
The chemical background of olfactory perception has been subject of intensive research, but no available model can fully explain the sense of smell. There are also inconsistent results on the role of the isotopology of molecules. In experiments with human subjects it was found that the isotope effect is weak with acetone and D6 -acetone. In contrast, clear differences were observed in the perception of octanoic acid and D15 -octanoic acid. Furthermore, a trained sniffer dog was initially able to distinguish between these isotopologues of octanoic acid. In chromatographic measurements, the respective deuterated molecule showed weaker interaction with a non-polar liquid phase. Quantum chemical calculations give evidence that deuterated octanoic acid binds more strongly to a model receptor than non-deuterated. In contrast, the binding of the non-deuterated molecule is stronger with acetone. The isotope effect is calculated in the framework of statistical mechanics. It results from a complicated interplay between various thermostatistical contributions to the non-covalent free binding energies and it turns out to be very molecule-specific. The vibrational terms including non-classical zero-point energies play about the same role as rotational/translational contributions and are larger than bond length effects for the differential isotope perception of odor for which general rules cannot be derived.
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Affiliation(s)
- Tunga Salthammer
- Department of Material Analysis and Indoor ChemistryFraunhofer WKI38108BraunschweigGermany
| | - Friederike Monegel
- Department of Material Analysis and Indoor ChemistryFraunhofer WKI38108BraunschweigGermany
| | - Nicole Schulz
- Department of Material Analysis and Indoor ChemistryFraunhofer WKI38108BraunschweigGermany
| | - Erik Uhde
- Department of Material Analysis and Indoor ChemistryFraunhofer WKI38108BraunschweigGermany
| | - Stefan Grimme
- Mulliken Center for Theoretical ChemistryInstitute for Physical and Theoretical ChemistryUniversity of Bonn53115BonnGermany
| | - Jakob Seibert
- Mulliken Center for Theoretical ChemistryInstitute for Physical and Theoretical ChemistryUniversity of Bonn53115BonnGermany
| | - Uwe Hohm
- Institute of Physical and Theoretical ChemistryUniversity of Braunschweig—Institute of Technology38106BraunschweigGermany
| | - Wolf‐Ulrich Palm
- Institute of Sustainable and Environmental ChemistryLeuphana University Lüneburg21335LüneburgGermany
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16
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Spicher S, Grimme S. Efficient Computation of Free Energy Contributions for Association Reactions of Large Molecules. J Phys Chem Lett 2020; 11:6606-6611. [PMID: 32787231 DOI: 10.1021/acs.jpclett.0c01930] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Modern density functional theory (DFT) methods are capable of providing accurate association energies for supramolecular systems and even protein-ligand complexes. However, the calculation of the essential harmonic vibrational frequencies needed to obtain free energies is often too computationally demanding. In this work, the corresponding thermostatistical contributions are computed in the well-established (modified) rigid-rotor-harmonic-oscillator approximation with structures and frequencies taken from low-cost quantum chemical methods, namely, GFN2-xTB and PM6-D3H4. Additionally, a recently developed new general force field (GFN-FF) is tested for this purpose. DFT reference values for 59 complexes composed of three standard noncovalent and supramolecular benchmark sets (S22, L7, and S30L) are used in the evaluation. Overall, the accuracy of the low-cost methods is remarkable with typical deviations of only 0.5-2 kcal mol-1 (5-10%) from the DFT reference values. In particular, the performance of the GFN-FF is promising considering the acceleration of 5 and 2-3 orders of magnitude compared to DFT and GFN2-xTB, respectively. This opens new perspectives for computing thermodynamic properties of, e.g., biomacromolecules as shown, for example, for the binding of retinol and rivaroxaban in protein complexes consisting of ≤4700 atoms.
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Affiliation(s)
- Sebastian Spicher
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstrasse 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstrasse 4, 53115 Bonn, Germany
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17
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Bannwarth C, Caldeweyher E, Ehlert S, Hansen A, Pracht P, Seibert J, Spicher S, Grimme S. Extended
tight‐binding
quantum chemistry methods. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1493] [Citation(s) in RCA: 218] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christoph Bannwarth
- Department of Chemistry and The PULSE Institute Stanford University Stanford California USA
| | - Eike Caldeweyher
- Mulliken Center for Theoretical Chemistry Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
| | - Sebastian Ehlert
- Mulliken Center for Theoretical Chemistry Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
| | - Philipp Pracht
- Mulliken Center for Theoretical Chemistry Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
| | - Jakob Seibert
- Mulliken Center for Theoretical Chemistry Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
| | - Sebastian Spicher
- Mulliken Center for Theoretical Chemistry Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
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18
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Adeshina YO, Deeds EJ, Karanicolas J. Machine learning classification can reduce false positives in structure-based virtual screening. Proc Natl Acad Sci U S A 2020; 117:18477-18488. [PMID: 32669436 PMCID: PMC7414157 DOI: 10.1073/pnas.2000585117] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
With the recent explosion in the size of libraries available for screening, virtual screening is positioned to assume a more prominent role in early drug discovery's search for active chemical matter. In typical virtual screens, however, only about 12% of the top-scoring compounds actually show activity when tested in biochemical assays. We argue that most scoring functions used for this task have been developed with insufficient thoughtfulness into the datasets on which they are trained and tested, leading to overly simplistic models and/or overtraining. These problems are compounded in the literature because studies reporting new scoring methods have not validated their models prospectively within the same study. Here, we report a strategy for building a training dataset (D-COID) that aims to generate highly compelling decoy complexes that are individually matched to available active complexes. Using this dataset, we train a general-purpose classifier for virtual screening (vScreenML) that is built on the XGBoost framework. In retrospective benchmarks, our classifier shows outstanding performance relative to other scoring functions. In a prospective context, nearly all candidate inhibitors from a screen against acetylcholinesterase show detectable activity; beyond this, 10 of 23 compounds have IC50 better than 50 μM. Without any medicinal chemistry optimization, the most potent hit has IC50 280 nM, corresponding to Ki of 173 nM. These results support using the D-COID strategy for training classifiers in other computational biology tasks, and for vScreenML in virtual screening campaigns against other protein targets. Both D-COID and vScreenML are freely distributed to facilitate such efforts.
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Affiliation(s)
- Yusuf O Adeshina
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111
- Center for Computational Biology, University of Kansas, Lawrence, KS 66045
| | - Eric J Deeds
- Center for Computational Biology, University of Kansas, Lawrence, KS 66045
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045
| | - John Karanicolas
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111;
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19
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Seritan S, Bannwarth C, Fales BS, Hohenstein EG, Isborn CM, Kokkila‐Schumacher SIL, Li X, Liu F, Luehr N, Snyder JW, Song C, Titov AV, Ufimtsev IS, Wang L, Martínez TJ. TeraChem
: A graphical processing unit
‐accelerated
electronic structure package for
large‐scale
ab initio molecular dynamics. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1494] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Stefan Seritan
- Department of Chemistry and the PULSE Institute Stanford University Stanford California USA
- SLAC National Accelerator Laboratory Menlo Park California USA
| | - Christoph Bannwarth
- Department of Chemistry and the PULSE Institute Stanford University Stanford California USA
- SLAC National Accelerator Laboratory Menlo Park California USA
| | - Bryan S. Fales
- Department of Chemistry and the PULSE Institute Stanford University Stanford California USA
- SLAC National Accelerator Laboratory Menlo Park California USA
| | - Edward G. Hohenstein
- Department of Chemistry and the PULSE Institute Stanford University Stanford California USA
- SLAC National Accelerator Laboratory Menlo Park California USA
| | - Christine M. Isborn
- Department of Chemistry University of California Merced Merced California USA
| | | | - Xin Li
- Division of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health KTH Royal Institute of Technology Stockholm Sweden
| | - Fang Liu
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
| | | | | | - Chenchen Song
- Department of Physics University of California Berkeley Berkeley California USA
- Molecular Foundry Lawrence Berkeley National Laboratory Berkeley California USA
| | | | - Ivan S. Ufimtsev
- Department of Structural Biology Stanford University School of Medicine Stanford California USA
| | - Lee‐Ping Wang
- Department of Chemistry University of California Davis Davis California USA
| | - Todd J. Martínez
- Department of Chemistry and the PULSE Institute Stanford University Stanford California USA
- SLAC National Accelerator Laboratory Menlo Park California USA
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20
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Dong C, Montes M, Al-Sawai WM. Xanthine oxidoreductase inhibition – A review of computational aspect. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2020. [DOI: 10.1142/s0219633620400088] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Xanthine Oxidoreductase (XOR) exists in a variety of organisms from bacteria to humans and catalyzes the oxidation of hypoxanthine to xanthine and from xanthine to uric acid. Excessive uric acid could lead to gout and hyperuricemia. In this paper, we have reviewed the recent computational studies on xanthine oxidase inhibition. Computational methods, such as molecular dynamics (molecular mechanics), quantum mechanics, and quantum mechanics/molecular mechanics (QM/MM), have been employed to investigate the binding affinity of xanthine oxidase with synthesized and isolated nature inhibitors. The limitations of different computational methods for xanthine oxidase inhibition studies were also discussed. Implications of the computational approach could be used to help to understand the existing arguments on substrate/product orientation in xanthine oxidase inhibition, which allows designing new inhibitors with higher efficacy.
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Affiliation(s)
- Chao Dong
- Department of Chemistry, The University of Texas of the Permian Basin, Odessa, Texas 79762, USA
| | - Milka Montes
- Department of Chemistry, The University of Texas of the Permian Basin, Odessa, Texas 79762, USA
| | - Wael M. Al-Sawai
- Department of Mathematics & Physics, The University of Texas of the Permian Basin, Odessa, Texas 79762, USA
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21
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Schmitz S, Seibert J, Ostermeir K, Hansen A, Göller AH, Grimme S. Quantum Chemical Calculation of Molecular and Periodic Peptide and Protein Structures. J Phys Chem B 2020; 124:3636-3646. [PMID: 32275425 DOI: 10.1021/acs.jpcb.0c00549] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Special-purpose classical force fields (FFs) provide good accuracy at very low computational cost, but their application is limited to systems for which potential energy functions are available. This excludes most metal-containing proteins or those containing cofactors. In contrast, the GFN2-xTB semiempirical quantum chemical method is parametrized for almost the entire periodic table. The accuracy of GFN2-xTB is assessed for protein structures with respect to experimental X-ray data. Furthermore, the results are compared with those of two special-purpose FFs, HF-3c, PM6-D3H4X, and PM7. The test sets include proteins without any prosthetic groups as well as metalloproteins. Crystal packing effects are examined for a set of smaller proteins to validate the molecular approach. For the proteins without prosthetic groups, the special purpose FF OPLS-2005 yields the smallest overall RMSD to the X-ray data but GFN2-xTB provides similarly good structures with even better bond-length distributions. For the metalloproteins with up to 5000 atoms, a good overall structural agreement is obtained with GFN2-xTB. The full geometry optimizations of protein structures with on average 1000 atoms in wall-times below 1 day establishes the GFN2-xTB method as a versatile tool for the computational treatment of various biomolecules with a good accuracy/computational cost ratio.
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Affiliation(s)
- Sarah Schmitz
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstraße 4, D-53115 Bonn, Germany
| | - Jakob Seibert
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstraße 4, D-53115 Bonn, Germany
| | - Katja Ostermeir
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstraße 4, D-53115 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstraße 4, D-53115 Bonn, Germany
| | - Andreas H Göller
- Computational Molecular Design, Pharmaceuticals, R&D, Bayer AG, D-42096 Wuppertal, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstraße 4, D-53115 Bonn, Germany
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22
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Cavasotto CN, Aucar MG. High-Throughput Docking Using Quantum Mechanical Scoring. Front Chem 2020; 8:246. [PMID: 32373579 PMCID: PMC7186494 DOI: 10.3389/fchem.2020.00246] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 03/16/2020] [Indexed: 11/13/2022] Open
Abstract
Today high-throughput docking is one of the most commonly used computational tools in drug lead discovery. While there has been an impressive methodological improvement in docking accuracy, docking scoring still remains an open challenge. Most docking programs are rooted in classical molecular mechanics. However, to better characterize protein-ligand interactions, the use of a more accurate quantum mechanical (QM) description would be necessary. In this work, we introduce a QM-based docking scoring function for high-throughput docking and evaluate it on 10 protein systems belonging to diverse protein families, and with different binding site characteristics. Outstanding results were obtained, with our QM scoring function displaying much higher enrichment (screening power) than a traditional docking method. It is acknowledged that developments in quantum mechanics theory, algorithms and computer hardware throughout the upcoming years will allow semi-empirical (or low-cost) quantum mechanical methods to slowly replace force-field calculations. It is thus urgently needed to develop and validate novel quantum mechanical-based scoring functions for high-throughput docking toward more accurate methods for the identification and optimization of modulators of pharmaceutically relevant targets.
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Affiliation(s)
- Claudio N Cavasotto
- Computational Drug Design and Biomedical Informatics Laboratory, Translational Medicine Research Institute (IIMT), CONICET-Universidad Austral, Pilar, Argentina.,Facultad de Ciencias Biomédicas and Facultad de Ingeniería, Universidad Austral, Pilar, Argentina.,Austral Institute for Applied Artificial Intelligence, Universidad Austral, Pilar, Argentina
| | - M Gabriela Aucar
- Computational Drug Design and Biomedical Informatics Laboratory, Translational Medicine Research Institute (IIMT), CONICET-Universidad Austral, Pilar, Argentina
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23
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Spicher S, Abdullin D, Grimme S, Schiemann O. Modeling of spin–spin distance distributions for nitroxide labeled biomacromolecules. Phys Chem Chem Phys 2020; 22:24282-24290. [DOI: 10.1039/d0cp04920d] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Combining CREST and MD simulations based on GFN-FF for the automated computation of distance distributions for nitroxide labeled (metallo-) proteins.
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Affiliation(s)
- Sebastian Spicher
- Mulliken Center for Theoretical Chemistry
- Institute of Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
| | - Dinar Abdullin
- Institute of Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry
- Institute of Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
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24
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Cavasotto CN. Binding Free Energy Calculation Using Quantum Mechanics Aimed for Drug Lead Optimization. Methods Mol Biol 2020; 2114:257-268. [PMID: 32016898 DOI: 10.1007/978-1-0716-0282-9_16] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The routine use of in silico tools is already established in drug lead design. Besides the use of molecular docking methods to screen large chemical libraries and thus prioritize compounds for purchase or synthesis, more accurate calculations of protein-ligand binding free energy has shown the potential to guide lead optimization, thus saving time and resources. Theoretical developments and advances in computing power have allowed quantum mechanical-based methods applied to calculations on biomacromolecules to be increasingly explored and used, with the purpose of providing a more accurate description of protein-ligand interactions and an enhanced level of accuracy in the calculation of binding affinities. It should be noted that the quantum mechanical formulation includes, in principle, all contributions to the energy, considering terms usually neglected in molecular mechanics force fields, such as electronic polarization, metal coordination, and covalent binding; moreover, quantum mechanical approaches are systematically improvable. By treating all elements and interactions on equal footing, and avoiding the need of system-dependent parameterizations, they provide a greater degree of transferability. In this review, we illustrate the increasing relevance of quantum mechanical methods for binding free energy calculation in the context of structure-based drug lead optimization, showing representative applications of the different approaches available.
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Affiliation(s)
- Claudio N Cavasotto
- Computational Drug Design and Biomedical Informatics Laboratory, Translational Medicine Research Institute (IIMT), CONICET-Universidad Austral, Derqui-Pilar, Buenos Aires, Argentina. .,Austral Institute for Applied Artificial Intelligence, Universidad Austral, Derqui-Pilar, Buenos Aires, Argentina. .,Facultad de Ciencias Biomédicas, Universidad Austral, Derqui-Pilar, Buenos Aires, Argentina. .,Facultad de Ingeniería, Universidad Austral, Derqui-Pilar, Buenos Aires, Argentina.
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25
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Abstract
Computational methods are a powerful and consolidated tool in the early stage of the drug lead discovery process. Among these techniques, high-throughput molecular docking has proved to be extremely useful in identifying novel bioactive compounds within large chemical libraries. In the docking procedure, the predominant binding mode of each small molecule within a target binding site is assessed, and a docking score reflective of the likelihood of binding is assigned to them. These methods also shed light on how a given hit could be modified in order to improve protein-ligand interactions and are thus able to guide lead optimization. The possibility of reducing time and cost compared to experimental approaches made this technology highly appealing. Due to methodological developments and the increase of computational power, the application of quantum mechanical methods to study macromolecular systems has gained substantial attention in the last decade. A quantum mechanical description of the interactions involved in molecular association of biomolecules may lead to better accuracy compared to molecular mechanics, since there are many physical phenomena that cannot be correctly described within a classical framework, such as covalent bond formation, polarization effects, charge transfer, bond rearrangements, halogen bonding, and others, that require electrons to be explicitly accounted for. Considering the fact that quantum mechanics-based approaches in biomolecular simulation constitute an active and important field of research, we highlight in this work the recent developments of quantum mechanical-based molecular docking and high-throughput docking.
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Affiliation(s)
- M Gabriela Aucar
- Computational Drug Design and Biomedical Informatics Laboratory, Translational Medicine Research Institute (IIMT), CONICET-Universidad Austral, Derqui-Pilar, Buenos Aires, Argentina
| | - Claudio N Cavasotto
- Computational Drug Design and Biomedical Informatics Laboratory, Translational Medicine Research Institute (IIMT), CONICET-Universidad Austral, Derqui-Pilar, Buenos Aires, Argentina.
- Austral Institute for Applied Artificial Intelligence, Universidad Austral, Derqui-Pilar, Buenos Aires, Argentina.
- Facultad de Ciencias Biomédicas, Universidad Austral, Derqui-Pilar, Buenos Aires, Argentina.
- Facultad de Ingeniería, Universidad Austral, Derqui-Pilar, Buenos Aires, Argentina.
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26
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Abstract
Quantum mechanics (QM) methods provide a fine description of receptor-ligand interactions and of chemical reactions. Their use in drug design and drug discovery is increasing, especially for complex systems including metal ions in the binding sites, for the design of highly selective inhibitors, for the optimization of bi-specific compounds, to understand enzymatic reactions, and for the study of covalent ligands and prodrugs. They are also used for generating molecular descriptors for predictive QSAR/QSPR models and for the parameterization of force fields. Thanks to the continuous increase of computational power offered by GPUs and to the development of sophisticated algorithms, QM methods are becoming part of the standard tools used in computer-aided drug design (CADD). We present the most used QM methods and software packages, and we discuss recent representative applications in drug design and drug discovery.
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Affiliation(s)
- Martin Kotev
- Global Research Informatics/Cheminformatics and Drug Design, Evotec (France) SAS, Toulouse, France
| | - Laurie Sarrat
- Global Research Informatics/Cheminformatics and Drug Design, Evotec (France) SAS, Toulouse, France
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27
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Doná L, Brandenburg JG, Civalleri B. Extending and assessing composite electronic structure methods to the solid state. J Chem Phys 2019; 151:121101. [PMID: 31575185 DOI: 10.1063/1.5123627] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A hierarchy of simplified Hartree-Fock (HF), density functional theory (DFT) methods, and their combinations has been recently proposed for the fast electronic structure computation of large systems. The covered methods are a minimal basis set Hartree-Fock (HF-3c), a small basis set global hybrid functional (PBEh-3c), and its screened exchange variant (HSE-3c), all augmented with semiclassical correction potentials. Here, we extend their applicability to inorganic covalent and ionic solids as well as layered materials. The new methods have been dubbed HFsol-3c, PBEsol0-3c, and HSEsol-3c, respectively, to indicate their parent functional as well as the correction potentials. They have been implemented in the CRYSTAL code to enable routine application for molecular as well as solid materials. We validate the new methods on diverse sets of solid state benchmarks that cover more than 90 solids ranging from covalent, ionic, semi-ionic, layered, and molecular crystals. While we focus on structural and energetic properties, we also test bandgaps, vibrational frequencies, elastic constants, and dielectric and piezoelectric tensors. HSEsol-3c appears to be most promising with mean absolute error for cohesive energies and unit cell volumes of molecular crystals of 1.5 kcal/mol and 2.8%, respectively. Lattice parameters of inorganic solids deviate by 3% from the references, and vibrational frequencies of α-quartz have standard deviations of 10 cm-1. Overall, this shows an accuracy competitive to converged basis set dispersion corrected DFT with a substantial increase in computational efficiency.
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Affiliation(s)
- L Doná
- Dipartimento di Chimica, Università di Torino and NIS (Nanostructured Interfaces and Surfaces) Centre, Via P. Giuria 5, 10125 Torino, Italy
| | - J G Brandenburg
- Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 205A, 69120 Heidelberg, Germany
| | - B Civalleri
- Dipartimento di Chimica, Università di Torino and NIS (Nanostructured Interfaces and Surfaces) Centre, Via P. Giuria 5, 10125 Torino, Italy
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28
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Giese TJ, York DM. Development of a Robust Indirect Approach for MM → QM Free Energy Calculations That Combines Force-Matched Reference Potential and Bennett's Acceptance Ratio Methods. J Chem Theory Comput 2019; 15:5543-5562. [PMID: 31507179 DOI: 10.1021/acs.jctc.9b00401] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We use the PBE0/6-31G* density functional method to perform ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations under periodic boundary conditions with rigorous electrostatics using the ambient potential composite Ewald method in order to test the convergence of MM → QM/MM free energy corrections for the prediction of 17 small-molecule solvation free energies and eight ligand binding free energies to T4 lysozyme. The "indirect" thermodynamic cycle for calculating free energies is used to explore whether a series of reference potentials improve the statistical quality of the predictions. Specifically, we construct a series of reference potentials that optimize a molecular mechanical (MM) force field's parameters to reproduce the ab initio QM/MM forces from a QM/MM simulation. The optimizations form a systematic progression of successively expanded parameters that include bond, angle, dihedral, and charge parameters. For each reference potential, we calculate benchmark quality reference values for the MM → QM/MM correction by performing the mixed MM and QM/MM Hamiltonians at 11 intermediate states, each for 200 ps. We then compare forward and reverse application of Zwanzig's relation, thermodynamic integration (TI), and Bennett's acceptance ratio (BAR) methods as a function of reference potential, simulation time, and the number of simulated intermediate states. We find that Zwanzig's equation is inadequate unless a large number of intermediate states are explicitly simulated. The TI and BAR mean signed errors are very small even when only the end-state simulations are considered, and the standard deviations of the TI and BAR errors are decreased by choosing a reference potential that optimizes the bond and angle parameters. We find a robust approach for the data sets of fairly rigid molecules considered here is to use bond + angle reference potential together with the end-state-only BAR analysis. This requires QM/MM simulations to be performed in order to generate reference data to parametrize the bond + angle reference potential, and then this same simulation serves a dual purpose as the full QM/MM end state. The convergence of the results with respect to time suggests that computational resources may be used more efficiently by running multiple simulations for no more than 50 ps, rather than running one long simulation.
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Affiliation(s)
- Timothy J Giese
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854-8087 , United States
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854-8087 , United States
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29
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Sokka IK, Ekholm FS, Johansson MP. Increasing the Potential of the Auristatin Cancer-Drug Family by Shifting the Conformational Equilibrium. Mol Pharm 2019; 16:3600-3608. [PMID: 31199662 PMCID: PMC6750905 DOI: 10.1021/acs.molpharmaceut.9b00437] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Monomethyl auristatin E and monomethyl
auristatin F are widely
used cytotoxic agents in antibody–drug conjugates (ADCs), a
group of promising cancer drugs. The ADCs specifically target cancer
cells, releasing the auristatins inside, which results in the prevention
of mitosis. The auristatins suffer from a potentially serious flaw,
however. In solution, the molecules exist in an equal mixture of two
conformers, cis and trans. Only the trans-isomer is biologically active
and the isomerization process, i.e., the conversion of cis to trans
is slow. This significantly diminishes the efficiency of the drugs
and their corresponding ADCs, and perhaps more importantly, raises
concerns over drug safety. The potency of the auristatins would be
enhanced by decreasing the amount of the biologically inactive isomer,
either by stabilizing the trans-isomer or destabilizing the cis-isomer.
Here, we follow the computer-aided design strategy of shifting the
conformational equilibrium and employ high-level quantum chemical
modeling to identify promising candidates for improved auristatins.
Coupled cluster calculations predict that a simple halogenation in
the norephedrine/phenylalanine residues shifts the isomer equilibrium
almost completely toward the active trans-conformation, due to enhanced
intramolecular interactions specific to the active isomer.
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Affiliation(s)
- Iris K Sokka
- Department of Chemistry , University of Helsinki , P.O. Box 55, FI-00014 Helsinki , Finland
| | - Filip S Ekholm
- Department of Chemistry , University of Helsinki , P.O. Box 55, FI-00014 Helsinki , Finland
| | - Mikael P Johansson
- Department of Chemistry , University of Helsinki , P.O. Box 55, FI-00014 Helsinki , Finland.,Helsinki Institute of Sustainability Science, HELSUS , FI-00014 Helsinki , Finland
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30
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Kairys V, Baranauskiene L, Kazlauskiene M, Matulis D, Kazlauskas E. Binding affinity in drug design: experimental and computational techniques. Expert Opin Drug Discov 2019; 14:755-768. [DOI: 10.1080/17460441.2019.1623202] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Visvaldas Kairys
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Lina Baranauskiene
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | | | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Egidijus Kazlauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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31
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Bauer MR, Mackey MD. Electrostatic Complementarity as a Fast and Effective Tool to Optimize Binding and Selectivity of Protein-Ligand Complexes. J Med Chem 2019; 62:3036-3050. [PMID: 30807144 DOI: 10.1021/acs.jmedchem.8b01925] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Electrostatic interactions between small molecules and their respective receptors are essential for molecular recognition and are also key contributors to the binding free energy. Assessing the electrostatic match of protein-ligand complexes therefore provides important insights into why ligands bind and what can be changed to improve binding. Ideally, the ligand and protein electrostatic potentials at the protein-ligand interaction interface should maximize their complementarity while minimizing desolvation penalties. In this work, we present a fast and efficient tool to calculate and visualize the electrostatic complementarity (EC) of protein-ligand complexes. We compiled benchmark sets demonstrating electrostatically driven structure-activity relationships (SAR) from literature data, including kinase, protein-protein interaction, and GPCR targets, and used these to demonstrate that the EC method can visualize, rationalize, and predict electrostatically driven ligand affinity changes and help to predict compound selectivity. The methodology presented here for the analysis of EC is a powerful and versatile tool for drug design.
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Affiliation(s)
- Matthias R Bauer
- Cresset, New Cambridge House , Bassingbourn Road , Litlington , Cambridgeshire SG8 0SS , U.K
| | - Mark D Mackey
- Cresset, New Cambridge House , Bassingbourn Road , Litlington , Cambridgeshire SG8 0SS , U.K
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32
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Cutini M, Civalleri B, Ugliengo P. Cost-Effective Quantum Mechanical Approach for Predicting Thermodynamic and Mechanical Stability of Pure-Silica Zeolites. ACS OMEGA 2019; 4:1838-1846. [PMID: 31459438 PMCID: PMC6648702 DOI: 10.1021/acsomega.8b03135] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/10/2019] [Indexed: 06/10/2023]
Abstract
Several computational techniques for solid-state applications have recently been proposed to enlarge the scope of computer simulations of large molecular systems. In this contribution, we focused on two of these, namely, HF-3c and PBEh-3c. They were recently proposed by the Grimme's group, as "low-cost" ab initio-based techniques for electronic structure calculation of large systems and were proved to be effective essentially for organic molecules. HF-3c is based on a Hartree-Fock Hamiltonian with a minimal Gaussian quality basis set, whereas PBEh-3c is a density functional theory (DFT) based method with a hybrid functional and a medium-quality basis set. Both HF-3c and PBEh-3c account for dispersion (London) interactions and are free from the basis set superposition error due to limited basis set size, through several pairwise semiempirical corrections. To the best of our knowledge, despite the promising results on the cost-accuracy side of molecular simulations of organic molecules, these methods have been used only in few cases for solid-state applications. In this contribution, we studied the performance of HF-3c and PBEh-3c for predicting the properties of inorganic crystals to enlarge the applicability of these cheap and fast methodologies. As a testing ground, we have chosen a well-known class of material, e.g., microporous all-silica zeolites. We benchmarked geometries, formation energies, vibrational features, and mechanical properties by comparing the results with literature data from both experiment and computer simulation. For structures, HF-3c is extremely accurate in predicting the zeolites cell volume, albeit we do not include any vibrational contribution, neither zero point nor thermal, on the computed volumes, which may introduce small variations in the predicted values. For the energetic, the relative stability of the zeolites using the DFT//HF-3c approach allows predictions within the experimental error for most of the cases taken into consideration when the experimental enthalpies were corrected back to electronic energies by using the HF-3c thermodynamic contributions computed in the harmonic approximation. This strategy is particularly convenient, as the slow step (geometry optimization) is carried out with the cheapest HF-3c method, whereas the fast step (single point energy evaluation) is carried out with costly DFT methods. In this sense, the use of the DFT//HF-3c approach results to be a promising one to predict the stability and structure of microporous materials. Finally, the HF-3c method predicts the mechanical properties of the zeolite set in reasonable agreement with respect to those computed with the state-of-the-art DFT simulations, indicating the HF-3c method as a possible technique for the mechanical stability screenings of microporous materials.
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Caldeweyher E, Brandenburg JG. Simplified DFT methods for consistent structures and energies of large systems. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:213001. [PMID: 29633964 DOI: 10.1088/1361-648x/aabcfb] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Kohn-Sham density functional theory (DFT) is routinely used for the fast electronic structure computation of large systems and will most likely continue to be the method of choice for the generation of reliable geometries in the foreseeable future. Here, we present a hierarchy of simplified DFT methods designed for consistent structures and non-covalent interactions of large systems with particular focus on molecular crystals. The covered methods are a minimal basis set Hartree-Fock (HF-3c), a small basis set screened exchange hybrid functional (HSE-3c), and a generalized gradient approximated functional evaluated in a medium-sized basis set (B97-3c), all augmented with semi-classical correction potentials. We give an overview on the methods design, a comprehensive evaluation on established benchmark sets for geometries and lattice energies of molecular crystals, and highlight some realistic applications on large organic crystals with several hundreds of atoms in the primitive unit cell.
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Affiliation(s)
- Eike Caldeweyher
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
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Cavasotto CN, Adler NS, Aucar MG. Quantum Chemical Approaches in Structure-Based Virtual Screening and Lead Optimization. Front Chem 2018; 6:188. [PMID: 29896472 PMCID: PMC5986912 DOI: 10.3389/fchem.2018.00188] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 05/09/2018] [Indexed: 12/05/2022] Open
Abstract
Today computational chemistry is a consolidated tool in drug lead discovery endeavors. Due to methodological developments and to the enormous advance in computer hardware, methods based on quantum mechanics (QM) have gained great attention in the last 10 years, and calculations on biomacromolecules are becoming increasingly explored, aiming to provide better accuracy in the description of protein-ligand interactions and the prediction of binding affinities. In principle, the QM formulation includes all contributions to the energy, accounting for terms usually missing in molecular mechanics force-fields, such as electronic polarization effects, metal coordination, and covalent binding; moreover, QM methods are systematically improvable, and provide a greater degree of transferability. In this mini-review we present recent applications of explicit QM-based methods in small-molecule docking and scoring, and in the calculation of binding free-energy in protein-ligand systems. Although the routine use of QM-based approaches in an industrial drug lead discovery setting remains a formidable challenging task, it is likely they will increasingly become active players within the drug discovery pipeline.
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Affiliation(s)
- Claudio N. Cavasotto
- Laboratory of Computational Chemistry and Drug Design, Instituto de Investigación en Biomedicina de Buenos Aires, CONICET, Partner Institute of the Max Planck Society, Buenos Aires, Argentina
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Cavasin AT, Hillisch A, Uellendahl F, Schneckener S, Göller AH. Reliable and Performant Identification of Low-Energy Conformers in the Gas Phase and Water. J Chem Inf Model 2018; 58:1005-1020. [PMID: 29717870 DOI: 10.1021/acs.jcim.8b00151] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Prediction of compound properties from structure via quantitative structure-activity relationship and machine-learning approaches is an important computational chemistry task in small-molecule drug research. Though many such properties are dependent on three-dimensional structures or even conformer ensembles, the majority of models are based on descriptors derived from two-dimensional structures. Here we present results from a thorough benchmark study of force field, semiempirical, and density functional methods for the calculation of conformer energies in the gas phase and water solvation as a foundation for the correct identification of relevant low-energy conformers. We find that the tight-binding ansatz GFN-xTB shows the lowest error metrics and highest correlation to the benchmark PBE0-D3(BJ)/def2-TZVP in the gas phase for the computationally fast methods and that in solvent OPLS3 becomes comparable in performance. MMFF94, AM1, and DFTB+ perform worse, whereas the performance-optimized but far more expensive functional PBEh-3c yields energies almost perfectly correlated to the benchmark and should be used whenever affordable. On the basis of our findings, we have implemented a reliable and fast protocol for the identification of low-energy conformers of drug-like molecules in water that can be used for the quantification of strain energy and entropy contributions to target binding as well as for the derivation of conformer-ensemble-dependent molecular descriptors.
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Affiliation(s)
| | - Alexander Hillisch
- Bayer AG , Drug Discovery, Chemical Research , 42096 Wuppertal , Germany
| | - Felix Uellendahl
- Bayer AG , Drug Discovery, Chemical Research , 42096 Wuppertal , Germany
| | - Sebastian Schneckener
- Bayer AG , Engineering & Technology, Applied Mathematics , 51368 Leverkusen , Germany
| | - Andreas H Göller
- Bayer AG , Drug Discovery, Chemical Research , 42096 Wuppertal , Germany
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Massolle A, Dresselhaus T, Eusterwiemann S, Doerenkamp C, Eckert H, Studer A, Neugebauer J. Towards reliable references for electron paramagnetic resonance parameters based on quantum chemistry: the case of verdazyl radicals. Phys Chem Chem Phys 2018; 20:7661-7675. [PMID: 29497710 DOI: 10.1039/c7cp05657e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present an efficient and accurate computational procedure to calculate properties measurable by EPR spectroscopy. We simulate a molecular dynamics (MD) trajectory by employing the quantum mechanically derived force field (QMDFF) [S. Grimme, J. Chem. Theory Comput., 2014, 10, 4497] and sample the trajectory at different time steps. For each snapshot EPR properties are calculated with a hybrid density functional theory (DFT) method. EPR spectra are simulated based on the averaged results. We applied the strategy to a number of previously published and novel verdazyl radicals, for which we recorded EPR spectra. The resulting simulated spectra are compatible with experiment already before employing an additional fitting step, in contrast to those from single point electronic-structure calculations. After the refinement, the experimental data are excellently reproduced, and the fitted EPR parameters do not deviate much from the calculated ones. This provides confidence in ascribing a direct physical meaning to the refined data in terms of experimental EPR parameters rather than merely considering them as mathematical fit parameters. We also find that couplings to hydrogen nuclei have a significant influence on the spectra of verdazyl radicals.
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Affiliation(s)
- Anja Massolle
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany.
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Brandenburg JG, Bannwarth C, Hansen A, Grimme S. B97-3c: A revised low-cost variant of the B97-D density functional method. J Chem Phys 2018; 148:064104. [DOI: 10.1063/1.5012601] [Citation(s) in RCA: 255] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Jan Gerit Brandenburg
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AH, United Kingdom
- Thomas Young Centre, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Christoph Bannwarth
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
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Parrish RM, Thompson KC, Martínez TJ. Large-Scale Functional Group Symmetry-Adapted Perturbation Theory on Graphical Processing Units. J Chem Theory Comput 2018; 14:1737-1753. [DOI: 10.1021/acs.jctc.7b01053] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Robert M. Parrish
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Keiran C. Thompson
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Todd J. Martínez
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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39
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Structure function relations in PDZ-domain-containing proteins: Implications for protein networks in cellular signalling. J Biosci 2017. [DOI: 10.1007/s12038-017-9727-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Grimme S, Schreiner PR. Computerchemie: das Schicksal aktueller Methoden und zukünftige Herausforderungen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201709943] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical Chemistry; Universität Bonn; Beringstraße 4 53115 Bonn Deutschland
| | - Peter R. Schreiner
- Institut für Organische Chemie; Justus-Liebig-Universität; Heinrich-Buff-Ring 17 35392 Gießen Deutschland
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Grimme S, Schreiner PR. Computational Chemistry: The Fate of Current Methods and Future Challenges. Angew Chem Int Ed Engl 2017; 57:4170-4176. [PMID: 29105929 DOI: 10.1002/anie.201709943] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Indexed: 11/12/2022]
Abstract
"Where do we go from here?" is the underlying question regarding the future (perhaps foreseeable) developments in computational chemistry. Although this young discipline has already permeated practically all of chemistry, it is likely to become even more powerful with the rapid development of computational hard- and software.
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Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115, Bonn, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
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Ekhteiari Salmas R, Serhat Is Y, Durdagi S, Stein M, Yurtsever M. A QM protein–ligand investigation of antipsychotic drugs with the dopamine D2 Receptor (D2R). J Biomol Struct Dyn 2017; 36:2668-2677. [DOI: 10.1080/07391102.2017.1365772] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | - Yusuf Serhat Is
- Department of Chemistry, Istanbul Technical University, Istanbul, Turkey
- Vocational School Department of Chemistry Technology, Istanbul Gedik University, Istanbul, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Matthias Stein
- Molecular Simulations and Design Group, Max-Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Mine Yurtsever
- Department of Chemistry, Istanbul Technical University, Istanbul, Turkey
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Frush EH, Sekharan S, Keinan S. In Silico Prediction of Ligand Binding Energies in Multiple Therapeutic Targets and Diverse Ligand Sets—A Case Study on BACE1, TYK2, HSP90, and PERK Proteins. J Phys Chem B 2017; 121:8142-8148. [DOI: 10.1021/acs.jpcb.7b07224] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Elizabeth Hatcher Frush
- Cloud Pharmaceuticals, Inc., 6 Davis Drive,
Research Triangle Park, North Carolina 27709, United States
| | - Sivakumar Sekharan
- Cloud Pharmaceuticals, Inc., 6 Davis Drive,
Research Triangle Park, North Carolina 27709, United States
| | - Shahar Keinan
- Cloud Pharmaceuticals, Inc., 6 Davis Drive,
Research Triangle Park, North Carolina 27709, United States
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