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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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Okiyama Y, Watanabe C, Fukuzawa K, Mochizuki Y, Nakano T, Tanaka S. Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson-Boltzmann Equation: II. Protein and Its Ligand-Binding System Studies. J Phys Chem B 2018; 123:957-973. [PMID: 30532968 DOI: 10.1021/acs.jpcb.8b09326] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, the electronic properties of bioactive proteins were analyzed using an ab initio fragment molecular orbital (FMO) methodology in solution: coupling with an implicit solvent model based on the Poisson-Boltzmann surface area called as FMO-PBSA. We investigated the solvent effects on practical and heterogeneous targets with uneven exposure to solvents unlike deoxyribonucleic acid analyzed in our recent study. Interfragment interaction energy (IFIE) and its decomposition analyses by FMO-PBSA revealed solvent-screening mechanisms that affect local stability inside ubiquitin protein: the screening suppresses excessiveness in bare charge-charge interactions and enables an intuitive IFIE analysis. The electrostatic character and associated solvation free energy also give consistent results as a whole to previous studies on the explicit solvent model. Moreover, by using the estrogen receptor alpha (ERα) protein bound to ligands, we elucidated the importance of specific interactions that depend on the electric charge and activatability as agonism/antagonism of the ligand while estimating the influences of the implicit solvent on the ligand and helix-12 bindings. The predicted ligand-binding affinities of bioactive compounds to ERα also show a good correlation with their in vitro activities. The FMO-PBSA approach would thus be a promising tool both for biological and pharmaceutical research targeting proteins.
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Affiliation(s)
- Yoshio Okiyama
- Institute of Industrial Science , The University of Tokyo , 4-6-1 Komaba , Meguro-ku, Tokyo 153-8505 , Japan.,Division of Medicinal Safety Science , National Institute of Health Sciences , 3-25-26 Tonomachi , Kawasaki-ku, Kawasaki , Kanagawa 210-9501 , Japan
| | - Chiduru Watanabe
- Institute of Industrial Science , The University of Tokyo , 4-6-1 Komaba , Meguro-ku, Tokyo 153-8505 , Japan.,RIKEN Center for Biosystems Dynamics Research , 1-7-22 Suehiro-cho , Tsurumi-ku, Yokohama , Kanagawa 230-0045 , Japan
| | - Kaori Fukuzawa
- Institute of Industrial Science , The University of Tokyo , 4-6-1 Komaba , Meguro-ku, Tokyo 153-8505 , Japan.,Faculty of Pharmaceutical Sciences , Hoshi University , 2-4-41 Ebara , Shinagawa-ku, Tokyo 142-8501 , Japan
| | - Yuji Mochizuki
- Institute of Industrial Science , The University of Tokyo , 4-6-1 Komaba , Meguro-ku, Tokyo 153-8505 , Japan.,Department of Chemistry and Research Center for Smart Molecules, Faculty of Science , Rikkyo University , 3-34-1 Nishi-ikebukuro , Toshima-ku, Tokyo 171-8501 , Japan
| | - Tatsuya Nakano
- Institute of Industrial Science , The University of Tokyo , 4-6-1 Komaba , Meguro-ku, Tokyo 153-8505 , Japan.,Division of Medicinal Safety Science , National Institute of Health Sciences , 3-25-26 Tonomachi , Kawasaki-ku, Kawasaki , Kanagawa 210-9501 , Japan
| | - Shigenori Tanaka
- Graduate School of System Informatics , Kobe University , 1-1 Rokkodai, Nada-ku, Kobe , Hyogo 657-8501 , Japan
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Thapa B, Beckett D, Erickson J, Raghavachari K. Theoretical Study of Protein–Ligand Interactions Using the Molecules-in-Molecules Fragmentation-Based Method. J Chem Theory Comput 2018; 14:5143-5155. [DOI: 10.1021/acs.jctc.8b00531] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Bishnu Thapa
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Daniel Beckett
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jon Erickson
- Lilly Research Laboratories, Eli Lilly & Co., Indianapolis, Indiana 47285, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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Ryde U, Söderhjelm P. Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods. Chem Rev 2016; 116:5520-66. [DOI: 10.1021/acs.chemrev.5b00630] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ulf Ryde
- Department of Theoretical
Chemistry and ‡Department of Biophysical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Pär Söderhjelm
- Department of Theoretical
Chemistry and ‡Department of Biophysical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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Chiniforoshan H, Pourrahim N, Tabrizi L, Tavakol H, Sabzalian MR, Notash B. Syntheses, studies and crystal structure of new coordination polymers of mercury (II) with phenylcyanamide derivative ligands. Inorganica Chim Acta 2014. [DOI: 10.1016/j.ica.2014.03.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Rodríguez Ortega MPG, Montejo M, López González JJ. Stabilizing factors of the molecular structure in silicon-based peptidomimetics in gas-phase and water solution. Assessment of the correlation between different descriptors of hydrogen bond strength. J Mol Model 2013; 19:4293-304. [PMID: 23900857 DOI: 10.1007/s00894-013-1945-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 07/12/2013] [Indexed: 10/26/2022]
Abstract
The use of DFT (B3LYP and M06L) and ab initio (MP2) computational methods allowed us to perform a thorough conformational study of N-[dihydroxy (methyl)silyl]methylformamide (DHSF) and 3-[dihydroxy (methyl) silyl] propanamide (DHSP), that could be considered simplified models of the environment of the silanediol group in silicon gem-diols that have proven efficiency as protease inhibitors. We have found a total of 13 molecular conformations that represent minima in the potential energy surfaces of DHSF (six conformers) and DHSP (seven conformers). The key feature in their molecular structure is the occurrence of intramolecular hydrogen bonding between the hydroxyl and aminocarbonyl groups. We have estimated the strength of each individual hydrogen bond in the mentioned species using the descriptors proposed by three different methodologies, i.e., the quantum theory of atoms in molecules (QTAIM), the natural bond orbitals population analysis (NBO), and the so-called empirical Rozenberg's enthalpy-distance relationship. We have found a good correlation among the calculated values for the different descriptors within the whole set of conformers in the molecular systems in this study. We have also discussed the predicted order of stabilities of the different conformers of each species in terms of the so-called ring anomeric effect (RAE) and generalized anomeric effect (GAE). Finally, we also analyzed the discrepancies found in the order of stability when going from the isolated molecule approximation to water solution (PCM).
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Affiliation(s)
- María Pilar Gema Rodríguez Ortega
- Department of Physical and Analytical Chemistry. Experimental Sciences Faculty, University of Jaén, Campus "Las Lagunillas", 23071, Jaén, Spain
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Rodríguez Ortega MPG, Montejo M, López González JJ. Interaction models of the Si(OH)2 functionality with Zn2+ cation in simplified biological environments: a DFT study. Struct Chem 2013. [DOI: 10.1007/s11224-013-0258-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Specific interactions and binding energies between thermolysin and potent inhibitors: Molecular simulations based on ab initio molecular orbital method. J Mol Graph Model 2012; 33:1-11. [DOI: 10.1016/j.jmgm.2011.10.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 10/18/2011] [Accepted: 10/18/2011] [Indexed: 11/19/2022]
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