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Watanabe K, Watanabe C, Honma T, Tian YS, Kawashima Y, Kawashita N, Takagi T, Fukuzawa K. Intermolecular Interaction Analyses on SARS-CoV-2 Spike Protein Receptor Binding Domain and Human Angiotensin-Converting Enzyme 2 Receptor-Blocking Antibody/Peptide Using Fragment Molecular Orbital Calculation. J Phys Chem Lett 2021; 12:4059-4066. [PMID: 33881894 PMCID: PMC8078196 DOI: 10.1021/acs.jpclett.1c00663] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/13/2021] [Indexed: 05/05/2023]
Abstract
The spike glycoprotein (S-protein) mediates SARS-CoV-2 entry via intermolecular interaction with human angiotensin-converting enzyme 2. The receptor binding domain (RBD) of the S-protein has been considered critical for this interaction and acts as the target of numerous neutralizing antibodies and antiviral peptides. This study used the fragment molecular orbital method to analyze the interactions between the RBD and antibodies/peptides and extracted crucial residues that can be used as epitopes. The interactions evaluated as interfragment interaction energy values between the RBD and 12 antibodies/peptides showed a fairly good correlation with the experimental activity pIC50 (R2 = 0.540). Nine residues (T415, K417, Y421, F456, A475, F486, N487, N501, and Y505) were confirmed as being crucial. Pair interaction energy decomposition analyses showed that hydrogen bonds, electrostatic interactions, and π-orbital interactions are important. Our results provide essential information for understanding SARS-CoV-2-antibody/peptide binding and may play roles in future antibody/antiviral drug design.
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Affiliation(s)
- Kazuki Watanabe
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Chiduru Watanabe
- Center
for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- JST
PRESTO, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Teruki Honma
- Center
for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yu-Shi Tian
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yusuke Kawashima
- School
of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41
Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Norihito Kawashita
- Graduate
School of Science and Engineering Research, Kindai University, 3-4-1
Kowakae, Higashiosaka, Osaka 577-8502, Japan
| | - Tatsuya Takagi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kaori Fukuzawa
- School
of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41
Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
- Department
of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
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2
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Watanabe C, Okiyama Y, Tanaka S, Fukuzawa K, Honma T. Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses. Chem Sci 2021; 12:4722-4739. [PMID: 35355624 PMCID: PMC8892577 DOI: 10.1039/d0sc06528e] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/21/2021] [Indexed: 12/18/2022] Open
Abstract
Due to the COVID-19 pandemic, researchers have attempted to identify complex structures of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein (S-protein) with angiotensin-converting enzyme 2 (ACE2) or a blocking antibody. However, the molecular recognition mechanism—critical information for drug and antibody design—has not been fully clarified at the amino acid residue level. Elucidating such a microscopic mechanism in detail requires a more accurate molecular interpretation that includes quantum mechanics to quantitatively evaluate hydrogen bonds, XH/π interactions (X = N, O, and C), and salt bridges. In this study, we applied the fragment molecular orbital (FMO) method to characterize the SARS-CoV-2 S-protein binding interactions with not only ACE2 but also the B38 Fab antibody involved in ACE2-inhibitory binding. By analyzing FMO-based interaction energies along a wide range of binding interfaces carefully, we identified amino acid residues critical for molecular recognition between S-protein and ACE2 or B38 Fab antibody. Importantly, hydrophobic residues that are involved in weak interactions such as CH–O hydrogen bond and XH/π interactions, as well as polar residues that construct conspicuous hydrogen bonds, play important roles in molecular recognition and binding ability. Moreover, through these FMO-based analyses, we also clarified novel hot spots and epitopes that had been overlooked in previous studies by structural and molecular mechanical approaches. Altogether, these hot spots/epitopes identified between S-protein and ACE2/B38 Fab antibody may provide useful information for future antibody design, evaluation of the binding property of the SARS-CoV-2 variants including its N501Y, and small or medium drug design against the SARS-CoV-2. Quantum chemical calculations investigated molecular recognition of SARS-CoV-2 spike glycoproteins including its N501Y variant for ACE2 and antibody. Hot spot and epitope analyses revealed key residues to design drugs and antibodies against COVID-19.![]()
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Affiliation(s)
| | - Yoshio Okiyama
- Division of Medicinal Safety Science
- National Institute of Health Sciences
- Kawasaki
- Japan
| | - Shigenori Tanaka
- Department of Computational Science
- Graduate School of System Informatics
- Kobe University
- Kobe
- Japan
| | - Kaori Fukuzawa
- School of Pharmacy and Pharmaceutical Sciences
- Hoshi University
- Tokyo 142-8501
- Japan
- Department of Biomolecular Engineering
| | - Teruki Honma
- Center for Biosystems Dynamics Research
- RIKEN
- Yokohama
- Japan
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3
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Takaya D, Niwa H, Mikuni J, Nakamura K, Handa N, Tanaka A, Yokoyama S, Honma T. Protein ligand interaction analysis against new CaMKK2 inhibitors by use of X-ray crystallography and the fragment molecular orbital (FMO) method. J Mol Graph Model 2020; 99:107599. [DOI: 10.1016/j.jmgm.2020.107599] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 01/30/2023]
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4
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Watanabe C, Watanabe H, Okiyama Y, Takaya D, Fukuzawa K, Tanaka S, Honma T. Development of an automated fragment molecular orbital (FMO) calculation protocol toward construction of quantum mechanical calculation database for large biomolecules . CHEM-BIO INFORMATICS JOURNAL 2019. [DOI: 10.1273/cbij.19.5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | - Hirofumi Watanabe
- Education Center on Computational Science and Engineering, Kobe University
| | - Yoshio Okiyama
- Center for Biosystems Dynamics Research, RIKEN
- National Institute of Health Sciences
| | | | - Kaori Fukuzawa
- Center for Biosystems Dynamics Research, RIKEN
- Department of Physical Chemistry, School of Pharmacy and Pharmaceutical Sciences, Hoshi University
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5
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Yamanaka M. <b>Random matrix theory for an inter-fragment interaction energy matrix in fragment molecular orbital method </b>. CHEM-BIO INFORMATICS JOURNAL 2018. [DOI: 10.1273/cbij.18.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Masanori Yamanaka
- Department of Physics, College of Science and Technology, Nihon University
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6
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Takaya D, Inaka K, Omura A, Takenuki K, Kawanishi M, Yabuki Y, Nakagawa Y, Tsuganezawa K, Ogawa N, Watanabe C, Honma T, Aritake K, Urade Y, Shirouzu M, Tanaka A. Characterization of crystal water molecules in a high-affinity inhibitor and hematopoietic prostaglandin D synthase complex by interaction energy studies. Bioorg Med Chem 2018; 26:4726-4734. [DOI: 10.1016/j.bmc.2018.08.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/07/2018] [Accepted: 08/10/2018] [Indexed: 10/28/2022]
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7
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Watanabe C, Watanabe H, Fukuzawa K, Parker LJ, Okiyama Y, Yuki H, Yokoyama S, Nakano H, Tanaka S, Honma T. Theoretical Analysis of Activity Cliffs among Benzofuranone-Class Pim1 Inhibitors Using the Fragment Molecular Orbital Method with Molecular Mechanics Poisson-Boltzmann Surface Area (FMO+MM-PBSA) Approach. J Chem Inf Model 2017; 57:2996-3010. [PMID: 29111719 DOI: 10.1021/acs.jcim.7b00110] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Significant activity changes due to small structural changes (i.e., activity cliffs) of serine/threonine kinase Pim1 inhibitors were studied theoretically using the fragment molecular orbital method with molecular mechanics Poisson-Boltzmann surface area (FMO+MM-PBSA) approach. This methodology enables quantum-chemical calculations for large biomolecules with solvation. In the course of drug discovery targeting Pim1, six benzofuranone-class inhibitors were found to differ only in the position of the indole-ring nitrogen atom. By comparing the various qualities of complex structures based on X-ray, classical molecular mechanics (MM)-optimized, and quantum/molecular mechanics (QM/MM)-optimized structures, we found that the QM/MM-optimized structures provided the best correlation (R2 = 0.85) between pIC50 and the calculated FMO+MM-PBSA binding energy. Combining the classical solvation energy with the QM binding energy was important to increase the correlation. In addition, decomposition of the interaction energy into various physicochemical components by pair interaction energy decomposition analysis suggested that CH-π and electrostatic interactions mainly caused the activity differences.
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Affiliation(s)
- Chiduru Watanabe
- RIKEN Center for Life Science Technologies , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,Institute of Industrial Science, The University of Tokyo , 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Hirofumi Watanabe
- RIKEN Center for Life Science Technologies , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Kaori Fukuzawa
- Institute of Industrial Science, The University of Tokyo , 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan.,Department of Physical Chemistry, School of Pharmacy and Pharmaceutical Sciences, Hoshi University , 2-4-41 Ebara, Shinagawa, Tokyo 142-8501, Japan
| | - Lorien J Parker
- RIKEN Structural Biology Laboratory , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,Department of Structural Biology, St. Vincent's Institute , 9 Princes Street, Fitzroy, Victoria 3065, Australia
| | - Yoshio Okiyama
- RIKEN Center for Life Science Technologies , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Hitomi Yuki
- RIKEN Center for Life Science Technologies , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN Structural Biology Laboratory , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Hirofumi Nakano
- Drug Discovery Initiative, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shigenori Tanaka
- Graduate School of System Informatics, Kobe University , 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Teruki Honma
- RIKEN Center for Life Science Technologies , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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8
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Zwitterionic structures: from physicochemical properties toward computer-aided drug designs. Future Med Chem 2016; 8:2245-2262. [DOI: 10.4155/fmc-2016-0176] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Zwitterions, used widely in chemical, biological and medicinal fields, show distinct physicochemical properties relative to ordinary ampholytes, which largely decide their bioavailability and biological activities. In the present manuscript, these properties are discussed in order to facilitate our understanding of zwitterionic structures, followed by various examples of zwitterionic drugs and the critical role these properties play. We specifically focus our discussions on neuraminidase inhibitors (NAIs), which are used in the treatment and prevention of influenza, covering their computer-assisted design, transformation to zwitterionic isomers and interaction mechanisms of NAIs with proteins. The discovery and development of NAIs provide useful insights that may assist in the exploration of new zwitterionic drugs.
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9
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Hydration of ligands of influenza virus neuraminidase studied by the fragment molecular orbital method. J Mol Graph Model 2016; 69:144-53. [DOI: 10.1016/j.jmgm.2016.08.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 07/29/2016] [Accepted: 08/10/2016] [Indexed: 11/18/2022]
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10
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Tagami U, Takahashi K, Igarashi S, Ejima C, Yoshida T, Takeshita S, Miyanaga W, Sugiki M, Tokumasu M, Hatanaka T, Kashiwagi T, Ishikawa K, Miyano H, Mizukoshi T. Interaction Analysis of FABP4 Inhibitors by X-ray Crystallography and Fragment Molecular Orbital Analysis. ACS Med Chem Lett 2016; 7:435-9. [PMID: 27096055 DOI: 10.1021/acsmedchemlett.6b00040] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 02/16/2016] [Indexed: 12/30/2022] Open
Abstract
X-ray crystal structural determination of FABP4 in complex with four inhibitors revealed the complex binding modes, and the resulting observations led to improvement of the inhibitory potency of FABP4 inhibitors. However, the detailed structure-activity relationship (SAR) could not be explained from these structural observations. For a more detailed understanding of the interactions between FABP4 and inhibitors, fragment molecular orbital analyses were performed. These analyses revealed that the total interfragment interaction energies of FABP4 and each inhibitor correlated with the ranking of the K i value for the four inhibitors. Furthermore, interactions between each inhibitor and amino acid residues in FABP4 were identified. The oxygen atom of Lys58 in FABP4 was found to be very important for strong interactions with FABP4. These results might provide useful information for the development of novel potent FABP4 inhibitors.
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Affiliation(s)
- Uno Tagami
- Institute
for Innovation, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki 210-8681, Japan
| | - Kazutoshi Takahashi
- Institute
for Innovation, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki 210-8681, Japan
| | - Shunsuke Igarashi
- Institute
for Innovation, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki 210-8681, Japan
| | - Chieko Ejima
- Research
Institute, Ajinomoto Pharmaceuticals Co., Ltd., 1-1 Suzuki-cho, Kawasaki 210-8681, Japan
| | - Tomomi Yoshida
- Institute
for Innovation, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki 210-8681, Japan
| | - Sen Takeshita
- Research
Institute, Ajinomoto Pharmaceuticals Co., Ltd., 1-1 Suzuki-cho, Kawasaki 210-8681, Japan
| | - Wataru Miyanaga
- Research
Institute, Ajinomoto Pharmaceuticals Co., Ltd., 1-1 Suzuki-cho, Kawasaki 210-8681, Japan
| | - Masayuki Sugiki
- Institute
for Innovation, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki 210-8681, Japan
| | - Munetaka Tokumasu
- Research
Institute, Ajinomoto Pharmaceuticals Co., Ltd., 1-1 Suzuki-cho, Kawasaki 210-8681, Japan
| | - Toshihiro Hatanaka
- Research
Institute, Ajinomoto Pharmaceuticals Co., Ltd., 1-1 Suzuki-cho, Kawasaki 210-8681, Japan
| | - Tatsuki Kashiwagi
- Institute
for Innovation, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki 210-8681, Japan
| | - Kohki Ishikawa
- Institute
for Innovation, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki 210-8681, Japan
| | - Hiroshi Miyano
- Institute
for Innovation, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki 210-8681, Japan
| | - Toshimi Mizukoshi
- Institute
for Innovation, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki 210-8681, Japan
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11
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Yoshida T, Hayashi T, Mashima A, Sasahara K, Chuman H. A simple and efficient dispersion correction to the Hartree–Fock theory (3): A comprehensive performance comparison of HF-Dtq with MP2 and DFT-Ds. Bioorg Med Chem Lett 2016; 26:589-593. [DOI: 10.1016/j.bmcl.2015.11.061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 11/14/2015] [Accepted: 11/19/2015] [Indexed: 11/25/2022]
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12
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Tanaka S, Mochizuki Y, Komeiji Y, Okiyama Y, Fukuzawa K. Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems. Phys Chem Chem Phys 2015; 16:10310-44. [PMID: 24740821 DOI: 10.1039/c4cp00316k] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent developments in the fragment molecular orbital (FMO) method for theoretical formulation, implementation, and application to nano and biomolecular systems are reviewed. The FMO method has enabled ab initio quantum-mechanical calculations for large molecular systems such as protein-ligand complexes at a reasonable computational cost in a parallelized way. There have been a wealth of application outcomes from the FMO method in the fields of biochemistry, medicinal chemistry and nanotechnology, in which the electron correlation effects play vital roles. With the aid of the advances in high-performance computing, the FMO method promises larger, faster, and more accurate simulations of biomolecular and related systems, including the descriptions of dynamical behaviors in solvent environments. The current status and future prospects of the FMO scheme are addressed in these contexts.
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Affiliation(s)
- Shigenori Tanaka
- Graduate School of System Informatics, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan.
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13
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Hitaoka S, Chuman H, Yoshizawa K. A QSAR study on the inhibition mechanism of matrix metalloproteinase-12 by arylsulfone analogs based on molecular orbital calculations. Org Biomol Chem 2015; 13:793-806. [DOI: 10.1039/c4ob01843e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The inhibition mechanism of matrix metalloproteinase-12 by arylsulfone analogs is revealed using a comprehensive computational approach including docking simulations, molecular orbital calculations, and QSAR.
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Affiliation(s)
- Seiji Hitaoka
- Institute for Materials Chemistry and Engineering and International Research Center for Molecular System
- Kyushu University
- Fukuoka 819-0395
- Japan
| | - Hiroshi Chuman
- Institute of Health Biosciences
- The University of Tokushima Graduate School
- Tokushima 770-8505
- Japan
| | - Kazunari Yoshizawa
- Institute for Materials Chemistry and Engineering and International Research Center for Molecular System
- Kyushu University
- Fukuoka 819-0395
- Japan
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14
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Multiscale quantum chemical approaches to QSAR modeling and drug design. Drug Discov Today 2014; 19:1921-7. [DOI: 10.1016/j.drudis.2014.09.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 08/01/2014] [Accepted: 09/26/2014] [Indexed: 12/24/2022]
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15
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Mashima A, Kurahashi M, Sasahara K, Yoshida T, Chuman H. Connecting Classical QSAR and LERE Analyses Using Modern Molecular Calculations, LERE-QSAR (VI): Hydrolysis of Substituted Hippuric Acid Phenyl Esters by Trypsin. Mol Inform 2014; 33:802-14. [PMID: 27485426 DOI: 10.1002/minf.201400099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 09/14/2014] [Indexed: 11/08/2022]
Abstract
The reaction mechanism of trypsin was studied by applying DFT and ab initio molecular orbital (MO) calculations to complexes of trypsin with a congeneric series of eight para-substituted hippuric acid phenyl esters, for which a previous quantitative structureactivity relationship (QSAR) study revealed nice linearity of Hammett substitution constant σ(-) with logarithmic values of the MichaelisMenten and catalytic rate constants. Based on the LERE procedure, we performed QSAR analyses on each elementary reaction step during the acylation process. The present calculations showed that the rate-determining step during the acylation process is the transition state (TS) between the enzymesubstrate complex (ES) and tetrahedral intermediate (TET), and that the proton transfer occurs from Ser195 to His57, not between His57 and Asp102. The LERE-QSAR analysis statistically suggested that the variation of overall free-energy changes leading to formation of TS is governed mostly by that of activation energies required to form TS from ES. In spite of a very limited number of congeneric ligands in the current work, it is critically essential to clarify and verify physicochemical meanings of a typical QSAR/Chemoinformatics parameter, Hammett σ(-) based on quantum chemical calculations on the proteinligand kinetics; how Hammett σ(-) behaves in terms of proteinligand interaction energies.
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Affiliation(s)
- Akira Mashima
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan phone/fax: +81-88-633-7257/+81-88-633-9508
| | - Masahiro Kurahashi
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan phone/fax: +81-88-633-7257/+81-88-633-9508
| | - Katsunori Sasahara
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan phone/fax: +81-88-633-7257/+81-88-633-9508
| | - Tatsusada Yoshida
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan phone/fax: +81-88-633-7257/+81-88-633-9508
| | - Hiroshi Chuman
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan phone/fax: +81-88-633-7257/+81-88-633-9508.
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16
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A simple and efficient dispersion correction to the Hartree–Fock theory. Bioorg Med Chem Lett 2014; 24:1037-42. [DOI: 10.1016/j.bmcl.2014.01.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 01/08/2014] [Accepted: 01/08/2014] [Indexed: 11/18/2022]
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17
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Mutation effects of neuraminidases and their docking with ligands: a molecular dynamics and free energy calculation study. J Comput Aided Mol Des 2013; 27:935-50. [DOI: 10.1007/s10822-013-9691-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 11/05/2013] [Indexed: 01/15/2023]
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18
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Pan P, Li L, Li Y, Li D, Hou T. Insights into susceptibility of antiviral drugs against the E119G mutant of 2009 influenza A (H1N1) neuraminidase by molecular dynamics simulations and free energy calculations. Antiviral Res 2013; 100:356-64. [DOI: 10.1016/j.antiviral.2013.09.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 09/07/2013] [Accepted: 09/10/2013] [Indexed: 12/11/2022]
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19
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Kubrycht J, Sigler K, Souček P, Hudeček J. Structures composing protein domains. Biochimie 2013; 95:1511-24. [DOI: 10.1016/j.biochi.2013.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 04/02/2013] [Indexed: 12/21/2022]
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20
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Three- and four-body corrected fragment molecular orbital calculations with a novel subdividing fragmentation method applicable to structure-based drug design. J Mol Graph Model 2013; 41:31-42. [PMID: 23467020 DOI: 10.1016/j.jmgm.2013.01.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 01/25/2013] [Accepted: 01/25/2013] [Indexed: 12/30/2022]
Abstract
We develop an inter-fragment interaction energy (IFIE) analysis based on the three- and four-body corrected fragment molecular orbital (FMO3 and FMO4) method to evaluate the interactions of functional group units in structure-based drug design context. The novel subdividing fragmentation method for a ligand (in units of their functional groups) and amino acid residues (in units of their main and side chains) enables us to understand the ligand-binding mechanism in more detail without sacrificing chemical accuracy of the total energy and IFIEs by using the FMO4 method. We perform FMO4 calculations with the second order Møller-Plesset perturbation theory for an estrogen receptor (ER) and the 17β-estradiol (EST) complex using the proposed fragmentation method and assess the interaction for each ligand-binding site by the FMO4-IFIE analysis. When the steroidal EST is divided into two functional units including "A ring" and "D ring", respectively, the FMO4-IFIE analysis reveals their binding affinity with surrounding fragments of the amino acid residues; the "A ring" of EST has polarization interaction with the main chain of Thr347 and two hydrogen bonds with the side chains of Glu353 and Arg394; the "D ring" of EST has a hydrogen bond with the side chain of His524. In particular, the CH/π interactions of the "A ring" of EST with the side chains of Leu387 and Phe404 are easily identified in cooperation with the CHPI program. The FMO4-IFIE analysis using our novel subdividing fragmentation method, which provides higher resolution than the conventional IFIE analysis in units of ligand and each amino acid reside in the framework of two-body approximation, is a useful tool for revealing ligand-binding mechanism and would be applicable to rational drug design such as structure-based drug design and fragment-based drug design.
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Li L, Li Y, Zhang L, Hou T. Theoretical Studies on the Susceptibility of Oseltamivir against Variants of 2009 A/H1N1 Influenza Neuraminidase. J Chem Inf Model 2012; 52:2715-29. [DOI: 10.1021/ci300375k] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Lin Li
- Institute of Functional Nano & Soft Materials (FUNSOM) and Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu 215123, China
| | - Youyong Li
- Institute of Functional Nano & Soft Materials (FUNSOM) and Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu 215123, China
| | - Liling Zhang
- Institute of Functional Nano & Soft Materials (FUNSOM) and Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu 215123, China
| | - Tingjun Hou
- Institute of Functional Nano & Soft Materials (FUNSOM) and Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu 215123, China
- College of
Pharmaceutical Sciences,
Soochow University, Suzhou, Jiangsu 215123, China
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22
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Yoshida T, Hitaoka S, Mashima A, Sugimoto T, Matoba H, Chuman H. Combined QM/MM (ONIOM) and QSAR approach to the study of complex formation of matrix metalloproteinase‑9 with a series of biphenylsulfonamides−LERE-QSAR analysis (V). J Phys Chem B 2012; 116:10283-9. [PMID: 22845734 DOI: 10.1021/jp305476x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We previously proposed a novel QSAR (quantitative structure-activity relationship) procedure called LERE (linear expression by representative energy terms)-QSAR involving molecular calculations such as an ab initio fragment molecular orbital ones. In the present work, we applied LERE-QSAR to complex formation of matrix metalloproteinase-9 (MMP-9) with a series of substituted biphenylsulfonamides. The results shows that the overall free-energy change accompanying complex formation is due to predominantly the contribution from the electrostatic interaction with the zinc atom in the active site of MMP-9. Carbonic anhydrase (CA) belongs to the zinc-containing protease family. In contrast to the current case of MMP-9, the overall free-energy change during complex formation of CA with a series of benzenesulfonamides is due to the contributions from the solvation and dissociation free-energy changes, as previously reported. Comparison of the two sets of results indicates quantitative differences in the relative contributions of free-energy components to the overall free-energy change between the two data sets, corresponding with those in the respective classical QSAR equations. The LERE-QSAR procedure was demonstrated to quantitatively reveal differences in the binding mechanisms between the two cases involving similar but different zinc-containing proteins at the electronic and atomic levels.
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Affiliation(s)
- Tatsusada Yoshida
- Institute of Health Biosciences, The University of Tokushima Graduate School , 1-78 Shomachi, Tokushima 770-8505, Japan
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23
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Fedorov DG, Nagata T, Kitaura K. Exploring chemistry with the fragment molecular orbital method. Phys Chem Chem Phys 2012; 14:7562-77. [DOI: 10.1039/c2cp23784a] [Citation(s) in RCA: 290] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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24
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Yoshida T, Shimizu M, Harada M, Hitaoka S, Chuman H. Reassessment of Hammett σ as an effective parameter representing intermolecular interaction energy-links between traditional and modern QSAR approaches. Bioorg Med Chem Lett 2011; 22:124-8. [PMID: 22172696 DOI: 10.1016/j.bmcl.2011.11.047] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2011] [Revised: 11/11/2011] [Accepted: 11/14/2011] [Indexed: 11/29/2022]
Abstract
The Hammett σ constant has for a long time been known to be one of most important linear free-energy related parameters that correlate with biological activity. It is a conventionally used electronic parameter in studies of enzymatic quantitative structure-activity relationships (QSAR). However, it is not necessarily obvious why σ represents variations in the free-energy change associated with the complex formation between a congeneric series of ligands with their target protein. So far, several powerful molecular calculations, such as the ab initio fragment molecular orbital (FMO) one, that are directly applicable to ligand-protein complexes have emerged. In this study, we comprehensively reevaluate experimentally derived parameter σ confirming it represents intermolecular interaction energy terms, by applying molecular orbital (MO) calculations to a simple ligand-protein complex model. The current results provide a rational and quantitative basis for bridging the gap between the traditional QSAR approach and 'the modern QSAR one', which involves the molecular calculations to evaluate the overall free-energy change for complex formation.
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Affiliation(s)
- Tatsusada Yoshida
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan
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25
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Hitaoka S, Matoba H, Harada M, Yoshida T, Tsuji D, Hirokawa T, Itoh K, Chuman H. Correlation Analyses on Binding Affinity of Sialic Acid Analogues and Anti-Influenza Drugs with Human Neuraminidase Using ab Initio MO Calculations on Their Complex Structures – LERE-QSAR Analysis (IV). J Chem Inf Model 2011; 51:2706-16. [DOI: 10.1021/ci2002395] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Seiji Hitaoka
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan
| | - Hiroshi Matoba
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan
| | - Masataka Harada
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan
| | - Tatsusada Yoshida
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan
| | - Daisuke Tsuji
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan
| | - Takatsugu Hirokawa
- Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Kohji Itoh
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan
| | - Hiroshi Chuman
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan
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26
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Gordon MS, Fedorov DG, Pruitt SR, Slipchenko LV. Fragmentation Methods: A Route to Accurate Calculations on Large Systems. Chem Rev 2011; 112:632-72. [DOI: 10.1021/cr200093j] [Citation(s) in RCA: 836] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Mark S. Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames Iowa 50011, United States
| | - Dmitri G. Fedorov
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Spencer R. Pruitt
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames Iowa 50011, United States
| | - Lyudmila V. Slipchenko
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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27
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Okiyama Y, Fukuzawa K, Yamada H, Mochizuki Y, Nakano T, Tanaka S. Counterpoise-corrected interaction energy analysis based on the fragment molecular orbital scheme. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.04.070] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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28
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Mazanetz MP, Ichihara O, Law RJ, Whittaker M. Prediction of cyclin-dependent kinase 2 inhibitor potency using the fragment molecular orbital method. J Cheminform 2011; 3:2. [PMID: 21219630 PMCID: PMC3032746 DOI: 10.1186/1758-2946-3-2] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 01/10/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The reliable and robust estimation of ligand binding affinity continues to be a challenge in drug design. Many current methods rely on molecular mechanics (MM) calculations which do not fully explain complex molecular interactions. Full quantum mechanical (QM) computation of the electronic state of protein-ligand complexes has recently become possible by the latest advances in the development of linear-scaling QM methods such as the ab initio fragment molecular orbital (FMO) method. This approximate molecular orbital method is sufficiently fast that it can be incorporated into the development cycle during structure-based drug design for the reliable estimation of ligand binding affinity. Additionally, the FMO method can be combined with approximations for entropy and solvation to make it applicable for binding affinity prediction for a broad range of target and chemotypes. RESULTS We applied this method to examine the binding affinity for a series of published cyclin-dependent kinase 2 (CDK2) inhibitors. We calculated the binding affinity for 28 CDK2 inhibitors using the ab initio FMO method based on a number of X-ray crystal structures. The sum of the pair interaction energies (PIE) was calculated and used to explain the gas-phase enthalpic contribution to binding. The correlation of the ligand potencies to the protein-ligand interaction energies gained from FMO was examined and was seen to give a good correlation which outperformed three MM force field based scoring functions used to appoximate the free energy of binding. Although the FMO calculation allows for the enthalpic component of binding interactions to be understood at the quantum level, as it is an in vacuo single point calculation, the entropic component and solvation terms are neglected. For this reason a more accurate and predictive estimate for binding free energy was desired. Therefore, additional terms used to describe the protein-ligand interactions were then calculated to improve the correlation of the FMO derived values to experimental free energies of binding. These terms were used to account for the polar and non-polar solvation of the molecule estimated by the Poisson-Boltzmann equation and the solvent accessible surface area (SASA), respectively, as well as a correction term for ligand entropy. A quantitative structure-activity relationship (QSAR) model obtained by Partial Least Squares projection to latent structures (PLS) analysis of the ligand potencies and the calculated terms showed a strong correlation (r2 = 0.939, q2 = 0.896) for the 14 molecule test set which had a Pearson rank order correlation of 0.97. A training set of a further 14 molecules was well predicted (r2 = 0.842), and could be used to obtain meaningful estimations of the binding free energy. CONCLUSIONS Our results show that binding energies calculated with the FMO method correlate well with published data. Analysis of the terms used to derive the FMO energies adds greater understanding to the binding interactions than can be gained by MM methods. Combining this information with additional terms and creating a scaled model to describe the data results in more accurate predictions of ligand potencies than the absolute values obtained by FMO alone.
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Affiliation(s)
- Michael P Mazanetz
- Evotec (UK) limited, 114 Milton Park, Abingdon, Oxfordshire, OX14 4SA, UK
| | - Osamu Ichihara
- Evotec (UK) limited, 114 Milton Park, Abingdon, Oxfordshire, OX14 4SA, UK
| | - Richard J Law
- Evotec (UK) limited, 114 Milton Park, Abingdon, Oxfordshire, OX14 4SA, UK
| | - Mark Whittaker
- Evotec (UK) limited, 114 Milton Park, Abingdon, Oxfordshire, OX14 4SA, UK
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Munei Y, Shimamoto K, Harada M, Yoshida T, Chuman H. Correlation analyses on binding affinity of substituted benzenesulfonamides with carbonic anhydrase using ab initio MO calculations on their complex structures (II). Bioorg Med Chem Lett 2011; 21:141-4. [PMID: 21130650 DOI: 10.1016/j.bmcl.2010.11.050] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 11/08/2010] [Accepted: 11/09/2010] [Indexed: 10/18/2022]
Abstract
We proposed a novel QSAR (quantitative structure-activity relationship) procedure called LERE (linear expression by representative energy terms)-QSAR involving molecular calculations such as ab initio fragment molecular orbital and generalized Born/surface area ones. We applied LERE-QSAR to two datasets for the free-energy changes during complex formation between carbonic anhydrase and a series of substituted benzenesulfonamides. The first compound set (Set I) and the second one (Set II) include relatively small substituents and alkyl chains of different lengths in the benzene ring, respectively. Variation of the inhibitory activity in Set I is expressed as the combination of Hammett σ and the hydrophobic substituent constant π in classical QSAR, and variation in Set II only by π. LERE-QSAR analyses clearly revealed that effects of σ and π on the activity variations in Sets I and II are consistently explainable with the energy terms in the LERE formulation, and provide more detailed and direct information as to the binding mechanism. The proposed procedure was demonstrated to provide a quantitative basis for understanding ligand-protein interactions at the electronic and atomic levels.
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Affiliation(s)
- Yohei Munei
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan
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