1
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Handa Y, Okuwaki K, Kawashima Y, Hatada R, Mochizuki Y, Komeiji Y, Tanaka S, Furuishi T, Yonemochi E, Honma T, Fukuzawa K. Prediction of Binding Pose and Affinity of Nelfinavir, a SARS-CoV-2 Main Protease Repositioned Drug, by Combining Docking, Molecular Dynamics, and Fragment Molecular Orbital Calculations. J Phys Chem B 2024; 128:2249-2265. [PMID: 38437183 PMCID: PMC10946393 DOI: 10.1021/acs.jpcb.3c05564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 03/06/2024]
Abstract
A novel in silico drug design procedure is described targeting the Main protease (Mpro) of the SARS-CoV-2 virus. The procedure combines molecular docking, molecular dynamics (MD), and fragment molecular orbital (FMO) calculations. The binding structure and properties of Mpro were predicted for Nelfinavir (NFV), which had been identified as a candidate compound through drug repositioning, targeting Mpro. Several poses of the Mpro and NFV complexes were generated by docking, from which four docking poses were selected by scoring with FMO energy. Then, each pose was subjected to MD simulation, 100 snapshot structures were sampled from each of the generated MD trajectories, and the structures were evaluated by FMO calculations to rank the pose based on binding energy. Several residues were found to be important in ligand recognition, including Glu47, Asp48, Glu166, Asp187, and Gln189, all of which interacted strongly with NFV. Asn142 is presumably regarded to form hydrogen bonds or CH/π interaction with NFV; however, in the present calculation, their interactions were transient. Moreover, the tert-butyl group of NFV had no interaction with Mpro. Identifying such strong and weak interactions provides candidates for maintaining and substituting ligand functional groups and important suggestions for drug discovery using drug repositioning. Besides the interaction between NFV and the amino acid residues of Mpro, the desolvation effect of the binding pocket also affected the ranking order. A similar procedure of drug design was applied to Lopinavir, and the calculated interaction energy and experimental inhibitory activity value trends were consistent. Our approach provides a new guideline for structure-based drug design starting from a candidate compound whose complex crystal structure has not been obtained.
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Affiliation(s)
- Yuma Handa
- Department
of Physical Chemistry, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
- Graduate
School of Pharmaceutical Sciences, Osaka
University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Koji Okuwaki
- Department
of Physical Chemistry, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, 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
| | - Yusuke Kawashima
- Department
of Physical Chemistry, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Ryo Hatada
- 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
| | - Yuji Mochizuki
- 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
- Institute
of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Yuto Komeiji
- Graduate
School of Pharmaceutical Sciences, Osaka
University, 1-6 Yamadaoka, Suita, Osaka 565-0871, 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
- Health
and Medical Research Institute, AIST, Tsukuba Central 6, Tsukuba, Ibaraki 305-8566, Japan
- RIKEN
Center
for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Shigenori Tanaka
- Graduate
School of System Informatics, Department of Computational Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Takayuki Furuishi
- Department
of Physical Chemistry, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Etsuo Yonemochi
- Department
of Physical Chemistry, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Teruki Honma
- RIKEN
Center
for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Kaori Fukuzawa
- Department
of Physical Chemistry, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
- Graduate
School of Pharmaceutical Sciences, Osaka
University, 1-6 Yamadaoka, Suita, Osaka 565-0871, 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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Abe-Sato K, Tabuse H, Kanazawa H, Kamitani M, Endo M, Tokura S, Wakabayashi S, Yahara T, Takeda T, Hitaka K, Gunji E, Kojima N, Oka Y. Structure-Based Optimization and Biological Evaluation of Potent and Selective MMP-7 Inhibitors for Kidney Fibrosis. J Med Chem 2023; 66:14653-14668. [PMID: 37861435 DOI: 10.1021/acs.jmedchem.3c01166] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Matrix metalloproteinase-7 (MMP-7) has been shown to play important roles in pathophysiological processes involved in the development/progression of diseases such as cancer and fibrosis. We discovered selective MMP-7 inhibitors composed of arylsulfonamide, carboxylate, and short peptides by a molecular hybridization approach. These compounds interacted with MMP-7 via multiple hydrogen bonds in the cocrystal structures. To obtain compounds for in vivo evaluation, we attempted structural optimization, particularly targeting Tyr167 at the S3 subsite through structure-based drug design, and identified compound 15 as showing improved MMP-7 potency and MMP subtype selectivity. A novel π-π stacking interaction with Tyr167 was achieved when 4-pyridylalanine was introduced as the P3 residue. Compound 15 suppressed the progression of kidney fibrosis in a dose-dependent manner in a mouse model of unilateral ureteral obstruction. Thus, we demonstrated, for the first time, that potent and selective MMP-7 inhibitors could prevent the progression of kidney fibrosis.
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Affiliation(s)
- Kumi Abe-Sato
- Medicinal Chemistry Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Hideaki Tabuse
- Medicinal Chemistry Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Harumi Kanazawa
- Medicinal Chemistry Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Masafumi Kamitani
- Discovery Technologies Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Mayumi Endo
- Discovery Technologies Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Seiken Tokura
- Discovery Technologies Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Satoshi Wakabayashi
- Drug Metabolism and Pharmacokinetics Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Tohru Yahara
- Drug Metabolism and Pharmacokinetics Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Takuya Takeda
- Pharmacology Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Kosuke Hitaka
- Pharmacology Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Emi Gunji
- Pharmacology Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Naoki Kojima
- Pharmacology Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Yusuke Oka
- Medicinal Chemistry Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
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3
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Watanabe C, Tanaka S, Okiyama Y, Yuki H, Ohyama T, Kamisaka K, Takaya D, Fukuzawa K, Honma T. Quantum Chemical Interaction Analysis between SARS-CoV-2 Main Protease and Ensitrelvir Compared with Its Initial Screening Hit. J Phys Chem Lett 2023; 14:3609-3620. [PMID: 37023394 PMCID: PMC10081834 DOI: 10.1021/acs.jpclett.2c03768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/17/2023] [Indexed: 06/19/2023]
Abstract
A non-covalent oral drug targeting SARS-CoV-2 main protease (Mpro), ensitrelvir (Xocova), has been developed using structure-based drug design (SBDD). To elucidate the factors responsible for enhanced inhibitory activities from an in silico screening hit compound to ensitrelvir, we analyzed the interaction energies of the inhibitors with each residue of Mpro using fragment molecular orbital (FMO) calculations. This analysis reveals that functional group conversion for P1' and P1 parts in the inhibitors increases the strength of existing interactions with Mpro and also provides novel interactions for ensitrelvir; the associated changes in the conformation of Mpro induce further interactions for ensitrelvir in other parts, including hydrogen bonds, a halogen bond, and π-orbital interactions. Thus, we illuminate the promising strategies of SBDD for leading ensitrelvir to get higher activity against Mpro by elucidating microscopic interactions through FMO-based analysis. These detailed mechanism findings, including water cross-linkings, will help to design novel inhibitors in SBDD.
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Affiliation(s)
- Chiduru Watanabe
- Center for Biosystems Dynamics Research,
RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa
230-0045, Japan
| | - Shigenori Tanaka
- Department of Computational Science, Graduate School
of System Informatics, Kobe University, 1-1 Rokkodai, Nada-ku,
Kobe, Hyogo 657-8501, Japan
| | - Yoshio Okiyama
- Department of Computational Science, Graduate School
of System Informatics, Kobe University, 1-1 Rokkodai, Nada-ku,
Kobe, Hyogo 657-8501, Japan
| | - Hitomi Yuki
- Center for Biosystems Dynamics Research,
RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa
230-0045, Japan
| | - Tatsuya Ohyama
- Frontier Institute for Biomolecular Engineering Research
(FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe
650-0047, Japan
| | - Kikuko Kamisaka
- Center for Biosystems Dynamics Research,
RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa
230-0045, Japan
| | - Daisuke Takaya
- Graduate School of Pharmaceutical Sciences,
Osaka University,1-6 Yamadaoka, Suita, Osaka 565-0871,
Japan
| | - Kaori Fukuzawa
- Graduate School of Pharmaceutical Sciences,
Osaka University,1-6 Yamadaoka, Suita, Osaka 565-0871,
Japan
| | - Teruki Honma
- Center for Biosystems Dynamics Research,
RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa
230-0045, Japan
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4
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Nakamura S, Akaki T, Nishiwaki K, Nakatani M, Kawase Y, Takahashi Y, Nakanishi I. System truncation accelerates binding affinity calculations with the fragment molecular orbital method: A benchmark study. J Comput Chem 2023; 44:824-831. [PMID: 36444861 DOI: 10.1002/jcc.27044] [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: 08/07/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 11/30/2022]
Abstract
The fragment molecular orbital (FMO) method is a fast quantum-mechanical method that divides systems into pieces of fragments and performs ab initio calculations. The system truncation enables further speed improvement. In this article, we systematically study the effects of system truncations on binding affinity calculations obtained with FMO in combination with either the polarizable continuum model (FMO/PCM) or in combination with the Møller-Plesset method (FMO-MP2). We have used five protein complexes with ligands of several charged states. The calculated binding energies of the size variants of the truncated system, including only a restricted number of atoms around the ligand, are compared to the energy obtained from a full system. The result shows that the systems could be truncated to a radius of 8 Å from neutral ligands within an error of 0.7 kcal/mol, and 12 Å from charged ligands within an error of 1.1 kcal/mol for calculating the binding energy in solution.
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Affiliation(s)
- Shinya Nakamura
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan
| | - Tatsuo Akaki
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan.,Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., Osaka, Japan
| | - Keiji Nishiwaki
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan
| | - Midori Nakatani
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan
| | - Yuji Kawase
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan
| | - Yuki Takahashi
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan
| | - Isao Nakanishi
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan
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5
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Tanaka S. Protein-Protein Interaction Modelling with the Fragment Molecular Orbital Method. Methods Mol Biol 2023; 2552:295-305. [PMID: 36346599 DOI: 10.1007/978-1-0716-2609-2_16] [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] [Indexed: 06/16/2023]
Abstract
Fragment molecular orbital (FMO) method enables ab initio quantum-chemical calculations for biomolecular systems with high accuracy and moderate computational cost. Through this analysis we can evaluate the inter-fragment interaction energies (IFIEs) that provide useful measures for effective interactions between the fragments representing amino-acid residues and ligand molecules. Here I describe how to prepare the input structures and perform the FMO calculations for protein-protein complex system. In addition to the pre-processing, some useful tools for the post-processing analysis are also illustrated.
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Affiliation(s)
- Shigenori Tanaka
- Graduate School of System Informatics, Kobe University, Kobe, Hyogo, Japan.
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6
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Sengoku T, Shiina M, Suzuki K, Hamada K, Sato K, Uchiyama A, Kobayashi S, Oguni A, Itaya H, Kasahara K, Moriwaki H, Watanabe C, Honma T, Okada C, Baba S, Ohta T, Motohashi H, Yamamoto M, Ogata K. Structural basis of transcription regulation by CNC family transcription factor, Nrf2. Nucleic Acids Res 2022; 50:12543-12557. [PMID: 36454022 PMCID: PMC9756947 DOI: 10.1093/nar/gkac1102] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/22/2022] [Accepted: 11/02/2022] [Indexed: 12/05/2022] Open
Abstract
Several basic leucine zipper (bZIP) transcription factors have accessory motifs in their DNA-binding domains, such as the CNC motif of CNC family or the EHR motif of small Maf (sMaf) proteins. CNC family proteins heterodimerize with sMaf proteins to recognize CNC-sMaf binding DNA elements (CsMBEs) in competition with sMaf homodimers, but the functional role of the CNC motif remains elusive. In this study, we report the crystal structures of Nrf2/NFE2L2, a CNC family protein regulating anti-stress transcriptional responses, in a complex with MafG and CsMBE. The CNC motif restricts the conformations of crucial Arg residues in the basic region, which form extensive contact with the DNA backbone phosphates. Accordingly, the Nrf2-MafG heterodimer has approximately a 200-fold stronger affinity for CsMBE than canonical bZIP proteins, such as AP-1 proteins. The high DNA affinity of the CNC-sMaf heterodimer may allow it to compete with the sMaf homodimer on target genes without being perturbed by other low-affinity bZIP proteins with similar sequence specificity.
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Affiliation(s)
- Toru Sengoku
- To whom correspondence should be addressed. Tel: +81 45 787 2590; Fax: +81 45 784 4530;
| | | | - Kae Suzuki
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Keisuke Hamada
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Ko Sato
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Akiko Uchiyama
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Shunsuke Kobayashi
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Asako Oguni
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Hayato Itaya
- College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Kota Kasahara
- College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Hirotomo Moriwaki
- RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan
| | - Chiduru Watanabe
- RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan,JST PRESTO, Yokohama 230-0045, Japan
| | - Teruki Honma
- RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan
| | - Chikako Okada
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Shiho Baba
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Tsutomu Ohta
- Department of Physical Therapy, Faculty of Health and Medical Sciences, Tokoha University, Hamamatsu 431-2102, Japan
| | - Hozumi Motohashi
- Department of Gene Expression Regulation, Institute of Development, Aging, and Cancer, Tohoku University, Sendai 980-8575, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8575, Japan
| | - Kazuhiro Ogata
- Correspondence may also be addressed to Kazuhiro Ogata. Tel: +81 45 787 2590; Fax: +81 45 784 4530;
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7
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Fujii M, Tanaka S. Interspecies Comparison of Interaction Energies between Photosynthetic Protein RuBisCO and 2CABP Ligand. Int J Mol Sci 2022; 23:ijms231911347. [PMID: 36232645 PMCID: PMC9570433 DOI: 10.3390/ijms231911347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/15/2022] [Accepted: 09/22/2022] [Indexed: 01/27/2023] Open
Abstract
Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) functions as the initial enzyme in the dark reactions of photosynthesis, catalyzing reactions that extract CO2 from the atmosphere and fix CO2 into organic compounds. RuBisCO is classified into four types (isoforms I–IV) according to sequence-based phylogenetic trees. Given its size, the computational cost of accurate quantum-chemical calculations for functional analysis of RuBisCO is high; however, recent advances in hardware performance and the use of the fragment molecular orbital (FMO) method have enabled the ab initio analyses of RuBisCO. Here, we performed FMO calculations on multiple structural datasets for various complexes with the 2′-carboxylarabinitol 1,5-bisphosphate (2CABP) ligand as a substrate analog and investigated whether phylogenetic relationships based on sequence information are physicochemically relevant as well as whether novel information unobtainable from sequence information can be revealed. We extracted features similar to the phylogenetic relationships found in sequence analysis, and in terms of singular value decomposition, we identified residues that strongly interacted with the ligand and the characteristics of the isoforms for each principal component. These results identified a strong correlation between phylogenetic relationships obtained by sequence analysis and residue interaction energies with the ligand. Notably, some important residues were located far from the ligand, making comparisons among species using only residues proximal to the ligand insufficient.
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8
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Fujii M, Watanabe C, Fukuzawa K, Tanaka S. Fragment molecular orbital calculations containing Mg<sup>2+</sup> ions: PPlase domain of Cyclophilin G. CHEM-BIO INFORMATICS JOURNAL 2022. [DOI: 10.1273/cbij.22.55] [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)
- Masayasu Fujii
- Department of Computational Science, Graduate School of System Informatics, Kobe University
| | | | - Kaori Fukuzawa
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Shigenori Tanaka
- Department of Computational Science, Graduate School of System Informatics, Kobe University
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9
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Niwa H, Watanabe C, Sato S, Harada T, Watanabe H, Tabusa R, Fukasawa S, Shiobara A, Hashimoto T, Ohno O, Nakamura K, Tsuganezawa K, Tanaka A, Shirouzu M, Honma T, Matsuno K, Umehara T. Structure–Activity Relationship and In Silico Evaluation of cis- and trans-PCPA-Derived Inhibitors of LSD1 and LSD2. ACS Med Chem Lett 2022; 13:1485-1492. [PMID: 36105323 PMCID: PMC9465824 DOI: 10.1021/acsmedchemlett.2c00294] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/04/2022] [Indexed: 12/15/2022] Open
Abstract
![]()
trans-2-Phenylcycloproylamine (trans-PCPA) has been used as the scaffold to develop covalent-binding
inhibitors against lysine-specific demethylase 1 (LSD1/KDM1A), a therapeutic
target for several cancers. However, the effects of different structural
moieties on the inhibitory activity, selectivity, and reactivity of
these derivatives, including the cis isomers, against
LSD1 and its paralogue LSD2/KDM1B are not fully understood. Here we
synthesized 65 cis- and trans-PCPA
derivatives and evaluated their inhibitory activity against LSD1 and
LSD2. One of the derivatives, 7c (cis-4-Br-2,5-F2-PCPA; S1024), inhibited LSD1
and LSD2 with Ki values of 0.094 μM
and 8.4 μM, respectively, and increased the level of dimethylated
histone H3 at K4 in CCRF-CEM cells. A machine learning-based regression
model (Q2 = 0.61) to predict LSD1-inhibitory
activity was also constructed and showed a good prediction accuracy
(R2 = 0.81) for 12 test-set compounds,
including 7c. The present methodology would be useful
when designing covalent-binding inhibitors for other enzymes.
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Affiliation(s)
- Hideaki Niwa
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Chiduru Watanabe
- Drug Discovery Computational Chemistry Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Shin Sato
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Toshiyuki Harada
- Drug Discovery Computational Chemistry Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hisami Watanabe
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Ryo Tabusa
- Laboratory of Medicinal Chemistry, Department of Chemistry and Life Science, School of Advanced Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan
| | - Shunsuke Fukasawa
- Laboratory of Medicinal Chemistry, Department of Chemistry and Life Science, School of Advanced Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan
| | - Ayane Shiobara
- Laboratory of Medicinal Chemistry, Department of Chemistry and Life Science, School of Advanced Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan
| | - Tomoko Hashimoto
- Laboratory of Medicinal Chemistry, Department of Chemistry and Life Science, School of Advanced Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan
| | - Osamu Ohno
- Laboratory of Medicinal Chemistry, Department of Chemistry and Life Science, School of Advanced Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan
| | - Kana Nakamura
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Keiko Tsuganezawa
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Akiko Tanaka
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Mikako Shirouzu
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Teruki Honma
- Drug Discovery Computational Chemistry Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Kenji Matsuno
- Laboratory of Medicinal Chemistry, Department of Chemistry and Life Science, School of Advanced Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan
- Department of Pharmacy, Faculty of Pharmacy, Yasuda Women’s University, 6-13-1 Yasuhigashi, Asaminami-ku, Hiroshima 731-0153, Japan
| | - Takashi Umehara
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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10
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Takaba K, Watanabe C, Tokuhisa A, Akinaga Y, Ma B, Kanada R, Araki M, Okuno Y, Kawashima Y, Moriwaki H, Kawashita N, Honma T, Fukuzawa K, Tanaka S. Protein-ligand binding affinity prediction of cyclin-dependent kinase-2 inhibitors by dynamically averaged fragment molecular orbital-based interaction energy. J Comput Chem 2022; 43:1362-1371. [PMID: 35678372 DOI: 10.1002/jcc.26940] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 03/27/2022] [Accepted: 04/02/2022] [Indexed: 01/16/2023]
Abstract
Fragment molecular orbital (FMO) method is a powerful computational tool for structure-based drug design, in which protein-ligand interactions can be described by the inter-fragment interaction energy (IFIE) and its pair interaction energy decomposition analysis (PIEDA). Here, we introduced a dynamically averaged (DA) FMO-based approach in which molecular dynamics simulations were used to generate multiple protein-ligand complex structures for FMO calculations. To assess this approach, we examined the correlation between the experimental binding free energies and DA-IFIEs of six CDK2 inhibitors whose net charges are zero. The correlation between the experimental binding free energies and snapshot IFIEs for X-ray crystal structures was R2 = 0.75. Using the DA-IFIEs, the correlation significantly improved to 0.99. When an additional CDK2 inhibitor with net charge of -1 was added, the DA FMO-based scheme with the dispersion energies still achieved R2 = 0.99, whereas R2 decreased to 0.32 employing all the energy terms of PIEDA.
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Affiliation(s)
- Kenichiro Takaba
- Pharmaceutical Research Center, Advanced Drug Discovery, Asahi Kasei Pharma Corporation, Shizuoka, Japan
| | - Chiduru Watanabe
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Atsushi Tokuhisa
- RIKEN Center for Computational Science, Chuo-ku, Kobe, Hyogo, Japan
| | - Yoshinobu Akinaga
- RIKEN Center for Computational Science, Chuo-ku, Kobe, Hyogo, Japan.,Project Development Department, VINAS Co., Ltd., Osaka, Japan
| | - Biao Ma
- RIKEN Center for Computational Science, Chuo-ku, Kobe, Hyogo, Japan
| | - Ryo Kanada
- RIKEN Center for Computational Science, Chuo-ku, Kobe, Hyogo, Japan
| | - Mitsugu Araki
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasushi Okuno
- RIKEN Center for Computational Science, Chuo-ku, Kobe, Hyogo, Japan.,Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yusuke Kawashima
- School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Tokyo, Japan
| | - Hirotomo Moriwaki
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | | | - Teruki Honma
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Kaori Fukuzawa
- School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Tokyo, Japan.,Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Shigenori Tanaka
- Graduate School of System Informatics, Kobe University, Kobe, Japan
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11
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Dawson W, Degomme A, Stella M, Nakajima T, Ratcliff LE, Genovese L. Density functional theory calculations of large systems: Interplay between fragments, observables, and computational complexity. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1574] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | | | - Martina Stella
- Department of Materials Imperial College London London UK
| | | | | | - Luigi Genovese
- Université Grenoble Alpes, INAC‐MEM, L_Sim Grenoble France
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12
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Fukuzawa K, Kato K, Watanabe C, Kawashima Y, Handa Y, Yamamoto A, Watanabe K, Ohyama T, Kamisaka K, Takaya D, Honma T. Special Features of COVID-19 in the FMODB: Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2-Related Proteins. J Chem Inf Model 2021; 61:4594-4612. [PMID: 34506132 PMCID: PMC8457332 DOI: 10.1021/acs.jcim.1c00694] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Indexed: 01/18/2023]
Abstract
SARS-CoV-2 is the causative agent of coronavirus (known as COVID-19), the virus causing the current pandemic. There are ongoing research studies to develop effective therapeutics and vaccines against COVID-19 using various methods and many results have been published. The structure-based drug design of SARS-CoV-2-related proteins is promising, however, reliable information regarding the structural and intra- and intermolecular interactions is required. We have conducted studies based on the fragment molecular orbital (FMO) method for calculating the electronic structures of protein complexes and analyzing their quantitative molecular interactions. This enables us to extensively analyze the molecular interactions in residues or functional group units acting inside the protein complexes. Such precise interaction data are available in the FMO database (FMODB) (https://drugdesign.riken.jp/FMODB/). Since April 2020, we have performed several FMO calculations on the structures of SARS-CoV-2-related proteins registered in the Protein Data Bank. We have published the results of 681 structures, including three structural proteins and 11 nonstructural proteins, on the COVID-19 special page (as of June 8, 2021). In this paper, we describe the entire COVID-19 special page of the FMODB and discuss the calculation results for various proteins. These data not only aid the interpretation of experimentally determined structures but also the understanding of protein functions, which is useful for rational drug design for COVID-19.
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Affiliation(s)
- Kaori Fukuzawa
- Department of Physical Chemistry, 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
| | - Koichiro Kato
- Department of Applied Chemistry, Graduate School of
Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka
819-0395, Japan
- Center for Molecular Systems (CMS),
Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395,
Japan
| | - Chiduru Watanabe
- RIKEN Center for Biosystems Dynamics
Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045,
Japan
- JST PRESTO, 4-1-8, Honcho,
Kawaguchi, Saitama 332-0012, Japan
| | - Yusuke Kawashima
- Department of Physical Chemistry, School of Pharmacy
and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara,
Shinagawa-ku, Tokyo 142-8501, Japan
| | - Yuma Handa
- Department of Physical Chemistry, School of Pharmacy
and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara,
Shinagawa-ku, Tokyo 142-8501, Japan
| | - Ami Yamamoto
- Department of Physical Chemistry, School of Pharmacy
and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara,
Shinagawa-ku, Tokyo 142-8501, Japan
| | - Kazuki Watanabe
- Graduate School of Pharmaceutical Sciences,
Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871,
Japan
- Graduate School of Pharmaceutical Sciences,
Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675,
Japan
| | - Tatsuya Ohyama
- RIKEN Center for Biosystems Dynamics
Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045,
Japan
- Frontier Institute for Biomolecular Engineering
Research (FIBER), Konan University, 7-1-20,
Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Kikuko Kamisaka
- RIKEN Center for Biosystems Dynamics
Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045,
Japan
| | - Daisuke Takaya
- RIKEN Center for Biosystems Dynamics
Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045,
Japan
| | - Teruki Honma
- RIKEN Center for Biosystems Dynamics
Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045,
Japan
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13
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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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14
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Waman VP, Sen N, Varadi M, Daina A, Wodak SJ, Zoete V, Velankar S, Orengo C. The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies. Brief Bioinform 2021; 22:742-768. [PMID: 33348379 PMCID: PMC7799268 DOI: 10.1093/bib/bbaa362] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 01/18/2023] Open
Abstract
SARS-CoV-2 is the causative agent of COVID-19, the ongoing global pandemic. It has posed a worldwide challenge to human health as no effective treatment is currently available to combat the disease. Its severity has led to unprecedented collaborative initiatives for therapeutic solutions against COVID-19. Studies resorting to structure-based drug design for COVID-19 are plethoric and show good promise. Structural biology provides key insights into 3D structures, critical residues/mutations in SARS-CoV-2 proteins, implicated in infectivity, molecular recognition and susceptibility to a broad range of host species. The detailed understanding of viral proteins and their complexes with host receptors and candidate epitope/lead compounds is the key to developing a structure-guided therapeutic design. Since the discovery of SARS-CoV-2, several structures of its proteins have been determined experimentally at an unprecedented speed and deposited in the Protein Data Bank. Further, specialized structural bioinformatics tools and resources have been developed for theoretical models, data on protein dynamics from computer simulations, impact of variants/mutations and molecular therapeutics. Here, we provide an overview of ongoing efforts on developing structural bioinformatics tools and resources for COVID-19 research. We also discuss the impact of these resources and structure-based studies, to understand various aspects of SARS-CoV-2 infection and therapeutic development. These include (i) understanding differences between SARS-CoV-2 and SARS-CoV, leading to increased infectivity of SARS-CoV-2, (ii) deciphering key residues in the SARS-CoV-2 involved in receptor-antibody recognition, (iii) analysis of variants in host proteins that affect host susceptibility to infection and (iv) analyses facilitating structure-based drug and vaccine design against SARS-CoV-2.
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Affiliation(s)
| | | | | | - Antoine Daina
- Molecular Modeling Group at SIB, Swiss Institute of Bioinformatics
| | | | - Vincent Zoete
- Department of Fundamental Oncology at the University of Lausanne and Group leader at SIB
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15
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Takaya D, Watanabe C, Nagase S, Kamisaka K, Okiyama Y, Moriwaki H, Yuki H, Sato T, Kurita N, Yagi Y, Takagi T, Kawashita N, Takaba K, Ozawa T, Takimoto-Kamimura M, Tanaka S, Fukuzawa K, Honma T. FMODB: The World's First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method. J Chem Inf Model 2021; 61:777-794. [PMID: 33511845 DOI: 10.1021/acs.jcim.0c01062] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We developed the world's first web-based public database for the storage, management, and sharing of fragment molecular orbital (FMO) calculation data sets describing the complex interactions between biomacromolecules, named FMO Database (https://drugdesign.riken.jp/FMODB/). Each entry in the database contains relevant background information on how the data was compiled as well as the total energy of each molecular system and interfragment interaction energy (IFIE) and pair interaction energy decomposition analysis (PIEDA) values. Currently, the database contains more than 13 600 FMO calculation data sets, and a comprehensive search function implemented at the front-end. The procedure for selecting target proteins, preprocessing the experimental structures, construction of the database, and details of the database front-end were described. Then, we demonstrated a use of the FMODB by comparing IFIE value distributions of hydrogen bond, ion-pair, and XH/π interactions obtained by FMO method to those by molecular mechanics approach. From the comparison, the statistical analysis of the data provided standard reference values for the three types of interactions that will be useful for determining whether each interaction in a given system is relatively strong or weak compared to the interactions contained within the data in the FMODB. In the final part, we demonstrate the use of the database to examine the contribution of halogen atoms to the binding affinity between human cathepsin L and its inhibitors. We found that the electrostatic term derived by PIEDA greatly correlated with the binding affinities of the halogen containing cathepsin L inhibitors, indicating the importance of QM calculation for quantitative analysis of halogen interactions. Thus, the FMO calculation data in FMODB will be useful for conducting statistical analyses to drug discovery, for conducting molecular recognition studies in structural biology, and for other studies involving quantum mechanics-based interactions.
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Affiliation(s)
- Daisuke Takaya
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Chiduru Watanabe
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,JST PRESTO, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Shunpei Nagase
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Kikuko Kamisaka
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshio Okiyama
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, Japan
| | - Hirotomo Moriwaki
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hitomi Yuki
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Tomohiro Sato
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
| | - Yoichiro Yagi
- Graduate School of Engineering, Okayama University of Science, Okayama, 1-1 Ridai-cho, Okayama 700-0005, Japan
| | - Tatsuya Takagi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Norihito Kawashita
- Faculty of Science and Engineering, Kindai University, 3-4-1 Kowakae, Higashiosaka, Osaka 577-8502, Japan
| | - Kenichiro Takaba
- Pharmaceutical Research Center, Laboratory for Medicinal Chemistry, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni, Shizuoka 410-2321, Japan
| | - Tomonaga Ozawa
- Kissei Pharmaceutical Co., LTD., Frontier Technology Research Lab., Research Div. 4365-1 Hotaka Kashiwabara, Azumino, Nagano 399-8304, Japan
| | - Midori Takimoto-Kamimura
- Teijin Institute for Biomedical Research, Teijin Pharma Ltd., 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan
| | - Shigenori Tanaka
- Graduate School of System Informatics, Department of Computational Science, Kobe University, 1-1 Rokkodai, Kobe, Hyogo 657-8501, Japan
| | - Kaori Fukuzawa
- School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa, Tokyo 142-8501, Japan.,Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Sendai, Miyagi 980-8579, Japan
| | - Teruki Honma
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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16
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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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17
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Hatada R, Okuwaki K, Mochizuki Y, Handa Y, Fukuzawa K, Komeiji Y, Okiyama Y, Tanaka S. Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease - Inhibitor N3 Complex (PDB ID: 6LU7). J Chem Inf Model 2020; 60:3593-3602. [PMID: 32539372 PMCID: PMC7318557 DOI: 10.1021/acs.jcim.0c00283] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Indexed: 01/23/2023]
Abstract
The worldwide spread of COVID-19 (new coronavirus found in 2019) is an emergent issue to be tackled. In fact, a great amount of works in various fields have been made in a rather short period. Here, we report a fragment molecular orbital (FMO) based interaction analysis on a complex between the SARS-CoV-2 main protease (Mpro) and its peptide-like inhibitor N3 (PDB ID: 6LU7). The target inhibitor molecule was segmented into five fragments in order to capture site specific interactions with amino acid residues of the protease. The interaction energies were decomposed into several contributions, and then the characteristics of hydrogen bonding and dispersion stabilization were made clear. Furthermore, the hydration effect was incorporated by the Poisson-Boltzmann (PB) scheme. From the present FMO study, His41, His163, His164, and Glu166 were found to be the most important amino acid residues of Mpro in interacting with the inhibitor, mainly due to hydrogen bonding. A guideline for optimizations of the inhibitor molecule was suggested as well based on the FMO analysis.
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Affiliation(s)
- Ryo Hatada
- 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
| | - Koji Okuwaki
- 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
| | - Yuji Mochizuki
- 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
- Institute of Industrial Science,
The University of Tokyo, 4-6-1
Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Yuma Handa
- School of Pharmacy and Pharmaceutical
Sciences, Hoshi University, 2-4-41 Ebara,
Shinagawa-Ku, Tokyo 142-8501, Japan
| | - Kaori Fukuzawa
- Institute of Industrial Science,
The University of Tokyo, 4-6-1
Komaba, Meguro-ku, Tokyo 153-8505, Japan
- School of Pharmacy and Pharmaceutical
Sciences, Hoshi University, 2-4-41 Ebara,
Shinagawa-Ku, Tokyo 142-8501, Japan
| | - Yuto Komeiji
- Health and Medical
Research Institute, AIST, Tsukuba Central 6,
Tsukuba, Ibaraki 305-8566, Japan
| | - Yoshio Okiyama
- Division of Medicinal Safety Science,
National Institute of Health
Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki,
Kanagawa 201-9501, Japan
| | - Shigenori Tanaka
- Graduate School of System Informatics,
Department of Computational Science, Kobe
University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501,
Japan
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18
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Kato K, Masuda T, Watanabe C, Miyagawa N, Mizouchi H, Nagase S, Kamisaka K, Oshima K, Ono S, Ueda H, Tokuhisa A, Kanada R, Ohta M, Ikeguchi M, Okuno Y, Fukuzawa K, Honma T. High-Precision Atomic Charge Prediction for Protein Systems Using Fragment Molecular Orbital Calculation and Machine Learning. J Chem Inf Model 2020; 60:3361-3368. [PMID: 32496771 DOI: 10.1021/acs.jcim.0c00273] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Here, we have constructed neural network-based models that predict atomic partial charges with high accuracy at low computational cost. The models were trained using high-quality data acquired from quantum mechanics calculations using the fragment molecular orbital method. We have succeeded in obtaining highly accurate atomic partial charges for three representative molecular systems of proteins, including one large biomolecule (approx. 2000 atoms). The novelty of our approach is the ability to take into account the electronic polarization in the system, which is a system-dependent phenomenon, being important in the field of drug design. Our high-precision models are useful for the prediction of atomic partial charges and expected to be widely applicable in structure-based drug designs such as structural optimization, high-speed and high-precision docking, and molecular dynamics calculations.
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Affiliation(s)
- Koichiro Kato
- Science Solutions Division, Mizuho Information & Research Institute, Inc., 2-3 Kanda Nishiki-cho, Chiyoda, Tokyo 101-8443, Japan.,Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.,Center for Molecular Systems (CMS), Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Tomohide Masuda
- Pharmaceutical Research Laboratories, Toray Industries, Inc., 6-10-1 Tebiro, Kamakura, Kanagawa 248-8555, Japan
| | - Chiduru Watanabe
- Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Naoki Miyagawa
- Science Solutions Division, Mizuho Information & Research Institute, Inc., 2-3 Kanda Nishiki-cho, Chiyoda, Tokyo 101-8443, Japan
| | - Hideo Mizouchi
- Science Solutions Division, Mizuho Information & Research Institute, Inc., 2-3 Kanda Nishiki-cho, Chiyoda, Tokyo 101-8443, Japan
| | - Shumpei Nagase
- Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,Masuda Keizai Kenkyusho, Y.K., Hillsidemasuda, 1-1-15 Teraya, Tsurumi-ku, Yokohama-shi, Kanagawa 230-0015, Japan
| | - Kikuko Kamisaka
- Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Kanji Oshima
- Biotechnology Research Laboratories, Kaneka Corporation, 1-8 Miyamae-cho, Takasago-cho, Takasago, Hyogo 676-8688, Japan
| | - Satoshi Ono
- Discovery Technology Laboratories, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
| | - Hiroshi Ueda
- Pharmaceutical Research Laboratories, Toray Industries, Inc., 6-10-1 Tebiro, Kamakura, Kanagawa 248-8555, Japan
| | - Atsushi Tokuhisa
- RIKEN Cluster for Science and Technology Hub, 6-3-5 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,RIKEN Center for Computational Science, 6-3-5 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,RIKEN Medical Sciences Innovation Hub Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Ryo Kanada
- RIKEN Cluster for Science and Technology Hub, 6-3-5 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Masateru Ohta
- Drug Development Data Intelligence Platform Group, Medical Science Innovation Hub Program, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yasushi Okuno
- RIKEN Medical Sciences Innovation Hub Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan.,RIKEN Compass to Healthy Life Research Complex Program, RIKEN, 6-7-1 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Kaori Fukuzawa
- School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Teruki Honma
- Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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19
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Sato T, Sekimata K, Sakai N, Watanabe H, Mishima-Tsumagari C, Taguri T, Matsumoto T, Fujii Y, Handa N, Tanaka A, Shirouzu M, Yokoyama S, Hashizume Y, Miyazono K, Koyama H, Honma T. Structural Basis of Activin Receptor-Like Kinase 2 (R206H) Inhibition by Bis-heteroaryl Pyrazole-Based Inhibitors for the Treatment of Fibrodysplasia Ossificans Progressiva Identified by the Integration of Ligand-Based and Structure-Based Drug Design Approaches. ACS OMEGA 2020; 5:11411-11423. [PMID: 32478230 PMCID: PMC7254505 DOI: 10.1021/acsomega.9b04245] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 03/19/2020] [Indexed: 05/11/2023]
Abstract
Fibrodysplasia ossificans progressiva (FOP) is a rare but severe genetic disorder in which acute inflammation elicits progressive heterotopic ossification in the muscles, tendons, and ligaments. Classic FOP is caused by the R206H mutation in ALK2/ACVR1. While several activin receptor-like kinase 2 (ALK2) inhibitors were found to be efficacious in animal models of FOP, most of the ALK2 (R206H) inhibitors lacked sufficient oral bioavailability for efficacy. Previously, the synthesis of a series of novel bis-heteroaryl pyrazole-based ALK2 (R206H) inhibitors that achieved both substantial potency and an improved ADMET profile was reported. In the present study, the detailed procedure of the in silico approach employed to identify the initial bis-heteroaryl pyrazole-based ALK2 (R206H) inhibitor RK-59638 and the analysis of the ALK2 (R206H) RK-59638 complex structure to guide the synthetic optimization of the chemical series, obtaining RK-71807 showing improved potency and metabolic stability, were described. According to the initial in silico screening, the screening efficiencies and chemical diversity of the hit compounds of both ligand-based and structure-based methods were evaluated. Then, X-ray structures of ALK2 (R206H) and the inhibitors were analyzed to assess the structure-activity relationships of the synthesized compounds. The 3D-RISM analysis indicated the existence of the additional hydrogen bond via water molecules restricting the attachment point in the pyrazole scaffold. The quantum mechanics calculation of the newly determined ALK2 (R206H) RK-71807 complex structure using a fragment molecular orbital method and pair interaction energy decomposition analysis was employed to evaluate the interaction energies between the inhibitor and each of the amino acid residues and decompose them to electrostatic, exchange-repulsion, and charge transfer energies. The pattern of decomposed interaction energies was then compared to that formed by RK-59638 and LDN-193189 to investigate the structural basis of ALK2 (R206H) inhibition.
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Affiliation(s)
- Tomohiro Sato
- Drug
Discovery Computational Chemistry Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1−7−22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Katsuhiko Sekimata
- Drug
Discovery Chemistry Platform Unit, RIKEN
Center for Sustainable Resource Science, 2−1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoki Sakai
- Drug
Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1−7−22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Hisami Watanabe
- Drug
Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1−7−22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Chiemi Mishima-Tsumagari
- Drug
Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1−7−22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Tomonori Taguri
- Drug
Discovery Chemistry Platform Unit, RIKEN
Center for Sustainable Resource Science, 2−1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Takehisa Matsumoto
- Drug
Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1−7−22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yoshifumi Fujii
- Crystallographic
Drug Discovery Platform Unit, RIKEN Systems
and Structural Biology Center, 1−7−22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Noriko Handa
- Crystallographic
Drug Discovery Platform Unit, RIKEN Systems
and Structural Biology Center, 1−7−22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Akiko Tanaka
- Drug
Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1−7−22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mikako Shirouzu
- Drug
Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1−7−22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Shigeyuki Yokoyama
- Crystallographic
Drug Discovery Platform Unit, RIKEN Systems
and Structural Biology Center, 1−7−22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yoshinobu Hashizume
- RIKEN
Program for Drug Discovery and Medical Technology Platforms, 2−1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kohei Miyazono
- Department
of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, 7−3−1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroo Koyama
- Drug
Discovery Chemistry Platform Unit, RIKEN
Center for Sustainable Resource Science, 2−1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Teruki Honma
- Drug
Discovery Computational Chemistry Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1−7−22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- . Phone: +81-45-503-9551. Fax: +81-45-503-9432
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20
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Nakliang P, Lazim R, Chang H, Choi S. Multiscale Molecular Modeling in G Protein-Coupled Receptor (GPCR)-Ligand Studies. Biomolecules 2020; 10:E631. [PMID: 32325877 PMCID: PMC7226129 DOI: 10.3390/biom10040631] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/13/2020] [Accepted: 04/17/2020] [Indexed: 12/17/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are major drug targets due to their ability to facilitate signal transduction across cell membranes, a process that is vital for many physiological functions to occur. The development of computational technology provides modern tools that permit accurate studies of the structures and properties of large chemical systems, such as enzymes and GPCRs, at the molecular level. The advent of multiscale molecular modeling permits the implementation of multiple levels of theories on a system of interest, for instance, assigning chemically relevant regions to high quantum mechanics (QM) level of theory while treating the rest of the system using classical force field (molecular mechanics (MM) potential). Multiscale QM/MM molecular modeling have far-reaching applications in the rational design of GPCR drugs/ligands by affording precise ligand binding configurations through the consideration of conformational plasticity. This enables the identification of key binding site residues that could be targeted to manipulate GPCR function. This review will focus on recent applications of multiscale QM/MM molecular simulations in GPCR studies that could boost the efficiency of future structure-based drug design (SBDD) strategies.
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Affiliation(s)
| | | | | | - Sun Choi
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea; (P.N.); (R.L.); (H.C.)
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