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Matsuoka S, Sakakura K, Akinaga Y, Akisawa K, Okuwaki K, Doi H, Mochizuki Y. Enhancement of energy decomposition analysis in fragment molecular orbital calculations. J Comput Chem 2024; 45:898-902. [PMID: 38158621 DOI: 10.1002/jcc.27297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/10/2023] [Accepted: 12/13/2023] [Indexed: 01/03/2024]
Abstract
Energy decomposition analysis is one of the most attractive features of fragment molecular orbital (FMO) calculations from the point of view of practical applications. Here we report some enhancements for PIEDA in the ABINIT-MP program. One is a separation of the dispersion-type stabilization from the electron correlation energy, traditionally referred to as the "dispersion interaction" (DI). Another is an alternative evaluation of the electrostatic (ES) interaction using the restrained electrostatic potential (RESP) charges. The GA:CT stacked base pair and the Trp-Cage miniprotein were used as illustrative examples.
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Affiliation(s)
- Sota Matsuoka
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, Tokyo, Japan
| | | | | | - Kazuki Akisawa
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, Tokyo, Japan
| | - Koji Okuwaki
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, Tokyo, Japan
- JSOL Corp., Kudan-Kaikan Terrace, Tokyo, Japan
| | - Hideo Doi
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, Tokyo, Japan
| | - Yuji Mochizuki
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, Tokyo, Japan
- Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
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2
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Fukumoto Y, Kyono R, Shibukawa Y, Tanaka YK, Suzuki N, Ogra Y. Differential molecular mechanisms of substrate recognition by selenium methyltransferases, INMT and TPMT, in selenium detoxification and excretion. J Biol Chem 2024; 300:105599. [PMID: 38159853 PMCID: PMC10844679 DOI: 10.1016/j.jbc.2023.105599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024] Open
Abstract
It is known that the recommended dietary allowance of selenium (Se) is dangerously close to its tolerable upper intake level. Se is detoxified and excreted in urine as trimethylselenonium ion (TMSe) when the amount ingested exceeds the nutritional level. Recently, we demonstrated that the production of TMSe requires two methyltransferases: thiopurine S-methyltransferase (TPMT) and indolethylamine N-methyltransferase (INMT). In this study, we investigated the substrate recognition mechanisms of INMT and TPMT in the Se-methylation reaction. Examination of the Se-methyltransferase activities of two paralogs of INMT, namely, nicotinamide N-methyltransferase and phenylethanolamine N-methyltransferase, revealed that only INMT exhibited Se-methyltransferase activity. Consistently, molecular dynamics simulations demonstrated that dimethylselenide was preferentially associated with the active center of INMT. Using the fragment molecular orbital method, we identified hydrophobic residues involved in the binding of dimethylselenide to the active center of INMT. The INMT-L164R mutation resulted in a deficiency in Se- and N-methyltransferase activities. Similarly, TPMT-R152, which occupies the same position as INMT-L164, played a crucial role in the Se-methyltransferase activity of TPMT. Our findings suggest that TPMT recognizes negatively charged substrates, whereas INMT recognizes electrically neutral substrates in the hydrophobic active center embedded within the protein. These observations explain the sequential requirement of the two methyltransferases in producing TMSe.
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Affiliation(s)
- Yasunori Fukumoto
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan.
| | - Rin Kyono
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Yuka Shibukawa
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Yu-Ki Tanaka
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Noriyuki Suzuki
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Yasumitsu Ogra
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
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3
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Yuan Z, Chen X, Fan S, Chang L, Chu L, Zhang Y, Wang J, Li S, Xie J, Hu J, Miao R, Zhu L, Zhao Z, Li H, Li S. Binding Free Energy Calculation Based on the Fragment Molecular Orbital Method and Its Application in Designing Novel SHP-2 Allosteric Inhibitors. Int J Mol Sci 2024; 25:671. [PMID: 38203841 PMCID: PMC10779950 DOI: 10.3390/ijms25010671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
The accurate prediction of binding free energy is a major challenge in structure-based drug design. Quantum mechanics (QM)-based approaches show promising potential in predicting ligand-protein binding affinity by accurately describing the behavior and structure of electrons. However, traditional QM calculations face computational limitations, hindering their practical application in drug design. Nevertheless, the fragment molecular orbital (FMO) method has gained widespread application in drug design due to its ability to reduce computational costs and achieve efficient ab initio QM calculations. Although the FMO method has demonstrated its reliability in calculating the gas phase potential energy, the binding of proteins and ligands also involves other contributing energy terms, such as solvent effects, the 'deformation energy' of a ligand's bioactive conformations, and entropy. Particularly in cases involving ionized fragments, the calculation of solvation free energy becomes particularly crucial. We conducted an evaluation of some previously reported implicit solvent methods on the same data set to assess their potential for improving the performance of the FMO method. Herein, we develop a new QM-based binding free energy calculation method called FMOScore, which enhances the performance of the FMO method. The FMOScore method incorporates linear fitting of various terms, including gas-phase potential energy, deformation energy, and solvation free energy. Compared to other widely used traditional prediction methods such as FEP+, MM/PBSA, MM/GBSA, and Autodock vina, FMOScore showed good performance in prediction accuracies. By constructing a retrospective case study, it was observed that incorporating calculations for solvation free energy and deformation energy can further enhance the precision of FMO predictions for binding affinity. Furthermore, using FMOScore-guided lead optimization against Src homology-2-containing protein tyrosine phosphatase 2 (SHP-2), we discovered a novel and potent allosteric SHP-2 inhibitor (compound 8).
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Affiliation(s)
- Zhen Yuan
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
| | - Xingyu Chen
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
| | - Sisi Fan
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
| | - Longfeng Chang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
| | - Linna Chu
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
| | - Ying Zhang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
| | - Jie Wang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
| | - Shuang Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
| | - Jinxin Xie
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
| | - Jianguo Hu
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
| | - Runyu Miao
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
| | - Lili Zhu
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
| | - Zhenjiang Zhao
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
- Innovation Center for AI and Drug Discovery, East China Normal University, Shanghai 200062, China
- Lingang Laboratory, Shanghai 200031, China
| | - Shiliang Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
- Innovation Center for AI and Drug Discovery, East China Normal University, Shanghai 200062, China
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4
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Jin H, Kim J, Lee O, Kim H, No KT. Leveraging the Fragment Molecular Orbital Method to Explore the PLK1 Kinase Binding Site and Polo-Box Domain for Potent Small-Molecule Drug Design. Int J Mol Sci 2023; 24:15639. [PMID: 37958623 PMCID: PMC10650754 DOI: 10.3390/ijms242115639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/19/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Polo-like kinase 1 (PLK1) plays a pivotal role in cell division regulation and emerges as a promising therapeutic target for cancer treatment. Consequently, the development of small-molecule inhibitors targeting PLK1 has become a focal point in contemporary research. The adenosine triphosphate (ATP)-binding site and the polo-box domain in PLK1 present crucial interaction sites for these inhibitors, aiming to disrupt the protein's function. However, designing potent and selective small-molecule inhibitors can be challenging, requiring a deep understanding of protein-ligand interaction mechanisms at these binding sites. In this context, our study leverages the fragment molecular orbital (FMO) method to explore these site-specific interactions in depth. Using the FMO approach, we used the FMO method to elucidate the molecular mechanisms of small-molecule drugs binding to these sites to design PLK1 inhibitors that are both potent and selective. Our investigation further entailed a comparative analysis of various PLK1 inhibitors, each characterized by distinct structural attributes, helping us gain a better understanding of the relationship between molecular structure and biological activity. The FMO method was particularly effective in identifying key binding features and predicting binding modes for small-molecule ligands. Our research also highlighted specific "hot spot" residues that played a critical role in the selective and robust binding of PLK1. These findings provide valuable insights that can be used to design new and effective PLK1 inhibitors, which can have significant implications for developing anticancer therapeutics.
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Affiliation(s)
- Haiyan Jin
- The Interdisciplinary Graduate Program in Integrative Biotechnology & Translational Medicine, Yonsei University, Incheon 21983, Republic of Korea; (H.J.); (O.L.)
| | - Jongwan Kim
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
- Bioinformatics and Molecular Design Research Center (BMDRC), Incheon 21983, Republic of Korea;
| | - Onju Lee
- The Interdisciplinary Graduate Program in Integrative Biotechnology & Translational Medicine, Yonsei University, Incheon 21983, Republic of Korea; (H.J.); (O.L.)
| | - Hyein Kim
- Bioinformatics and Molecular Design Research Center (BMDRC), Incheon 21983, Republic of Korea;
| | - Kyoung Tai No
- The Interdisciplinary Graduate Program in Integrative Biotechnology & Translational Medicine, Yonsei University, Incheon 21983, Republic of Korea; (H.J.); (O.L.)
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
- Bioinformatics and Molecular Design Research Center (BMDRC), Incheon 21983, Republic of Korea;
- Baobab AiBIO Co., Ltd., Incheon 21983, Republic of Korea
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5
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Shi J, Kanoya R, Tani Y, Ishikawa S, Maeda R, Suzuki S, Kawanami F, Miyagawa N, Takahashi K, Oku T, Yamamoto A, Fukuzawa K, Nakajima M, Irimura T, Higashi N. Sulfated Hyaluronan Binds to Heparanase and Blocks Its Enzymatic and Cellular Actions in Carcinoma Cells. Int J Mol Sci 2022; 23:ijms23095055. [PMID: 35563446 PMCID: PMC9102160 DOI: 10.3390/ijms23095055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/20/2022] [Accepted: 04/28/2022] [Indexed: 11/17/2022] Open
Abstract
We examined whether sulfated hyaluronan exerts inhibitory effects on enzymatic and biological actions of heparanase, a sole endo-beta-glucuronidase implicated in cancer malignancy and inflammation. Degradation of heparan sulfate by human and mouse heparanase was inhibited by sulfated hyaluronan. In particular, high-sulfated hyaluronan modified with approximately 2.5 sulfate groups per disaccharide unit effectively inhibited the enzymatic activity at a lower concentration than heparin. Human and mouse heparanase bound to immobilized sulfated hyaluronan. Invasion of heparanase-positive colon-26 cells and 4T1 cells under 3D culture conditions was significantly suppressed in the presence of high-sulfated hyaluronan. Heparanase-induced release of CCL2 from colon-26 cells was suppressed in the presence of sulfated hyaluronan via blocking of cell surface binding and subsequent intracellular NF-κB-dependent signaling. The inhibitory effect of sulfated hyaluronan is likely due to competitive binding to the heparanase molecule, which antagonizes the heparanase-substrate interaction. Fragment molecular orbital calculation revealed a strong binding of sulfated hyaluronan tetrasaccharide to the heparanase molecule based on electrostatic interactions, particularly characterized by interactions of (−1)- and (−2)-positioned sulfated sugar residues with basic amino acid residues composing the heparin-binding domain-1 of heparanase. These results propose a relevance for sulfated hyaluronan in the blocking of heparanase-mediated enzymatic and cellular actions.
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Affiliation(s)
- Jia Shi
- Department of Biochemistry, Hoshi University School of Pharmacy, 2-4-41, Ebara, Shinagawa-ku, Tokyo 144-8501, Japan; (J.S.); (R.K.); (Y.T.); (S.I.); (R.M.); (S.S.); (F.K.); (N.M.); (K.T.)
| | - Riku Kanoya
- Department of Biochemistry, Hoshi University School of Pharmacy, 2-4-41, Ebara, Shinagawa-ku, Tokyo 144-8501, Japan; (J.S.); (R.K.); (Y.T.); (S.I.); (R.M.); (S.S.); (F.K.); (N.M.); (K.T.)
| | - Yurina Tani
- Department of Biochemistry, Hoshi University School of Pharmacy, 2-4-41, Ebara, Shinagawa-ku, Tokyo 144-8501, Japan; (J.S.); (R.K.); (Y.T.); (S.I.); (R.M.); (S.S.); (F.K.); (N.M.); (K.T.)
| | - Sodai Ishikawa
- Department of Biochemistry, Hoshi University School of Pharmacy, 2-4-41, Ebara, Shinagawa-ku, Tokyo 144-8501, Japan; (J.S.); (R.K.); (Y.T.); (S.I.); (R.M.); (S.S.); (F.K.); (N.M.); (K.T.)
| | - Rino Maeda
- Department of Biochemistry, Hoshi University School of Pharmacy, 2-4-41, Ebara, Shinagawa-ku, Tokyo 144-8501, Japan; (J.S.); (R.K.); (Y.T.); (S.I.); (R.M.); (S.S.); (F.K.); (N.M.); (K.T.)
| | - Sana Suzuki
- Department of Biochemistry, Hoshi University School of Pharmacy, 2-4-41, Ebara, Shinagawa-ku, Tokyo 144-8501, Japan; (J.S.); (R.K.); (Y.T.); (S.I.); (R.M.); (S.S.); (F.K.); (N.M.); (K.T.)
| | - Fumiya Kawanami
- Department of Biochemistry, Hoshi University School of Pharmacy, 2-4-41, Ebara, Shinagawa-ku, Tokyo 144-8501, Japan; (J.S.); (R.K.); (Y.T.); (S.I.); (R.M.); (S.S.); (F.K.); (N.M.); (K.T.)
| | - Naoko Miyagawa
- Department of Biochemistry, Hoshi University School of Pharmacy, 2-4-41, Ebara, Shinagawa-ku, Tokyo 144-8501, Japan; (J.S.); (R.K.); (Y.T.); (S.I.); (R.M.); (S.S.); (F.K.); (N.M.); (K.T.)
| | - Katsuhiko Takahashi
- Department of Biochemistry, Hoshi University School of Pharmacy, 2-4-41, Ebara, Shinagawa-ku, Tokyo 144-8501, Japan; (J.S.); (R.K.); (Y.T.); (S.I.); (R.M.); (S.S.); (F.K.); (N.M.); (K.T.)
| | - Teruaki Oku
- Department of Microbiology, Hoshi University School of Pharmacy, 2-4-41, Ebara, Shinagawa-ku, Tokyo 144-8501, Japan;
| | - Ami Yamamoto
- Department of Physical Chemistry, Hoshi University School of Pharmacy, 2-4-41, Ebara, Shinagawa-ku, Tokyo 144-8501, Japan; (A.Y.); (K.F.)
| | - Kaori Fukuzawa
- Department of Physical Chemistry, Hoshi University School of Pharmacy, 2-4-41, Ebara, Shinagawa-ku, Tokyo 144-8501, Japan; (A.Y.); (K.F.)
| | - Motowo Nakajima
- SBI Pharmaceuticals Co., Ltd., 1-6-1, Roppongi, Minato-ku, Tokyo 106-6019, Japan;
| | - Tatsuro Irimura
- Division of Glycobiologics, Intractable Disease Research Center, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-ku, Tokyo 104-8520, Japan;
| | - Nobuaki Higashi
- Department of Biochemistry, Hoshi University School of Pharmacy, 2-4-41, Ebara, Shinagawa-ku, Tokyo 144-8501, Japan; (J.S.); (R.K.); (Y.T.); (S.I.); (R.M.); (S.S.); (F.K.); (N.M.); (K.T.)
- Correspondence: ; Tel.: +81-3-5498-5775
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7
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Ma X, Higashi K, Fukuzawa K, Ueda K, Kadota K, Tozuka Y, Yonemochi E, Moribe K. Computational approach to elucidate the formation and stabilization mechanism of amorphous formulation using molecular dynamics simulation and fragment molecular orbital calculation. Int J Pharm 2022; 615:121477. [PMID: 35051536 DOI: 10.1016/j.ijpharm.2022.121477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/05/2022] [Accepted: 01/11/2022] [Indexed: 11/25/2022]
Abstract
α-Glycosyl rutin (Rutin-G) consists of a flavonol skeleton and sugar groups and is a promising additive for amorphous formulations. In our previous study, experimental approaches suggested an interaction between the model drug carbamazepine (CBZ) and flavonol skeleton of Rutin-G that stabilizes amorphous formulations. In the present study, the formation and stabilization mechanisms of CBZ/Rutin-G amorphous formulation were investigated using a computational approach. The CBZ/Rutin-G amorphous formulation was obtained via molecular dynamics (MD) simulation, which mimicked the melt-quenching method. Root mean square deviation analysis revealed that the translational motion of CBZ during the cooling process was suppressed by adding Rutin-G. Monitoring the atomic distance during the cooling process revealed that hydrogen bonds via carboxamide oxygen of CBZ with hydroxyl hydrogen of Rutin-G were preferentially formed with flavonol skeletons than sugar groups. The simulated amorphous formulation was then calculated using fragment molecular orbital (FMO) method. The quantitative evaluation of multiple interactions revealed that the hydrogen bond energy was higher in CBZ-sugar groups than in CBZ-flavonol skeleton, while the π-type of interaction energy was higher in CBZ-flavonol skeleton than in CBZ-sugar groups. The computational approach combining MD simulation and FMO calculation provides information on various interactions that are difficult to detect using experimental approaches, which helps understand the formation and stabilization mechanism of amorphous formulations.
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Affiliation(s)
- Xiaohan Ma
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Kenjirou Higashi
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Kaori Fukuzawa
- School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41, Ebara, Shinagawa, Tokyo 142-8501, Japan
| | - Keisuke Ueda
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Kazunori Kadota
- Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Yuichi Tozuka
- Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Etsuo Yonemochi
- School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41, Ebara, Shinagawa, Tokyo 142-8501, Japan
| | - Kunikazu Moribe
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
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Kim J, Lim H, Moon S, Cho SY, Kim M, Park JH, Park HW, No KT. Hot Spot Analysis of YAP-TEAD Protein-Protein Interaction Using the Fragment Molecular Orbital Method and Its Application for Inhibitor Discovery. Cancers (Basel) 2021; 13:4246. [PMID: 34439400 PMCID: PMC8391968 DOI: 10.3390/cancers13164246] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 08/19/2021] [Indexed: 02/02/2023] Open
Abstract
The Hippo pathway is an important signaling pathway modulating growth control and cancer cell proliferation. Dysregulation of the Hippo pathway is a common feature of several types of cancer cells. The modulation of the interaction between yes-associated protein (YAP) and transcriptional enhancer associated domain (TEAD) in the Hippo pathway is considered an attractive target for cancer therapeutic development, although the inhibition of PPI is a challenging task. In order to investigate the hot spots of the YAP and TEAD1 interacting complex, an ab initio Fragment Molecular Orbital (FMO) method was introduced. With the hot spots, pharmacophores for the inhibitor design were constructed, then virtual screening was performed to an in-house library. Next, we performed molecular docking simulations and FMO calculations for screening results to study the binding modes and affinities between PPI inhibitors and TEAD1. As a result of the virtual screening, three compounds were selected as virtual hit compounds. In order to confirm their biological activities, cellular (luciferase activity, proximity ligation assay and wound healing assay in A375 cells, qRT-PCR in HEK 293T cells) and biophysical assays (surface plasmon resonance assays) were performed. Based on the findings of the study, we propose a novel PPI inhibitor BY03 and demonstrate a profitable strategy to analyze YAP-TEAD PPI and discover novel PPI inhibitors.
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Affiliation(s)
- Jongwan Kim
- Department of Biotechnology, Yonsei University, Seoul 03722, Korea;
- Bioinformatics and Molecular Design Research Center (BMDRC), Incheon 21983, Korea
| | - Hocheol Lim
- The Interdisciplinary Graduate Program in Integrative Biotechnology and Translational Medicine, Yonsei University, Incheon 21983, Korea;
| | - Sungho Moon
- Baobab AiBIO Co., Ltd., Incheon 21983, Korea; (S.M.); (S.Y.C.); (M.K.)
| | - Seon Yeon Cho
- Baobab AiBIO Co., Ltd., Incheon 21983, Korea; (S.M.); (S.Y.C.); (M.K.)
| | - Minhye Kim
- Baobab AiBIO Co., Ltd., Incheon 21983, Korea; (S.M.); (S.Y.C.); (M.K.)
| | - Jae Hyung Park
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea; (J.H.P.); (H.W.P.)
| | - Hyun Woo Park
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea; (J.H.P.); (H.W.P.)
| | - Kyoung Tai No
- Bioinformatics and Molecular Design Research Center (BMDRC), Incheon 21983, Korea
- Baobab AiBIO Co., Ltd., Incheon 21983, Korea; (S.M.); (S.Y.C.); (M.K.)
- Institute of Convergence Science and Technology, Yonsei University, Incheon 21983, Korea
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9
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Fujita T, Noguchi Y, Hoshi T. Revisiting the Charge-Transfer States at Pentacene/C 60 Interfaces with the GW/Bethe-Salpeter Equation Approach. Materials (Basel) 2020; 13:E2728. [PMID: 32560127 PMCID: PMC7345661 DOI: 10.3390/ma13122728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/11/2020] [Accepted: 06/13/2020] [Indexed: 11/16/2022]
Abstract
Molecular orientations and interfacial morphologies have critical effects on the electronic states of donor/acceptor interfaces and thus on the performance of organic photovoltaic devices. In this study, we explore the energy levels and charge-transfer states at the organic donor/acceptor interfaces on the basis of the fragment-based GW and Bethe-Salpeter equation approach. The face-on and edge-on orientations of pentacene/C60 bilayer heterojunctions have employed as model systems. GW+Bethe-Salpeter equation calculations were performed for the local interface structures in the face-on and edge-on bilayer heterojunctions, which contain approximately 2000 atoms. Calculated energy levels and charge-transfer state absorption spectra are in reasonable agreements with those obtained from experimental measurements. We found that the dependence of the energy levels on interfacial morphology is predominantly determined by the electrostatic contribution of polarization energy, while the effects of induction contribution in the edge-on interface are similar to those in the face-on. Moreover, the delocalized charge-transfer states contribute to the main absorption peak in the edge-on interface, while the face-on interface features relatively localized charge-transfer states in the main absorption peak. The impact of the interfacial morphologies on the polarization and charge delocalization effects is analyzed in detail.
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Affiliation(s)
| | - Yoshifumi Noguchi
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University, Hamamatsu, Shizuoka 432-8561, Japan;
| | - Takeo Hoshi
- Department of Applied Mathematics and Physics, Tottori University, Tottori 680-8550, Japan;
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10
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Akinaga Y, Kato K, Nakano T, Fukuzawa K, Mochizuki Y. Fragmentation at sp 2 carbon atoms in fragment molecular orbital method. J Comput Chem 2020; 41:1416-1420. [PMID: 32196699 DOI: 10.1002/jcc.26190] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/13/2020] [Accepted: 03/04/2020] [Indexed: 11/06/2022]
Abstract
In the fragment molecular orbital (FMO) method, a given molecular system is usually fragmented at sp3 carbon atoms. However, fragmentation at different sites sometimes becomes necessary. Hence, we propose fragmentation at sp2 carbon atoms in the FMO method. Projection operators are constructed using sp2 local orbitals. To maintain practical accuracy, it is essential to consider the three-body effect. In order to suppress the corresponding increase of computational cost, we propose approximate models considering local trimers. Numerical verification shows that the present models are as accurate as or better than the standard FMO2 method in total energy with fragmentation at sp3 carbon atoms.
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Affiliation(s)
| | - Koichiro Kato
- Mizuho Information & Research Institute, Inc., Tokyo, Japan
| | - Tatsuya Nakano
- Division of Medicinal Safety and Science, National Institute of Health Sciences, Kawasaki, Japan
| | - Kaori Fukuzawa
- Department of Physical Chemistry, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Tokyo, Japan.,Center for Research on Innovative Simulation Software (CISS), Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
| | - Yuji Mochizuki
- Center for Research on Innovative Simulation Software (CISS), Institute of Industrial Science, The University of Tokyo, Tokyo, Japan.,Department of Chemistry, Rikkyo University, Tokyo, Japan
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11
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Ishikawa T, Sakakura K, Mochizuki Y. RI-MP3 calculations of biomolecules based on the fragment molecular orbital method. J Comput Chem 2018; 39:1970-1978. [PMID: 30277590 DOI: 10.1002/jcc.25368] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/04/2018] [Accepted: 05/09/2018] [Indexed: 12/24/2022]
Abstract
In this study, the third-order Møller-Plesset perturbation (MP3) theory using the resolution of the identity (RI) approximation was combined with the fragment molecular orbital (FMO) method to efficiently calculate a high-order electron correlation energy of biomolecular systems. We developed a new algorithm for the RI-MP3 calculation, which can be used with the FMO scheme. After test calculations using a small molecule, the FMO-RI-MP3 calculations were performed for two biomolecular systems comprising a protein and a ligand. The computational cost of these calculations was only around 5 and 4 times higher than those of the FMO-RHF calculations. The error associated with the RI approximation was around 2.0% of the third-order correlation contribution to the total energy. However, the RI approximation error in the interaction energy between the protein and ligand molecule was insignificantly small, which reflected the negligible error in the inter fragment interaction energy. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Takeshi Ishikawa
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Kota Sakakura
- 1st Government and Public Solutions Division, NEC Corporation, 7-1, Shiba 5-chome, Minato-ku, Tokyo, 108-8001, 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
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12
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Tsuchiya Y, Namiuchi Y, Wako H, Tsurui H. A study of CDR3 loop dynamics reveals distinct mechanisms of peptide recognition by T-cell receptors exhibiting different levels of cross-reactivity. Immunology 2017; 153:466-478. [PMID: 28992359 DOI: 10.1111/imm.12849] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 10/04/2017] [Accepted: 10/05/2017] [Indexed: 01/09/2023] Open
Abstract
T-cell receptors (TCRs) can productively interact with many different peptides bound within the MHC binding groove. This property varies with the level of cross-reactivity of TCRs; some TCRs are particularly hyper cross-reactive while others exhibit greater specificity. To elucidate the mechanism behind these differences, we studied five TCRs in complex with the same class II MHC (1Ab )-peptide (3K), that are known to exhibit different levels of cross-reactivity. Although these complexes have similar binding affinities, the interface areas between the TCR and the peptide-MHC (pMHC) differ significantly. We investigated static and dynamic structural features of the TCR-pMHC complexes and of TCRs in a free state, as well as the relationship between binding affinity and interface area. It was found that the TCRs known to exhibit lower levels of cross-reactivity bound to pMHC using an induced-fitting mechanism, forming large and tight interfaces rich in specific hydrogen bonds. In contrast, TCRs known to exhibit high levels of cross-reactivity used a more rigid binding mechanism where non-specific π-interactions involving the bulky Trp residue in CDR3β dominated. As entropy loss upon binding in these highly degenerate and rigid TCRs is smaller than that in less degenerate TCRs, they can better tolerate changes in residues distal from the major contacts with MHC-bound peptide. Hence, our dynamics study revealed that differences in the peptide recognition mechanisms by TCRs appear to correlate with the levels of T-cell cross-reactivity.
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Affiliation(s)
- Yuko Tsuchiya
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | | | - Hiroshi Wako
- School of Social Sciences, Waseda University, Tokyo, Japan
| | - Hiromichi Tsurui
- Department of Pathology, Juntendo University School of Medicine, Tokyo, Japan
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13
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Abstract
The second-order Møller-Plesset perturbation theory (MP2) gradient using resolution of the identity approximation (RI-MP2 gradient) was combined with the fragment molecular orbital (FMO) method to evaluate the gradient including electron correlation for large molecules. In this study, we adopted a direct implementation of the RI-MP2 gradient, in which a characteristic feature of the FMO scheme was utilized. Test calculations with a small peptide presented a computational advantage of the RI-MP2 gradient over the canonical MP2 gradient. In addition, it was shown that the error of the RI-MP2 gradient, caused by RI approximation, was negligible. As an illustrative example, we performed gradient calculations for two biomolecules-a prion protein with GN8 and a human immunodeficiency virus type 1 (HIV1) protease with lopinavir (LPV). These calculations demonstrated that the gradient including the correlation effect could be evaluated with only about twice the computational effort of the Hartree-Fock (HF) gradient.
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Affiliation(s)
- Takeshi Ishikawa
- †Division of Prion Research, Center for Emerging Infectious Disease, Gifu University, 1-1 Yanagido, Gifu 501-1194, Japan
- ‡CREST Project, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Kazuo Kuwata
- †Division of Prion Research, Center for Emerging Infectious Disease, Gifu University, 1-1 Yanagido, Gifu 501-1194, Japan
- ‡CREST Project, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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