π (FMO) [4] Ligand 4 FMO FMO Gordon Schmidt (DHODH) de novo DNA RNA T. cruzi DHODH X DHODH- T. cruzi [5] DHODH DHODH FMN FMN FMNH 2 2 3
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1 FMO , ,2 X Protein-ligand interaction energy analysis between anti-trypanosome drug candidate and target protein using fragment molecular orbital RYUNOSUKE YOSHINO 1 NOBUAKI YASUO 2 YOHSUKE HAGIWARA 3 KAZUKI OHNO 3 MASAYA ORITA 1,3 MASAYUKI INOUE 4 SHIGEHARU HARADA 5 TERUKI HONMA 6 INAOKA DANIEL KEN 6 KIYOSHI KITA 6 MASAKAZU SEKIJIMA 1,2 Abstract : Chagas' disease caused by Trypanosoma cruzi is known as neglected tropical diseases (NTD s). To develop effective anti-trypanosome drug, we remarked dihydroorotate dehydrogenase which assumed synthesis of orotic acid and studied inhibitor of the enzyme. Although X-ray structure of target protein with inhibitor is clarified, important protein-ligand interaction is not determined for elucidation of inhibition mechanism. Then, in this research, we analyzed interaction energy between target proteins and inhibitors using fragment molecular orbital method. As a result, it was revealed that hydrogen bonding with Lys and Asn was important. It is expected that these results are useful for anti-trypanosome drug design. Keyword : Tropical diseases, Trypanosoma cruzi, Dihydroorotate dehydrogenase, Fragment molecular orbital method 1. 1 Global Scientific Information and Computing Center, Tokyo Institute of Technology, Meguro, Tokyo , Japan 2 Department of Computer Science, Tokyo Institute of Technology, Meguro, Tokyo , Japan 3 Chemistry Research Labs, Drug Discovery Research, Astellas Pharma Inc, Tsukuba, Ibaraki , Japan. 4 Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo , Japan 5 Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo, Kyoto , Japan 6 Graduate School of Medicine, The University of Tokyo, Bunkyo, Tokyo , Japan Trypanosoma cruzi (T. cruzi) 20 [1] 1500 [2] X [3] c 2013 Information Processing Society of Japan 1
![π (FMO) [4] Ligand 4 FMO FMO Gordon Schmidt 2. 2.1 (DHODH) de novo 1 2.](/docs-images/89/99459908/images/2-2.jpg "1. DNA RNA T. cruzi DHODH X DHODH- T.")
![cruzi [5] DHODH DHODH FMN FMN FMNH 2 2 3 DHODH FMN π-π FMN 3 DHODH](/docs-images/89/99459908/images/2-3.jpg "Ligand DHODH DHODH 2.2 FMO FMO 1999 Schrödinger 3.")
2 π (FMO) [4] Ligand 4 FMO FMO Gordon Schmidt (DHODH) de novo DNA RNA T. cruzi DHODH X DHODH- T. cruzi [5] DHODH DHODH FMN FMN FMNH DHODH FMN π-π FMN 3 DHODH Ligand DHODH DHODH 2.2 FMO FMO 1999 Schrödinger 3. DHODH c 2013 Information Processing Society of Japan 2
![GAMESS [6] FMO 6 Lys43, Asn67, Asn194 Asn FMN π-π -6.29 kcal/mol 4. Fedorov Pair interaction energy decomposition analysis [7] Facio [8] 5 Ligand N C Ligand PDB Ligand Lys401 Phe408 6.](/docs-images/89/99459908/images/3-0.jpg "DHODH- (kcal/mol) 5. (kcal/mol) FMO Ligand π-π π-cation, CH-π DHODH FMO Ligand 3. DHODH Discovery Studio FMO MP2/6-31G 3.1 DHODH- DHODH 7.")
3 GAMESS [6] FMO 6 Lys43, Asn67, Asn194 Asn FMN π-π kcal/mol 4. Fedorov Pair interaction energy decomposition analysis [7] Facio [8] 5 Ligand N C Ligand PDB Ligand Lys401 Phe DHODH- (kcal/mol) 5. (kcal/mol) FMO Ligand π-π π-cation, CH-π DHODH FMO Ligand 3. DHODH Discovery Studio FMO MP2/6-31G 3.1 DHODH- DHODH 7. c 2013 Information Processing Society of Japan 3
4 7 Asn67, Asn194 2 DHODH 3.2 DHODH- DHODH 43 DHODH 5 ( 8) 4 Lys43, Asn67, Asn194, FMN DHODH (kcal/mol) 8. PDBID Compound Lys43 Asn67 Asn194 FMN 3W1R W1T W1U W1X W2J W2K W2L W2M W2N W2U W3O W W W6Y W7C W7D W7E W7G W7H W7I W7J W7K W7L W7M W7N W7O W7P W7Q W W W W W W W W W W W W W JD JDB c 2013 Information Processing Society of Japan 4
5 Asn67, Asn Leu 71, Cys Leu71, Cys130 Leu71 5 Cys131 α 5 CH-π 2. DOHD (kcal/mol) PDBID Compound Leu71 Cys130 Lys214 3W1R W1T W1U W1X W2J W2K W2L W2M W2N W2U W3O W W W6Y W7C W7D W7E W7G W7H W7I W7J W7K W7L W7M W7N W7O W7P W7Q W W W W W W W W W W W W W JD JDB Leu71, Cys130 (kcal/mol) c 2013 Information Processing Society of Japan 5
6 Lys Lys 214 5, 8, 10, Lys Lys214 Lys214 Ligand Lys , 27 Lys Lys Lys214 Ligand CH-π DHODH , 27 Lys FMO Lys43, Asn67, Asn194 FMN π-π Leu71, Cys130 CH-π Lys214 Ligand 12 Lys Asn Leu71 Cys130 DHODH 12. Acc : Acceptor, Don : Donor Aro : Aromatic, Hyd : Hydrophobic [1] Schmunis G.A., Yadon Z.E.: Chagas disease a Latin American health problem becoming a world health problem, Acta Trop., 2010, 115, [2] World Health Organization(TDR GTC ) Reporte sobre la enfermedad de Chagas. Grupo de trabajo cientfico. Ginebra: World Health Organization. [3] Inaoka D.K., Sakamoto S., Shimizu H., et al.: c 2013 Information Processing Society of Japan 6
7 Structures of Trypanosoma cruzi Dihydroorotate Dehydrogenase Complexed with Substrates and Products, Biochemistry, 2008, 47, [4] K. Kitaura, T. Sawai, et al.: Pair interaction molecular orbital method: an approximate computational method for molecular interactions, Chem. Phys. Lett., 1999, 312, [5] Annoura T., Nara T., et al.: The Origin of Dihydroorotate Dehydrogenase Genes of Kinetoplastids, with Special Reference to Their Biological Significance and Adaptation to Anaerobic, Parasitic Conditions, J. Mol. Evol., 2005, 60, [6] M.W. Schmidt, K. K. Baldridge, et al.: General atomic and molecular electronic structure system, J. Comput. Chem., 1993, [7] Fedorov D.G., Kitaura K.: Pair interaction energy decomposition analysis, J. Comput. Chem., 2007, 28, [8] c 2013 Information Processing Society of Japan 7
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