101
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Yamaguchi H, Akitaya T, Yu T, Kidachi Y, Kamiie K, Noshita T, Umetsu H, Ryoyama K. Molecular docking and structural analysis of cofactor-protein interaction between NAD⁺ and 11β-hydroxysteroid dehydrogenase type 2. J Mol Model 2011; 18:1037-48. [PMID: 21667072 DOI: 10.1007/s00894-011-1140-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 05/27/2011] [Indexed: 11/28/2022]
Abstract
Molecular docking and structural analysis of the cofactor-protein interaction between NAD(+) and human (h) or mouse (m) 11β-hydroxysteroid dehydrogenase type 2 (11βHSD2) were performed with the molecular operating environment (MOE). 11βHSD1 (PDB code: 3HFG) was selected as a template for the 3D structure modeling of 11βHSD2. The MOE docking (MOE-dock) and the alpha sphere and excluded volume-based ligand-protein docking (ASE-dock) showed that both NAD(+)-h11βHSD2 and NAD(+)-m11βHSD2 models have a similar binding orientation to the template cofactor-protein model. Our present study also revealed that Asp91, Phe94, Tyr232 and Thr267 could be of importance in the interaction between NAD(+) and 11βHSD2. NADP(+) was incapable of entering into the cofactor-binding site of the 11βHSD2 models. The present study proposes the latest models for 11βHSD2 and its cofactor NAD(+), and to the best of our knowledge, this is the first report of a m11βHSD2 model with NAD(+).
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Affiliation(s)
- Hideaki Yamaguchi
- Department of Pharmacy, Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tenpaku, Nagoya 468-8503, Japan.
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102
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Yamakawa N, Suemasu S, Matoyama M, Tanaka KI, Katsu T, Miyata K, Okamoto Y, Otsuka M, Mizushima T. Synthesis and biological evaluation of loxoprofen derivatives. Bioorg Med Chem 2011; 19:3299-311. [DOI: 10.1016/j.bmc.2011.04.050] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 04/26/2011] [Accepted: 04/28/2011] [Indexed: 10/18/2022]
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103
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Iwai Y, Murakami K, Gomi Y, Hashimoto T, Asakawa Y, Okuno Y, Ishikawa T, Hatakeyama D, Echigo N, Kuzuhara T. Anti-influenza activity of marchantins, macrocyclic bisbibenzyls contained in liverworts. PLoS One 2011; 6:e19825. [PMID: 21625478 PMCID: PMC3098833 DOI: 10.1371/journal.pone.0019825] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 04/18/2011] [Indexed: 11/22/2022] Open
Abstract
The H1N1 influenza A virus of swine-origin caused pandemics throughout the world in 2009 and the highly pathogenic H5N1 avian influenza virus has also caused epidemics in Southeast Asia in recent years. The threat of influenza A thus remains a serious global health issue and novel drugs that target these viruses are highly desirable. Influenza A possesses an endonuclease within its RNA polymerase which comprises PA, PB1 and PB2 subunits. To identify potential new anti-influenza compounds in our current study, we screened 33 different types of phytochemicals using a PA endonuclease inhibition assay in vitro and an anti-influenza A virus assay. The marchantins are macrocyclic bisbibenzyls found in liverworts, and plagiochin A and perrottetin F are marchantin-related phytochemicals. We found from our screen that marchantin A, B, E, plagiochin A and perrottetin F inhibit influenza PA endonuclease activity in vitro. These compounds have a 3,4-dihydroxyphenethyl group in common, indicating the importance of this moiety for the inhibition of PA endonuclease. Docking simulations of marchantin E with PA endonuclease suggest a putative “fitting and chelating model” as the mechanism underlying PA endonuclease inhibition. The docking amino acids are well conserved between influenza A and B. In a cultured cell system, marchantin E was further found to inhibit the growth of both H3N2 and H1N1 influenza A viruses, and marchantin A, E and perrotein F showed inhibitory properties towards the growth of influenza B. These marchantins also decreased the viral infectivity titer, with marchantin E showing the strongest activity in this assay. We additionally identified a chemical group that is conserved among different anti-influenza chemicals including marchantins, green tea catechins and dihydroxy phenethylphenylphthalimides. Our present results indicate that marchantins are candidate anti-influenza drugs and demonstrate the utility of the PA endonuclease assay in the screening of phytochemicals for anti-influenza characteristics.
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Affiliation(s)
- Yuma Iwai
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima, Japan
| | - Kouki Murakami
- Research group, Research and Production Technology Division, Kanonji Institute, The Research Foundation for Microbial Diseases of Osaka University, Kanonji, Kagawa, Japan
| | - Yasuyuki Gomi
- Research group, Research and Production Technology Division, Kanonji Institute, The Research Foundation for Microbial Diseases of Osaka University, Kanonji, Kagawa, Japan
| | - Toshihiro Hashimoto
- Laboratory of Pharmacognosy, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima, Japan
| | - Yoshinori Asakawa
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima, Japan
| | - Yoshinobu Okuno
- Research group, Research and Production Technology Division, Kanonji Institute, The Research Foundation for Microbial Diseases of Osaka University, Kanonji, Kagawa, Japan
| | - Toyokazu Ishikawa
- Research group, Research and Production Technology Division, Kanonji Institute, The Research Foundation for Microbial Diseases of Osaka University, Kanonji, Kagawa, Japan
| | - Dai Hatakeyama
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima, Japan
| | - Noriko Echigo
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima, Japan
| | - Takashi Kuzuhara
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima, Japan
- * E-mail:
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104
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Rognan D. Docking Methods for Virtual Screening: Principles and Recent Advances. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2011. [DOI: 10.1002/9783527633326.ch6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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105
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Watanabe Y, Ibrahim MS, Ellakany HF, Kawashita N, Mizuike R, Hiramatsu H, Sriwilaijaroen N, Takagi T, Suzuki Y, Ikuta K. Acquisition of human-type receptor binding specificity by new H5N1 influenza virus sublineages during their emergence in birds in Egypt. PLoS Pathog 2011; 7:e1002068. [PMID: 21637809 PMCID: PMC3102706 DOI: 10.1371/journal.ppat.1002068] [Citation(s) in RCA: 173] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 03/30/2011] [Indexed: 01/18/2023] Open
Abstract
Highly pathogenic avian influenza A virus subtype H5N1 is currently widespread in Asia, Europe, and Africa, with 60% mortality in humans. In particular, since 2009 Egypt has unexpectedly had the highest number of human cases of H5N1 virus infection, with more than 50% of the cases worldwide, but the basis for this high incidence has not been elucidated. A change in receptor binding affinity of the viral hemagglutinin (HA) from α2,3- to α2,6-linked sialic acid (SA) is thought to be necessary for H5N1 virus to become pandemic. In this study, we conducted a phylogenetic analysis of H5N1 viruses isolated between 2006 and 2009 in Egypt. The phylogenetic results showed that recent human isolates clustered disproportionally into several new H5 sublineages suggesting that their HAs have changed their receptor specificity. Using reverse genetics, we found that these H5 sublineages have acquired an enhanced binding affinity for α2,6 SA in combination with residual affinity for α2,3 SA, and identified the amino acid mutations that produced this new receptor specificity. Recombinant H5N1 viruses with a single mutation at HA residue 192 or a double mutation at HA residues 129 and 151 had increased attachment to and infectivity in the human lower respiratory tract but not in the larynx. These findings correlated with enhanced virulence of the mutant viruses in mice. Interestingly, these H5 viruses, with increased affinity to α2,6 SA, emerged during viral diversification in bird populations and subsequently spread to humans. Our findings suggested that emergence of new H5 sublineages with α2,6 SA specificity caused a subsequent increase in human H5N1 influenza virus infections in Egypt, and provided data for understanding the virus's pandemic potential.
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MESH Headings
- Animals
- Cell Line
- Cells, Cultured
- Chickens
- Disease Models, Animal
- Ducks
- Egypt
- Female
- Hemagglutinins, Viral/genetics
- Hemagglutinins, Viral/metabolism
- Humans
- Influenza A Virus, H5N1 Subtype/genetics
- Influenza A Virus, H5N1 Subtype/metabolism
- Influenza in Birds/epidemiology
- Influenza in Birds/metabolism
- Influenza, Human/epidemiology
- Influenza, Human/pathology
- Influenza, Human/virology
- Mice
- Mice, Inbred BALB C
- Mutation/genetics
- N-Acetylneuraminic Acid/metabolism
- Pandemics
- Phylogeny
- Prevalence
- Protein Binding/genetics
- Receptors, Virus/metabolism
- Respiratory Mucosa/pathology
- Respiratory Mucosa/virology
- Retrospective Studies
- Virus Replication/physiology
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Affiliation(s)
- Yohei Watanabe
- Department of Virology, Research Institute for Microbial Diseases (BIKEN), Osaka University, Osaka, Japan
| | - Madiha S. Ibrahim
- Department of Virology, Research Institute for Microbial Diseases (BIKEN), Osaka University, Osaka, Japan
- Department of Microbiology, Faculty of Veterinary Medicine, Alexandria University, Damanhour Branch, Egypt
| | - Hany F. Ellakany
- Department of Poultry Diseases and Hygiene, Faculty of Veterinary Medicine, Alexandria University, Edfina Branch, Egypt
| | - Norihito Kawashita
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Rika Mizuike
- Department of Virology, Research Institute for Microbial Diseases (BIKEN), Osaka University, Osaka, Japan
| | - Hiroaki Hiramatsu
- Health Scientific Hills, College of Life and Health Sciences, Chubu University, Aichi, Japan
| | - Nogluk Sriwilaijaroen
- Health Scientific Hills, College of Life and Health Sciences, Chubu University, Aichi, Japan
- Faculty of Medicine, Thammasat University (Rangsit Campus), PathumThani, Thailand
| | - Tatsuya Takagi
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yasuo Suzuki
- Health Scientific Hills, College of Life and Health Sciences, Chubu University, Aichi, Japan
| | - Kazuyoshi Ikuta
- Department of Virology, Research Institute for Microbial Diseases (BIKEN), Osaka University, Osaka, Japan
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106
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Selective toxicity of glycyrrhetinic acid against tumorigenic r/m HM-SFME-1 cells is potentially attributed to downregulation of glutathione. Biochimie 2011; 93:1172-8. [PMID: 21539886 DOI: 10.1016/j.biochi.2011.04.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 04/20/2011] [Indexed: 01/11/2023]
Abstract
Natural products from plants are expected to play significant roles in creating new, safe and improved chemopreventive and therapeutic antitumor agents. Selectivity is also an important issue in cancer prevention and therapy. The present study was designed to extend our previous study on the c-Ha-ras and c-myc-induced tumor cell-selective antiproliferative effects of a licorice component, glycyrrhetinic acid (GA). An in silico ligand-receptor docking simulation revealed that GA acts as an 11β-hydroxysteroid dehydrogenase type 2 inhibitor. GA disrupted the redox balance in tumor cells through upregulation of reactive oxygen species and downregulation of glutathione (GSH). The GA-induced GSH reduction and cytotoxicity were enhanced by an inhibitor of GSH, l-buthionine-[S,R]-sulfoximine. N-acetyl-l-cysteine, an antioxidant and precursor of GSH, restored the GA-induced GSH reduction and cytotoxicity in tumor cells. Taken together, these data highlighting the downregulation of GSH by GA and the efficacy of GSH in ameliorating GA-mediated cytotoxicity support the notion that GSH is involved in the selective toxicity of GA toward tumor cells.
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107
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LaPlante SR, Gillard JR, Jakalian A, Aubry N, Coulombe R, Brochu C, Tsantrizos YS, Poirier M, Kukolj G, Beaulieu PL. Importance of ligand bioactive conformation in the discovery of potent indole-diamide inhibitors of the hepatitis C virus NS5B. J Am Chem Soc 2011; 132:15204-12. [PMID: 20942454 DOI: 10.1021/ja101358s] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Significant advances have led to receptor induced-fit and conformational selection models for describing bimolecular recognition, but a more comprehensive view must evolve to also include ligand shape and conformational changes. Here, we describe an example where a ligand's "structural hinge" influences potency by inducing an "L-shape" bioactive conformation, and due to its solvent exposure in the complex, reasonable conformation-activity-relationships can be qualitatively attributed. From a ligand design perspective, this feature was exploited by successful linker hopping to an alternate "structural hinge" that led to a new and promising chemical series which matched the ligand bioactive conformation and the pocket bioactive space. Using a combination of X-ray crystallography, NMR and modeling with support from binding-site resistance mutant studies and photoaffinity labeling experiments, we were able to derive inhibitor-polymerase complexes for various chemical series.
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Affiliation(s)
- Steven R LaPlante
- Department of Chemistry, Boehringer Ingelheim (Canada) Ltd., 2100 Cunard St., Laval, Quebec, Canada, H7S2G5.
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108
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Sassa A, Niimi N, Fujimoto H, Katafuchi A, Grúz P, Yasui M, Gupta RC, Johnson F, Ohta T, Nohmi T. Phenylalanine 171 is a molecular brake for translesion synthesis across benzo[a]pyrene-guanine adducts by human DNA polymerase kappa. Mutat Res 2010; 718:10-7. [PMID: 21078407 DOI: 10.1016/j.mrgentox.2010.11.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 11/05/2010] [Accepted: 11/05/2010] [Indexed: 10/18/2022]
Abstract
Human cells possess multiple specialized DNA polymerases (Pols) that bypass a variety of DNA lesions which otherwise would block chromosome replication. Human polymerase kappa (Pol κ) bypasses benzo[a]pyrene diolepoxide-N(2)-deoxyguanine (BPDE-N(2)-dG) DNA adducts in an almost error-free manner. To better understand the relationship between the structural features in the active site and lesion bypass by Pol κ, we mutated codons corresponding to amino acids appearing close to the adducts in the active site, and compared bypass efficiencies. Remarkably, the substitution of alanine for phenylalanine 171 (F171), an amino acid conserved between Pol κ and its bacterial counterpart Escherichia coli DinB, enhanced the efficiencies of dCMP incorporation opposite (-)- and (+)-trans-anti-BPDE-N(2)-dG 18-fold. This substitution affected neither the fidelity of TLS nor the efficiency of dCMP incorporation opposite normal guanine. This amino acid change also enhanced the binding affinity of Pol κ to template/primer DNA containing (-)-trans-anti-BPDE-N(2)-dG. These results suggest that F171 functions as a molecular brake for TLS across BPDE-N(2)-dG by Pol κ and that the F171A derivative of Pol κ bypasses these DNA lesions more actively than does the wild-type enzyme.
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MESH Headings
- 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide/analogs & derivatives
- 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide/chemistry
- 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide/metabolism
- Amino Acid Substitution
- Base Sequence
- Benzo(a)pyrene/chemistry
- Benzo(a)pyrene/metabolism
- Catalytic Domain/genetics
- DNA Adducts/chemistry
- DNA Adducts/metabolism
- DNA Damage
- DNA Primers/genetics
- DNA Repair
- DNA-Directed DNA Polymerase/chemistry
- DNA-Directed DNA Polymerase/genetics
- DNA-Directed DNA Polymerase/metabolism
- Deoxyguanosine/analogs & derivatives
- Deoxyguanosine/chemistry
- Deoxyguanosine/metabolism
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Humans
- In Vitro Techniques
- Kinetics
- Models, Molecular
- Mutagenesis, Site-Directed
- Phenylalanine/chemistry
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Substrate Specificity
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Affiliation(s)
- Akira Sassa
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
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109
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Hawkins PCD, Skillman AG, Warren GL, Ellingson BA, Stahl MT. Conformer generation with OMEGA: algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database. J Chem Inf Model 2010; 50:572-84. [PMID: 20235588 PMCID: PMC2859685 DOI: 10.1021/ci100031x] [Citation(s) in RCA: 1154] [Impact Index Per Article: 82.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
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Here, we present the algorithm and validation for OMEGA, a systematic, knowledge-based conformer generator. The algorithm consists of three phases: assembly of an initial 3D structure from a library of fragments; exhaustive enumeration of all rotatable torsions using values drawn from a knowledge-based list of angles, thereby generating a large set of conformations; and sampling of this set by geometric and energy criteria. Validation of conformer generators like OMEGA has often been undertaken by comparing computed conformer sets to experimental molecular conformations from crystallography, usually from the Protein Databank (PDB). Such an approach is fraught with difficulty due to the systematic problems with small molecule structures in the PDB. Methods are presented to identify a diverse set of small molecule structures from cocomplexes in the PDB that has maximal reliability. A challenging set of 197 high quality, carefully selected ligand structures from well-solved models was obtained using these methods. This set will provide a sound basis for comparison and validation of conformer generators in the future. Validation results from this set are compared to the results using structures of a set of druglike molecules extracted from the Cambridge Structural Database (CSD). OMEGA is found to perform very well in reproducing the crystallographic conformations from both these data sets using two complementary metrics of success.
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Affiliation(s)
- Paul C D Hawkins
- OpenEye Scientific Software, 9 Bisbee Court, Suite D, Santa Fe, New Mexico 87508, USA.
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110
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Nakamura S, Takahira K, Tanabe G, Morikawa T, Sakano M, Ninomiya K, Yoshikawa M, Muraoka O, Nakanishi I. Docking and SAR studies of salacinol derivatives as alpha-glucosidase inhibitors. Bioorg Med Chem Lett 2010; 20:4420-3. [PMID: 20598536 DOI: 10.1016/j.bmcl.2010.06.059] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Revised: 06/03/2010] [Accepted: 06/09/2010] [Indexed: 11/28/2022]
Abstract
Salacinol is a potent alpha-glucosidase inhibitor isolated from Salacia reticulata, and a good lead compound for an antidiabetic drug. It is essential to clarify the binding state of salacinol to alpha-glucosidase for efficient optimization study using structure-based drug design. Redocking simulations of two inhibitors, acarbose and casuarine whose complex structures are known, were performed to assure the appropriate docking pose prediction. The simulation reproduced both experimental binding states with accuracy. Then, using the same simulation protocol, the binding mode of salacinol and its derivatives has been predicted. Salacinol bound to the protein with a similar binding mode as casuarine, and the predicted structures could explain most of the structure-activity relationships of salacinol derivatives.
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Affiliation(s)
- Shinya Nakamura
- Faculty of Pharmacy, Kinki University, Higashi-osaka, Osaka 577-8502, Japan.
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111
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A novel inhibitor of plasminogen activator inhibitor-1 provides antithrombotic benefits devoid of bleeding effect in nonhuman primates. J Cereb Blood Flow Metab 2010; 30:904-12. [PMID: 20087372 PMCID: PMC2949193 DOI: 10.1038/jcbfm.2009.272] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Inhibition of plasminogen activator inhibitor (PAI)-1 is useful to treat several disorders including thrombosis. An inhibitor of PAI-1 (TM5275) was newly identified by an extensive study of structure-activity relationship based on a lead compound (TM5007) which was obtained through virtual screening by docking simulations. Its antithrombotic efficacy and adverse effects were tested in vivo in rats and nonhuman primates (cynomolgus monkey). TM5275, administered orally in rats (1 to 10 mg/kg), has an antithrombotic effect equivalent to that of ticlopidine (500 mg/kg) in an arterial venous shunt thrombosis model and to that of clopidogrel (3 mg/kg) in a ferric chloride-treated carotid artery thrombosis model. TM5275 does not modify activated partial thromboplastin time and prothrombin time or platelet activity and does not prolong bleeding time. Combined with tissue plasminogen activator, TM5275 improves the latter's therapeutic efficacy and reduces its adverse effect. Administered to a monkey model of photochemical induced arterial thrombosis, TM5275 (10 mg/kg) has the same antithrombotic effect as clopidogrel (10 mg/kg), without enhanced bleeding. This study documents the antithrombotic benefits of a novel, more powerful, PAI-1 inhibitor in rats and, for the first time, in nonhuman primates. These effects are obtained without adverse effect on bleeding time.
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112
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Muta H, Hirayama N. Alpha sphere filter method: Application of pseudomolecular descriptors in virtual screening of 2D chemical structures. J Comput Chem 2010; 31:2225-32. [DOI: 10.1002/jcc.21517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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113
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Yokoyama M, Mori H, Sato H. Allosteric regulation of HIV-1 reverse transcriptase by ATP for nucleotide selection. PLoS One 2010; 5:e8867. [PMID: 20111609 PMCID: PMC2810339 DOI: 10.1371/journal.pone.0008867] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2009] [Accepted: 01/05/2010] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) is a DNA polymerase that converts viral RNA genomes into proviral DNAs. How HIV-1 RT regulates nucleotide selectivity is a central issue for genetics and the nucleoside analog RT inhibitor (NRTI) resistance of HIV-1. METHODOLOGY/PRINCIPAL FINDINGS Here we show that an ATP molecule at physiological concentrations acts as an allosteric regulator of HIV-1 RT to decrease the K(m) value of the substrate, decrease the k(cat) value, and increase the K(i) value of NRTIs for RT. Computer-assisted structural analyses and mutagenesis studies suggested the positions of the ATP molecule and NRTI-resistance mutations during a catalytic reaction, which immediately predict possible influences on nucleotide insertion into the catalytic site, the DNA polymerization, and the excision reaction. CONCLUSIONS/SIGNIFICANCE These data imply that the ATP molecule and NRTI mutations can modulate nucleotide selectivity by altering the fidelity of the geometric selection of nucleotides and the probability of an excision reaction.
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Affiliation(s)
- Masaru Yokoyama
- Pathogen Genomics Center, National Institute of Infectious Diseases, Musashi Murayama-shi, Tokyo, Japan.
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114
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Toda K, Goto J, Hirayama N. A novel target-based de novo ligand design by use of pseudomolecular probe. MEDCHEMCOMM 2010. [DOI: 10.1039/c0md00121j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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115
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Nakamura T, Yamaguchi A, Kondo H, Watanabe H, Kurihara T, Esaki N, Hirono S, Tanaka S. Roles of K151 and D180 in L-2-haloacid dehalogenase fromPseudomonassp. YL: Analysis by molecular dynamics andab initiofragment molecular orbital calculations. J Comput Chem 2009; 30:2625-34. [DOI: 10.1002/jcc.21273] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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116
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Masada S, Terasaka K, Oguchi Y, Okazaki S, Mizushima T, Mizukami H. Functional and structural characterization of a flavonoid glucoside 1,6-glucosyltransferase from Catharanthus roseus. PLANT & CELL PHYSIOLOGY 2009; 50:1401-1415. [PMID: 19561332 DOI: 10.1093/pcp/pcp088] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Sugar-sugar glycosyltransferases play an important role in structural diversity of small molecule glycosides in higher plants. We isolated a cDNA clone encoding a sugar-sugar glucosyltransferase (CaUGT3) catalyzing 1,6-glucosylation of flavonol and flavone glucosides for the first time from Catharanthus roseus. CaUGT3 exhibited a unique glucosyl chain elongation activity forming not only gentiobioside but also gentiotrioside and gentiotetroside in a sequential manner. We investigated the functional properties of CaUGT3 using homology modeling and site-directed mutagenesis, and identified amino acids positioned in the acceptor-binding pocket as crucial for providing enough space to accommodate flavonoid glucosides instead of flavonoid aglycones. These results provide basic information for understanding and engineering the catalytic functions of sugar-sugar glycosyltransferases involved in biosynthesis of plant glycosides.
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Affiliation(s)
- Sayaka Masada
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
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117
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Akt is a direct target for myricetin to inhibit cell transformation. Mol Cell Biochem 2009; 332:33-41. [PMID: 19504174 DOI: 10.1007/s11010-009-0171-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Accepted: 05/21/2009] [Indexed: 10/20/2022]
Abstract
Akt, a serine/threonine kinase, is a critical regulator in many cellular processes including cell growth, proliferation, and apoptosis. In this study, we found that myricetin, a typical flavonol existing in many fruits and vegetables, could directly target Akt to inhibit cell transformation. Binding assay revealed that myricetin bound to Akt directly by competing with ATP. In vitro and ex vivo data confirmed that myricetin inhibited the phosphorylation and kinase activity of Akt. Molecular modeling suggested that myricetin easily docks to the ATP-binding site of Akt with hydrogen bonds. Signaling analysis data further demonstrated that myricetin inhibited Akt-mediated activator protein-1 (AP-1) transactivation, cyclin D1 expression and cell transformation. Overall, our results indicate that Akt is a direct target for myricetin to inhibit cell transformation.
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Le Guilloux V, Schmidtke P, Tuffery P. Fpocket: an open source platform for ligand pocket detection. BMC Bioinformatics 2009; 10:168. [PMID: 19486540 PMCID: PMC2700099 DOI: 10.1186/1471-2105-10-168] [Citation(s) in RCA: 851] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Accepted: 06/02/2009] [Indexed: 11/29/2022] Open
Abstract
Background Virtual screening methods start to be well established as effective approaches to identify hits, candidates and leads for drug discovery research. Among those, structure based virtual screening (SBVS) approaches aim at docking collections of small compounds in the target structure to identify potent compounds. For SBVS, the identification of candidate pockets in protein structures is a key feature, and the recent years have seen increasing interest in developing methods for pocket and cavity detection on protein surfaces. Results Fpocket is an open source pocket detection package based on Voronoi tessellation and alpha spheres built on top of the publicly available package Qhull. The modular source code is organised around a central library of functions, a basis for three main programs: (i) Fpocket, to perform pocket identification, (ii) Tpocket, to organise pocket detection benchmarking on a set of known protein-ligand complexes, and (iii) Dpocket, to collect pocket descriptor values on a set of proteins. Fpocket is written in the C programming language, which makes it a platform well suited for the scientific community willing to develop new scoring functions and extract various pocket descriptors on a large scale level. Fpocket 1.0, relying on a simple scoring function, is able to detect 94% and 92% of the pockets within the best three ranked pockets from the holo and apo proteins respectively, outperforming the standards of the field, while being faster. Conclusion Fpocket provides a rapid, open source and stable basis for further developments related to protein pocket detection, efficient pocket descriptor extraction, or drugablity prediction purposes. Fpocket is freely available under the GNU GPL license at .
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Affiliation(s)
- Vincent Le Guilloux
- ICOA - Institut de chimie organique et analytique - UMR CNRS 6005, Div. of chemoinformatics and molecular modeling, University of Orléans, Orléans, France.
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Hirakawa H, Akita H, Fujiwara T, Sugai M, Kuhara S. Structural insight into the binding mode between the targeting domain of ALE-1 (92AA) and pentaglycine of peptidoglycan. Protein Eng Des Sel 2009; 22:385-91. [DOI: 10.1093/protein/gzp014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Tatara Y, Lin YC, Bamba Y, Mori T, Uchida T. Dipentamethylene thiuram monosulfide is a novel inhibitor of Pin1. Biochem Biophys Res Commun 2009; 384:394-8. [PMID: 19422802 DOI: 10.1016/j.bbrc.2009.04.144] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Accepted: 04/29/2009] [Indexed: 01/29/2023]
Abstract
Pin1 is involved in eukaryotic cell proliferation by changing the structure and function of phosphorylated proteins. PiB, the Pin1 specific inhibitor, blocks cancer cell proliferation. However, low solubility of PiB in DMSO has limited studies of its effectiveness. We screened for additional Pin1 inhibitors and identified the DMSO-soluble compound dipentamethylene thiuram monosulfide (DTM) that inhibits Pin1 activity with an EC50 value of 4.1 microM. Molecular modeling and enzyme kinetic analysis indicated that DTM competitively inhibits Pin1 activity, with a K(i) value of 0.05 microM. The K(D) value of DTM with Pin1 was determined to be 0.06 microM by SPR technology. Moreover, DTM specifically inhibited peptidyl-prolyl cis/trans isomerase activity in HeLa cells. FACS analysis showed that DTM induced G0 arrest of the HCT116 cells. Our results suggest that DTM has the potential to guide the development of novel antifungal and/or anticancer drugs.
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Affiliation(s)
- Yota Tatara
- Molecular Enzymology, Department of Molecular and Cell Biology, Graduate School of Agricultural Science, Tohoku University, 1-1 Amamiya, Tsutsumidori, Aoba, Sendai, Miyagi 981-8555, Japan
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Vainio MJ, Puranen JS, Johnson MS. ShaEP: Molecular Overlay Based on Shape and Electrostatic Potential. J Chem Inf Model 2009; 49:492-502. [DOI: 10.1021/ci800315d] [Citation(s) in RCA: 157] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Mikko J. Vainio
- Structural Bioinformatics Laboratory, Department of Biochemistry and Pharmacy, Åbo Akademi University, Tykistökatu 6A (BioCity), FI-20520 Turku, Finland
| | - J. Santeri Puranen
- Structural Bioinformatics Laboratory, Department of Biochemistry and Pharmacy, Åbo Akademi University, Tykistökatu 6A (BioCity), FI-20520 Turku, Finland
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Department of Biochemistry and Pharmacy, Åbo Akademi University, Tykistökatu 6A (BioCity), FI-20520 Turku, Finland
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Azuma M, Kabe Y, Kuramori C, Kondo M, Yamaguchi Y, Handa H. Adenine nucleotide translocator transports haem precursors into mitochondria. PLoS One 2008; 3:e3070. [PMID: 18728780 PMCID: PMC2516936 DOI: 10.1371/journal.pone.0003070] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2008] [Accepted: 08/04/2008] [Indexed: 11/18/2022] Open
Abstract
Haem is a prosthetic group for haem proteins, which play an essential role in oxygen transport, respiration, signal transduction, and detoxification. In haem biosynthesis, the haem precursor protoporphyrin IX (PP IX) must be accumulated into the mitochondrial matrix across the inner membrane, but its mechanism is largely unclear. Here we show that adenine nucleotide translocator (ANT), the inner membrane transporter, contributes to haem biosynthesis by facilitating mitochondrial accumulation of its precursors. We identified that haem and PP IX specifically bind to ANT. Mitochondrial uptake of PP IX was inhibited by ADP, a known substrate of ANT. Conversely, ADP uptake into mitochondria was competitively inhibited by haem and its precursors, suggesting that haem-related porphyrins are accumulated into mitochondria via ANT. Furthermore, disruption of the ANT genes in yeast resulted in a reduction of haem biosynthesis by blocking the translocation of haem precursors into the matrix. Our results represent a new model that ANT plays a crucial role in haem biosynthesis by facilitating accumulation of its precursors into the mitochondrial matrix.
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Affiliation(s)
- Motoki Azuma
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
| | - Yasuaki Kabe
- Department of Integrative Medical Biology, School of Medicine, Keio University, Shinjuku-ku, Tokyo, Japan
| | - Chikanori Kuramori
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
| | - Masao Kondo
- Department of Early Childhood Care and Education, Toyoko Gakuen Women's College, , Setagaya-ku, Tokyo, Japan
| | - Yuki Yamaguchi
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
| | - Hiroshi Handa
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
- Solutions Research Organization, Integrated Research Institute, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
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