1
|
Hossain MS, Roney M, Bin Mohd Yunus MY, Shariffuddin JH. Virtual screening, molecular docking, molecular dynamics, and MM-GBSA approaches identify prospective fructose-1,6-bisphosphatase inhibitors from pineapple for diabetes management. J Biomol Struct Dyn 2023:1-16. [PMID: 37916669 DOI: 10.1080/07391102.2023.2276889] [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: 05/24/2023] [Accepted: 10/22/2023] [Indexed: 11/03/2023]
Abstract
Diabetes affects millions globally and poses treatment challenges. Targeting the enzyme fructose-1,6-bisphosphatase (FBPase) in gluconeogenesis and exploring plant-based therapies offer potential solutions for improving diabetes management while supporting sustainability and medicinal advancements. Utilizing pineapple (Ananas comosus L. Merr.) waste as a source of drug precursors could be valuable for health and environmental care due to its medicinal benefits and abundant yearly biomass production. Therefore, this study conducted a virtual screening to identify potential natural compounds from pineapple that could inhibit FBPase activity. A total of 112 compounds were screened for drug-likeness and ADMET properties, and molecular docking simulations were performed on 20 selected compounds using blind docking. The lead compound, butane-2,3-diyl diacetate, was subjected to 100 ns MD simulations, revealing a binding energy of -5.4 kcal/mol comparable to metformin (-5.6 kcal/mol). The MD simulation also confirmed stable complexes with crucial hydrogen bonds. Glu20, Ala24, Thr27, Gly28, Glu29, Leu30, Val160, Met177, Asp178, and Cys179 were identified as key amino acids that stabilized the human liver FBPase-butane-2,3-diyl diacetate complex, while Tyr215 and Asp218 played a crucial role in the human liver FBPase-Metformin complex. Our study indicates that the lead compound has high intestinal solubility. Therefore, it would show rapid bloodstream distribution and effective action on the target protein, making butane-2,3-diyl diacetate a potential antidiabetic drug candidate. However, further investigations in vitro, preclinical, and clinical trials are required to thoroughly assess its efficacy and safety.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Md Sanower Hossain
- Centre for Sustainability of Mineral and Resource Recovery Technology (Pusat SMaRRT), Universiti Malaysia Pahang Al-Sultan Abdullah, Kuantan, Malaysia
| | - Miah Roney
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, Kuantan, Malaysia
| | - Mohd Yusri Bin Mohd Yunus
- Centre for Sustainability of Mineral and Resource Recovery Technology (Pusat SMaRRT), Universiti Malaysia Pahang Al-Sultan Abdullah, Kuantan, Malaysia
- Faculty of Chemical and Process Engineering Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, Kuantan, Malaysia
| | - Jun Haslinda Shariffuddin
- Centre for Sustainability of Mineral and Resource Recovery Technology (Pusat SMaRRT), Universiti Malaysia Pahang Al-Sultan Abdullah, Kuantan, Malaysia
- Faculty of Chemical and Process Engineering Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, Kuantan, Malaysia
| |
Collapse
|
2
|
Wang X, Zhao R, Ji W, Zhou J, Liu Q, Zhao L, Shen Z, Liu S, Xu B. Discovery of Novel Indole Derivatives as Fructose-1,6-bisphosphatase Inhibitors and X-ray Cocrystal Structures Analysis. ACS Med Chem Lett 2021; 13:118-127. [PMID: 35059131 PMCID: PMC8762752 DOI: 10.1021/acsmedchemlett.1c00613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/15/2021] [Indexed: 01/16/2023] Open
Abstract
Liver fructose-1,6-bisphosphatase (FBPase) is a key enzyme in the gluconeogenesis, and its inhibitors are expected to be novel antidiabetic agents. Herein, a series of new indole and benzofuran analogues were designed and synthesized to evaluate the inhibitory activity against FBPase. As a result, the novel FBPase inhibitors bearing N-acylsulfonamide moiety on the 3-position of the indole-2-carboxylic acid scaffold (compounds 22f and 22g) were identified with IC50s at the submicromolar levels. Three X-ray crystal structures of the complexes were solved and revealed the structural basis for the inhibitory activity. The chemoinformatics analysis further disclosed the distinct binding features of this class of inhibitors, providing an insight for further modifications to create structurally distinct FBPase inhibitors with high potency and drug-like properties.
Collapse
Affiliation(s)
- Xiaoyu Wang
- Beijing
Key Laboratory of Active Substances Discovery and Druggability Evaluation,
Institute of Materia Medica, Chinese Academy
of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Rui Zhao
- Beijing
Key Laboratory of Active Substances Discovery and Druggability Evaluation,
Institute of Materia Medica, Chinese Academy
of Medical Sciences and Peking Union Medical College, Beijing, 100050, China,School
of Pharmaceutical Engineering, Shenyang
Pharmaceutical University, Shenyang, 100016, China
| | - Wenming Ji
- State
Key Laboratory of Bioactive Substances and Functions of Natural Medicines,
Institute of Materia Medica, Chinese Academy
of Medical Sciences and Peking Union Medical College, Beijing, 100050, China,Diabetes
Research Center, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Jie Zhou
- Beijing
Key Laboratory of Active Substances Discovery and Druggability Evaluation,
Institute of Materia Medica, Chinese Academy
of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Quan Liu
- State
Key Laboratory of Bioactive Substances and Functions of Natural Medicines,
Institute of Materia Medica, Chinese Academy
of Medical Sciences and Peking Union Medical College, Beijing, 100050, China,Diabetes
Research Center, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Linxiang Zhao
- School
of Pharmaceutical Engineering, Shenyang
Pharmaceutical University, Shenyang, 100016, China
| | - Zhufang Shen
- State
Key Laboratory of Bioactive Substances and Functions of Natural Medicines,
Institute of Materia Medica, Chinese Academy
of Medical Sciences and Peking Union Medical College, Beijing, 100050, China,Diabetes
Research Center, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Shuainan Liu
- State
Key Laboratory of Bioactive Substances and Functions of Natural Medicines,
Institute of Materia Medica, Chinese Academy
of Medical Sciences and Peking Union Medical College, Beijing, 100050, China,Diabetes
Research Center, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing, 100050, China,S.L. email,
| | - Bailing Xu
- Beijing
Key Laboratory of Active Substances Discovery and Druggability Evaluation,
Institute of Materia Medica, Chinese Academy
of Medical Sciences and Peking Union Medical College, Beijing, 100050, China,B.X.: email,
| |
Collapse
|
3
|
Vanillin exerts therapeutic effects against hyperglycemia-altered glucose metabolism and purinergic activities in testicular tissues of diabetic rats. Reprod Toxicol 2021; 102:24-34. [PMID: 33823243 DOI: 10.1016/j.reprotox.2021.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/07/2021] [Accepted: 03/25/2021] [Indexed: 01/04/2023]
Abstract
Testicular dysfunctions leading to male infertility has been reported in type 2 diabetes (T2D), with glucose dysmetabolism, cholinergic and purinergic dysfunction being major contributors. In the present study, the effect of vanillin on glucose metabolism, purinergic and cholinergic dysfunctions were investigated in testicular tissues of T2D rats. Male Sprague-Dawley rats were divided into 6 groups containing 5 rats each. T2D was induced in rats by administering 10 % fructose ad libitum for 14 days followed by a single intraperitoneal injection (40 mg/kg body weight) of streptozotocin. T2D rats were orally administered with vanillin at 150 and 300 mg/kg body weight (bw). Diabetic control (DC) consisted of untreated diabetic rats, while normal control (NC) consisted of normal rats and they were administered with distilled water only. Metformin was used as the standard antidiabetic drug. After 5 weeks treatment, the rats were sacrificed, and the testes were harvested. Induction of T2D led to significantly depleted testicular levels of glutathione, glycogen content, superoxide dismutase and catalase enzyme activities, with concomitantly elevated levels of nitric oxide, malondialdehyde, acetylcholinesterase, glucose-6-phosphatase, fructose-1,6-biphophastase, glycogen phosphorylase, amylase and lipase activities. These activities and levels were significantly reversed to near normal in rats treated with both doses of vanillin as compared with metformin. These results, when taken together, suggest the therapeutic effect of vanillin against hyperglycemia-mediated metabolic dysfunctions in testes of T2D rats. This is depicted by the ability of the phenolic to attenuate oxidative imbalance, purinergic and cholinergic dysfunctions, while suppressing glucose dysmetabolism.
Collapse
|
4
|
Curran DM, Grote A, Nursimulu N, Geber A, Voronin D, Jones DR, Ghedin E, Parkinson J. Modeling the metabolic interplay between a parasitic worm and its bacterial endosymbiont allows the identification of novel drug targets. eLife 2020; 9:e51850. [PMID: 32779567 PMCID: PMC7419141 DOI: 10.7554/elife.51850] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 07/14/2020] [Indexed: 12/17/2022] Open
Abstract
The filarial nematode Brugia malayi represents a leading cause of disability in the developing world, causing lymphatic filariasis in nearly 40 million people. Currently available drugs are not well-suited to mass drug administration efforts, so new treatments are urgently required. One potential vulnerability is the endosymbiotic bacteria Wolbachia-present in many filariae-which is vital to the worm. Genome scale metabolic networks have been used to study prokaryotes and protists and have proven valuable in identifying therapeutic targets, but have only been applied to multicellular eukaryotic organisms more recently. Here, we present iDC625, the first compartmentalized metabolic model of a parasitic worm. We used this model to show how metabolic pathway usage allows the worm to adapt to different environments, and predict a set of 102 reactions essential to the survival of B. malayi. We validated three of those reactions with drug tests and demonstrated novel antifilarial properties for all three compounds.
Collapse
Affiliation(s)
- David M Curran
- Program in Molecular Medicine, Hospital for Sick ChildrenTorontoCanada
| | - Alexandra Grote
- Department of Biology, Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
| | - Nirvana Nursimulu
- Program in Molecular Medicine, Hospital for Sick ChildrenTorontoCanada
- Department of Computer Science, University of TorontoTorontoCanada
| | - Adam Geber
- Department of Biology, Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
| | | | - Drew R Jones
- Department of Biochemistry and Molecular Pharmacology, New York University School of MedicineNew YorkUnited States
| | - Elodie Ghedin
- Department of Biology, Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
- Department of Epidemiology, School of Global Public Health, New York UniversityNew YorkUnited States
| | - John Parkinson
- Program in Molecular Medicine, Hospital for Sick ChildrenTorontoCanada
- Department of Computer Science, University of TorontoTorontoCanada
- Department of Biochemistry, University of TorontoTorontoCanada
- Department of Molecular Genetics, University of TorontoTorontoCanada
| |
Collapse
|
5
|
Wu F, Zhuo L, Wang F, Huang W, Hao G, Yang G. Auto In Silico Ligand Directing Evolution to Facilitate the Rapid and Efficient Discovery of Drug Lead. iScience 2020; 23:101179. [PMID: 32498019 PMCID: PMC7267738 DOI: 10.1016/j.isci.2020.101179] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/25/2020] [Accepted: 05/13/2020] [Indexed: 12/21/2022] Open
Abstract
Motivated by the growing demand for reducing the chemical optimization burden of H2L, we developed auto in silico ligand directing evolution (AILDE, http://chemyang.ccnu.edu.cn/ccb/server/AILDE), an efficient and general approach for the rapid identification of drug leads in accessible chemical space. This computational strategy relies on minor chemical modifications on the scaffold of a hit compound, and it is primarily intended for identifying new lead compounds with minimal losses or, in some cases, even increases in ligand efficiency. We also described how AILDE greatly reduces the chemical optimization burden in the design of mesenchymal-epithelial transition factor (c-Met) kinase inhibitors. We only synthesized eight compounds and found highly efficient compound 5g, which showed an ∼1,000-fold improvement in in vitro activity compared with the hit compound. 5g also displayed excellent in vivo antitumor efficacy as a drug lead. We believe that AILDE may be applied to a large number of studies for rapid design and identification of drug leads. AILDE was developed for the rapid identification of drug leads A potent drug lead targeted to c-Met was found by synthesizing only eight compounds
Collapse
Affiliation(s)
- Fengxu Wu
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China
| | - Linsheng Zhuo
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China
| | - Fan Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China
| | - Wei Huang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China.
| | - Gefei Hao
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China.
| | - Guangfu Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China; Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, P. R. China.
| |
Collapse
|
6
|
El Guesmi N, Hussein EM, Asghar BH, Obaid RJ, Jassas RS, Alharbi A, Altass HM, Althagafi II, Morad M, Moussa Z, Ahmed SA. Nucleophilicity and solvent effects on the kinetics of 4-(pyren-1-yl)thiazol-2-amine interaction with 4,6-dinitrobenzofuroxan. ARAB J CHEM 2020. [DOI: 10.1016/j.arabjc.2019.12.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
7
|
Singh S, Harmalkar DS, Choi Y, Lee K. Fructose-1,6-bisphosphatase Inhibitors: A Review of Recent (2000- 2017) Advances and Structure-Activity Relationship Studies. Curr Med Chem 2019; 26:5542-5563. [DOI: 10.2174/0929867325666180831133734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 05/01/2018] [Accepted: 07/20/2018] [Indexed: 11/22/2022]
Abstract
:
Diabetes mellitus, commonly referred to as diabetes, is the 8th leading cause of
death worldwide. As of 2015, approximately 415 million people were estimated to be diabetic
worldwide, type 2 diabetes being the most common accounting for approximately 90-95% of
all diagnosed cases with increasing prevalence. Fructose-1,6-bisphosphatase is one of the important
therapeutic targets recently discovered to treat this chronic disease. In this focused
review, we have highlighted recent advances and structure-activity relationship studies in the
discovery and development of different fructose-1,6-bisphosphatase inhibitors reported since
the year 2000.
Collapse
Affiliation(s)
- Sarbjit Singh
- College of Pharmacy, Dongguk University-Seoul, Goyang, 10326, Korea
| | | | - Yongseok Choi
- College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea
| | - Kyeong Lee
- College of Pharmacy, Dongguk University-Seoul, Goyang, 10326, Korea
| |
Collapse
|
8
|
Huang Y, Chi B, Xu Y, Song R, Wei L, Rao L, Feng L, Ren Y, Wan J. In silico screening of a novel scaffold for fructose-1,6-bisphosatase (FBPase) inhibitors. J Mol Graph Model 2018; 86:142-148. [PMID: 30366190 DOI: 10.1016/j.jmgm.2018.10.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 09/27/2018] [Accepted: 10/17/2018] [Indexed: 12/22/2022]
Abstract
Fructose-1, 6-bisphosphatase (FBPase) has been regarded as an attractive drug target to control blood glucose against Type 2 diabetes (T2D). In this study, by using the strategy of pharmacophore-based virtual screening, a novel scaffold inhibitor targeted the AMP allosteric site of human liver FBPase were screened, their inhibitory activities were further tested. The experimental results showed that compound H27 exhibited high inhibitory activities with the IC50 value of 5.3 μM. Therefore, compound H27 was chosen as the probe molecule, it's possible binding conformation targeted into FBPase was identified by using DOX2.0 strategy. The importance of key residues (T27, T31, K112 and R140) in allosteric site of FBPase for the binding inhibitors were validated by mutation experiments. The agreement between theory and experiment suggest that the interactional information of FBPase and inhibitors (H27) were reliable. On basis of these rational interactional information, the compound H29 was further designed to exhibit more potential FBPase inhibition (IC50 = 2.5 μM).
Collapse
Affiliation(s)
- Yunyuan Huang
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Bo Chi
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Yanhong Xu
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Rongrong Song
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Lin Wei
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Li Rao
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Lingling Feng
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Yanliang Ren
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan, 430079, China.
| | - Jian Wan
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan, 430079, China.
| |
Collapse
|
9
|
Kaur R, Dahiya L, Kumar M. Fructose-1,6-bisphosphatase inhibitors: A new valid approach for management of type 2 diabetes mellitus. Eur J Med Chem 2017; 141:473-505. [DOI: 10.1016/j.ejmech.2017.09.029] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 09/14/2017] [Accepted: 09/16/2017] [Indexed: 11/27/2022]
|
10
|
Yuan M, Vásquez-Valdivieso MG, McNae IW, Michels PAM, Fothergill-Gilmore LA, Walkinshaw MD. Structures of Leishmania Fructose-1,6-Bisphosphatase Reveal Species-Specific Differences in the Mechanism of Allosteric Inhibition. J Mol Biol 2017; 429:3075-3089. [PMID: 28882541 PMCID: PMC5639204 DOI: 10.1016/j.jmb.2017.08.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 08/14/2017] [Accepted: 08/17/2017] [Indexed: 11/29/2022]
Abstract
The gluconeogenic enzyme fructose-1,6-bisphosphatase has been proposed as a potential drug target against Leishmania parasites that cause up to 20,000-30,000 deaths annually. A comparison of three crystal structures of Leishmania major fructose-1,6-bisphosphatase (LmFBPase) along with enzyme kinetic data show how AMP acts as an allosteric inhibitor and provides insight into its metal-dependent reaction mechanism. The crystal structure of the apoenzyme form of LmFBPase is a homotetramer in which the dimer of dimers adopts a planar conformation with disordered "dynamic loops". The structure of LmFBPase, complexed with manganese and its catalytic product phosphate, shows the dynamic loops locked into the active sites. A third crystal structure of LmFBPase complexed with its allosteric inhibitor AMP shows an inactive form of the tetramer, in which the dimer pairs are rotated by 18° relative to each other. The three structures suggest an allosteric mechanism in which AMP binding triggers a rearrangement of hydrogen bonds across the large and small interfaces. Retraction of the "effector loop" required for AMP binding releases the side chain of His23 from the dimer-dimer interface. This is coupled with a flip of the side chain of Arg48 which ties down the key catalytic dynamic loop in a disengaged conformation and also locks the tetramer in an inactive rotated T-state. The structure of the effector site of LmFBPase shows different structural features compared with human FBPases, thereby offering a potential and species-specific drug target.
Collapse
Affiliation(s)
- Meng Yuan
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Montserrat G Vásquez-Valdivieso
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Iain W McNae
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Paul A M Michels
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Linda A Fothergill-Gilmore
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Malcolm D Walkinshaw
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK.
| |
Collapse
|
11
|
Ruf A, Tetaz T, Schott B, Joseph C, Rudolph MG. Quadruple space-group ambiguity owing to rotational and translational noncrystallographic symmetry in human liver fructose-1,6-bisphosphatase. Acta Crystallogr D Struct Biol 2016; 72:1212-1224. [PMID: 27841754 PMCID: PMC5108348 DOI: 10.1107/s2059798316016715] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 10/18/2016] [Indexed: 11/17/2022] Open
Abstract
Fructose-1,6-bisphosphatase (FBPase) is a key regulator of gluconeogenesis and a potential drug target for type 2 diabetes. FBPase is a homotetramer of 222 symmetry with a major and a minor dimer interface. The dimers connected via the minor interface can rotate with respect to each other, leading to the inactive T-state and active R-state conformations of FBPase. Here, the first crystal structure of human liver FBPase in the R-state conformation is presented, determined at a resolution of 2.2 Å in a tetragonal setting that exhibits an unusual arrangement of noncrystallographic symmetry (NCS) elements. Self-Patterson function analysis and various intensity statistics revealed the presence of pseudo-translation and the absence of twinning. The space group is P41212, but structure determination was also possible in space groups P43212, P4122 and P4322. All solutions have the same arrangement of three C2-symmetric dimers spaced by 1/3 along an NCS axis parallel to the c axis located at (1/4, 1/4, z), which is therefore invisible in a self-rotation function analysis. The solutions in the four space groups are related to one another and emulate a body-centred lattice. If all NCS elements were crystallographic, the space group would be I4122 with a c axis three times shorter and a single FBPase subunit in the asymmetric unit. I4122 is a minimal, non-isomorphic supergroup of the four primitive tetragonal space groups, explaining the space-group ambiguity for this crystal.
Collapse
Affiliation(s)
- Armin Ruf
- pRED, Therapeutic Modalities, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Tim Tetaz
- pRED, Therapeutic Modalities, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Brigitte Schott
- pRED, Therapeutic Modalities, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Catherine Joseph
- pRED, Therapeutic Modalities, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| | - Markus G. Rudolph
- pRED, Therapeutic Modalities, F. Hoffmann-La Roche, 4070 Basel, Switzerland
| |
Collapse
|
12
|
Bie J, Liu S, Li Z, Mu Y, Xu B, Shen Z. Discovery of novel indole derivatives as allosteric inhibitors of fructose-1,6-bisphosphatase. Eur J Med Chem 2014; 90:394-405. [PMID: 25461330 DOI: 10.1016/j.ejmech.2014.11.049] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Revised: 10/30/2014] [Accepted: 11/24/2014] [Indexed: 11/30/2022]
Abstract
A series of novel indole derivatives was designed and synthesized as inhibitors of fructose-1,6-bisphosphatase (FBPase). The most potent compound 14c was identified with an IC50 value of 0.10 μM by testing the inhibitory activity against recombinant human FBPase. The structure-activity relationships were investigated on the substitution at 4- and 5-position of the indole scaffold. The binding interactions of the title compounds at AMP binding site of FBPase were predicted using CDOCKER algorithm.
Collapse
Affiliation(s)
- Jianbo Bie
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences&Peking Union Medical College, Beijing 100050, China
| | - Shuainan Liu
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences&Peking Union Medical College, Beijing 100050, China
| | - Zhanmei Li
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences&Peking Union Medical College, Beijing 100050, China
| | - Yongzhao Mu
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences&Peking Union Medical College, Beijing 100050, China
| | - Bailing Xu
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences&Peking Union Medical College, Beijing 100050, China.
| | - Zhufang Shen
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences&Peking Union Medical College, Beijing 100050, China.
| |
Collapse
|
13
|
Synthesis, photophysical properties and TD-DFT calculation of fluorescent dyes based on pyrenylthiazoles. Chem Res Chin Univ 2014. [DOI: 10.1007/s40242-014-3467-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
14
|
Zhou M, Ning C, Liu R, He Y, Yu N. Design, synthesis and biological evaluation of indeno[1,2-d]thiazole derivatives as potent histone deacetylase inhibitors. Bioorg Med Chem Lett 2013; 23:3200-3. [DOI: 10.1016/j.bmcl.2013.04.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2012] [Revised: 03/22/2013] [Accepted: 04/01/2013] [Indexed: 11/16/2022]
|
15
|
Tayyem RF, Zalloum HM, Elmaghrabi MR, Yousef AM, Mubarak MS. Ligand-based designing, in silico screening, and biological evaluation of new potent fructose-1,6-bisphosphatase (FBPase) inhibitors. Eur J Med Chem 2012; 56:70-95. [DOI: 10.1016/j.ejmech.2012.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2012] [Revised: 07/27/2012] [Accepted: 08/02/2012] [Indexed: 10/28/2022]
|
16
|
Yang F, Li J, Li JY, He HB, Zhou YY, Liu T, Tang J, Gong XP, Qiu WW. Design, Synthesis and Biological Activity Evaluation of 2,5-Diphenyl-1,3,4-oxadiazole Derivatives as Novel Inhibitors of Fructose-1,6-bisphosphatase. HETEROCYCLES 2012. [DOI: 10.3987/com-12-12565] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
17
|
Murai T, Hori F, Maruyama T. Intramolecular Cyclization of in Situ Generated Adducts Formed between Thioamide Dianions and Thioformamides Leading to Generation of 5-Amino-2-thiazolines and 5-Aminothiazoles, and Their Fluorescence Properties. Org Lett 2011; 13:1718-21. [DOI: 10.1021/ol200231z] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Toshiaki Murai
- Department of Chemistry, Faculty of Engineering, Gifu University, Yanagido, Gifu 501-1193, Japan
| | - Fumihiko Hori
- Department of Chemistry, Faculty of Engineering, Gifu University, Yanagido, Gifu 501-1193, Japan
| | - Toshifumi Maruyama
- Department of Chemistry, Faculty of Engineering, Gifu University, Yanagido, Gifu 501-1193, Japan
| |
Collapse
|
18
|
Yi P, Di YT, Liu W, Hao XJ, Ming Y, Huang DS, Yang J, Yi ZZ, Li ZJ, Yang RD, Zhang JC. Protein-based alignment in 3D-QSAR of FBPase inhibitors. Eur J Med Chem 2011; 46:885-92. [DOI: 10.1016/j.ejmech.2010.12.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 10/07/2010] [Accepted: 12/31/2010] [Indexed: 10/18/2022]
|
19
|
Lan P, Chen WN, Huang ZJ, Sun PH, Chen WM. Understanding the structure-activity relationship of betulinic acid derivatives as anti-HIV-1 agents by using 3D-QSAR and docking. J Mol Model 2010; 17:1643-59. [DOI: 10.1007/s00894-010-0870-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Accepted: 10/05/2010] [Indexed: 10/18/2022]
|
20
|
3D-QSAR studies and molecular docking on [5-(4-amino-1H-benzoimidazol-2-yl)-furan-2-yl]-phosphonic acid derivatives as fructose-1,6-biphophatase inhibitors. J Comput Aided Mol Des 2010; 24:993-1008. [DOI: 10.1007/s10822-010-9391-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Accepted: 10/06/2010] [Indexed: 10/18/2022]
|
21
|
Tsukada T, Kanno O, Yamane T, Tanaka J, Yoshida T, Okuno A, Shiiki T, Takahashi M, Nishi T. Discovery of potent and orally active tricyclic-based FBPase inhibitors. Bioorg Med Chem 2010; 18:5346-51. [DOI: 10.1016/j.bmc.2010.05.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 05/13/2010] [Accepted: 05/14/2010] [Indexed: 11/28/2022]
|
22
|
Tsukada T, Tamaki K, Tanaka J, Takagi T, Yoshida T, Okuno A, Shiiki T, Takahashi M, Nishi T. A prodrug approach towards the development of tricyclic-based FBPase inhibitors. Bioorg Med Chem Lett 2010; 20:2938-41. [PMID: 20359891 DOI: 10.1016/j.bmcl.2010.03.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2009] [Revised: 03/03/2010] [Accepted: 03/04/2010] [Indexed: 11/18/2022]
Abstract
For the purpose of reducing the strong CYP3A4 inhibitory potency of diamide prodrug 4, cyclic prodrugs of tricyclic-based FBPase inhibitors were synthesized. Extensive SAR studies led to the discovery of pyridine-containing cyclic prodrug 20, which strongly inhibited glucose production in monkey hepatocytes and also showed weak CYP3A4 inhibitory potency.
Collapse
Affiliation(s)
- Tomoharu Tsukada
- Medicinal Chemistry Research Laboratories I, Daiichi Sankyo Co., Ltd, 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|