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Ma S, Yu H, Wang M, Cui T, Zhao Y, Zhang X, Wang C, Li M, Zhang L, Dong J. Natural product drupacine acting on a novel herbicidal target shikimate dehydrogenase. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 194:105480. [PMID: 37532346 DOI: 10.1016/j.pestbp.2023.105480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 08/04/2023]
Abstract
Natural products are one of the important sources for the creation of new pesticides. Drupacine ((1R,11S,12S,13R,15S)-13-methoxy-5,7,21-trioxa-19-azahexacyclo[11.7.1.02,10.04,8.011,15.015,19]henicosa-2,4(8),9-trien-12-ol), isolated from Cephalotaxus sinensis (Chinese plum-yew), is a potent herbicidal compound containing an oxo-bridged oxygen bond structure. However, its molecular target still remains unknown. In this study, the targets of drupacine in Amaranthus retroflexus were identified by combining drug affinity responsive target stability (DARTS), cellular thermal shift assay coupled with mass spectrometry (CETSA MS), RNA-seq transcriptomic, and TMT proteomic analyses. Fifty-one and sixty-eight main binding proteins were identified by DARTS and CETSA MS, respectively, including nine co-existing binding proteins. In drupacine-treated A. retroflexus seedlings we identified 1389 up-regulated genes and 442 down-regulated genes, 34 up-regulated proteins, and 194 down-regulated proteins, respectively. Combining the symptoms and the biochemical profiles, Profilin, Shikimate dehydrogenase (SkDH), and Zeta-carotene desaturase were predicted to be the drupacine potential target proteins. At the same time, drupacine was found to bind SkDH stronger by molecular docking, and its inhibition on ArSkDH increased with the treatment concentration increase. Our results suggest that the molecular target of drupacine is SkDH, a new herbicide target, which lay a foundation for the rational design of herbicides based on new targets from natural products and enrich the target resources for developing green herbicides.
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Affiliation(s)
- Shujie Ma
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology/College of Plant Protection, Hebei Agricultural University, Baoding 071000, China.
| | - Hualong Yu
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology/College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Mingyu Wang
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology/College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Tingru Cui
- Baoding Meteorological Bureau, Baoding 071000, China
| | - Yujing Zhao
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology/College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Xinxin Zhang
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology/College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Caixia Wang
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology/College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Mengmeng Li
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology/College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Lihui Zhang
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology/College of Plant Protection, Hebei Agricultural University, Baoding 071000, China.
| | - Jingao Dong
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology/College of Plant Protection, Hebei Agricultural University, Baoding 071000, China.
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2
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Rajput VS, Runthala A, Khan IA. Shikimate Kinase Inhibitors: An Update on Promising Strategy against Mycobacterium tuberculosis. Curr Drug Targets 2023; 24:388-405. [PMID: 36752299 DOI: 10.2174/1389450124666230208102645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 11/16/2022] [Accepted: 11/25/2022] [Indexed: 02/09/2023]
Abstract
Humanity has been battling with tuberculosis (TB) for a long period, and despite the availability of drugs well-known to act against the deadly microbe, the menace is still very far from reaching its end. Moreover, problems related to TB chemotherapy, such as lengthy treatment periods leading to poor patient compliance, increasing drug resistance, and association with another deadlier disease HIV-AIDS, make the situation alarming, thereby pressing the need for the discovery of new potent drugs urgently. Therefore, a drug target that is essential for survival and exclusive to M. tuberculosis presents a promising platform to explore novel molecules against the microorganism for better pathogen clearance with minimal toxicity. The shikimate pathway that leads to the synthesis of essential aromatic amino acids is one such attractive target. Shikimate kinase, the fifth enzyme of this pathway, converts shikimate to shikimate-3-phosphate by using ATP as a cosubstrate. Targeting shikimate kinase could be an effective strategy in light of its essentiality and absence of any homologue in mammals. This review discusses different strategies adopted for discovering novel compounds or scaffolds targeting M. tuberculosis shikimate kinase (MtSK) in vitro. The application of substrate analogues, their structure, and ligand-based approach for screening a library of anti-mycobacterial compounds, marine-derived molecules, and commercially available libraries have yielded promising MtSK inhibitors exhibiting micro-molar activities. To develop these leads into future drugs with minimum off-target effects on the host microenvironment, the molecules need to be structurally optimized for improved activities against enzymes and whole-cell organisms.
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Affiliation(s)
- Vikrant Singh Rajput
- Department of Biomedical Engineering, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817, Ajmer, Rajasthan, India
| | - Ashish Runthala
- Department of Bio-Technology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, AP, India
| | - Inshad Ali Khan
- Department of Microbiology, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817, Ajmer, Rajasthan, India
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3
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Mackie ERR, Barrow AS, Christoff RM, Abbott BM, Gendall AR, Soares da Costa TP. A dual-target herbicidal inhibitor of lysine biosynthesis. eLife 2022; 11:78235. [PMID: 35723913 PMCID: PMC9208756 DOI: 10.7554/elife.78235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/10/2022] [Indexed: 11/29/2022] Open
Abstract
Herbicides with novel modes of action are urgently needed to safeguard global agricultural industries against the damaging effects of herbicide-resistant weeds. We recently developed the first herbicidal inhibitors of lysine biosynthesis, which provided proof-of-concept for a promising novel herbicide target. In this study, we expanded upon our understanding of the mode of action of herbicidal lysine biosynthesis inhibitors. We previously postulated that these inhibitors may act as proherbicides. Here, we show this is not the case. We report an additional mode of action of these inhibitors, through their inhibition of a second lysine biosynthesis enzyme, and investigate the molecular determinants of inhibition. Furthermore, we extend our herbicidal activity analyses to include a weed species of global significance.
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Affiliation(s)
- Emily R R Mackie
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia.,School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Waite Campus, Glen Osmond, Australia
| | - Andrew S Barrow
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Rebecca M Christoff
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Belinda M Abbott
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Anthony R Gendall
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, AgriBio, La Trobe University, Bundoora, Australia.,Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Australia
| | - Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia.,School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Waite Campus, Glen Osmond, Australia
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4
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Carroll MJ, Garcia-Reyero N, Perkins EJ, Lauffenburger DA. Translatable pathways classification (TransPath-C) for inferring processes germane to human biology from animal studies data: example application in neurobiology. Integr Biol (Camb) 2021; 13:237-245. [PMID: 34849940 DOI: 10.1093/intbio/zyab016] [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: 07/19/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 11/13/2022]
Abstract
How to translate insights gained from studies in one organismal species for what is most likely to be germane in another species, such as from mice to humans, is a ubiquitous challenge in basic biology as well as biomedicine. This is an especially difficult problem when there are few molecular features that are obviously important in both species for a given phenotype of interest. Neuropathologies are a prominent realm of this complication. Schizophrenia is complex psychiatric disorder that affects 1% of the population. Many genetic factors have been proposed to drive the development of schizophrenia, and the 22q11 microdeletion (MD) syndrome has been shown to dramatically increase this risk. Due to heterogeneity of presentation of symptoms, diagnosis and formulation of treatment options for patients can often be delayed, and there is an urgent need for novel therapeutics directed toward the treatment of schizophrenia. Here, we present a novel computational approach, Translational Pathways Classification (TransPath-C), that can be used to identify shared pathway dysregulation between mouse models and human schizophrenia cohorts. This method uses variation of pathway activation in the mouse model to predict both mouse and human disease phenotype. Analysis of shared dysregulated pathways called out by both the mouse and human classifiers of TransPath-C can identify pathways that can be targeted in both preclinical and human cohorts of schizophrenia. In application to the 22q11 MD mouse model, our findings suggest that PAR1 pathway activation found upregulated in this mouse phenotype is germane for the corresponding human schizophrenia cohort such that inhibition of PAR1 may offer a novel therapeutic target.
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Affiliation(s)
- Molly J Carroll
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Natàlia Garcia-Reyero
- Environmental Laboratory, US Army Engineer Research & Development Center, Vicksburg, MS, USA
| | - Edward J Perkins
- Environmental Laboratory, US Army Engineer Research & Development Center, Vicksburg, MS, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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5
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Pathak N, Chen YT, Hsu YC, Hsu NY, Kuo CJ, Tsai HP, Kang JJ, Huang CH, Chang SY, Chang YH, Liang PH, Yang JM. Uncovering Flexible Active Site Conformations of SARS-CoV-2 3CL Proteases through Protease Pharmacophore Clusters and COVID-19 Drug Repurposing. ACS NANO 2021; 15:857-872. [PMID: 33373194 DOI: 10.1021/acsnano.0c07383] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The infectious SARS-CoV-2 causes COVID-19, which is now a global pandemic. Aiming for effective treatments, we focused on the key drug target, the viral 3C-like (3CL) protease. We modeled a big dataset with 42 SARS-CoV-2 3CL protease-ligand complex structures from ∼98.7% similar SARS-CoV 3CL protease with abundant complex structures. The diverse flexible active site conformations identified in the dataset were clustered into six protease pharmacophore clusters (PPCs). For the PPCs with distinct flexible protease active sites and diverse interaction environments, we identified pharmacophore anchor hotspots. A total of 11 "PPC consensus anchors" (a distinct set observed in each PPC) were observed, of which three "PPC core anchors" EHV2, HV1, and V3 are strongly conserved across PPCs. The six PPC cavities were then applied in virtual screening of 2122 FDA drugs for repurposing, using core anchor-derived "PPC scoring S" to yield seven drug candidates. Experimental testing by SARS-CoV-2 3CL protease inhibition assay and antiviral cytopathic effect assays discovered active hits, Boceprevir and Telaprevir (HCV drugs) and Nelfinavir (HIV drug). Specifically, Boceprevir showed strong protease inhibition with micromolar IC50 of 1.42 μM and an antiviral activity with EC50 of 49.89 μM, whereas Telaprevir showed moderate protease inhibition only with an IC50 of 11.47 μM. Nelfinavir solely showed antiviral activity with a micromolar EC50 value of 3.28 μM. Analysis of binding mechanisms of protease inhibitors revealed the role of PPC core anchors. Our PPCs revealed the flexible protease active site conformations, which successfully enabled drug repurposing.
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Affiliation(s)
- Nikhil Pathak
- TIGP Bioinformatics Program, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Yun-Ti Chen
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Yen-Chao Hsu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Nung-Yu Hsu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Chih-Jung Kuo
- Department of Veterinary Medicine, National Chung Hsing University, Taichung 402, Taiwan
| | - Hui Ping Tsai
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei City 114, Taiwan
| | - Jaw-Jou Kang
- National Yang-Ming University, Taipei 112, Taiwan
| | - Chih-Heng Huang
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei City 114, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical Center, New Taipei City 114, Taiwan
| | - Sui-Yuan Chang
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei 100, Taiwan
- National Taiwan University College of Medicine, Taipei 100, Taiwan
| | - Yu-Hsiu Chang
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei City 114, Taiwan
| | - Po-Huang Liang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
| | - Jinn-Moon Yang
- TIGP Bioinformatics Program, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices, National Chiao Tung University, Hsinchu 300, Taiwan
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6
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de Oliveira MD, Araújo JDO, Galúcio JMP, Santana K, Lima AH. Targeting shikimate pathway: In silico analysis of phosphoenolpyruvate derivatives as inhibitors of EPSP synthase and DAHP synthase. J Mol Graph Model 2020; 101:107735. [PMID: 32947107 DOI: 10.1016/j.jmgm.2020.107735] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/13/2020] [Accepted: 08/31/2020] [Indexed: 02/03/2023]
Abstract
The shikimate pathway consists of seven enzymatic steps involved in the conversion of erythrose-4-phosphate and phosphoenolpyruvate to chorismate and also responsible to the production of aromatic amino acids, such as phenylalanine, tyrosine, and tryptophan which are essential to the bacterial metabolism. The 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHPS) and 5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) catalyze important steps in the shikimate pathway using as substrate the phosphoenolpyruvate (PEP). Due to the importance of PEP in shikimate pathway, its structure has been investigated to develop new bioinspired competitive inhibitors against DAHPS and EPSPS. In the present study, we perform a literature survey of 28 PEP derivatives, then we analyzed the selectivity and affinity of these compounds against the EPSPS and DAHPS structures using consensual molecular docking, pharmacophore prediction, molecular dynamics (MD) simulations, and binding free energy calculations. Here, we propose consistent binding modes of the selected ligands and indicate that their structures show interesting pharmacophoric properties related to multi-targets inhibitors for both enzymes. Our computational results are supported by previous experimental findings related to the interactions of PEP derivatives with DAHPS and EPSPS structures.
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Affiliation(s)
- Maycon D de Oliveira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, 66075-110, Belém, Pará, Brazil
| | - Jéssica de O Araújo
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, 66075-110, Belém, Pará, Brazil
| | - João M P Galúcio
- Instituto de Biodiversidade. Universidade Federal do Oeste do Pará, 68035-110, Santarém, Pará, Brazil
| | - Kauê Santana
- Instituto de Biodiversidade. Universidade Federal do Oeste do Pará, 68035-110, Santarém, Pará, Brazil
| | - Anderson H Lima
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, 66075-110, Belém, Pará, Brazil.
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7
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A site-moiety map and virtual screening approach for discovery of novel 5-LOX inhibitors. Sci Rep 2020; 10:10510. [PMID: 32601404 PMCID: PMC7324578 DOI: 10.1038/s41598-020-67420-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/04/2020] [Indexed: 11/09/2022] Open
Abstract
The immune system works in conjunction with inflammation. Excessive inflammation underlies various human diseases, such as asthma, diabetes and heart disease. Previous studies found that 5-lipoxygenase (5-LOX) plays a crucial role in metabolizing arachidonic acid into inflammatory mediators and is a potential therapeutic target. In this study, we performed an in silico approach to establish a site-moiety map (SiMMap) to screen for new 5-LOX inhibitors. The map is composed of several anchors that contain key residues, moiety preferences, and their interaction types (i.e., electrostatic (E), hydrogen-bonding (H), and van der Waals (V) interactions) within the catalytic site. In total, we identified one EH, one H, and five V anchors, within the 5-LOX catalytic site. Based on the SiMMap, three 5-LOX inhibitors (YS1, YS2, and YS3) were identified. An enzyme-based assay validated inhibitory activity of YS1, YS2, and YS3 against 5-LOX with an IC50 value of 2.7, 4.2, and 5.3 μM, respectively. All three inhibitors significantly decrease LPS-induced TNF-α and IL-6 production, which suggests its potential use an anti-inflammatory agent. In addition, the identified 5-LOX inhibitors contain a novel scaffold. The discovery of these inhibitors presents an opportunity for designing specific anti-inflammatory drugs.
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8
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Pathak N, Kuo YP, Chang TY, Huang CT, Hung HC, Hsu JTA, Yu GY, Yang JM. Zika Virus NS3 Protease Pharmacophore Anchor Model and Drug Discovery. Sci Rep 2020; 10:8929. [PMID: 32488021 PMCID: PMC7265434 DOI: 10.1038/s41598-020-65489-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 04/29/2020] [Indexed: 11/28/2022] Open
Abstract
Zika virus (ZIKV) of the flaviviridae family, is the cause of emerging infections characterized by fever, Guillain-Barré syndrome (GBS) in adults and microcephaly in newborns. There exists an urgent unmet clinical need for anti-ZIKV drugs for the treatment of infected individuals. In the current work, we aimed at the promising virus drug target, ZIKV NS3 protease and constructed a Pharmacophore Anchor (PA) model for the active site. The PA model reveals a total of 12 anchors (E, H, V) mapped across the active site subpockets. We further identified five of these anchors to be critical core anchors (CEH1, CH3, CH7, CV1, CV3) conserved across flaviviral proteases. The ZIKV protease PA model was then applied in anchor-enhanced virtual screening yielding 14 potential antiviral candidates, which were tested by in vitro assays. We discovered FDA drugs Asunaprevir and Simeprevir to have potent anti-ZIKV activities with EC50 values 4.7 µM and 0.4 µM, inhibiting the viral protease with IC50 values 6.0 µM and 2.6 µM respectively. Additionally, the PA model anchors aided in the exploration of inhibitor binding mechanisms. In conclusion, our PA model serves as a promising guide map for ZIKV protease targeted drug discovery and the identified ‘previr’ FDA drugs are promising for anti-ZIKV treatments.
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Affiliation(s)
- Nikhil Pathak
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, 11529, Taiwan.,Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Yi-Ping Kuo
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, 35053, Taiwan
| | - Teng-Yuan Chang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, 35053, Taiwan
| | - Chin-Ting Huang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, 35053, Taiwan
| | - Hui-Chen Hung
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, 35053, Taiwan
| | - John Tsu-An Hsu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, 35053, Taiwan
| | - Guann-Yi Yu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, 35053, Taiwan
| | - Jinn-Moon Yang
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, 11529, Taiwan. .,Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 30010, Taiwan. .,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 30010, Taiwan.
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9
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Li J, Wu G, Fu Q, Ge H, Liu S, Li X, Cheng B. Exploring the influence of conserved lysine69 on the catalytic activity of the helicobacter pylori shikimate dehydrogenase: A combined QM/MM and MD simulations. Comput Biol Chem 2019; 83:107098. [DOI: 10.1016/j.compbiolchem.2019.107098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/22/2019] [Accepted: 08/04/2019] [Indexed: 12/29/2022]
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10
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Lee CC, Chang WH, Chang YS, Yang JM, Chang CS, Hsu KC, Chen YT, Liu TY, Chen YC, Lin SY, Wu YC, Chang JG. Alternative splicing in human cancer cells is modulated by the amiloride derivative 3,5-diamino-6-chloro-N-(N-(2,6-dichlorobenzoyl)carbamimidoyl)pyrazine-2-carboxide. Mol Oncol 2019; 13:1744-1762. [PMID: 31152681 PMCID: PMC6670021 DOI: 10.1002/1878-0261.12524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 04/30/2019] [Accepted: 05/30/2019] [Indexed: 12/11/2022] Open
Abstract
Alternative splicing (AS) is a process that enables the generation of multiple protein isoforms with different biological properties from a single mRNA. Cancer cells often use the maneuverability conferred by AS to produce proteins that contribute to growth and survival. In our previous studies, we identified that amiloride modulates AS in cancer cells. However, the effective concentration of amiloride required to modulate AS is too high for use in cancer treatment. In this study, we used computational algorithms to screen potential amiloride derivatives for their ability to regulate AS in cancer cells. We found that 3,5-diamino-6-chloro-N-(N-(2,6-dichlorobenzoyl)carbamimidoyl)pyrazine-2-carboxamide (BS008) can regulate AS of apoptotic gene transcripts, including HIPK3, SMAC, and BCL-X, at a lower concentration than amiloride. This splicing regulation involved various splicing factors, and it was accompanied by a change in the phosphorylation state of serine/arginine-rich proteins (SR proteins). RNA sequencing was performed to reveal that AS of many other apoptotic gene transcripts, such as AATF, ATM, AIFM1, NFKB1, and API5, was also modulated by BS008. In vivo experiments further indicated that treatment of tumor-bearing mice with BS008 resulted in a marked decrease in tumor size. BS008 also had inhibitory effects in vitro, either alone or in a synergistic combination with the cytotoxic chemotherapeutic agents sorafenib and nilotinib. BS008 enabled sorafenib dose reduction without compromising antitumor activity. These findings suggest that BS008 may possess therapeutic potential for cancer treatment.
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Affiliation(s)
- Chien-Chin Lee
- Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan
| | - Wen-Hsin Chang
- Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan.,Department of Primary Care Medicine, Taipei Medical University Hospital, Taiwan
| | - Ya-Sian Chang
- Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan.,Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan.,Center for Precision Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Jinn-Moon Yang
- TIGP-Bioinformatics, Institute of Information Science, Academia Sinica, Taipei, Taiwan.,Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Chih-Shiang Chang
- Graduate Institute of Pharmaceutical Chemistry, China Medical University, Taichung, Taiwan
| | - Kai-Cheng Hsu
- Graduate Institute of Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taiwan
| | - Yun-Ti Chen
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Ting-Yuan Liu
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Yu-Chia Chen
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Shyr-Yi Lin
- Department of Primary Care Medicine, Taipei Medical University Hospital, Taiwan.,Department of General Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taiwan.,TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taiwan
| | - Yang-Chang Wu
- Graduate Institute of Natural Products, Kaohsiung Medical University, Taiwan.,Research Center for Natural Products and Drug Development, Kaohsiung Medical University, Taiwan.,Department of Medical Research, Kaohsiung Medical University Hospital, Taiwan.,Chinese Medicine Research and Development Center, China Medical University Hospital, Taichung, Taiwan
| | - Jan-Gowth Chang
- Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan.,Department of Primary Care Medicine, Taipei Medical University Hospital, Taiwan.,Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
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11
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Díaz-Quiroz DC, Cardona-Félix CS, Viveros-Ceballos JL, Reyes-González MA, Bolívar F, Ordoñez M, Escalante A. Synthesis, biological activity and molecular modelling studies of shikimic acid derivatives as inhibitors of the shikimate dehydrogenase enzyme of Escherichia coli. J Enzyme Inhib Med Chem 2018; 33:397-404. [PMID: 29363372 PMCID: PMC6009893 DOI: 10.1080/14756366.2017.1422125] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/22/2017] [Accepted: 12/23/2017] [Indexed: 11/25/2022] Open
Abstract
Shikimic acid (SA) pathway is the common route used by bacteria, plants, fungi, algae, and certain Apicomplexa parasites for the biosynthesis of aromatic amino acids and other secondary metabolites. As this essential pathway is absent in mammals designing inhibitors against implied enzymes may lead to the development of antimicrobial and herbicidal agents harmless to humans. Shikimate dehydrogenase (SDH) is the fourth enzyme of the SA pathway. In this contribution, a series of SA amide derivatives were synthesised and evaluated for in vitro SDH inhibition and antibacterial activity against Escherichia coli. All tested compounds showed to be mixed type inhibitors; diamide derivatives displayed more inhibitory activity than synthesised monoamides. Among the evaluated compounds, molecules called 4a and 4b were the most active derivatives with IC50 588 and 589 µM, respectively. Molecular modelling studies suggested two different binding modes of monoamide and diamide derivatives to the SDH enzyme of E. coli.
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Affiliation(s)
- Dulce Catalina Díaz-Quiroz
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - César Salvador Cardona-Félix
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
- CONACyT – Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, La Paz, México
| | | | | | - Franciso Bolívar
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Mario Ordoñez
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, México
| | - Adelfo Escalante
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
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Pharmacophore anchor models of flaviviral NS3 proteases lead to drug repurposing for DENV infection. BMC Bioinformatics 2017; 18:548. [PMID: 29297305 PMCID: PMC5751397 DOI: 10.1186/s12859-017-1957-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Viruses of the flaviviridae family are responsible for some of the major infectious viral diseases around the world and there is an urgent need for drug development for these diseases. Most of the virtual screening methods in flaviviral drug discovery suffer from a low hit rate, strain-specific efficacy differences, and susceptibility to resistance. It is because they often fail to capture the key pharmacological features of the target active site critical for protein function inhibition. So in our current work, for the flaviviral NS3 protease, we summarized the pharmacophore features at the protease active site as anchors (subsite-moiety interactions). Results For each of the four flaviviral NS3 proteases (i.e., HCV, DENV, WNV, and JEV), the anchors were obtained and summarized into ‘Pharmacophore anchor (PA) models’. To capture the conserved pharmacophore anchors across these proteases, were merged the four PA models. We identified five consensus core anchors (CEH1, CH3, CH7, CV1, CV3) in all PA models, represented as the “Core pharmacophore anchor (CPA) model” and also identified specific anchors unique to the PA models. Our PA/CPA models complied with 89 known NS3 protease inhibitors. Furthermore, we proposed an integrated anchor-based screening method using the anchors from our models for discovering inhibitors. This method was applied on the DENV NS3 protease to screen FDA drugs discovering boceprevir, telaprevir and asunaprevir as promising anti-DENV candidates. Experimental testing against DV2-NGC virus by in-vitro plaque assays showed that asunaprevir and telaprevir inhibited viral replication with EC50 values of 10.4 μM & 24.5 μM respectively. The structure-anchor-activity relationships (SAAR) showed that our PA/CPA model anchors explained the observed in-vitro activities of the candidates. Also, we observed that the CEH1 anchor engagement was critical for the activities of telaprevir and asunaprevir while the extent of inhibitor anchor occupation guided their efficacies. Conclusion These results validate our NS3 protease PA/CPA models, anchors and the integrated anchor-based screening method to be useful in inhibitor discovery and lead optimization, thus accelerating flaviviral drug discovery. Electronic supplementary material The online version of this article (10.1186/s12859-017-1957-5) contains supplementary material, which is available to authorized users.
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Sutton KA, Breen J, Russo TA, Schultz LW, Umland TC. Crystal structure of 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase from the ESKAPE pathogen Acinetobacter baumannii. Acta Crystallogr F Struct Biol Commun 2016; 72:179-87. [PMID: 26919521 PMCID: PMC4774876 DOI: 10.1107/s2053230x16001114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 01/19/2016] [Indexed: 01/01/2023] Open
Abstract
The enzyme 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase catalyzes the sixth step of the seven-step shikimate pathway. Chorismate, the product of the pathway, is a precursor for the biosynthesis of aromatic amino acids, siderophores and metabolites such as folate, ubiquinone and vitamin K. The shikimate pathway is present in bacteria, fungi, algae, plants and apicomplexan parasites, but is absent in humans. The EPSP synthase enzyme produces 5-enolpyruvylshikimate 3-phosphate and phosphate from phosphoenolpyruvate and shikimate 3-phosphate via a transferase reaction, and is the target of the herbicide glyphosate. The Acinetobacter baumannii gene encoding EPSP synthase, aroA, has previously been demonstrated to be essential during host infection for the growth and survival of this clinically important drug-resistant ESKAPE pathogen. Prephenate dehydrogenase is also encoded by the bifunctional A. baumannii aroA gene, but its activity is dependent upon EPSP synthase since it operates downstream of the shikimate pathway. As part of an effort to evaluate new antimicrobial targets, recombinant A. baumannii EPSP (AbEPSP) synthase, comprising residues Ala301-Gln756 of the aroA gene product, was overexpressed in Escherichia coli, purified and crystallized. The crystal structure, determined to 2.37 Å resolution, is described in the context of a potential antimicrobial target and in comparison to EPSP synthases that are resistant or sensitive to the herbicide glyphosate.
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Affiliation(s)
- Kristin A. Sutton
- Hauptman–Woodward Medical Research Institute, Buffalo, NY 14203, USA
| | - Jennifer Breen
- Hauptman–Woodward Medical Research Institute, Buffalo, NY 14203, USA
| | - Thomas A. Russo
- Department of Medicine and The Witebsky Center for Microbial Pathogenesis, University at Buffalo, State University of New York, Buffalo, NY 14214, USA
- Veterans Administration Western New York Healthcare System and Department of Microbiology and Immunology, University at Buffalo, State University of New York, Buffalo, NY 14214, USA
| | - L. Wayne Schultz
- Hauptman–Woodward Medical Research Institute, Buffalo, NY 14203, USA
- Department of Structural Biology, University at Buffalo, State University of New York, Buffalo, NY 14203, USA
| | - Timothy C. Umland
- Hauptman–Woodward Medical Research Institute, Buffalo, NY 14203, USA
- Department of Structural Biology, University at Buffalo, State University of New York, Buffalo, NY 14203, USA
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14
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Modelling of compound combination effects and applications to efficacy and toxicity: state-of-the-art, challenges and perspectives. Drug Discov Today 2015; 21:225-38. [PMID: 26360051 DOI: 10.1016/j.drudis.2015.09.003] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 07/30/2015] [Accepted: 09/01/2015] [Indexed: 01/18/2023]
Abstract
The development of treatments involving combinations of drugs is a promising approach towards combating complex or multifactorial disorders. However, the large number of compound combinations that can be generated, even from small compound collections, means that exhaustive experimental testing is infeasible. The ability to predict the behaviour of compound combinations in biological systems, whittling down the number of combinations to be tested, is therefore crucial. Here, we review the current state-of-the-art in the field of compound combination modelling, with the aim to support the development of approaches that, as we hope, will finally lead to an integration of chemical with systems-level biological information for predicting the effect of chemical mixtures.
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15
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Sutton KA, Breen J, MacDonald U, Beanan JM, Olson R, Russo TA, Schultz LW, Umland TC. Structure of shikimate kinase, an in vivo essential metabolic enzyme in the nosocomial pathogen Acinetobacter baumannii, in complex with shikimate. ACTA ACUST UNITED AC 2015; 71:1736-44. [PMID: 26249354 DOI: 10.1107/s139900471501189x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 06/22/2015] [Indexed: 11/10/2022]
Abstract
Acinetobacter baumannii is an opportunistic Gram-negative pathogen that is an important cause of healthcare-associated infections exhibiting high mortality rates. Clinical isolates of multidrug-resistant (MDR) and extremely drug-resistant (XDR) A. baumannii strains are increasingly being observed. Compounding this concern is the dearth of new antibacterial agents in late-stage development that are effective against MDR and XDR A. baumannii. As part of an effort to address these concerns, two genes (aroA and aroC) of the shikimate pathway have previously been determined to be essential for the growth and survival of A. baumannii during host infection (i.e. to be essential in vivo). This study expands upon these results by demonstrating that the A. baumannii aroK gene, encoding shikimate kinase (SK), is also essential in vivo in a rat soft-tissue infection model. The crystal structure of A. baumannii SK in complex with the substrate shikimate and a sulfate ion that mimics the binding interactions expected for the β-phosphate of ATP was then determined to 1.91 Å resolution and the enzyme kinetics were characterized. The flexible shikimate-binding domain and LID region are compared with the analogous regions in other SK crystal structures. The impact of structural differences and sequence divergence between SKs from pathogenic bacteria that may influence antibiotic-development efforts is discussed.
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Affiliation(s)
- Kristin A Sutton
- Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA
| | - Jennifer Breen
- Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA
| | - Ulrike MacDonald
- Department of Medicine and The Witebsky Center for Microbial Pathogenesis, University at Buffalo, State University of New York, Buffalo, NY 14214, USA
| | - Janet M Beanan
- Department of Medicine and The Witebsky Center for Microbial Pathogenesis, University at Buffalo, State University of New York, Buffalo, NY 14214, USA
| | - Ruth Olson
- Department of Medicine and The Witebsky Center for Microbial Pathogenesis, University at Buffalo, State University of New York, Buffalo, NY 14214, USA
| | - Thomas A Russo
- Department of Medicine and The Witebsky Center for Microbial Pathogenesis, University at Buffalo, State University of New York, Buffalo, NY 14214, USA
| | - L Wayne Schultz
- Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA
| | - Timothy C Umland
- Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA
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16
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Chen H, Yao K, Chang X, Shim JH, Kim HG, Malakhova M, Kim DJ, Bode AM, Dong Z. Computational and Biochemical Discovery of RSK2 as a Novel Target for Epigallocatechin Gallate (EGCG). PLoS One 2015; 10:e0130049. [PMID: 26083344 PMCID: PMC4470687 DOI: 10.1371/journal.pone.0130049] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 05/15/2015] [Indexed: 11/30/2022] Open
Abstract
The most active anticancer component in green tea is epigallocatechin-3-gallate (EGCG). Protein interaction with EGCG is a critical step for mediating the effects of EGCG on the regulation of various key molecules involved in signal transduction. By using computational docking screening methods for protein identification, we identified a serine/threonine kinase, 90-kDa ribosomal S6 kinase (RSK2), as a novel molecular target of EGCG. RSK2 includes two kinase catalytic domains in the N-terminal (NTD) and the C-terminal (CTD) and RSK2 full activation requires phosphorylation of both terminals. The computer prediction was confirmed by an in vitro kinase assay in which EGCG inhibited RSK2 activity in a dose-dependent manner. Pull-down assay results showed that EGCG could bind with RSK2 at both kinase catalytic domains in vitro and ex vivo. Furthermore, results of an ATP competition assay and a computer-docking model showed that EGCG binds with RSK2 in an ATP-dependent manner. In RSK2+/+ and RSK2-/- murine embryonic fibroblasts, EGCG decreased viability only in the presence of RSK2. EGCG also suppressed epidermal growth factor-induced neoplastic cell transformation by inhibiting phosphorylation of histone H3 at Ser10. Overall, these results indicate that RSK2 is a novel molecular target of EGCG.
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Affiliation(s)
- Hanyong Chen
- The Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN, 55912, United States of America
| | - Ke Yao
- The Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN, 55912, United States of America
| | - Xiaoyu Chang
- The Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN, 55912, United States of America
| | - Jung-Hyun Shim
- The Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN, 55912, United States of America
| | - Hong-Gyum Kim
- The Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN, 55912, United States of America
| | - Margarita Malakhova
- The Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN, 55912, United States of America
| | - Dong-Joon Kim
- The Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN, 55912, United States of America
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN, 55912, United States of America
| | - Zigang Dong
- The Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN, 55912, United States of America
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17
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Hsu KC, Sung TY, Lin CT, Chiu YY, Hsu JTA, Hung HC, Sun CM, Barve I, Chen WL, Huang WC, Huang CT, Chen CH, Yang JM. Anchor-based classification and type-C inhibitors for tyrosine kinases. Sci Rep 2015; 5:10938. [PMID: 26077136 PMCID: PMC4468516 DOI: 10.1038/srep10938] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 05/08/2015] [Indexed: 12/13/2022] Open
Abstract
Tyrosine kinases regulate various biological processes and are drug targets for cancers. At present, the design of selective and anti-resistant inhibitors of kinases is an emergent task. Here, we inferred specific site-moiety maps containing two specific anchors to uncover a new binding pocket in the C-terminal hinge region by docking 4,680 kinase inhibitors into 51 protein kinases, and this finding provides an opportunity for the development of kinase inhibitors with high selectivity and anti-drug resistance. We present an anchor-based classification for tyrosine kinases and discover two type-C inhibitors, namely rosmarinic acid (RA) and EGCG, which occupy two and one specific anchors, respectively, by screening 118,759 natural compounds. Our profiling reveals that RA and EGCG selectively inhibit 3% (EGFR and SYK) and 14% of 64 kinases, respectively. According to the guide of our anchor model, we synthesized three RA derivatives with better potency. These type-C inhibitors are able to maintain activities for drug-resistant EGFR and decrease the invasion ability of breast cancer cells. Our results show that the type-C inhibitors occupying a new pocket are promising for cancer treatments due to their kinase selectivity and anti-drug resistance.
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Affiliation(s)
- Kai-Cheng Hsu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Tzu-Ying Sung
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Chih-Ta Lin
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Yi-Yuan Chiu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - John T-A Hsu
- 1] Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan [2] Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan
| | - Hui-Chen Hung
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan
| | - Chung-Ming Sun
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu, Taiwan
| | - Indrajeet Barve
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu, Taiwan
| | - Wen-Liang Chen
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Wen-Chien Huang
- Department of Thoracic Surgery, Mackay Memorial Hospital, Taipei City, Taiwan
| | - Chin-Ting Huang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan
| | - Chun-Hwa Chen
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan
| | - Jinn-Moon Yang
- 1] Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan [2] Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
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18
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Gordon S, Simithy J, Goodwin DC, Calderón AI. Selective Mycobacterium tuberculosis Shikimate Kinase Inhibitors as Potential Antibacterials. PERSPECTIVES IN MEDICINAL CHEMISTRY 2015; 7:9-20. [PMID: 25861218 PMCID: PMC4362912 DOI: 10.4137/pmc.s13212] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 01/19/2015] [Accepted: 01/27/2015] [Indexed: 11/08/2022]
Abstract
Owing to the persistence of tuberculosis (TB) as well as the emergence of multidrug-resistant and extensively drug-resistant (XDR) forms of the disease, the development of new antitubercular drugs is crucial. Developing inhibitors of shikimate kinase (SK) in the shikimate pathway will provide a selective target for antitubercular agents. Many studies have used in silico technology to identify compounds that are anticipated to interact with and inhibit SK. To a much more limited extent, SK inhibition has been evaluated by in vitro methods with purified enzyme. Currently, there are no data on in vivo activity of Mycobacterium tuberculosis shikimate kinase (MtSK) inhibitors available in the literature. In this review, we present a summary of the progress of SK inhibitor discovery and evaluation with particular attention toward development of new antitubercular agents.
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Affiliation(s)
- Sara Gordon
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA
| | - Johayra Simithy
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA
| | - Douglas C Goodwin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL, USA
| | - Angela I Calderón
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA
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19
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Peek J, Christendat D. The shikimate dehydrogenase family: functional diversity within a conserved structural and mechanistic framework. Arch Biochem Biophys 2014; 566:85-99. [PMID: 25524738 DOI: 10.1016/j.abb.2014.12.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 11/19/2014] [Accepted: 12/07/2014] [Indexed: 11/19/2022]
Abstract
Shikimate dehydrogenase (SDH) catalyzes the NADPH-dependent reduction of 3-deydroshikimate to shikimate, an essential reaction in the biosynthesis of the aromatic amino acids and a large number of other secondary metabolites in plants and microbes. The indispensible nature of this enzyme makes it a potential target for herbicides and antimicrobials. SDH is the archetypal member of a large protein family, which contains at least four additional functional classes with diverse metabolic roles. The different members of the SDH family share a highly similar three-dimensional structure and utilize a conserved catalytic mechanism, but exhibit distinct substrate preferences, making the family a particularly interesting system for studying modes of substrate recognition used by enzymes. Here, we review our current understanding of the biochemical and structural properties of each of the five previously identified SDH family functional classes.
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Affiliation(s)
- James Peek
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Dinesh Christendat
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada; Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada.
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20
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Peek J, Shi T, Christendat D. Identification of Novel Polyphenolic Inhibitors of Shikimate Dehydrogenase (AroE). ACTA ACUST UNITED AC 2014; 19:1090-8. [DOI: 10.1177/1087057114527127] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 02/17/2014] [Indexed: 11/15/2022]
Abstract
Shikimate dehydrogenase (AroE) is an attractive target for herbicides and antimicrobial agents due to its conserved and essential nature in plants, fungi, and bacteria. Here, we have performed an in vitro screen using a collection of more than 5500 compounds and identified 24 novel inhibitors of AroE from Pseudomonas putida. The IC50 values for the two most potent inhibitors we identified, epigallocatechin gallate (EGCG) and epicatechin gallate (ECG), were 3.0 ± 0.2 µM and 3.7 ± 0.5 µM, respectively. Based on the high level of structural conservation between AroE orthologs, we predicted that the identified compounds would also inhibit AroE enzymes from other organisms. Consistent with this hypothesis, we found that EGCG and ECG inhibit the AroE domain of the bifunctional dehydroquinate dehydratase-shikimate dehydrogenase (DHQ-SDH) from Arabidopsis thaliana with IC50 values of 2.1 ± 0.3 µM and 2.0 ± 0.2 µM, respectively.
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Affiliation(s)
- James Peek
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Thomas Shi
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Dinesh Christendat
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
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21
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Trosset JY, Carbonell P. Synergistic Synthetic Biology: Units in Concert. Front Bioeng Biotechnol 2013; 1:11. [PMID: 25022769 PMCID: PMC4090895 DOI: 10.3389/fbioe.2013.00011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 10/01/2013] [Indexed: 01/31/2023] Open
Abstract
Synthetic biology aims at translating the methods and strategies from engineering into biology in order to streamline the design and construction of biological devices through standardized parts. Modular synthetic biology devices are designed by means of an adequate elimination of cross-talk that makes circuits orthogonal and specific. To that end, synthetic constructs need to be adequately optimized through in silico modeling by choosing the right complement of genetic parts and by experimental tuning through directed evolution and craftsmanship. In this review, we consider an additional and complementary tool available to the synthetic biologist for innovative design and successful construction of desired circuit functionalities: biological synergies. Synergy is a prevalent emergent property in biological systems that arises from the concerted action of multiple factors producing an amplification or cancelation effect compared with individual actions alone. Synergies appear in domains as diverse as those involved in chemical and protein activity, polypharmacology, and metabolic pathway complementarity. In conventional synthetic biology designs, synergistic cross-talk between parts and modules is generally attenuated in order to verify their orthogonality. Synergistic interactions, however, can induce emergent behavior that might prove useful for synthetic biology applications, like in functional circuit design, multi-drug treatment, or in sensing and delivery devices. Synergistic design principles are therefore complementary to those coming from orthogonal design and may provide added value to synthetic biology applications. The appropriate modeling, characterization, and design of synergies between biological parts and units will allow the discovery of yet unforeseeable, novel synthetic biology applications.
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Affiliation(s)
| | - Pablo Carbonell
- BioRetroSynth Laboratory, Institute of Systems and Synthetic Biology, University of Evry-Val d'Essonne , Evry , France ; BioRetroSynth Laboratory, Institute of Systems and Synthetic Biology, CNRS , Evry , France
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