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Rios-Soto L, Hernández-Campos A, Tovar-Escobar D, Castillo R, Sierra-Campos E, Valdez-Solana M, Téllez-Valencia A, Avitia-Domínguez C. Inhibition of Shikimate Kinase from Methicillin-Resistant Staphylococcus aureus by Benzimidazole Derivatives. Kinetic, Computational, Toxicological, and Biological Activity Studies. Int J Mol Sci 2024; 25:5077. [PMID: 38791117 PMCID: PMC11121535 DOI: 10.3390/ijms25105077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/26/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024] Open
Abstract
Antimicrobial resistance (AMR) is one of the biggest threats in modern times. It was estimated that in 2019, 1.27 million deaths occurred around the globe due to AMR. Methicillin-resistant Staphylococcus aureus (MRSA) strains, a pathogen considered of high priority by the World Health Organization, have proven to be resistant to most of the actual antimicrobial treatments. Therefore, new treatments are required to be able to manage this increasing threat. Under this perspective, an important metabolic pathway for MRSA survival, and absent in mammals, is the shikimate pathway, which is involved in the biosynthesis of chorismate, an intermediate for the synthesis of aromatic amino acids, folates, and ubiquinone. Therefore, the enzymes of this route have been considered good targets to design novel antibiotics. The fifth step of the route is performed by shikimate kinase (SK). In this study, an in-house chemical library of 170 benzimidazole derivatives was screened against MRSA shikimate kinase (SaSK). This effort led to the identification of the first SaSK inhibitors, and the two inhibitors with the greatest inhibition activity (C1 and C2) were characterized. Kinetic studies showed that both compounds were competitive inhibitors with respect to ATP and non-competitive for shikimate. Structural analysis through molecular docking and molecular dynamics simulations indicated that both inhibitors interacted with ARG113, an important residue involved in ATP binding, and formed stable complexes during the simulation period. Biological activity evaluation showed that both compounds were able to inhibit the growth of a MRSA strain. Mitochondrial assays showed that both compounds modify the activity of electron transport chain complexes. Finally, ADMETox predictions suggested that, in general, C1 and C2 can be considered as potential drug candidates. Therefore, the benzimidazole derivatives reported here are the first SaSK inhibitors, representing a promising scaffold and a guide to design new drugs against MRSA.
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Affiliation(s)
- Lluvia Rios-Soto
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny, Anitúa S/N, Durango 34000, Mexico;
| | - Alicia Hernández-Campos
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, México City 04510, Mexico; (A.H.-C.); (D.T.-E.); (R.C.)
| | - David Tovar-Escobar
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, México City 04510, Mexico; (A.H.-C.); (D.T.-E.); (R.C.)
| | - Rafael Castillo
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, México City 04510, Mexico; (A.H.-C.); (D.T.-E.); (R.C.)
| | - Erick Sierra-Campos
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Av. Artículo 123 S/N Fracc. Filadelfia, Gómez Palacio 35010, Mexico; (E.S.-C.); (M.V.-S.)
| | - Mónica Valdez-Solana
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Av. Artículo 123 S/N Fracc. Filadelfia, Gómez Palacio 35010, Mexico; (E.S.-C.); (M.V.-S.)
| | - Alfredo Téllez-Valencia
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny, Anitúa S/N, Durango 34000, Mexico;
| | - Claudia Avitia-Domínguez
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny, Anitúa S/N, Durango 34000, Mexico;
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Hu S, Kamimura N, Sakamoto S, Nagano S, Takata N, Liu S, Goeminne G, Vanholme R, Uesugi M, Yamamoto M, Hishiyama S, Kim H, Boerjan W, Ralph J, Masai E, Mitsuda N, Kajita S. Rerouting of the lignin biosynthetic pathway by inhibition of cytosolic shikimate recycling in transgenic hybrid aspen. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:358-376. [PMID: 35044002 DOI: 10.1111/tpj.15674] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Lignin is a phenolic polymer deposited in the plant cell wall, and is mainly polymerized from three canonical monomers (monolignols), i.e. p-coumaryl, coniferyl and sinapyl alcohols. After polymerization, these alcohols form different lignin substructures. In dicotyledons, monolignols are biosynthesized from phenylalanine, an aromatic amino acid. Shikimate acts at two positions in the route to the lignin building blocks. It is part of the shikimate pathway that provides the precursor for the biosynthesis of phenylalanine, and is involved in the transesterification of p-coumaroyl-CoA to p-coumaroyl shikimate, one of the key steps in the biosynthesis of coniferyl and sinapyl alcohols. The shikimate residue in p-coumaroyl shikimate is released in later steps, and the resulting shikimate becomes available again for the biosynthesis of new p-coumaroyl shikimate molecules. In this study, we inhibited cytosolic shikimate recycling in transgenic hybrid aspen by accelerated phosphorylation of shikimate in the cytosol through expression of a bacterial shikimate kinase (SK). This expression elicited an increase in p-hydroxyphenyl units of lignin and, by contrast, a decrease in guaiacyl and syringyl units. Transgenic plants with high SK activity produced a lignin content comparable to that in wild-type plants, and had an increased processability via enzymatic saccharification. Although expression of many genes was altered in the transgenic plants, elevated SK activity did not exert a significant effect on the expression of the majority of genes responsible for lignin biosynthesis. The present results indicate that cytosolic shikimate recycling is crucial to the monomeric composition of lignin rather than for lignin content.
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Affiliation(s)
- Shi Hu
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Naofumi Kamimura
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Shingo Sakamoto
- Plant Gene Regulation Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Smart CO2 Utilization Research Team, Global Zero Emission Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Soichiro Nagano
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitachi, Ibaraki, Japan
| | - Naoki Takata
- Forest Bio-Research Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitachi, Ibaraki, Japan
| | - Sarah Liu
- Department of Biochemistry, and US Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
| | - Geert Goeminne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ruben Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Metabolomics Core Ghent, VIB, Ghent, Belgium
| | - Mikiko Uesugi
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Masanobu Yamamoto
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Shojiro Hishiyama
- Department of Forest Resource Chemistry, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tsukuba, Japan
| | - Hoon Kim
- Department of Biochemistry, and US Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - John Ralph
- Department of Biochemistry, and US Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
| | - Eiji Masai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Nobutaka Mitsuda
- Plant Gene Regulation Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Smart CO2 Utilization Research Team, Global Zero Emission Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Shinya Kajita
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
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Rios-Soto L, Téllez-Valencia A, Sierra-Campos E, Valdez-Solana M, Cisneros-Martínez J, Gómez Palacio-Gastélum M, Castillo-Villanueva A, Avitia-Domínguez C. Finding the First Potential Inhibitors of Shikimate Kinase from Methicillin Resistant Staphylococcus aureus through Computer-Assisted Drug Design. Molecules 2021; 26:molecules26216736. [PMID: 34771148 PMCID: PMC8587801 DOI: 10.3390/molecules26216736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 11/17/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is an important threat as it causes serious hospital and community acquired infections with deathly outcomes oftentimes, therefore, development of new treatments against this bacterium is a priority. Shikimate kinase, an enzyme in the shikimate pathway, is considered a good target for developing antimicrobial drugs; this is given because of its pathway, which is essential in bacteria whereas it is absent in mammals. In this work, a computer-assisted drug design strategy was used to report the first potentials inhibitors for Shikimate kinase from methicillin-resistant Staphylococcus aureus (SaSK), employing approximately 5 million compounds from ZINC15 database. Diverse filtering criteria, related to druglike characteristics and virtual docking screening in the shikimate binding site, were performed to select structurally diverse potential inhibitors from SaSK. Molecular dynamics simulations were performed to elucidate the dynamic behavior of each SaSK–ligand complex. The potential inhibitors formed important interactions with residues that are crucial for enzyme catalysis, such as Asp37, Arg61, Gly82, and Arg138. Therefore, the compounds reported provide valuable information and can be seen as the first step toward developing SaSK inhibitors in the search of new drugs against MRSA.
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Affiliation(s)
- Lluvia Rios-Soto
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitua S/N, Durango 34000, Mexico; (L.R.-S.); (J.C.-M.)
| | - Alfredo Téllez-Valencia
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitua S/N, Durango 34000, Mexico; (L.R.-S.); (J.C.-M.)
- Correspondence: (A.T.-V.); (C.A.-D.); Tel./Fax: +52(618)8271382 (A.T.-V. & C.A.-D.)
| | - Erick Sierra-Campos
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Av. Artículo 123 S/N Fracc. Filadelfia, Gómez Palacio, Durango 35010, Mexico; (E.S.-C.); (M.V.-S.)
| | - Mónica Valdez-Solana
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Av. Artículo 123 S/N Fracc. Filadelfia, Gómez Palacio, Durango 35010, Mexico; (E.S.-C.); (M.V.-S.)
| | - Jorge Cisneros-Martínez
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitua S/N, Durango 34000, Mexico; (L.R.-S.); (J.C.-M.)
| | - Marcelo Gómez Palacio-Gastélum
- Facultad de Odontología, Universidad Juárez del Estado de Durango, Predio Canoas S/N, Los Angeles, Durango 34070, Mexico;
| | - Adriana Castillo-Villanueva
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de Mexico 04530, Mexico;
| | - Claudia Avitia-Domínguez
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitua S/N, Durango 34000, Mexico; (L.R.-S.); (J.C.-M.)
- Correspondence: (A.T.-V.); (C.A.-D.); Tel./Fax: +52(618)8271382 (A.T.-V. & C.A.-D.)
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Yang X, Deng M, Zhang X, Wang Y, Song K, Cong R, Meng L, Zhang J. Design, synthesis, and biological evaluation of thieno[3,2‐d]pyrimidine derivatives as potential simplified phosphatidylinositol 3‐kinase alpha inhibitors. Chem Biol Drug Des 2019; 94:2013-2022. [DOI: 10.1111/cbdd.13425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 10/11/2018] [Accepted: 10/18/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Xiuyan Yang
- Department of PathophysiologyKey Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of EducationShanghai Jiao Tong University School of Medicine Shanghai China
| | - Meng Deng
- Department of PathophysiologyKey Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of EducationShanghai Jiao Tong University School of Medicine Shanghai China
| | - Xi Zhang
- Division of Anti‐tumor PharmacologyShanghai Institute of Materia MedicaChinese Academy of Sciences Shanghai China
| | - Yi Wang
- Division of Anti‐tumor PharmacologyShanghai Institute of Materia MedicaChinese Academy of Sciences Shanghai China
| | - Kun Song
- Department of PathophysiologyKey Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of EducationShanghai Jiao Tong University School of Medicine Shanghai China
| | - Ruan Cong
- Department of PathophysiologyKey Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of EducationShanghai Jiao Tong University School of Medicine Shanghai China
| | - Linghua Meng
- Division of Anti‐tumor PharmacologyShanghai Institute of Materia MedicaChinese Academy of Sciences Shanghai China
| | - Jian Zhang
- Department of PathophysiologyKey Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of EducationShanghai Jiao Tong University School of Medicine Shanghai China
- Basic Clinical Research CenterRenji HospitalShanghai Jiao Tong University School of Medicine Shanghai China
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Fong P, Hao CH, Io CC, Sin PI, Meng LR. In Silico and In Vitro Anti- Helicobacter Pylori Effects of Combinations of Phytochemicals and Antibiotics. Molecules 2019; 24:E3608. [PMID: 31591315 PMCID: PMC6804086 DOI: 10.3390/molecules24193608] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/04/2019] [Accepted: 10/04/2019] [Indexed: 12/16/2022] Open
Abstract
Helicobacter pylori infection is a WHO class 1 carcinogenic factor of gastric adenocarcinoma. In the past decades, many studies have demonstrated the increasing trend of antibiotic resistance and pointed out the necessity of new effective treatment. This study was aimed at identifying phytochemicals that can inhibit H. pylori and possibly serve as adjuvant treatments. Here, in silico molecular docking and drug-like properties analyses were performed to identify potential inhibitors of urease, shikimate kinase and aspartate-semialdehyde dehydrogenase. These three enzymes are targets of the treatment of H. pylori. Susceptibility and synergistic testing were performed on the selected phytochemicals and the positive control antibiotic, amoxicillin. The in-silico study revealed that oroxindin, rosmarinic acid and verbascoside are inhibitors of urease, shikimate kinase and aspartate-semialdehyde dehydrogenase, respectively, in which, oroxindin has the highest potency against H. pylori, indicated by a minimum inhibitory concentration (MIC) value of 50 μg/mL. A combination of oroxindin and amoxicillin demonstrated additive effects against H. pylori, as indicated by a fractional inhibitory concentration (FIC) value of 0.75. This study identified phytochemicals that deserve further investigation for the development of adjuvant therapeutic agents to current antibiotics against H. pylori.
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Affiliation(s)
- Pedro Fong
- School of Health Sciences and Sports, Macao Polytechnic Institute, Macao, China.
| | - Chon-Hou Hao
- School of Health Sciences and Sports, Macao Polytechnic Institute, Macao, China.
| | - Chi-Cheng Io
- School of Health Sciences and Sports, Macao Polytechnic Institute, Macao, China.
| | - Pou-Io Sin
- School of Health Sciences and Sports, Macao Polytechnic Institute, Macao, China.
| | - Li-Rong Meng
- School of Health Sciences and Sports, Macao Polytechnic Institute, Macao, China.
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An X, Lu S, Song K, Shen Q, Huang M, Yao X, Liu H, Zhang J. Are the Apo Proteins Suitable for the Rational Discovery of Allosteric Drugs? J Chem Inf Model 2018; 59:597-604. [PMID: 30525607 DOI: 10.1021/acs.jcim.8b00735] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Allosteric modulators, by targeting the less-conserved allosteric sites, represent an innovative strategy in drug discovery. These modulators have a distinctive advantage over orthosteric ligands that attach to the conserved, functional orthosteric sites. However, in structure-based drug design, it remains unclear whether allosteric protein structures determined without orthosteric ligand binding are suitable for allosteric drug screening. In this study, we performed large-scale conformational samplings of six representative allosteric proteins uncomplexed ( apo) and complexed ( holo) with orthosteric ligands to explore the effect of orthosteric site binding on the conformational dynamics of allosteric sites. The results, coupled with the redocking evaluation of allosteric modulators to their apo and holo proteins using their MD trajectories, indicated that orthosteric site binding had an effect on the dynamics of the allosteric sites and allosteric modulators preferentially bound to their holo proteins. According to the analysis data, we constructed a new correlation model for quantifying the allosteric site change driven by substrate binding to the orthosteric site. These results highlight the strong demand to select holo allosteric proteins as initial inputs in structure-based allosteric drug screening when the distance between orthosteric and allosteric sites in the protein is below 5 Å, which is expected to contribute to allosteric drug discovery.
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Affiliation(s)
- Xiaoli An
- Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai 200127 , China.,School of Pharmacy , Lanzhou University , Lanzhou 730000 , China
| | - Shaoyong Lu
- Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai 200127 , China
| | - Kun Song
- Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai 200127 , China
| | - Qiancheng Shen
- Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai 200127 , China
| | - Meilan Huang
- School of Chemistry and Chemical Engineering , Queen's University Belfast , Northern Ireland BT9 5AG , United Kingdom
| | - Xiaojun Yao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health , Macau University of Science and Technology , Taipa , Macau 999078 , China
| | - Huanxiang Liu
- School of Pharmacy , Lanzhou University , Lanzhou 730000 , China
| | - Jian Zhang
- Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai 200127 , China.,Medicinal Bioinformatics Center , Shanghai Jiao Tong University, School of Medicine , Shanghai , 200025 , China
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Yang X, Zhong J, Zhang Q, Qian J, Song K, Ruan C, Xu J, Ding K, Zhang J. Rational Design and Structure Validation of a Novel Peptide Inhibitor of the Adenomatous-Polyposis-Coli (APC)-Rho-Guanine-Nucleotide-Exchange-Factor-4 (Asef) Interaction. J Med Chem 2018; 61:8017-8028. [PMID: 30095910 DOI: 10.1021/acs.jmedchem.8b01112] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In colorectal cancer, adenomatous polyposis coli (APC) interacts with Rho guanine-nucleotide-exchange factor 4 (Asef), thereby stimulating aberrant colorectal-cancer-cell migration. Consequently, the APC-Asef interaction represents a promising therapeutic target for mitigating colorectal-cancer migration. In this study, we adopted the rational-design strategy involving the introduction of intramolecular hydrogen bonds and optimization of the lipophilic substituents to improve the binding affinities of peptides, leading to the discovery of MAI-400, the best inhibitor of the APC-Asef interaction known to date ( Kd = 0.012 μM, IC50 = 0.25 μM). Comprehensive evaluation of MAI-400 by biochemical and biophysical assays revealed the formation and effect of an intramolecular hydrogen bond. A cell-based assay showed MAI-400 efficiently blocking the APC-Asef interaction in a dose-dependent manner. Therefore, our study provides a best-in-class inhibitor, MAI-400, based on the rational drug design and structural validation, that can effectively inhibit the APC-Asef interaction.
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Affiliation(s)
| | | | | | | | | | | | | | - Ke Ding
- School of Pharmacy , Jinan University , 601 Huangpu Avenue West , Guangzhou 510632 , China
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An integrated computational hierarchy for identification of potent inhibitors against Shikimate Kinase enzyme from Shigella sonnei , a major cause of global dysentery. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.04.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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9
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Debraekeleer A, Remaut H. Future perspective for potentialHelicobacter pylorieradication therapies. Future Microbiol 2018; 13:671-687. [DOI: 10.2217/fmb-2017-0115] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Ayla Debraekeleer
- Department of Structural & Molecular Microbiology, VIB Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Department of Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Han Remaut
- Department of Structural & Molecular Microbiology, VIB Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Department of Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
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Parthasarathy A, Cross PJ, Dobson RCJ, Adams LE, Savka MA, Hudson AO. A Three-Ring Circus: Metabolism of the Three Proteogenic Aromatic Amino Acids and Their Role in the Health of Plants and Animals. Front Mol Biosci 2018; 5:29. [PMID: 29682508 PMCID: PMC5897657 DOI: 10.3389/fmolb.2018.00029] [Citation(s) in RCA: 160] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 03/21/2018] [Indexed: 12/19/2022] Open
Abstract
Tyrosine, phenylalanine and tryptophan are the three aromatic amino acids (AAA) involved in protein synthesis. These amino acids and their metabolism are linked to the synthesis of a variety of secondary metabolites, a subset of which are involved in numerous anabolic pathways responsible for the synthesis of pigment compounds, plant hormones and biological polymers, to name a few. In addition, these metabolites derived from the AAA pathways mediate the transmission of nervous signals, quench reactive oxygen species in the brain, and are involved in the vast palette of animal coloration among others pathways. The AAA and metabolites derived from them also have integral roles in the health of both plants and animals. This review delineates the de novo biosynthesis of the AAA by microbes and plants, and the branching out of AAA metabolism into major secondary metabolic pathways in plants such as the phenylpropanoid pathway. Organisms that do not possess the enzymatic machinery for the de novo synthesis of AAA must obtain these primary metabolites from their diet. Therefore, the metabolism of AAA by the host animal and the resident microflora are important for the health of all animals. In addition, the AAA metabolite-mediated host-pathogen interactions in general, as well as potential beneficial and harmful AAA-derived compounds produced by gut bacteria are discussed. Apart from the AAA biosynthetic pathways in plants and microbes such as the shikimate pathway and the tryptophan pathway, this review also deals with AAA catabolism in plants, AAA degradation via the monoamine and kynurenine pathways in animals, and AAA catabolism via the 3-aryllactate and kynurenine pathways in animal-associated microbes. Emphasis will be placed on structural and functional aspects of several key AAA-related enzymes, such as shikimate synthase, chorismate mutase, anthranilate synthase, tryptophan synthase, tyrosine aminotransferase, dopachrome tautomerase, radical dehydratase, and type III CoA-transferase. The past development and current potential for interventions including the development of herbicides and antibiotics that target key enzymes in AAA-related pathways, as well as AAA-linked secondary metabolism leading to antimicrobials are also discussed.
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Affiliation(s)
- Anutthaman Parthasarathy
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Penelope J. Cross
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
| | - Lily E. Adams
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Michael A. Savka
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
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11
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Screening and biological evaluation of a novel STAT3 signaling pathway inhibitor against cancer. Bioorg Med Chem Lett 2016; 26:5172-5176. [DOI: 10.1016/j.bmcl.2016.09.073] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/07/2016] [Accepted: 09/29/2016] [Indexed: 01/10/2023]
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12
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Prado V, Lence E, Thompson P, Hawkins AR, González-Bello C. Freezing the Dynamic Gap for Selectivity: Motion-Based Design of Inhibitors of the Shikimate Kinase Enzyme. Chemistry 2016; 22:17988-18000. [DOI: 10.1002/chem.201602923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Verónica Prado
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Paul Thompson
- Institute of Cell and Molecular Biosciences, Medical School; University of Newcastle upon Tyne, Catherine Cookson Building; Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Alastair R. Hawkins
- Institute of Cell and Molecular Biosciences, Medical School; University of Newcastle upon Tyne, Catherine Cookson Building; Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
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13
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Prado V, Lence E, Maneiro M, Vázquez-Ucha JC, Beceiro A, Thompson P, Hawkins AR, González-Bello C. Targeting the Motion of Shikimate Kinase: Development of Competitive Inhibitors that Stabilize an Inactive Open Conformation of the Enzyme. J Med Chem 2016; 59:5471-87. [DOI: 10.1021/acs.jmedchem.6b00483] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Verónica Prado
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS)
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, calle Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Emilio Lence
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS)
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, calle Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - María Maneiro
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS)
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, calle Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Juan C. Vázquez-Ucha
- Servicio de Microbioloxía-INIBIC, Complexo Hospitalario Universitario A Coruña (CHUAC), 15006 A Coruña, Spain
| | - Alejandro Beceiro
- Servicio de Microbioloxía-INIBIC, Complexo Hospitalario Universitario A Coruña (CHUAC), 15006 A Coruña, Spain
| | - Paul Thompson
- Institute of Cell and Molecular Biosciences,
Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, U.K
| | - Alastair R. Hawkins
- Institute of Cell and Molecular Biosciences,
Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, U.K
| | - Concepción González-Bello
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS)
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, calle Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
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14
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Mehra R, Rajput VS, Gupta M, Chib R, Kumar A, Wazir P, Khan IA, Nargotra A. Benzothiazole Derivative as a Novel Mycobacterium tuberculosis Shikimate Kinase Inhibitor: Identification and Elucidation of Its Allosteric Mode of Inhibition. J Chem Inf Model 2016; 56:930-40. [PMID: 27149193 DOI: 10.1021/acs.jcim.6b00056] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mycobacterium tuberculosis shikimate kinase (Mtb-SK) is a key enzyme involved in the biosynthesis of aromatic amino acids through the shikimate pathway. Since it is proven to be essential for the survival of the microbe and is absent from mammals, it is a promising target for anti-TB drug discovery. In this study, a combined approach of in silico similarity search and pharmacophore building using already reported inhibitors was used to screen a procured library of 20,000 compounds of the commercially available ChemBridge database. From the in silico screening, 15 hits were identified, and these hits were evaluated in vitro for Mtb-SK enzyme inhibition. Two compounds presented significant enzyme inhibition with IC50 values of 10.69 ± 0.9 and 46.22 ± 1.2 μM. The best hit was then evaluated for the in vitro mode of inhibition where it came out to be an uncompetitive and noncompetitive inhibitor with respect to shikimate (SKM) and ATP, respectively, suggesting its binding at an allosteric site. Potential binding sites of Mtb-SK were identified which confirmed the presence of an allosteric binding pocket apart from the ATP and SKM binding sites. The docking simulations were performed at this pocket in order to find the mode of binding of the best hit in the presence of substrates and the products of the enzymatic reaction. Molecular dynamics (MD) simulations elucidated the probability of inhibitor binding at the allosteric site in the presence of ADP and shikimate-3-phosphate (S-3-P), that is, after the formation of products of the reaction. The inhibitor binding may prevent the release of the product from Mtb-SK, thereby inhibiting its activity. The binding stability and the key residue interactions of the inhibitor to this product complex were also revealed by the MD simulations. Residues ARG43, ILE45, and PHE57 were identified as crucial that were involved in interactions with the best hit. This is the first report of an allosteric binding site of Mtb-SK, which could largely address the selectivity issue associated with kinase inhibitors.
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Affiliation(s)
- Rukmankesh Mehra
- Discovery Informatics Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
| | - Vikrant Singh Rajput
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
| | - Monika Gupta
- Discovery Informatics Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
| | - Reena Chib
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
| | - Amit Kumar
- Discovery Informatics Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
| | - Priya Wazir
- Instrumentation Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
| | - Inshad Ali Khan
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
| | - Amit Nargotra
- Discovery Informatics Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
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15
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Kaur P, Datta S, Shandil RK, Kumar N, Robert N, Sokhi UK, Guptha S, Narayanan S, Anbarasu A, Ramaiah S. Unravelling the Secrets of Mycobacterial Cidality through the Lens of Antisense. PLoS One 2016; 11:e0154513. [PMID: 27144597 PMCID: PMC4856384 DOI: 10.1371/journal.pone.0154513] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/14/2016] [Indexed: 01/13/2023] Open
Abstract
One of the major impediments in anti-tubercular drug discovery is the lack of a robust grammar that governs the in-vitro to the in-vivo translation of efficacy. Mycobacterium tuberculosis (Mtb) is capable of growing both extracellular as well as intracellular; encountering various hostile conditions like acidic milieu, free radicals, starvation, oxygen deprivation, and immune effector mechanisms. Unique survival strategies of Mtb have prompted researchers to develop in-vitro equivalents to simulate in-vivo physiologies and exploited to find efficacious inhibitors against various phenotypes. Conventionally, the inhibitors are screened on Mtb under the conditions that are unrelated to the in-vivo disease environments. The present study was aimed to (1). Investigate cidality of Mtb targets using a non-chemical inhibitor antisense-RNA (AS-RNA) under in-vivo simulated in-vitro conditions.(2). Confirm the cidality of the targets under in-vivo in experimental tuberculosis. (3). Correlate in-vitro vs. in-vivo cidality data to identify the in-vitro condition that best predicts in-vivo cidality potential of the targets. Using cidality as a metric for efficacy, and AS-RNA as a target-specific inhibitor, we delineated the cidality potential of five target genes under six different physiological conditions (replicating, hypoxia, low pH, nutrient starvation, nitrogen depletion, and nitric oxide).In-vitro cidality confirmed in experimental tuberculosis in BALB/c mice using the AS-RNA allowed us to identify cidal targets in the rank order of rpoB>aroK>ppk>rpoC>ilvB. RpoB was used as the cidality control. In-vitro and in-vivo studies feature aroK (encoding shikimate kinase) as an in-vivo mycobactericidal target suitable for anti-TB drug discovery. In-vitro to in-vivo cidality correlations suggested the low pH (R = 0.9856) in-vitro model as best predictor of in-vivo cidality; however, similar correlation studies in pathologically relevant (Kramnik) mice are warranted. In the acute infection phase for the high fidelity translation, the compound efficacy may also be evaluated in the low pH, in addition to the standard replication condition.
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Affiliation(s)
- Parvinder Kaur
- Research Area, Drug Discovery, AstraZeneca India Private Limited, Bangalore, India
- * E-mail:
| | | | | | - Naveen Kumar
- Research Area, Drug Discovery, AstraZeneca India Private Limited, Bangalore, India
| | - Nanduri Robert
- Research Area, Drug Discovery, AstraZeneca India Private Limited, Bangalore, India
| | - Upneet K. Sokhi
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, New York, United States of America
| | - Supreeth Guptha
- Research Area, Drug Discovery, AstraZeneca India Private Limited, Bangalore, India
| | - Shridhar Narayanan
- Research Area, Drug Discovery, AstraZeneca India Private Limited, Bangalore, India
| | - Anand Anbarasu
- School of Biosciences and Technology, VIT University, Vellore, India
| | - Sudha Ramaiah
- School of Biosciences and Technology, VIT University, Vellore, India
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16
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Screening of antitubercular compound library identifies novel shikimate kinase inhibitors of Mycobacterium tuberculosis. Appl Microbiol Biotechnol 2016; 100:5415-26. [DOI: 10.1007/s00253-015-7268-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 11/26/2015] [Accepted: 12/22/2015] [Indexed: 10/22/2022]
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17
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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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18
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Simithy J, Gill G, Wang Y, Goodwin DC, Calderón AI. Development of an ESI-LC-MS-Based Assay for Kinetic Evaluation of Mycobacterium tuberculosis Shikimate Kinase Activity and Inhibition. Anal Chem 2015; 87:2129-36. [DOI: 10.1021/ac503210n] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Johayra Simithy
- Department
of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, 4306 Walker Building, Auburn, Alabama 36849, United States
| | - Gobind Gill
- Department
of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, Alabama 36849, United States
| | - Yu Wang
- Department
of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, Alabama 36849, United States
| | - Douglas C. Goodwin
- Department
of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, Alabama 36849, United States
| | - Angela I. Calderón
- Department
of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, 4306 Walker Building, Auburn, Alabama 36849, United States
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19
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Dahlin JL, Walters MA. The essential roles of chemistry in high-throughput screening triage. Future Med Chem 2014; 6:1265-90. [PMID: 25163000 PMCID: PMC4465542 DOI: 10.4155/fmc.14.60] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
It is increasingly clear that academic high-throughput screening (HTS) and virtual HTS triage suffers from a lack of scientists trained in the art and science of early drug discovery chemistry. Many recent publications report the discovery of compounds by screening that are most likely artifacts or promiscuous bioactive compounds, and these results are not placed into the context of previous studies. For HTS to be most successful, it is our contention that there must exist an early partnership between biologists and medicinal chemists. Their combined skill sets are necessary to design robust assays and efficient workflows that will weed out assay artifacts, false positives, promiscuous bioactive compounds and intractable screening hits, efforts that ultimately give projects a better chance at identifying truly useful chemical matter. Expertise in medicinal chemistry, cheminformatics and purification sciences (analytical chemistry) can enhance the post-HTS triage process by quickly removing these problematic chemotypes from consideration, while simultaneously prioritizing the more promising chemical matter for follow-up testing. It is only when biologists and chemists collaborate effectively that HTS can manifest its full promise.
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Affiliation(s)
- Jayme L Dahlin
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
- Medical Scientist Training Program, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Michael A Walters
- Institute for Therapeutics Discovery & Development, University of Minnesota, Minneapolis, MN 55414, USA
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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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Meslamani J, Bhajun R, Martz F, Rognan D. Computational profiling of bioactive compounds using a target-dependent composite workflow. J Chem Inf Model 2013; 53:2322-33. [PMID: 23941602 DOI: 10.1021/ci400303n] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Computational target fishing is a chemoinformatic method aimed at determining main and secondary targets of bioactive compounds in order to explain their mechanism of action, anticipate potential side effects, or repurpose existing drugs for novel therapeutic indications. Many existing successes in this area have been based on a use of a single computational method to estimate potentially new target-ligand associations. We herewith present an automated workflow using several methods to optimally browse target-ligand space according to existing knowledge on either ligand and target space under investigation. The protocol uses four ligand-based (SVM classification, SVR affinity prediction, nearest neighbors interpolation, shape similarity) and two structure-based approaches (docking, protein-ligand pharmacophore match) in series, according to well-defined ligand and target property checks. The workflow was remarkably accurate (72%) in identifying the main target of 189 clinical candidates and proposed two novel off-targets which could be experimentally validated. Rolofylline, an adenosine A1 receptor antagonist, was confirmed to inhibit phosphodiesterase 5 with a moderate affinity (IC50 = 13.8 μM). More interestingly, we describe a strong binding (IC50 = 142 nM) of a claimed selective phosphodiesterase 10 A inhibitor (PF-2545920) with the cysteinyl leukotriene type 1 G protein-coupled receptor.
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Affiliation(s)
- Jamel Meslamani
- Laboratory for Therapeutical Innovation, UMR 7200 Université de Strasbourg/CNRS, MEDALIS Drug Discovery Center , F-67400 Illkirch, France
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22
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Kapnick SM, Zhang Y. New tuberculosis drug development: targeting the shikimate pathway. Expert Opin Drug Discov 2013; 3:565-77. [PMID: 23484927 DOI: 10.1517/17460441.3.5.565] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Tuberculosis (TB) remains a leading cause of morbidity and mortality worldwide, yet no new drugs have been developed in the last 40 years. OBJECTIVE The exceedingly lengthy TB chemotherapy and the increasing emergence of drug resistance complicated by HIV co-infection call for the development of new TB drugs. These problems are further compounded by a poor understanding of the biology of persister bacteria. METHODS New molecular tools have offered insights into potential new drug targets, particularly the enzymes of the shikimate pathway, which is the focus of this review. RESULTS/CONCLUSION Shikimate pathway enzymes, especially shikimate kinase, may offer attractive targets for new TB drug and vaccine development.
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Affiliation(s)
- Senta M Kapnick
- Johns Hopkins University, Department of Molecular Microbiology & Immunology, Bloomberg School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA +1 410 614 2975 ; +1 410 955 0105 ;
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23
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Cheng WC, Chen YF, Wang HJ, Hsu KC, Lin SC, Chen TJ, Yang JM, Wang WC. Structures of Helicobacter pylori shikimate kinase reveal a selective inhibitor-induced-fit mechanism. PLoS One 2012; 7:e33481. [PMID: 22438938 PMCID: PMC3306394 DOI: 10.1371/journal.pone.0033481] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 02/14/2012] [Indexed: 12/13/2022] Open
Abstract
Shikimate kinase (SK), which catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid in the presence of ATP, is the enzyme in the fifth step of the shikimate pathway for biosynthesis of aromatic amino acids. This pathway is present in bacteria, fungi, and plants but absent in mammals and therefore represents an attractive target pathway for the development of new antimicrobial agents, herbicides, and antiparasitic agents. Here we investigated the detailed structure–activity relationship of SK from Helicobacter pylori (HpSK). Site-directed mutagenesis and isothermal titration calorimetry studies revealed critical conserved residues (D33, F48, R57, R116, and R132) that interact with shikimate and are therefore involved in catalysis. Crystal structures of HpSK·SO4, R57A, and HpSK•shikimate-3-phosphate•ADP show a characteristic three-layer architecture and a conformationally elastic region consisting of F48, R57, R116, and R132, occupied by shikimate. The structure of the inhibitor complex, E114A•162535, was also determined, which revealed a dramatic shift in the elastic LID region and resulted in conformational locking into a distinctive form. These results reveal considerable insight into the active-site chemistry of SKs and a selective inhibitor-induced-fit mechanism.
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Affiliation(s)
- Wen-Chi Cheng
- Institute of Molecular and Cellular Biology and Department of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan
- Biomedical Science and Engineering Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Yen-Fu Chen
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Hung-Jung Wang
- Institute of Molecular and Cellular Biology and Department of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan
- Biomedical Science and Engineering Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Kai-Cheng Hsu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Shuang-Chih Lin
- Institute of Molecular and Cellular Biology and Department of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan
| | - Tzu-Jung Chen
- Institute of Molecular and Cellular Biology and Department of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan
| | - Jinn-Moon Yang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
- * E-mail: (J-MY); (W-CW)
| | - Wen-Ching Wang
- Institute of Molecular and Cellular Biology and Department of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan
- Biomedical Science and Engineering Center, National Tsing Hua University, Hsinchu, Taiwan
- * E-mail: (J-MY); (W-CW)
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24
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Mulabagal V, Calderón AI. Development of an Ultrafiltration-Liquid Chromatography/Mass Spectrometry (UF-LC/MS) Based Ligand-Binding Assay and an LC/MS Based Functional Assay for Mycobacterium tuberculosis Shikimate Kinase. Anal Chem 2010; 82:3616-21. [DOI: 10.1021/ac902849g] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vanisree Mulabagal
- Department of Pharmacal Sciences, Harrison School of Pharmacy, 4306B Walker Building, Auburn University, Auburn, Alabama 36849
| | - Angela I. Calderón
- Department of Pharmacal Sciences, Harrison School of Pharmacy, 4306B Walker Building, Auburn University, Auburn, Alabama 36849
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25
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Duckworth MJ, Okoli AS, Mendz GL. Novel Helicobacter pylori therapeutic targets: the unusual suspects. Expert Rev Anti Infect Ther 2009; 7:835-67. [PMID: 19735225 DOI: 10.1586/eri.09.61] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding the current status of the discovery and development of anti-Helicobacter therapies requires an overview of the searches for therapeutic targets performed to date. A summary is given of the very substantial body of work conducted in the quest to find Helicobacter pylori genes that could be suitable candidates for therapeutic intervention. The products of most of these genes perform metabolic functions, and others have roles in growth, cell motility and colonization. The genes identified as potential targets have been organized into three categories according to their degree of characterization. A short description and evaluation is provided of the main candidates in each category. Investigations of potential therapeutic targets have generated a wealth of information about the physiology and genetics of H. pylori, and its interactions with the host, but have yielded little by way of new therapies.
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Affiliation(s)
- Megan J Duckworth
- School of Medicine, Sydney, The University of Notre Dame Australia, 160 Oxford Street, Darlinghurst, NSW 2010, Australia.
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26
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Rich RL, Myszka DG. Survey of the year 2007 commercial optical biosensor literature. J Mol Recognit 2008; 21:355-400. [DOI: 10.1002/jmr.928] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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