1
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Shojazadeh T, Zolghadr L, Gharaghani S, JafarKhani S, Molaabasi F, Piri H, Gheibi N. New insights into the inhibitory effect of phenol carboxylic acid antioxidants on mushroom tyrosinase by molecular dynamic studies and experimental assessment. J Biomol Struct Dyn 2023; 41:13404-13414. [PMID: 36856125 DOI: 10.1080/07391102.2023.2175038] [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: 09/20/2022] [Accepted: 01/21/2023] [Indexed: 03/02/2023]
Abstract
The inhibitory effects of ferulic and chlorogenic acids on tyrosinase activity were investigated through multi-spectroscopic and molecular docking techniques. Ferulic and chlorogenic acids, flavonoid compounds, demonstrated inhibitory monophenolase activities of tyrosinase. The inhibitor effects against monophenolase activity were in a reversible and competitive manner with ki value equal to 6.8 and 7.5 µM respectively. The affinity between tyrosinase and L-DOPA decreased when fatty acids were added to the solution. The multi-spectroscopic techniques like UV-vis, fluorescence, and isothermal calorimetry are employed to investigate changes. Intrinsic fluorescence quenching and conformational changes of tyrosinase by hydrophobic interaction were confirmed. Tyrosinase had two and three binding sites for ferulic and chlorogenic acids with a binding constant in the order of magnitude of -6.8 and -7.2 kcal/mol. In addition, the secondary structural changes with Circular dichroism (CD) analysis, secondary structure (DSSP), radius of gyration (Rg) and analysis of hydrogen bonds (H-bonds) confirmed. Ferulic acid effect can be observed obviously and also content of α-helix decreased. Thermodynamic parameters indicated that the interaction between enzyme and ferulic and chlorogenic acids followed a spontaneous reaction dynamic manner with ΔG = -14.78 kJ/mol and ΔG = -14.61 kJ/mol (298k). The findings highlighted the potential applications of ferulic acid and chlorogenic acids in food and drug industries as potent inhibitors of tyrosinase.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Tahereh Shojazadeh
- Department of Clinical Biochemistry and Genetic, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Leila Zolghadr
- Department of Chemistry, Imam Khomeini International University, Qazvin, Iran
| | - Sajjad Gharaghani
- Laboratory of Bioinformatics and Drug Design, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Saeed JafarKhani
- Division of Biomedical Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Fatemeh Molaabasi
- Biomaterials and Tissue Engineering Research Group, Department of Interdisciplinary Technologies, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Hossein Piri
- Cellular and Molecular Research Center, Research Institute for Prevention of Non-Communicable Diseases, Qazvin University of Medical Sciences, Qazvin, Iran
- Department of Biochemistry and Genetics, School of Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Nematollah Gheibi
- Cellular and Molecular Research Center, Research Institute for Prevention of Non-Communicable Diseases, Qazvin University of Medical Sciences, Qazvin, Iran
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2
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Zolghadr L, Behbehani GR, PakBin B, Hosseini SA, Divsalar A, Gheibi N. Molecular dynamics simulations, molecular docking, and kinetics study of kaempferol interaction on Jack bean urease: Comparison of extended solvation model. Food Sci Nutr 2022; 10:3585-3597. [DOI: 10.1002/fsn3.2956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/30/2022] [Accepted: 05/25/2022] [Indexed: 11/11/2022] Open
Affiliation(s)
- Leila Zolghadr
- Department of Chemistry Faculty of Science Imam Khomeini International University Qazvin Iran
| | | | - Babak PakBin
- Department of Food Hygiene and Quality of Control Faculty of Veterinary Medicine University of Tehran Tehran Iran
- Medical Microbiology Research Center University of Medical sciences Qazvin Iran
| | - Seied Ali Hosseini
- Electrical Engineering Department Faculty of Engineering Imam Khomeini International University Qazvin Iran
| | - Adeleh Divsalar
- Department of Cell and Molecular Sciences Kharazmi University Tehran Iran
| | - Nematollah Gheibi
- Cellular and Molecular Research Center, Research Institute for Prevention of Non‐Communicable Diseases Qazvin University of Medical Sciences Qazvin Iran
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3
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Lizarme-Salas Y, Yu TT, de Bruin-Dickason C, Kumar N, Hunter L. Fluorinated quorum sensing inhibitors: enhancement of potency through conformational control. Org Biomol Chem 2021; 19:9629-9636. [PMID: 34709279 DOI: 10.1039/d1ob01649k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The bacterial quorum sensing (QS) system is a target for non-lethal antibacterial agents that do not encourage the development of resistance. QS inhibitors commonly contain a polar "head" moiety and a lipidic "tail" moiety. In this work, we synthesised novel QS inhibitor candidates in which the lipidic "tail" is decorated with stereospecifically positioned fluorine atoms. The presence of fluorine is shown to bias the molecules into distinctive conformations that are pre-organised for binding to the QS receptor. This translates into significant increases in QS inhibitory potency.
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Affiliation(s)
- Yuvixza Lizarme-Salas
- School of Chemistry, The University of New South Wales (UNSW), Sydney 2052, Australia.
| | - Tsz Tin Yu
- School of Chemistry, The University of New South Wales (UNSW), Sydney 2052, Australia.
| | | | - Naresh Kumar
- School of Chemistry, The University of New South Wales (UNSW), Sydney 2052, Australia.
| | - Luke Hunter
- School of Chemistry, The University of New South Wales (UNSW), Sydney 2052, Australia.
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4
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Chidambaram S, Ali D, Alarifi S, Gurusamy R, Radhakrishnan S, Akbar I. Tyrosinase-mediated synthesis of larvicidal active 1,5-diphenyl pent-4-en-1-one derivatives against Culex quinquefasciatus and investigation of their ichthyotoxicity. Sci Rep 2021; 11:20730. [PMID: 34671085 PMCID: PMC8528871 DOI: 10.1038/s41598-021-98281-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 08/30/2021] [Indexed: 12/02/2022] Open
Abstract
1,5-diphenylpent-4-en-1-one derivatives were synthesised using the grindstone method with Cu(II)-tyrosinase used as a catalyst. This method showed a high yield under mild reaction conditions. The synthesised compounds were identified by FTIR, 1H NMR, 13C NMR, mass spectrometry, and elemental analysis. In this study, a total of 17 compounds (1a-1q) were synthesised, and their larvicidal and antifeedant activities were evaluated. Compound 1i (1-(5-oxo-1,5-diphenylpent-1-en-3-yl)-3-(3-phenylallylidene)thiourea) was notably more active (LD50: 28.5 µM) against Culex quinquefasciatus than permethrin(54.6 µM) and temephos(37.9 µM), whereas compound 1i at 100 µM caused 0% mortality in Oreochromis mossambicus within 24 h in an antifeedant screening, with ichthyotoxicity determined as the death ratio (%) at 24 h. Compounds 1a, 1e, 1f, 1j, and 1k were found to be highly toxic, whereas 1i was not toxic in antifeedant screening. Compound 1i was found to possess a high larvicidal activity against C. quinquefasciatus and was non-toxic to non-target aquatic species. Molecular docking studies also supported the finding that 1i is a potent larvicide with higher binding energy than the control (- 10.0 vs. - 7.6 kcal/mol) in the 3OGN protein. Lead molecules are important for their larvicidal properties and application as insecticides.
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Affiliation(s)
- SathishKumar Chidambaram
- Research Department of Chemistry, Nehru Memorial College (Affiliated to Bharathidasan University), Puthanampatti, Tiruchchirappalli District, Tamil Nadu, 621007, India
| | - Daoud Ali
- Department of Zoology, College of Sciences, King Saud University (KSU), P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Saud Alarifi
- Department of Zoology, College of Sciences, King Saud University (KSU), P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Raman Gurusamy
- Department of Life Sciences, Yeungnam University, Gyeongsan, 38541, Gyeongsan-buk, South Korea
| | - SurendraKumar Radhakrishnan
- Research Department of Chemistry, Nehru Memorial College (Affiliated to Bharathidasan University), Puthanampatti, Tiruchchirappalli District, Tamil Nadu, 621007, India
| | - Idhayadhulla Akbar
- Research Department of Chemistry, Nehru Memorial College (Affiliated to Bharathidasan University), Puthanampatti, Tiruchchirappalli District, Tamil Nadu, 621007, India.
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5
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Wu M, Sun Y, Zhu M, Zhu L, Lü J, Geng F. Molecular Dynamics-Based Allosteric Prediction Method to Design Key Residues in Threonine Dehydrogenase for Amino-Acid Production. ACS OMEGA 2021; 6:10975-10983. [PMID: 34056250 PMCID: PMC8153896 DOI: 10.1021/acsomega.1c00798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/01/2021] [Indexed: 06/12/2023]
Abstract
Allosteric proteins are considered as one of the most critical targets to design cell factories via synthetic biology approaches. Here, we proposed a molecular dynamics-based allosteric prediction method (MBAP) to screen indirect-binding sites and potential mutations for protein re-engineering. Using this MBAP method, we have predicted new sites to relieve the allosteric regulation of threonine dehydrogenase (TD) by isoleucine. An obtained mutation P441L has been verified with the ability to significantly reduce the allosteric regulation of TD in vitro assays and with the fermentation application in vivo for amino-acid production. These findings have proved the MBAP method as an effective and efficient predicting tool to find new positions of the allosteric enzymes, thus opening a new path to constructing cell factories in synthetic biology.
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Affiliation(s)
- Mingyu Wu
- School
of Pharmacy, Binzhou Medical University, No. 346 Guanhai Road, Yantai 264003, China
| | - Yu Sun
- School
of Pharmacy, Binzhou Medical University, No. 346 Guanhai Road, Yantai 264003, China
| | - Meiru Zhu
- School
of Pharmacy, Binzhou Medical University, No. 346 Guanhai Road, Yantai 264003, China
| | - Laiyu Zhu
- School
of Pharmacy, Binzhou Medical University, No. 346 Guanhai Road, Yantai 264003, China
| | - Junhong Lü
- School
of Pharmacy, Binzhou Medical University, No. 346 Guanhai Road, Yantai 264003, China
- Zhangjiang
Laboratory, Shanghai Advanced Research Institute,
Chinese Academy of Sciences, No. 239 Zhangheng Road, Pudong New District, Shanghai 201203, China
| | - Feng Geng
- School
of Pharmacy, Binzhou Medical University, No. 346 Guanhai Road, Yantai 264003, China
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6
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Park H, Jin UH, Karki K, Allred C, Davidson LA, Chapkin RS, Orr AA, Nowshad F, Jayaraman A, Tamamis P, Safe S. Hydroxylated Chalcones as Aryl Hydrocarbon Receptor Agonists: Structure-Activity Effects. Toxicol Sci 2021; 180:148-159. [PMID: 33263770 PMCID: PMC7916741 DOI: 10.1093/toxsci/kfaa179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Hydroxylated chalcones are phytochemicals which are biosynthetic precursors of flavonoids and their 1,3-diaryl-prop-2-en-1-one structure is used as a scaffold for drug development. In this study, the structure-dependent activation of aryl hydrocarbon receptor (AhR)-responsive CYP1A1, CYP1B1, and UGT1A1 genes was investigated in Caco2 colon cancer cells and in non-transformed young adult mouse colonocytes (YAMC) cells. The effects of a series of di- and trihydroxychalcones as AhR agonists was structure dependent with maximal induction of CYP1A1, CYP1B1, and UGT1A1 in Caco2 cells observed for compounds containing 2,2'-dihydroxy substituents and this included 2,2'-dihydroxy-, 2,2',4'-trihydroxy-, and 2,2',5'-trihydroxychalcones. In contrast, 2',4,5'-, 2'3',4'-, 2',4,4'-trihydroxy, and 2',3-, 2',4-, 2',4'-, and 2',5-dihydroxychalcones exhibited low to non-detectable AhR activity in Caco2 cells. In addition, all of the hydroxychalcones exhibited minimal to non-detectable activity in YAMC cells, whereas 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) induced CYP1A1, CYP1B1, and UGT1A1 in Caco2 and YAMC cells. The activity of AhR-active chalcones was confirmed by determining their effects in AhR-deficient Caco2 cells. In addition, 2,2'-dihydroxychalcone induced CYP1A1 protein and formation of an AhR-DNA complex in an in vitro assay. Simulation and modeling studies of hydroxylated chalcones confirmed their interactions with the AhR ligand-binding domain and were consistent with their structure-dependent activity as AhR ligands. Thus, this study identifies hydroxylated chalcones as AhR agonists with potential for these phytochemicals to impact AhR-mediated colonic pathways.
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Affiliation(s)
- Hyejin Park
- Department of Veterinary Physiology and Pharmacology, College Station, Texas 77843, USA
| | - Un-Ho Jin
- Department of Veterinary Physiology and Pharmacology, College Station, Texas 77843, USA
| | - Keshav Karki
- Department of Veterinary Physiology and Pharmacology, College Station, Texas 77843, USA
| | - Clinton Allred
- Departments of Nutrition and Biochemistry and Biophysics, College Station, Texas 77843, USA
| | - Laurie A Davidson
- Departments of Nutrition and Biochemistry and Biophysics, College Station, Texas 77843, USA
| | - Robert S Chapkin
- Departments of Nutrition and Biochemistry and Biophysics, College Station, Texas 77843, USA
| | - Asuka A Orr
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, USA
| | - Farrhin Nowshad
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, USA
| | - Arul Jayaraman
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, USA
| | - Phanourios Tamamis
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, USA
| | - Stephen Safe
- Department of Veterinary Physiology and Pharmacology, College Station, Texas 77843, USA
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7
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Valojerdi FM, Farasat A, Shariatifar H, Gheibi N. Study of HSA interactions with arachidonic acid using spectroscopic methods revealing molecular dynamics of HSA-AA interactions. Biomed Rep 2020; 12:125-133. [PMID: 32042421 PMCID: PMC7006104 DOI: 10.3892/br.2019.1270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 09/20/2019] [Indexed: 12/14/2022] Open
Abstract
The interaction between human serum albumin (HSA) and arachidonic acid (AA) as an unsaturated fatty acid were investigated in the present study using methods including UV-VIS spectrophotometry, fluorescence and circular dichroism (CD) spectroscopy, lifetime measurements, fluorescence anisotropy measurements and visual molecular dynamics (MD). The thermodynamic parameters were assessed from HSA thermal and chemical denaturation in the presence and absence of AA. From the thermal denaturation, the Tm and ΔG˚(298K) magnitudes obtained were 327.7 K and 88 kJ/mol, respectively, for HSA alone, and 323.4 K and 85 kJ/mol, respectively, following treatment with a 10 µM AA concentration. The same manner of reduction in Gibbs free energy as a criterion of protein stability was achieved during chemical denaturation by urea in the presence of AA. The present study investigates HSA binding nature through MD approaches, and the results indicated that the binding affinity of AA to the subdomain IIA of HSA is greater compared with that of subdomain IIIA. Although the HSA regular secondary structure evaluation by CD exhibited a minor change following incubation with AA, its tertiary structure revealed an observable fluctuation. Thus, it appears that the interaction between AA and HSA requires minor instability and partial structural changes.
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Affiliation(s)
| | - Alireza Farasat
- Cellular and Molecular Research Center, Qazvin University of Medical Sciences, Qazvin 3419915315, Iran
| | - Hanifeh Shariatifar
- Cellular and Molecular Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj 6618634683, Iran
| | - Nematollah Gheibi
- Cellular and Molecular Research Center, Qazvin University of Medical Sciences, Qazvin 3419915315, Iran
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8
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Aroche DP, Vargas JP, Nogara PA, da Silveira Santos F, da Rocha JBT, Lüdtke DS, Rodembusch FS. Glycoconjugates Based on Supramolecular Tröger's Base Scaffold: Synthesis, Photophysics, Docking, and BSA Association Study. ACS OMEGA 2019; 4:13509-13519. [PMID: 31460480 PMCID: PMC6705216 DOI: 10.1021/acsomega.9b01857] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 07/18/2019] [Indexed: 05/03/2023]
Abstract
This study presents new Tröger's bases bearing glycosyl moieties obtained from a copper-catalyzed azide-alkyne cycloaddition reaction. The Tröger's bases present absorption maxima close to 275 nm related to fully spin and symmetry-allowed electronic transitions. The main fluorescence emission located at 350 nm was observed with no influence on the glycosyl moieties. Furthermore, protein detection studies have been performed using bovine serum albumin (BSA) as a model protein, and results have shown a strong interaction between some of the compounds through a static fluorescence suppression mechanism related to the formation of a glycoconjugate-BSA complex favored by the glycosyl subunit. Moreover, docking was also studied for better understanding the suppression mechanism and indicated that the glycosyl and triazole moieties increase the affinity with BSA.
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Affiliation(s)
- Débora
Muller Pimentel Aroche
- Grupo
de Pesquisa em Fotoquímica Orgânica Aplicada, Universidade Federal do Rio Grande do Sul, UFRGS,
Instituto de Química, Av. Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, RS, Brazil
| | - Jaqueline Pinto Vargas
- Instituto
de Química, Universidade Federal
do Rio Grande do Sul, UFRGS, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS, Brazil
| | - Pablo Andrei Nogara
- Departamento
de Bioquímica e Biologia Molecular, Centro de Ciências
Naturais e Exatas, Universidade Federal
de Santa Maria, UFSM, 97105-900 Santa Maria, RS, Brazil
| | - Fabiano da Silveira Santos
- Grupo
de Pesquisa em Fotoquímica Orgânica Aplicada, Universidade Federal do Rio Grande do Sul, UFRGS,
Instituto de Química, Av. Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, RS, Brazil
| | - João Batista Teixeira da Rocha
- Departamento
de Bioquímica e Biologia Molecular, Centro de Ciências
Naturais e Exatas, Universidade Federal
de Santa Maria, UFSM, 97105-900 Santa Maria, RS, Brazil
| | - Diogo Seibert Lüdtke
- Instituto
de Química, Universidade Federal
do Rio Grande do Sul, UFRGS, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS, Brazil
| | - Fabiano Severo Rodembusch
- Grupo
de Pesquisa em Fotoquímica Orgânica Aplicada, Universidade Federal do Rio Grande do Sul, UFRGS,
Instituto de Química, Av. Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, RS, Brazil
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9
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Pillarisetti P, Myers KA. Identification and characterization of agnuside, a natural proangiogenic small molecule. Eur J Med Chem 2018; 160:193-206. [PMID: 30340142 PMCID: PMC6287603 DOI: 10.1016/j.ejmech.2018.10.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 10/02/2018] [Indexed: 12/29/2022]
Abstract
Due to its important role in regulating angiogenesis, vascular homeostasis and remodeling, and arteriogenesis in blood vascular and lymphatic endothelial cells, VEGFR2 stimulation has demonstrated promise in preclinical studies as an endovascular treatment for ischemic myocardial and peripheral disease. However, the short half-life of protein- and cytokine-based strategies and transduction inefficiency of vector-based modalities have hindered its clinical therapeutic applications. In the present study, we used a streamlined bioinformatics strategy combining ligand-based pharmacophore development and validation, virtual screening, and molecular docking to identify agnuside, a non-toxic, natural small molecule extract of Vitex agnus-castus possessing strong binding affinity, druggable physiochemical properties, and conformationally stable hydrogen bond and hydrophobic interactions with catalytically important residues within VEGFR2's active and allosteric sites. In-vitro proliferation, tube formation, and scratch wound migration assays provide evidence that agnuside promotes endothelial cell angiogenesis. Agnuside increases HUVEC proliferation with an EC50 of 1.376 μg/mL, stimulates tubulogenesis dose-dependently, and increases scratch wound migration rate. An additional angiogenesis assay suggests that agnuside may actively compete with a VEGFR2 inhibitor for VEGFR2 binding site occupancy to increase total length and branching length of HUVEC tubular networks. Chemometric analysis of molecular interaction fields (MIFs) by partial least squares (PLS)-derived quantitative structure activity relationship (QSAR) analysis and MIF contours provides the framework for the formulation of agnuside analogues possessing greater potency. Our research supports that agnuside may be a lead molecule for therapeutic angiogenesis.
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Affiliation(s)
- Piyush Pillarisetti
- Department of Biology, University of Pennsylvania, 433 S University Avenue, Philadelphia, PA, 19104, USA.
| | - Kenneth A Myers
- Department of Biological Sciences, 600 S 43rd Street, Philadelphia, PA, 19104, USA.
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10
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Liang Z, Li QX. Discovery of Selective, Substrate-Competitive, and Passive Membrane Permeable Glycogen Synthase Kinase-3β Inhibitors: Synthesis, Biological Evaluation, and Molecular Modeling of New C-Glycosylflavones. ACS Chem Neurosci 2018; 9:1166-1183. [PMID: 29381861 DOI: 10.1021/acschemneuro.8b00010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Glycogen synthase kinase-3β (GSK-3β) is a key enzyme responsible for tau hyperphosphorylation and is a viable therapeutic target of Alzheimer's disease (AD). We developed a new class of GSK-3β inhibitors based on the 6- C-glycosylflavone isoorientin (1). The new inhibitors are passive membrane permeable and constitutively attenuate GSK-3β mediated tau hyperphosphorylation and amyloid neurotoxicity in an AD cellular model. Enzymatic assays and kinetic studies demonstrated that compound 30 is a GSK-3β substrate-competitive inhibitor with distinct kinase selectivity, isoform-selectivity and over 310-fold increased potency as compared to 1. Structure-activity relationship analyses and in silico modeling suggest the mechanism of actions by which the hydrophobic, π-cation, and orthogonal multipolar interactions of 30 with the substrate site are critical for the GSK-3β inhibition and selectivity. The results provide new insights into GSK-3β drug discovery. The new inhibitors are valuable chemical probes and drug leads with therapeutic potential to tackle AD and other GSK-3β relevant diseases.
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Affiliation(s)
- Zhibin Liang
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| | - Qing X. Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
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11
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Miao Y, Baudry J, Smith JC, McCammon JA. General trends of dihedral conformational transitions in a globular protein. Proteins 2016; 84:501-14. [PMID: 26799251 DOI: 10.1002/prot.24996] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 12/28/2015] [Accepted: 01/08/2016] [Indexed: 11/06/2022]
Abstract
Dihedral conformational transitions are analyzed systematically in a model globular protein, cytochrome P450cam, to examine their structural and chemical dependences through combined conventional molecular dynamics (cMD), accelerated molecular dynamics (aMD) and adaptive biasing force (ABF) simulations. The aMD simulations are performed at two acceleration levels, using dihedral and dual boost, respectively. In comparison with cMD, aMD samples protein dihedral transitions approximately two times faster on average using dihedral boost, and ∼ 3.5 times faster using dual boost. In the protein backbone, significantly higher dihedral transition rates are observed in the bend, coil, and turn flexible regions, followed by the β bridge and β sheet, and then the helices. Moreover, protein side chains of greater length exhibit higher transition rates on average in the aMD-enhanced sampling. Side chains of the same length (particularly Nχ = 2) exhibit decreasing transition rates with residues when going from hydrophobic to polar, then charged and aromatic chemical types. The reduction of dihedral transition rates is found to be correlated with increasing energy barriers as identified through ABF free energy calculations. These general trends of dihedral conformational transitions provide important insights into the hierarchical dynamics and complex free energy landscapes of functional proteins.
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Affiliation(s)
- Yinglong Miao
- Howard Hughes Medical Institute, University of California at San Diego, La Jolla, California, 92093.,Department of Pharmacology, University of California at San Diego, La Jolla, California, 92093
| | - Jerome Baudry
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, 37996
| | - Jeremy C Smith
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, 37996
| | - J Andrew McCammon
- Howard Hughes Medical Institute, University of California at San Diego, La Jolla, California, 92093.,Department of Pharmacology, University of California at San Diego, La Jolla, California, 92093.,Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California, 92093
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12
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Antunes DA, Devaurs D, Kavraki LE. Understanding the challenges of protein flexibility in drug design. Expert Opin Drug Discov 2015; 10:1301-13. [DOI: 10.1517/17460441.2015.1094458] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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13
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Discovery of small molecule inhibitors of MyD88-dependent signaling pathways using a computational screen. Sci Rep 2015; 5:14246. [PMID: 26381092 PMCID: PMC4585646 DOI: 10.1038/srep14246] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 08/21/2015] [Indexed: 01/09/2023] Open
Abstract
In this study, we used high-throughput computational screening to discover drug-like inhibitors of the host MyD88 protein-protein signaling interaction implicated in the potentially lethal immune response associated with Staphylococcal enterotoxins. We built a protein-protein dimeric docking model of the Toll-interleukin receptor (TIR)-domain of MyD88 and identified a binding site for docking small molecules. Computational screening of 5 million drug-like compounds led to testing of 30 small molecules; one of these molecules inhibits the TIR-TIR domain interaction and attenuates pro-inflammatory cytokine production in human primary cell cultures. Compounds chemically similar to this hit from the PubChem database were observed to be more potent with improved drug-like properties. Most of these 2nd generation compounds inhibit Staphylococcal enterotoxin B (SEB)-induced TNF-α, IFN-γ, IL-6, and IL-1β production at 2–10 μM in human primary cells. Biochemical analysis and a cell-based reporter assay revealed that the most promising compound, T6167923, disrupts MyD88 homodimeric formation, which is critical for its signaling function. Furthermore, we observed that administration of a single dose of T6167923 completely protects mice from lethal SEB-induced toxic shock. In summary, our in silico approach has identified anti-inflammatory inhibitors against in vitro and in vivo toxin exposure with promise to treat other MyD88-related pro-inflammatory diseases.
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Yuriev E, Holien J, Ramsland PA. Improvements, trends, and new ideas in molecular docking: 2012-2013 in review. J Mol Recognit 2015; 28:581-604. [PMID: 25808539 DOI: 10.1002/jmr.2471] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Revised: 01/16/2015] [Accepted: 02/05/2015] [Indexed: 12/11/2022]
Abstract
Molecular docking is a computational method for predicting the placement of ligands in the binding sites of their receptor(s). In this review, we discuss the methodological developments that occurred in the docking field in 2012 and 2013, with a particular focus on the more difficult aspects of this computational discipline. The main challenges and therefore focal points for developments in docking, covered in this review, are receptor flexibility, solvation, scoring, and virtual screening. We specifically deal with such aspects of molecular docking and its applications as selection criteria for constructing receptor ensembles, target dependence of scoring functions, integration of higher-level theory into scoring, implicit and explicit handling of solvation in the binding process, and comparison and evaluation of docking and scoring methods.
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Affiliation(s)
- Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Jessica Holien
- ACRF Rational Drug Discovery Centre and Structural Biology Laboratory, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, 3065, Australia
| | - Paul A Ramsland
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, 3004, Australia.,Department of Surgery Austin Health, University of Melbourne, Melbourne, Victoria, 3084, Australia.,Department of Immunology, Monash University, Alfred Medical Research and Education Precinct, Melbourne, Victoria, 3004, Australia.,School of Biomedical Sciences, CHIRI Biosciences, Curtin University, Perth, Western Australia, 6845, Australia
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Gajbhiye JM, More NA, Patil MD, Ummanni R, Kotapalli SS, Yogeeswari P, Sriram D, Masand VH. Discovery of Rimonabant and its potential analogues as anti-TB drug candidates. Med Chem Res 2015. [DOI: 10.1007/s00044-015-1346-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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López-Camacho E, García Godoy MJ, García-Nieto J, Nebro AJ, Aldana-Montes JF. Solving molecular flexible docking problems with metaheuristics: A comparative study. Appl Soft Comput 2015. [DOI: 10.1016/j.asoc.2014.10.049] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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17
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Chen SJ, Ren JL. Identification of a potential anticancer target of danshensu by inverse docking. Asian Pac J Cancer Prev 2014; 15:111-6. [PMID: 24528010 DOI: 10.7314/apjcp.2014.15.1.111] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE To study potential targets of Danshensu via dual inverse docking. METHOD PharmMapper and idTarget servers were used as tools, and the results were checked with the molecular docking program autodock vina in PyRx 0.8. RESULT The disease-related target HRas was rated top, with a pharmacophore model matching well the molecular features of Danshensu. In addition, docking results indicated that the complex was also matched in terms of structure, H-bonds, and hydrophobicity. CONCLUSION Dual inverse docking indicates that HRas may be a potential anticancer target of Danshensu. This approach can provide useful information for studying pharmacological effects of agents of interest.
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Affiliation(s)
- Shao-Jun Chen
- Department of Traditional Chinese Medicine, Zhejiang Pharmaceutical College, Ningbo, China E-mail :
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Chaillon A, Gianella S, Vazquez H, Ignacio C, Zweig AC, Richman DD, Smith DM. Novel codon insert in HIV type 1 clade B reverse transcriptase associated with low-level viremia during antiretroviral therapy. AIDS Res Hum Retroviruses 2014; 30:165-9. [PMID: 24020934 DOI: 10.1089/aid.2013.0202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We investigated the pol genotype in two phylogenetically and epidemiologically linked partners, who were both experiencing persistent low-level viremia during antiretroviral therapy. In one partner we identified a new residue insertion between codon 248 and 249 of the HIV-1 RNA reverse transcriptase (RT) coding region (HXB2 numbering). We then investigated the potential impact of identified mutations in RT and antiretroviral binding affinity using a novel computational approach.
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Affiliation(s)
- Antoine Chaillon
- University of California, San Diego, La Jolla, California
- Inserm UMR U966, Tours, France
| | - Sara Gianella
- University of California, San Diego, La Jolla, California
| | - Homero Vazquez
- University of California, San Diego, La Jolla, California
| | | | - Adam C. Zweig
- Scripps Clinic and Research Foundation, La Jolla, California
| | - Douglas D. Richman
- University of California, San Diego, La Jolla, California
- Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Davey M. Smith
- University of California, San Diego, La Jolla, California
- Veterans Affairs San Diego Healthcare System, San Diego, California
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Li H, Leung KS, Ballester PJ, Wong MH. istar: a web platform for large-scale protein-ligand docking. PLoS One 2014; 9:e85678. [PMID: 24475049 PMCID: PMC3901662 DOI: 10.1371/journal.pone.0085678] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 12/05/2013] [Indexed: 11/18/2022] Open
Abstract
Protein-ligand docking is a key computational method in the design of starting points for the drug discovery process. We are motivated by the desire to automate large-scale docking using our popular docking engine idock and thus have developed a publicly-accessible web platform called istar. Without tedious software installation, users can submit jobs using our website. Our istar website supports 1) filtering ligands by desired molecular properties and previewing the number of ligands to dock, 2) monitoring job progress in real time, and 3) visualizing ligand conformations and outputting free energy and ligand efficiency predicted by idock, binding affinity predicted by RF-Score, putative hydrogen bonds, and supplier information for easy purchase, three useful features commonly lacked on other online docking platforms like DOCK Blaster or iScreen. We have collected 17,224,424 ligands from the All Clean subset of the ZINC database, and revamped our docking engine idock to version 2.0, further improving docking speed and accuracy, and integrating RF-Score as an alternative rescoring function. To compare idock 2.0 with the state-of-the-art AutoDock Vina 1.1.2, we have carried out a rescoring benchmark and a redocking benchmark on the 2,897 and 343 protein-ligand complexes of PDBbind v2012 refined set and CSAR NRC HiQ Set 24Sept2010 respectively, and an execution time benchmark on 12 diverse proteins and 3,000 ligands of different molecular weight. Results show that, under various scenarios, idock achieves comparable success rates while outperforming AutoDock Vina in terms of docking speed by at least 8.69 times and at most 37.51 times. When evaluated on the PDBbind v2012 core set, our istar platform combining with RF-Score manages to reproduce Pearson's correlation coefficient and Spearman's correlation coefficient of as high as 0.855 and 0.859 respectively between the experimental binding affinity and the predicted binding affinity of the docked conformation. istar is freely available at http://istar.cse.cuhk.edu.hk/idock.
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Affiliation(s)
- Hongjian Li
- Department of Computer Science and Engineering, Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- * E-mail: (HL); (PJB)
| | - Kwong-Sak Leung
- Department of Computer Science and Engineering, Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Pedro J. Ballester
- European Bioinformatics Institute, Cambridge, United Kingdom
- * E-mail: (HL); (PJB)
| | - Man-Hon Wong
- Department of Computer Science and Engineering, Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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Molecular Dynamics Simulation of VEGFR2 with Sorafenib and Other Urea-Substituted Aryloxy Compounds. ACTA ACUST UNITED AC 2013. [DOI: 10.1155/2013/739574] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The binding mode of sorafenib with VEGFR2 was studied using molecular docking and molecular dynamics method. The docking results show that sorafenib forms hydrogen bonds with Asp1046, Cys919, and Glu885 of VEGFR2 receptor. Molecular dynamics simulation suggests that the hydrogen bond involving Asp1046 is the most stable one, and it is almost preserved during all the MD simulation time. The hydrogen bond formed with Cys919 occurs frequently after 6 ns, while the bifurcated hydrogen bonds involving Glu885 occurs occasionally. Meantime, molecular dynamics simulations of VEGFR2 with 11 other urea-substituted aryloxy compounds have also been performed, and the results indicate that a potent VEGFR2 inhibitor should have lower interaction energy with VEGFR2 and create at least 2 hydrogen bonds with VEGFR2.
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Kar RK, Suryadevara P, Sahoo BR, Sahoo GC, Dikhit MR, Das P. Exploring novel KDR inhibitors based on pharmaco-informatics methodology. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2013; 24:215-234. [PMID: 23437769 DOI: 10.1080/1062936x.2013.765912] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Kinase-insert domain-containing receptor (KDR) is one of the important mediators of Vascular endothelial growth factor (VEGF) function in endothelial cells. Inhibition of KDR can be therapeutically advantageous for treatment of a number of diseases. The present study focuses on exploring novel KDR inhibitors by means of pharmaco-informatics methodologies. Three-dimensional quantitative structure-activity relationship (3D-QSAR) analysis by atom-based pharmacophore mapping over a set of 85 molecules provides a proposition regarding the molecular fingerprint that can be optimized for designing more active inhibitors. The model was statistically validated with Q(2) = 0.865 for training and r(2) = 0.789, Pearson-r = 0.903 for test set molecules; r(2)(0.925) by external validation suggests model robustness and indicates it as a strong query for screening any compound library. Virtual screening shows the importance of active site and hinge region residue for interaction with KDR inhibitors. Remarkably the retrieved hits contain a urea backbone, implicating urea derivatives as promising candidate for designing KDR inhibitors. The hydrophobicity of active site, which has until now been overlooked, has been raised into the picture by this study. This can impact on KDR drug development. The study thus quantifies crucial structural requirements necessary for a favourable interaction with the receptor binding site while the cooperative pattern provides important structural clues to chemists for framing potent medicinal agents in future.
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Affiliation(s)
- R K Kar
- Biomedical Informatics Centre, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
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Clementi N, Mancini N, Castelli M, Clementi M, Burioni R. Characterization of epitopes recognized by monoclonal antibodies: experimental approaches supported by freely accessible bioinformatic tools. Drug Discov Today 2012. [PMID: 23178804 DOI: 10.1016/j.drudis.2012.11.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Monoclonal antibodies (mAbs) have been used successfully both in research and for clinical purposes. The possible use of protective mAbs directed against different microbial pathogens is currently being considered. The fine definition of the epitope recognized by a protective mAb is an important aspect to be considered for possible development in epitope-based vaccinology. The most accurate approach to this is the X-ray resolution of mAb/antigen crystal complex. Unfortunately, this approach is not always feasible. Under this perspective, several surrogate epitope mapping strategies based on the use of bioinformatics have been developed. In this article, we review the most common, freely accessible, bioinformatic tools used for epitope characterization and provide some basic examples of molecular visualization, editing and computational analysis.
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Affiliation(s)
- Nicola Clementi
- Microbiology and Virology Unit, 'Vita-Salute San Raffaele' University, 20132 Milan, Italy.
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