1
|
Yenigün S, Başar Y, İpek Y, Behçet L, Özen T, Demirtaş İ. Determination of antioxidant, DNA protection, enzyme inhibition potential and molecular docking studies of a biomarker ursolic acid in Nepeta species. J Biomol Struct Dyn 2024; 42:5799-5816. [PMID: 37394807 DOI: 10.1080/07391102.2023.2229440] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/17/2023] [Indexed: 07/04/2023]
Abstract
Ursolic acid (UA), which has many biological properties such as anti-cancer, anti-inflammatory and antioxidant, and regulates some pharmacological processes, has been isolated from the flowers, leaves, berries and fruits of many plant species. In this work, UA was purified from the methanol-chloroform crude extract of Nepeta species (N. aristata, N. baytopii, N. italica, N. trachonitica, N. stenantha) using a silica gel column with chloroform or ethyl acetate solvents via bioactivity-guided isolation. The most active sub-fractions were determined under bioactivities using antioxidant and DNA protection activities and enzyme inhibitions. UA was purified from these fractions and its structure was elucidated by NMR spectroscopy techniques. The highest amount of UA was found in N. stenantha (8.53 mg UA/g), while the lowest amount of UA was found in N. trachonitica (1.92 mg UA/g). The bioactivities of UA were evaluated with antioxidant and DNA protection activities, enzyme inhibitions, kinetics and interactions. The inhibition values (IC50) of α-amylase, α-glucosidase, urease, CA, tyrosinase, lipase, AChE, and BChE were determined between 5.08 and 181.96 µM. In contrast, Ki values of enzyme inhibition kinetics were observed between 0.04 and 0.20 mM. In addition, Ki values of these enzymes for enzyme-UA interactions were calculated as 0.38, 0.86, 0.45, 1.01, 0.23, 0.41, 0.01 and 2.24 µM, respectively. It is supported that UA can be widely used as a good antioxidant against oxidative damage, an effective DNA protector against genetic diseases, and a suitable inhibitor for metabolizing enzymes.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Semiha Yenigün
- Faculty of Science, Department of Chemistry, Ondokuz Mayıs University, Samsun, Turkey
| | - Yunus Başar
- Faculty of Arts and Sciences, Department of Biochemistry, Iğdır University, Iğdır, Turkey
| | - Yaşar İpek
- Faculty of Science, Department of Chemistry, Çankırı Karatekin University, Çankırı, Turkey
| | - Lütfi Behçet
- Faculty of Arts and Sciences, Department of Molecular Biology and Genetics, Bingöl University, Bingöl, Turkey
| | - Tevfik Özen
- Faculty of Science, Department of Chemistry, Ondokuz Mayıs University, Samsun, Turkey
| | - İbrahim Demirtaş
- Faculty of Arts and Sciences, Department of Biochemistry, Iğdır University, Iğdır, Turkey
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ondokuz Mayıs University, Samsun, Turkey
| |
Collapse
|
2
|
de Castro AA, Franco JH, de Andrade AR, Ramalho TC. Rationalizing the activity of a hybrid biocatalyst for ethanol oxidation. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
|
3
|
Kumar GS, Sobhia ME, Ghosh K. Binding affinity analysis of quinolone and dione inhibitors with Mtb-DNA gyrase emphasising the crystal water molecular transfer energy to the protein–ligand association. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2042530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- G. Siva Kumar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Punjab, India
| | - M. Elizabeth Sobhia
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Punjab, India
| | - Ketan Ghosh
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Punjab, India
| |
Collapse
|
4
|
Cathepsin K inhibitors based on 2-amino-1,3,4-oxadiazole derivatives. Bioorg Chem 2021; 109:104662. [PMID: 33626452 DOI: 10.1016/j.bioorg.2021.104662] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 01/06/2021] [Accepted: 01/12/2021] [Indexed: 11/22/2022]
Abstract
Two new series of hitherto unknown dipeptides, containing an electrophilic nitrile or a non-electrophilic 2-amino-1,3,4-oxadiazole moiety were synthesized and evaluated in vitro as Cathepsin K (Cat K) inhibitors. From 14 compounds obtained, the oxadiazole derivatives 10a, 10b, 10e, and 10g acted as enzymatic competitive inhibitors with Ki values between 2.13 and 7.33 µM. Molecular docking calculations were carried out and demonstrated that all inhibitors performed hydrogen bonds with residues from the enzyme active site, such as Asn18. The best inhibitors (10a, 10b, 10g) could also perform these bonds with Cys25, and 10a showed the most stabilizing interaction energy (-134.36 kcal mol-1) with the active cavity. For the first time, derivatives based in 2-amino-1,3,4-oxadiazole scaffolds were evaluated, and the results suggested that this core displays a remarkable potential as a building block for Cat K inhibitors.
Collapse
|
5
|
Bretz RR, de Castro AA, Lara Ferreira IF, Ramalho TC, Silva MC. Experimental and theoretical affinity and catalysis studies between halogenated phenols and peroxidases: Understanding the bioremediation potential. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 202:110895. [PMID: 32615496 DOI: 10.1016/j.ecoenv.2020.110895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 06/08/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
Halogenated phenols, such as 2,4-dichlorophenol (2,4-DCP) and 4-bromophenol (4-BP) are pollutants generated by a various industrial sectors like chemical, dye, paper bleaching, pharmaceuticals or in an agriculture as pesticides. The use of Horseradish peroxidase (HRP) in the halogenated phenols treatment has already been mentioned, but it is not well understood how the different phenolic substrates can bind in the peroxidase active site nor how these specific interactions can influence in the bioremediation potential. In this work, different removal efficiencies were obtained for phenolic compounds investigated using HRP as catalyst (93.87 and 59.19% to 4BP and 2,4 DCP, respectively). Thus, to rationalize this result based on the interactions of phenols with active center of HRP, we combine computational and experimental methodologies. The theoretical approaches utilized include density functional theory (DFT) calculations, docking simulation and quantum mechanics/molecular mechanics (QM/MM) technique. Michaelis Menten constant (Km) obtained through experimental methodologies were 2.3 and 0.95 mM to 2,4-DCP and 4-BP, respectively, while the specificity constant (Kcat/Km) found was 1.44 mM-1 s-1 and 0.62 mM-1 s-1 for 4-BP and 2,4-DCP, respectively. The experimental parameters appointed to the highest affinity of HRP to 4-BP. According to the molecular docking calculations, both ligands have shown stabilizing intermolecular interaction energies within the HRP active site, however, the 4-BP showed more stabilizing interaction energy (-53.00 kcal mol-1) than 2,4-dichlorophenol (-49.23 kcal mol-1). Besides that, oxidative mechanism of 4-BP and 2,4-DCP was investigated by the hybrid QM/MM approach. This study showed that the lowest activation energy values for transition states investigated were obtained for 4-BP. Therefore, by theoretical approach, the compound 4-BP showed the more stabilizing interaction and activation energy values related to the interaction within the enzyme and the oxidative reaction mechanism, respectively, which corroborates with experimental parameters obtained. The combination between experimental and theoretical approaches was essential to understand how the degradation potential of the HRP enzyme depends on the interactions between substrate and the active center cavity of the enzyme.
Collapse
Affiliation(s)
- Raphael Resende Bretz
- Department of Natural Sciences (DCNAT), Federal University of São João del-Rei, São João del Rei, Brazil
| | | | - Igor F Lara Ferreira
- Department of Natural Sciences (DCNAT), Federal University of São João del-Rei, São João del Rei, Brazil
| | - Teodorico C Ramalho
- Department of Chemistry, Federal University of Lavras, Lavras, Brazil; Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Maria Cristina Silva
- Department of Natural Sciences (DCNAT), Federal University of São João del-Rei, São João del Rei, Brazil.
| |
Collapse
|
6
|
Understanding the Interaction Modes and Reactivity of Trimedoxime toward MmAChE Inhibited by Nerve Agents: Theoretical and Experimental Aspects. Int J Mol Sci 2020; 21:ijms21186510. [PMID: 32899591 PMCID: PMC7554915 DOI: 10.3390/ijms21186510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 11/17/2022] Open
Abstract
Organophosphorus (OP) compounds are used as both chemical weapons and pesticides. However, these agents are very dangerous and toxic to humans, animals, and the environment. Thus, investigations with reactivators have been deeply developed in order to design new antidotes with better efficiency, as well as a greater spectrum of action in the acetylcholinesterase (AChE) reactivation process. With that in mind, in this work, we investigated the behavior of trimedoxime toward the Mus musculus acetylcholinesterase (MmAChE) inhibited by a range of nerve agents, such as chemical weapons. From experimental assays, reactivation percentages were obtained for the reactivation of different AChE–OP complexes. On the other hand, theoretical calculations were performed to assess the differences in interaction modes and the reactivity of trimedoxime within the AChE active site. Comparing theoretical and experimental data, it is possible to notice that the oxime, in most cases, showed better reactivation percentages at higher concentrations, with the best result for the reactivation of the AChE–VX adduct. From this work, it was revealed that the mechanistic process contributes most to the oxime efficiency than the interaction in the site. In this way, this study is important to better understand the reactivation process through trimedoxime, contributing to the proposal of novel antidotes.
Collapse
|
7
|
Liu C, Jiang J, Li J, Liang X, Zhou Y, Chen H, Ma Z. Synthesis, structural characterization and antiproliferative potential of copper 4′-phenyl-terpyridine complexes constructed from building block reaction. Polyhedron 2020. [DOI: 10.1016/j.poly.2020.114465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
8
|
Polisel DA, de Castro AA, Mancini DT, da Cunha EFF, França TCC, Ramalho TC, Kuca K. Slight difference in the isomeric oximes K206 and K203 makes huge difference for the reactivation of organophosphorus-inhibited AChE: Theoretical and experimental aspects. Chem Biol Interact 2019; 309:108671. [PMID: 31207225 DOI: 10.1016/j.cbi.2019.05.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/28/2019] [Accepted: 05/22/2019] [Indexed: 01/26/2023]
Abstract
Studies with oximes have been extensively developed to design new reactivators with better efficiency, and greater spectrum of action. In this study, we aimed to analyze the influence of the Carbamoyl group position change in two isomeric oximes, K203 and K206, on the reactivation percentage of Mus musculus Acetylcholinesterase (MmAChE), inhibited by different nerve agents. Theoretical calculations were performed to assess the difference for the oxime activity with inhibited AChE-complexes and the factors that govern this difference. Comparing theoretical and experimental data, it is possible to observe that this change between the oximes results in different reactivation percentage for the same nerve agent, due to the different interaction modes and activation energy for the studied systems.
Collapse
Affiliation(s)
- Daniel A Polisel
- Department of Chemistry, Federal University of Lavras, Lavras, Brazil
| | | | - Daiana T Mancini
- Department of Chemistry, Federal University of Lavras, Lavras, Brazil
| | - Elaine F F da Cunha
- Department of Chemistry, Federal University of Lavras, Lavras, Brazil; Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro, Brazil
| | - Tanos C C França
- Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro, Brazil; Center for Basic and Applied Research, Faculty of Informatics and Management, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Teodorico C Ramalho
- Department of Chemistry, Federal University of Lavras, Lavras, Brazil; Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic.
| | - Kamil Kuca
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic; Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic.
| |
Collapse
|
9
|
Pereira AF, de Castro AA, Soares FV, Soares Leal DH, da Cunha EFF, Mancini DT, Ramalho TC. Development of technologies applied to the biodegradation of warfare nerve agents: Theoretical evidence for asymmetric homogeneous catalysis. Chem Biol Interact 2019; 308:323-331. [PMID: 31173750 DOI: 10.1016/j.cbi.2019.06.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/21/2019] [Accepted: 06/03/2019] [Indexed: 01/31/2023]
Abstract
Organophosphorus compounds have been widely employed to the development of warfare nerve agents and pesticides, resulting in a huge number of people intoxicated annually, being a serious problem of public health. Efforts worldwide have been done in order to design new technologies that are capable of combating or even reversing the poisoning caused by these OP nerve agents. In this line, the bioremediation arises as a promising and efficient alternative for this purpose. As an example of degrading enzymes, there is the organophosphate-degrading (OpdA) enzyme from Agrobacterium radiobacter, which has been quite investigated experimentally due to its high performance in the degradation of neurotoxic nerve agents. This work aims to look into the structural and electronic details that govern the interaction modes of these compounds in the OpdA active site, with the posterior hydrolysis reaction prediction. Our findings have brought about data about the OpdA performance towards different nerve agents, and among them, we may realize that the degradation efficiency strongly depends on the nerve agent structure and its stereochemistry, being in this case the compound Tabun the one more effectively hydrolyzed. By means of the chemical bonds (AIM) and orbitals (FERMO) analysis, it is suggested that the initial reactivity of the OP nerve agents in the OpdA active site does not necessarily dictate the reactivity and interaction modes over the reaction coordinate.
Collapse
Affiliation(s)
- Ander Francisco Pereira
- Laboratory of Molecular Modeling, Department of Chemistry, Federal University of Lavras, Lavras, MG, 37200-000, Brazil
| | - Alexandre A de Castro
- Laboratory of Molecular Modeling, Department of Chemistry, Federal University of Lavras, Lavras, MG, 37200-000, Brazil
| | - Flavia Villela Soares
- Laboratory of Molecular Modeling, Department of Chemistry, Federal University of Lavras, Lavras, MG, 37200-000, Brazil
| | - Daniel Henriques Soares Leal
- Laboratory of Molecular Modeling, Department of Chemistry, Federal University of Lavras, Lavras, MG, 37200-000, Brazil; Department of Health Sciences, Federal University of Espírito Santo, São Mateus, ES, 29932-540, Brazil
| | - Elaine F F da Cunha
- Laboratory of Molecular Modeling, Department of Chemistry, Federal University of Lavras, Lavras, MG, 37200-000, Brazil
| | - Daiana Teixeira Mancini
- Laboratory of Molecular Modeling, Department of Chemistry, Federal University of Lavras, Lavras, MG, 37200-000, Brazil
| | - Teodorico C Ramalho
- Laboratory of Molecular Modeling, Department of Chemistry, Federal University of Lavras, Lavras, MG, 37200-000, Brazil; Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic.
| |
Collapse
|
10
|
de Castro AA, Soares FV, Pereira AF, Silva TC, Silva DR, Mancini DT, Caetano MS, da Cunha EFF, Ramalho TC. Asymmetric biodegradation of the nerve agents Sarin and VX by human dUTPase: chemometrics, molecular docking and hybrid QM/MM calculations. J Biomol Struct Dyn 2019; 37:2154-2164. [PMID: 30044197 DOI: 10.1080/07391102.2018.1478751] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Organophosphorus compounds (OP) nerve agents are among the most toxic chemical substances known. Their toxicity is due to their ability to bind to acetylcholinesterase. Currently, some enzymes, such as phosphotriesterase, human serum paraoxonase 1 and diisopropyl fluorophosphatase, capable of degrading OP, have been characterized. Regarding the importance of bioremediation methods for detoxication of OP, this work aims to study the interaction modes between the human human deoxyuridine triphosphate nucleotidohydrolase (dUTPase) and Sarin and VX, considering their Rp and Sp enantiomers, to evaluate the asymmetric catalysis of those compounds. In previous work, this enzyme has shown good potential to degrade phosphotriesters, and based on this characteristic, we have applied the human dUTPase to the OP degradation. Molecular docking, chemometrics and mixed quantum and molecular mechanics calculations have been employed, showing a good interaction between dUTPase and OP. Two possible reaction mechanisms were tested, and according to our theoretical results, the catalytic degradation of OP by dUTPase can take place via both mechanisms, beyond being stereoselective, that is, dUTPase cleaves one enantiomer preferentially in relation to other. Chemometric techniques provided excellent assistance for performing this theoretical investigation. The dUTPase study shows importance by the fact of it being a human enzyme. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Alexandre A de Castro
- a Laboratory of Molecular Modeling, Chemistry Department , Federal University of Lavras , Lavras , Brazil
| | - Flávia Villela Soares
- a Laboratory of Molecular Modeling, Chemistry Department , Federal University of Lavras , Lavras , Brazil
| | - Ander Francisco Pereira
- a Laboratory of Molecular Modeling, Chemistry Department , Federal University of Lavras , Lavras , Brazil
| | - Telles Cardoso Silva
- a Laboratory of Molecular Modeling, Chemistry Department , Federal University of Lavras , Lavras , Brazil
| | - Daniela Rodrigues Silva
- a Laboratory of Molecular Modeling, Chemistry Department , Federal University of Lavras , Lavras , Brazil
| | - Daiana Teixeira Mancini
- a Laboratory of Molecular Modeling, Chemistry Department , Federal University of Lavras , Lavras , Brazil
| | - Melissa Soares Caetano
- b Institute of Exact and Biological Sciences, Federal University of Ouro Preto, University Campus , Ouro Preto , Brazil
| | - Elaine F F da Cunha
- a Laboratory of Molecular Modeling, Chemistry Department , Federal University of Lavras , Lavras , Brazil
| | - Teodorico C Ramalho
- a Laboratory of Molecular Modeling, Chemistry Department , Federal University of Lavras , Lavras , Brazil.,c Center for Basic and Applied research, University Hradec Kralove , Hradec Kralove , Czech Republic
| |
Collapse
|
11
|
Kuca K, Musilek K, Jun D, Nepovimova E, Soukup O, Korabecny J, França TCC, de Castro AA, Krejcar O, da Cunha EFF, Ramalho TC. Oxime K074 – in vitro and in silico reactivation of acetylcholinesterase inhibited by nerve agents and pesticides. TOXIN REV 2018. [DOI: 10.1080/15569543.2018.1485702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Kamil Musilek
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Daniel Jun
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
- Department of Toxicology and Military Pharmacy, Faculty of Military Health Sciences, University of Defence, Hradec Kralove, Czech Republic
| | - Eugenie Nepovimova
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Ondrej Soukup
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Jan Korabecny
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Tanos C. C. França
- Center for Basic and Applied Research, Faculty of Informatics and Management, University of Hradec Kralove, Hradec Kralove, Czech Republic
- Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro, Brazil
| | | | - Ondrej Krejcar
- Center for Basic and Applied Research, Faculty of Informatics and Management, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | | | - Teodorico C. Ramalho
- Center for Basic and Applied Research, Faculty of Informatics and Management, University of Hradec Kralove, Hradec Kralove, Czech Republic
- Department of Chemistry, Federal University of Lavras, Lavras, Brazil
| |
Collapse
|
12
|
Alagumuthu M, Muralidharan VP, Andrew M, Ahmed MH, Iyer SK, Arumugam S. Computational Approaches to Develop Isoquinoline Based Antibiotics through DNA Gyrase Inhibition Mechanisms Unveiled through Antibacterial Evaluation and Molecular Docking. Mol Inform 2018; 37:e1800048. [DOI: 10.1002/minf.201800048] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 07/16/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Manikandan Alagumuthu
- Dept. of Biotechnology, School of Bio-Sciences and Technology; Vellore Institute of Technology; Vellore- 632014 India
| | - Vivek Panyam Muralidharan
- Dept. of Chemistry, School of Advanced Sciences; Vellore Institute of Technology; Vellore- 632014 India
| | - Monic Andrew
- Dept. of Biotechnology, School of Bio-Sciences and Technology; Vellore Institute of Technology; Vellore- 632014 India
| | - Mohammed Habeeb Ahmed
- Dept. of Biotechnology, School of Bio-Sciences and Technology; Vellore Institute of Technology; Vellore- 632014 India
| | | | - Sivakumar Arumugam
- Dept. of Biotechnology, School of Bio-Sciences and Technology; Vellore Institute of Technology; Vellore- 632014 India
| |
Collapse
|
13
|
Cardona-Pemberthy V, Rendón M, Beltrán JC, Soto-Ospina A, Muñoz-Gomez A, Araque-Marín P, Corredor M, Bedoya G, Cardona-Castro N. Genetic variants, structural, and functional changes of Myelin Protein Zero and Mannose-Binding Lectin 2 protein involved in immune response and its allelic transmission in families of patients with leprosy in Colombia. INFECTION GENETICS AND EVOLUTION 2018; 61:215-223. [DOI: 10.1016/j.meegid.2018.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 03/09/2018] [Accepted: 04/01/2018] [Indexed: 10/17/2022]
|
14
|
Soares FV, de Castro AA, Pereira AF, Leal DHS, Mancini DT, Krejcar O, Ramalho TC, da Cunha EFF, Kuca K. Theoretical Studies Applied to the Evaluation of the DFPase Bioremediation Potential against Chemical Warfare Agents Intoxication. Int J Mol Sci 2018; 19:E1257. [PMID: 29690585 PMCID: PMC5979579 DOI: 10.3390/ijms19041257] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 04/16/2018] [Accepted: 04/19/2018] [Indexed: 11/30/2022] Open
Abstract
Organophosphorus compounds (OP) are part of a group of compounds that may be hazardous to health. They are called neurotoxic agents because of their action on the nervous system, inhibiting the acetylcholinesterase (AChE) enzyme and resulting in a cholinergic crisis. Their high toxicity and rapid action lead to irreversible damage to the nervous system, drawing attention to developing new treatment methods. The diisopropyl fluorophosphatase (DFPase) enzyme has been considered as a potent biocatalyst for the hydrolysis of toxic OP and has potential for bioremediation of this kind of intoxication. In order to investigate the degradation process of the nerve agents Tabun, Cyclosarin and Soman through the wild-type DFPase, and taking into account their stereochemistry, theoretical studies were carried out. The intermolecular interaction energy and other parameters obtained from the molecular docking calculations were used to construct a data matrix, which were posteriorly treated by statistical analyzes of chemometrics, using the PCA (Principal Components Analysis) multivariate analysis. The analyzed parameters seem to be quite important for the reaction mechanisms simulation (QM/MM). Our findings showed that the wild-type DFPase enzyme is stereoselective in hydrolysis, showing promising results for the catalytic degradation of the neurotoxic agents under study, with the degradation mechanism performed through two proposed pathways.
Collapse
Affiliation(s)
- Flávia V Soares
- Laboratory of Molecular Modeling, Chemistry Department, Federal University of Lavras, 37200-000 Lavras, MG, Brazil.
| | - Alexandre A de Castro
- Laboratory of Molecular Modeling, Chemistry Department, Federal University of Lavras, 37200-000 Lavras, MG, Brazil.
| | - Ander F Pereira
- Laboratory of Molecular Modeling, Chemistry Department, Federal University of Lavras, 37200-000 Lavras, MG, Brazil.
| | - Daniel H S Leal
- Laboratory of Molecular Modeling, Chemistry Department, Federal University of Lavras, 37200-000 Lavras, MG, Brazil.
- Department of Health Sciences, Federal University of Espírito Santo, 29932-540 São Mateus, ES, Brazil.
| | - Daiana T Mancini
- Laboratory of Molecular Modeling, Chemistry Department, Federal University of Lavras, 37200-000 Lavras, MG, Brazil.
| | - Ondrej Krejcar
- Center for Basic and Applied Research, Faculty of Informatics and Management, University Hradec Kralove, 50003 Hradec Kralove, Czech Republic.
| | - Teodorico C Ramalho
- Laboratory of Molecular Modeling, Chemistry Department, Federal University of Lavras, 37200-000 Lavras, MG, Brazil.
- Center for Basic and Applied Research, Faculty of Informatics and Management, University Hradec Kralove, 50003 Hradec Kralove, Czech Republic.
| | - Elaine F F da Cunha
- Laboratory of Molecular Modeling, Chemistry Department, Federal University of Lavras, 37200-000 Lavras, MG, Brazil.
| | - Kamil Kuca
- Center for Basic and Applied Research, Faculty of Informatics and Management, University Hradec Kralove, 50003 Hradec Kralove, Czech Republic.
| |
Collapse
|
15
|
Kuca K, Musilek K, Jun D, Zdarova-Karasova J, Nepovimova E, Soukup O, Hrabinova M, Mikler J, Franca TCC, Da Cunha EFF, De Castro AA, Valis M, Ramalho TC. A newly developed oxime K203 is the most effective reactivator of tabun-inhibited acetylcholinesterase. BMC Pharmacol Toxicol 2018; 19:8. [PMID: 29467029 PMCID: PMC5822599 DOI: 10.1186/s40360-018-0196-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 01/25/2018] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Based on in vitro and in vivo rat experiments, the newly developed acetylcholinesterase (AChE) reactivator, K203, appears to be much more effective in the treatment of tabun poisonings than currently fielded oximes. METHODS To determine if this reactivating efficacy would extend to humans, studies were conducted in vitro using human brain homogenate as the source of AChE. The efficacy of K203 was compared with commercially available oximes; pralidoxime, obidoxime and asoxime (HI-6). RESULTS Reactivation studies showed that K203 was the most effective reactivator with a second order kinetic constant (kr) of 2142 min- 1. M- 1, which was 51 times higher than that obtained for obidoxime (kr = 42 min- 1. M- 1). Both pralidoxime and asoxime (HI-6) failed to significantly reactivate tabun-inhibited human AChE. DISCUSSION According to these results and previous studies, using K203, it appears that oxime K203 is the most effective reactivator of tabun-inhibited cholinesterase in several species including humans and should be considered as a possible medical countermeasure to tabun exposure.
Collapse
Affiliation(s)
- Kamil Kuca
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic.
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic.
| | - Kamil Musilek
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Daniel Jun
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
- Faculty of Military Health Sciences, University of Defence, Hradec Kralove, Czech Republic
| | - Jana Zdarova-Karasova
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
- Faculty of Military Health Sciences, University of Defence, Hradec Kralove, Czech Republic
| | - Eugenie Nepovimova
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Ondrej Soukup
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
- Faculty of Military Health Sciences, University of Defence, Hradec Kralove, Czech Republic
| | - Martina Hrabinova
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
- Faculty of Military Health Sciences, University of Defence, Hradec Kralove, Czech Republic
| | - John Mikler
- Defence Research and Development Canada - Suffield Research Centre, Department of National Defence, Suffield, Alberta, Canada
| | - Tanos C C Franca
- Center for Basic and Applied Research, Faculty of Informatics and Management, University of Hradec Kralove, Hradec Kralove, Czech Republic
- Department of Chemical Engineering, Military Institute of Engineering, Rio de Janeiro, RJ, 22290-270, Brazil
| | | | | | - Martin Valis
- Neurology Clinic, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Teodorico C Ramalho
- Center for Basic and Applied Research, Faculty of Informatics and Management, University of Hradec Kralove, Hradec Kralove, Czech Republic
- Department of Chemistry, Federal University of Lavras, Lavras/MG, Brazil
| |
Collapse
|
16
|
Franco JH, Silva BFD, Oliveira RV, Meireles G, de Oliveira DP, Castro AAD, Ramalho TC, Zanoni MVB. Identification of biotransformation products of disperse dyes with rat liver microsomes by LC-MS/MS and theoretical studies with DNA: Structure-mutagenicity relationship using Salmonella/microsome assay. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 613-614:1093-1103. [PMID: 28950671 DOI: 10.1016/j.scitotenv.2017.08.271] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/07/2017] [Accepted: 08/27/2017] [Indexed: 06/07/2023]
Abstract
Azo dyes are known as a group of substances with DNA damage potential that depend on the nature and number of azo groups connected to aromatic rings (benzene and naphthalene), chemical properties, e.g. solubility and reactive functional groups, which significantly affect their toxicological and ecological risks. In this paper, we used in vitro models to evaluate the metabolism of selected textile dyes: Disperse Red 73 (DR 73), Disperse Red 78 (DR 78) and Disperse Red 167 (DR 167). To evaluate the mutagenic potential of the textile dyes, the Salmonella mutagenicity assay (Ames test) with strains TA 98 and TA 100 in the presence and absence of the exogenous metabolic system (S9) was used. DR73 was considered the most mutagenic compound, inducing both replacement base pairs (TA 100) and also changing frameshift (TA 98) mutations that are reduced in the presence of the S9 mixture. Furthermore, we used rat liver microsomes in the same experimental conditions of the S9 mixture to metabolize the dyes and the resultant solutions were analyzed using a liquid chromatography coupled to a quadrupole linear ion trap mass spectrometry (LC-MS/MS) to investigate the metabolites formed by the in vitro biotransformation. Based on this experiment, we detected and identified two biotransformation products for each textile dye substrate analyzed. Furthermore, to evaluate the interaction and reactivity of these compounds with DNA, theoretical calculations were also carried out. The results showed that the chemical reaction occurred preferentially at the azo group and the nitro group, indicating that there was a reduction in these groups by the CYP P450 enzymes presented in the rat microsomal medium. Our results clearly demonstrated that the reduction of these dyes by biological systems is a great environmental concern due to increased genotoxicity for the body of living beings, especially for humans.
Collapse
Affiliation(s)
- Jefferson Honorio Franco
- Institute of Chemistry-State University "Julio de Mesquita Filho"-UNESP-Avenida Professor Francisco Degni, 55, Quitandinha, 14800-900 Araraquara, SP, Brazil
| | - Bianca F da Silva
- Institute of Chemistry-State University "Julio de Mesquita Filho"-UNESP-Avenida Professor Francisco Degni, 55, Quitandinha, 14800-900 Araraquara, SP, Brazil
| | - Regina V Oliveira
- Federal University of São Carlos, UFSCar, Department of Chemistry, Rod. Washington Luiz Km 235, Monjolinho, 13565-905 São Carlos, SP, Brazil
| | - Gabriela Meireles
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo - FCFRP/USP, Ribeirão Preto, São Paulo, Brazil
| | - Danielle Palma de Oliveira
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo - FCFRP/USP, Ribeirão Preto, São Paulo, Brazil.
| | | | - Teodorico C Ramalho
- Department of Chemistry, Federal University of Lavras, 37200-000 Lavras, Brazil
| | - Maria V B Zanoni
- Institute of Chemistry-State University "Julio de Mesquita Filho"-UNESP-Avenida Professor Francisco Degni, 55, Quitandinha, 14800-900 Araraquara, SP, Brazil
| |
Collapse
|
17
|
Pereira-Maia EC, Souza IP, Nunes KJRC, Castro AA, Ramalho TC, Steffler F, Duarte HA, Pacheli A, Chagas P, Oliveira LCA. Peroxoniobium inhibits leukemia cell growth. RSC Adv 2018; 8:10310-10313. [PMID: 35540472 PMCID: PMC9078932 DOI: 10.1039/c8ra00898a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 03/08/2018] [Indexed: 12/27/2022] Open
Abstract
A new class of polyoxoniobate complex has been synthesized and characterized as a novel anticancer agent for photodynamic therapy. The complex inhibits the growth of chronic myelogenous leukemia cells with an IC50 value of 30 μM, in the dark. However, upon exposure to light (365 nm) there is a fivefold increase in the cytotoxic activity. Light radiation activate the complex with the formation of radical species capable of interacting with DNA according to our experimental and theoretical data. A new class of polyoxoniobate complex has been synthesized and characterized as a novel anticancer agent for photodynamic therapy.![]()
Collapse
Affiliation(s)
| | - Ivina P. Souza
- Universidade Federal de Minas Gerais
- Department of Chemistry
- Belo Horizonte
- Brazil
| | | | | | | | - Fernando Steffler
- Universidade Federal de Minas Gerais
- Department of Chemistry
- Belo Horizonte
- Brazil
| | - Helio A. Duarte
- Universidade Federal de Minas Gerais
- Department of Chemistry
- Belo Horizonte
- Brazil
| | - Ana Pacheli
- Universidade Federal de Minas Gerais
- Department of Chemistry
- Belo Horizonte
- Brazil
| | - Poliana Chagas
- Universidade Federal de Minas Gerais
- Department of Chemistry
- Belo Horizonte
- Brazil
| | - Luiz C. A. Oliveira
- Universidade Federal de Minas Gerais
- Department of Chemistry
- Belo Horizonte
- Brazil
| |
Collapse
|
18
|
de Oliveira Viana J, Scotti MT, Scotti L. Molecular Docking Studies in Multitarget Antitubercular Drug Discovery. METHODS IN PHARMACOLOGY AND TOXICOLOGY 2018. [DOI: 10.1007/7653_2018_28] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
|
19
|
Sales TA, Marcussi S, da Cunha EFF, Kuca K, Ramalho TC. Can Inhibitors of Snake Venom Phospholipases A₂ Lead to New Insights into Anti-Inflammatory Therapy in Humans? A Theoretical Study. Toxins (Basel) 2017; 9:E341. [PMID: 29068410 PMCID: PMC5705956 DOI: 10.3390/toxins9110341] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 10/20/2017] [Accepted: 10/21/2017] [Indexed: 11/16/2022] Open
Abstract
Human phospholipase A₂ (hPLA₂) of the IIA group (HGIIA) catalyzes the hydrolysis of membrane phospholipids, producing arachidonic acid and originating potent inflammatory mediators. Therefore, molecules that can inhibit this enzyme are a source of potential anti-inflammatory drugs, with different action mechanisms of known anti-inflammatory agents. For the study and development of new anti-inflammatory drugs with this action mechanism, snake venom PLA₂ (svPLA₂) can be employed, since the svPLA₂ has high similarity with the human PLA₂ HGIIA. Despite the high similarity between these secretory PLA₂s, it is still not clear if these toxins can really be employed as an experimental model to predict the interactions that occur with the human PLA₂ HGIIA and its inhibitors. Thus, the present study aims to compare and evaluate, by means of theoretical calculations, docking and molecular dynamics simulations, as well as experimental studies, the interactions of human PLA₂ HGIIA and two svPLA₂s,Bothrops toxin II and Crotoxin B (BthTX-II and CB, respectively). Our theoretical findings corroborate experimental data and point out that the human PLA₂ HGIIA and svPLA₂ BthTX-II lead to similar interactions with the studied compounds. From our results, the svPLA₂ BthTX-II can be used as an experimental model for the development of anti-inflammatory drugs for therapy in humans.
Collapse
Affiliation(s)
- Thaís A Sales
- Department of Chemistry, Federal University of Lavras, P.O. Box 3037, 37200-000 Lavras, MG, Brazil.
| | - Silvana Marcussi
- Department of Chemistry, Federal University of Lavras, P.O. Box 3037, 37200-000 Lavras, MG, Brazil.
| | - Elaine F F da Cunha
- Department of Chemistry, Federal University of Lavras, P.O. Box 3037, 37200-000 Lavras, MG, Brazil.
| | - Kamil Kuca
- Biomedical Research Center, University Hospital Hradec Kralove, 500 05 Hradec Kralove, Czech Republic.
- Center for Basic and Applied Research, Faculty of Informatics and Management, University of Hradec Kralove, Rokitanskeho 62, 500 03 Hradec Kralove, Czech Republic.
| | - Teodorico C Ramalho
- Department of Chemistry, Federal University of Lavras, P.O. Box 3037, 37200-000 Lavras, MG, Brazil.
- Center for Basic and Applied Research, Faculty of Informatics and Management, University of Hradec Kralove, Rokitanskeho 62, 500 03 Hradec Kralove, Czech Republic.
| |
Collapse
|
20
|
Molecular docking, discovery, synthesis, and pharmacological properties of new 6-substituted-2-(3-phenoxyphenyl)-4-phenyl quinoline derivatives; an approach to developing potent DNA gyrase inhibitors/antibacterial agents. Bioorg Med Chem 2017; 25:1448-1455. [DOI: 10.1016/j.bmc.2017.01.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/03/2017] [Accepted: 01/05/2017] [Indexed: 12/23/2022]
|
21
|
Wang M, Xie W, Li A, Xu S. Structural Basis and Mechanism of Chiral Benzedrine Molecules Interacting With Third Dopamine Receptor. Chirality 2016; 28:674-85. [PMID: 27581600 DOI: 10.1002/chir.22630] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 07/12/2016] [Accepted: 07/15/2016] [Indexed: 11/09/2022]
Abstract
In order to investigate the chiral benzedrine molecules corresponding to their different characteristics in biochemical systems, we studied their interaction with D3 R using the docking method, molecular dynamic simulation, and quantum chemistry. The obtained results indicate that the active residues for R-benzedrine (RAT) bound with D3 R are Ala132, Asp133, and Tyr55, while Asn57, Asp133, Asp168, Cys172, Gly54, Trp24, and Vall136 act as the active residues for S-benzedrine (SAT). The different active pockets are observed for ART or SAT because they possess different active residues. The binding energies between RAT and SAT with D3 R were determined to be -44.0 kJ.mol(-1) and -71.2 kJ.mol(-1) , respectively. These results demonstrate that SAT within the studied pocket of D3 R has a stronger capability of binding with D3 R, while it is more feasible for RAT to leave from the interior positions of D3 R. In addition, the results suggest that the D3 R protein can recognize chiral benzedrine molecules and influence their different addictive and pharmacological effects in biochemical systems. Chirality 28:674-685, 2016. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Ming Wang
- Key Laboratory of Education Ministry for Medicinal Chemistry of Natural Resource, College of Chemical Science and Technology, Yunnan University, Kunming, China
| | - Wei Xie
- Key Laboratory of Education Ministry for Medicinal Chemistry of Natural Resource, College of Chemical Science and Technology, Yunnan University, Kunming, China
| | - Aijing Li
- Key Laboratory of Education Ministry for Medicinal Chemistry of Natural Resource, College of Chemical Science and Technology, Yunnan University, Kunming, China
| | - Sichuan Xu
- Key Laboratory of Education Ministry for Medicinal Chemistry of Natural Resource, College of Chemical Science and Technology, Yunnan University, Kunming, China.
| |
Collapse
|
22
|
Asymmetric biocatalysis of the nerve agent VX by human serum paraoxonase 1: molecular docking and reaction mechanism calculations. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1704-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
23
|
Silva MC, Torres JA, Castro AA, da Cunha EF, Alves de Oliveira LC, Corrêa AD, Ramalho TC. Combined experimental and theoretical study on the removal of pollutant compounds by peroxidases: affinity and reactivity toward a bioremediation catalyst. J Biomol Struct Dyn 2016; 34:1839-48. [DOI: 10.1080/07391102.2015.1063456] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Maria Cristina Silva
- Department of Chemistry, Federal University of Minas Gerais, 31270-901 Belo Horizonte, Brazil
| | | | - Alexandre A. Castro
- Department of Chemistry, Federal University of Lavras, 37200-000 Lavras, Brazil
| | | | | | | | - Teodorico C. Ramalho
- Department of Chemistry, Federal University of Lavras, 37200-000 Lavras, Brazil
- Center for Basic and Applied Research, University Hradec Kralove, Hradec Kralove, Czech Republic
| |
Collapse
|
24
|
Fakhar Z, Naiker S, Alves CN, Govender T, Maguire GEM, Lameira J, Lamichhane G, Kruger HG, Honarparvar B. A comparative modeling and molecular docking study on Mycobacterium tuberculosis targets involved in peptidoglycan biosynthesis. J Biomol Struct Dyn 2016; 34:2399-417. [PMID: 26612108 DOI: 10.1080/07391102.2015.1117397] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
An alarming rise of multidrug-resistant Mycobacterium tuberculosis strains and the continuous high global morbidity of tuberculosis have reinvigorated the need to identify novel targets to combat the disease. The enzymes that catalyze the biosynthesis of peptidoglycan in M. tuberculosis are essential and noteworthy therapeutic targets. In this study, the biochemical function and homology modeling of MurI, MurG, MraY, DapE, DapA, Alr, and Ddl enzymes of the CDC1551 M. tuberculosis strain involved in the biosynthesis of peptidoglycan cell wall are reported. Generation of the 3D structures was achieved with Modeller 9.13. To assess the structural quality of the obtained homology modeled targets, the models were validated using PROCHECK, PDBsum, QMEAN, and ERRAT scores. Molecular dynamics simulations were performed to calculate root mean square deviation (RMSD) and radius of gyration (Rg) of MurI and MurG target proteins and their corresponding templates. For further model validation, RMSD and Rg for selected targets/templates were investigated to compare the close proximity of their dynamic behavior in terms of protein stability and average distances. To identify the potential binding mode required for molecular docking, binding site information of all modeled targets was obtained using two prediction algorithms. A docking study was performed for MurI to determine the potential mode of interaction between the inhibitor and the active site residues. This study presents the first accounts of the 3D structural information for the selected M. tuberculosis targets involved in peptidoglycan biosynthesis.
Collapse
Affiliation(s)
- Zeynab Fakhar
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
| | - Suhashni Naiker
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
| | - Claudio N Alves
- b Laboratório de Planejamento de Fármacos, Instituto de Ciências Exatas e Naturais , Instituto de Ciências Biológicas, Universidade Federal do Pará , CEP 66075-110, Belém , Pará , Brazil
| | - Thavendran Govender
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
| | - Glenn E M Maguire
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa.,c School of Chemistry and Physics , University of KwaZulu-Natal , 4001 Durban , South Africa
| | - Jeronimo Lameira
- b Laboratório de Planejamento de Fármacos, Instituto de Ciências Exatas e Naturais , Instituto de Ciências Biológicas, Universidade Federal do Pará , CEP 66075-110, Belém , Pará , Brazil
| | - Gyanu Lamichhane
- d Division of Infectious Diseases, Center for Tuberculosis Research , Johns Hopkins University School of Medicine , Baltimore , MD 21205 , USA
| | - Hendrik G Kruger
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
| | - Bahareh Honarparvar
- a Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
| |
Collapse
|
25
|
Njogu PM, Guantai EM, Pavadai E, Chibale K. Computer-Aided Drug Discovery Approaches against the Tropical Infectious Diseases Malaria, Tuberculosis, Trypanosomiasis, and Leishmaniasis. ACS Infect Dis 2016; 2:8-31. [PMID: 27622945 DOI: 10.1021/acsinfecdis.5b00093] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Despite the tremendous improvement in overall global health heralded by the adoption of the Millennium Declaration in the year 2000, tropical infections remain a major health problem in the developing world. Recent estimates indicate that the major tropical infectious diseases, namely, malaria, tuberculosis, trypanosomiasis, and leishmaniasis, account for more than 2.2 million deaths and a loss of approximately 85 million disability-adjusted life years annually. The crucial role of chemotherapy in curtailing the deleterious health and economic impacts of these infections has invigorated the search for new drugs against tropical infectious diseases. The research efforts have involved increased application of computational technologies in mainstream drug discovery programs at the hit identification, hit-to-lead, and lead optimization stages. This review highlights various computer-aided drug discovery approaches that have been utilized in efforts to identify novel antimalarial, antitubercular, antitrypanosomal, and antileishmanial agents. The focus is largely on developments over the past 5 years (2010-2014).
Collapse
Affiliation(s)
- Peter M. Njogu
- Department of Pharmaceutical Chemistry and ‡Division of Pharmacology, School of Pharmacy, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
- Department of Chemistry, ⊗Institute of Infectious
Disease and Molecular Medicine, and ΘSouth African Medical Research Council Drug
Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa
| | - Eric M. Guantai
- Department of Pharmaceutical Chemistry and ‡Division of Pharmacology, School of Pharmacy, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
- Department of Chemistry, ⊗Institute of Infectious
Disease and Molecular Medicine, and ΘSouth African Medical Research Council Drug
Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa
| | - Elumalai Pavadai
- Department of Pharmaceutical Chemistry and ‡Division of Pharmacology, School of Pharmacy, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
- Department of Chemistry, ⊗Institute of Infectious
Disease and Molecular Medicine, and ΘSouth African Medical Research Council Drug
Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa
| | - Kelly Chibale
- Department of Pharmaceutical Chemistry and ‡Division of Pharmacology, School of Pharmacy, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
- Department of Chemistry, ⊗Institute of Infectious
Disease and Molecular Medicine, and ΘSouth African Medical Research Council Drug
Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa
| |
Collapse
|
26
|
Evaluation of the effect of the chiral centers of Taxol on binding to β-tubulin: A docking and molecular dynamics simulation study. Comput Biol Chem 2015; 56:33-40. [DOI: 10.1016/j.compbiolchem.2015.02.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 02/26/2015] [Accepted: 02/26/2015] [Indexed: 11/17/2022]
|
27
|
Chi S, Xie W, Zhang J, Xu S. Theoretical insight into the structural mechanism for the binding of vinblastine with tubulin. J Biomol Struct Dyn 2015; 33:2234-54. [PMID: 25588192 DOI: 10.1080/07391102.2014.999256] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Vinblastine (VLB) is one of vinca alkaloids with high cytotoxicity toward cancer cells approved for clinical use. However, because of drug resistance, toxicity, and other side effects caused from the use of VLB, new vinca alkaloids with higher cytotoxicity toward cancer cells and other good qualities need to develop. One strategy is to further study and better understand the essence why VLB possesses the high cytotoxicity toward cancer cells. In present work, by using molecular simulation, molecular docking, density functional calculation, and the crystal structure of α,β-tubulin complex, we find two modes labeled in catharanthine moiety (CM) and vindoline moiety (VM) modes of VLB bound with the interface of α,β-tubulin to probe the essence why VLB has the high cytotoxicity toward cancer cells. In the CM mode, nine key residues B-Ser178, B-Asp179, B-Glu183, B-Tyr210, B-Asp226, C-Lys326, C-Asp327, C-Lys336, and C-Lys352 from the α,β-tubulin complex are determined as the active sites for the interaction of VLB with α,β-tubulin. Some of them such as B-Ser178, B-Glu183, B-Tyr210, B-Asp226, C-Lys326, C-Asp327, and C-Lys336 are newly identified as the active sites in present work. The affinity between VLB and the active pocket within the interface of α,β-tubulin is -60.8 kJ mol(-1) in the CM mode. In the VM mode, that is a new mode established in present paper, nine similar key residues B-Lys176, B-Ser178, B-Asp179, B-Glu183, B-Tyr210, B-Asp226, C-Lys326, C-Asp327, and C-Lys336 from the α,β-tubulin complex are found as the active sites for the interaction with VLB. The difference is from one key residue C-Lys352 in the CM mode changed to the key residue B-Lys176 in the VM mode. The affinity between VLB and the active pocket within the interface of α,β-tubulin is -96.3 kJ mol(-1) in the VM mode. Based on the results obtained in present work, and because VLB looks like two faces, composed of CM and VM both to have similar polar active groups, to interact with the active sites, we suggest double-faces sticking mechanism for the binding of VLB to the interface of α,β-tubulin. The double-faces sticking mechanism can be used to qualitatively explain high cytotoxicity toward cancer cells of vinca alkaloids including vinblastine, vincristine, vindestine, and vinorelbine approved for clinical use and vinflunine still in a phase III clinical trial. Furthermore, this mechanism will be applied to develop novel vinca alkaloids with much higher cytotoxicity toward cancer cells.
Collapse
Affiliation(s)
- Shaoming Chi
- a Key Laboratory of Education Ministry for Medicinal Chemistry of Natural Resource , College of Chemical Science and Technology, Yunnan University , Kunming 650091 , China
| | | | | | | |
Collapse
|
28
|
Sun J, Lv PC, Yin Y, Yuan RJ, Ma J, Zhu HL. Synthesis, structure and antibacterial activity of potent DNA gyrase inhibitors: N'-benzoyl-3-(4-bromophenyl)-1H-pyrazole-5-carbohydrazide derivatives. PLoS One 2013; 8:e69751. [PMID: 23922790 PMCID: PMC3726784 DOI: 10.1371/journal.pone.0069751] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 06/12/2013] [Indexed: 12/31/2022] Open
Abstract
A total of 19 novel (3a-3s) N'-benzoyl-3-(4-bromophenyl)-1H-pyrazole-5-carbohydrazide analogs were designed, synthesized, and evaluated for biological activities as potential DNA gyrase inhibitors. The results showed that compound 3k can strongly inhibit Staphylococcus aureus DNA gyrase and Bacillus subtilis DNA gyrase (with IC50 of 0.15 µg/mL and 0.25 µg/mL, respectively). Structure-activity relationships were also discussed base on the biological and docking simulation results.
Collapse
Affiliation(s)
- Juan Sun
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Peng-Cheng Lv
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Yong Yin
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Rong-Ju Yuan
- School of Life Sciences, Shandong University of Technology, Zibo, China
| | - Jian Ma
- School of Life Sciences, Shandong University of Technology, Zibo, China
| | - Hai-Liang Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
- School of Life Sciences, Shandong University of Technology, Zibo, China
| |
Collapse
|
29
|
Shi G, Wang Y, Jin Y, Chi S, Shi Q, Ge M, Wang S, Zhang X, Xu S. Structural insight into the mechanism of epothilone A bound to beta-tubulin and its mutants at Arg282Gln and Thr274Ile. J Biomol Struct Dyn 2012; 30:559-73. [DOI: 10.1080/07391102.2012.687522] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
30
|
Matos KS, da Cunha EF, da Silva Gonçalves A, Wilter A, Kuča K, França TC, Ramalho TC. First principles calculations of thermodynamics and kinetic parameters and molecular dynamics simulations of acetylcholinesterase reactivators: can mouse data provide new insights into humans? J Biomol Struct Dyn 2012; 30:546-58. [DOI: 10.1080/07391102.2012.687521] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
|
31
|
Wang ZJ, Si YX, Oh S, Yang JM, Yin SJ, Park YD, Lee J, Qian GY. The effect of fucoidan on tyrosinase: computational molecular dynamics integrating inhibition kinetics. J Biomol Struct Dyn 2012; 30:460-73. [PMID: 22694253 DOI: 10.1080/07391102.2012.682211] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fucoidan is a complex sulfated polysaccharide extracted from brown seaweed and has a wide variety of biological activities. In this study, we investigated the inhibitory effect of fucoidan on tyrosinase via a combination of inhibition kinetics and computational simulations. Fucoidan reversibly inhibited tyrosinase in a mixed-type manner. Time-interval kinetics showed that the inhibition was processed as first order with biphasic processes. For further insight, we simulated dockings with various sizes of molecular models (monomer to decamer) of fucoidan and showed that the best binding energy change results were obtained from the pentamer (-1.89 kcal/mol) and the hexamer (-1.97 kcal/mol) models of AutoDock Vina. The molecular dynamics simulation confirmed the binding mechanisms between tyrosinase and fucoidan and suggested that fucoidan mostly interacts with several residues including copper ions located in the active site. Our study suggests that fucoidan might be a potential natural antipigment agent.
Collapse
Affiliation(s)
- Zhi-Jiang Wang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, P.R. China
| | | | | | | | | | | | | | | |
Collapse
|
32
|
Tou WI, Chen CYC. Traditional Chinese medicine as dual guardians against hypertension and cancer? J Biomol Struct Dyn 2012; 30:299-317. [PMID: 22694277 DOI: 10.1080/07391102.2012.680030] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This study utilizes the comprehensive traditional Chinese medicine database TCM Database@Taiwan ( http://tcm.cmu.edu.tw/ ) in conjunction with structure-based and ligand-based drug design to identify multi-function Src inhibitors. The three potential TCM candidates identified as having suitable docking conformations and bioactivity profiles were Angeliferulate, (3R)-2'-hydroxy-3',4'-dimethoxyisoflavan-7-O-beta-D-glucoside (HMID), and 3-[2',6-dihydroxy-5'-(2-propenyl)[1,1'-biphenyl]3-yl]-(E)-2-propenoic acid (3PA). Molecular dynamics simulation demonstrated that the TCM candidates have more stable interactions with the cleft and in complex with Src kinase compared to Saracatinib. Angeliferulate and HMID, both originated from Angelica sinensis, not only interact with Lys298 and amino acids from different loops in the cleft, but also with Asp407 located on the activation loop. These interactions are important to reduce the opening of the activation loop due to phosphorylation, hence stabilize the Src kinase cleft structure and inhibit activation. The TCM candidates also exhibited high affinity to other cancer-related target proteins (EGFR, HER2, and HSP90). Our observations suggest that the TCM candidates might have multi-targeting effects in hypertension and cancer.
Collapse
Affiliation(s)
- Weng Ieong Tou
- School of Medicine, China Medical University, Taichung, Taiwan
| | | |
Collapse
|
33
|
Alijanianzadeh M, Saboury AA, Ganjali MR, Hadi-Alijanvand H, Moosavi-Movahedi AA. Inhibition of mushroom tyrosinase by a newly synthesized ligand: inhibition kinetics and computational simulations. J Biomol Struct Dyn 2012; 30:448-59. [PMID: 22686596 DOI: 10.1080/07391102.2012.682210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Alterations in the synthesis of melanin contribute to a number of diseases; therefore, the design of new tyrosinase inhibitors is very important. Mushroom tyrosinase (MT) is a metalloenzyme, which plays an important role in melanin biosynthesis. In this study, the inhibitory effect of a novel designed compound, i.e. 2-((1Z)-(2-(2,4-dinitrophenyl)hydrazin-1-ylidene)methyl)phenol, as a specific ligand which can bind to the copper ion of MT, has been assessed. The ligand was found to competitively inhibit both the cresolase and catecholase activities of MT, with small inhibition constants of 2.8 and 2.6 μM, respectively. Intrinsic fluorescence studies were performed to gain more information on the binding constants. Docking results indicated that the ligand binds to copper ions in the active site of MT via the OH group of the ligand. The ligand makes four hydrogen bonds with aspartic acid and one hydrogen bond with the histidine residue in the active site. Molecular dynamics results show that ligand binds to the MT via both electrostatic and hydrophobic interactions with its different parts.
Collapse
|
34
|
Majumder R, Roy S, Thakur AR. Analysis of Delta–Notch interaction by molecular modeling and molecular dynamic simulation studies. J Biomol Struct Dyn 2012; 30:13-29. [DOI: 10.1080/07391102.2012.674184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
35
|
Divsalar A, Saboury AA, Ahadi L, Zemanatiyar E, Mansouri-Torshizi H, Ajloo D, Sarma RH. Biological evaluation and interaction of a newly designed anti-cancer Pd(II) complex and human serum albumin. J Biomol Struct Dyn 2012; 29:283-96. [PMID: 21875149 DOI: 10.1080/07391102.2011.10507385] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The pharmacokinetics and pharmacodynamics of any drug will depend, largely, on the interaction that has with human serum albumin (HSA), the most abundant plasma protein. The interaction between newly synthesized Pd(II) complexe, 2,2'-bipyridin Butylglycinato Pd(II) nitrate, an anti-tumor component, with HSA was studied at different temperatures by fluorescence, far UV circular dichroism (CD), UV-visible spectrophotometry and theoretical approaches. The Pd(II) complex has a strong ability to quench the intrinsic fluorescence of HSA through a dynamic quenching procedure. The binding parameters and thermodynamic parameters, including δH°, δS° and δG° were calculated by fluorescence quenching method, indicated that hydrophobic forces play a major role in the interaction of Pd(II) complex with HSA. Based on Autodock, FRET (fluorescence resonance energy transfer) and fluorescence quenching data, it may be concluded that one of the binding sites in the complex of HSA is near the only one Trp of HSA (Trp214) in sub domain IIA of the protein. Far-UV-CD results indicated that Pd(II)-complex induced increase in the α-helical content of the protein. The anti-tumor property of the synthesized Pd(II) complex was studied by testing it on human tumor cell line K562. The 50% cytotoxic concentration (Cc₅₀) of complex was determined using MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide) assay. Also, fluorescence staining with DAPI (4,6-diamidino-2-phenylindole) revealed some typical nuclear changes that are characteristic of apoptosis which is induced at Cc₅₀ concentration of Pd(II) complex in K562 cell line after 24 h incubation. Our results suggest that Pd(II) complex is a promising anti-proliferative agent and should execute its biological effects by inducing apoptosis.
Collapse
Affiliation(s)
- Adeleh Divsalar
- Institute of Biochemistry and Biophysics, University of Tehran. Tehran, Iran.
| | | | | | | | | | | | | |
Collapse
|
36
|
Abstract
Cardiac troponin C (cTnC) is the Ca²⁺ dependent switch for contraction in heart muscle making it a potential target for drug research in the therapy of heart failure. Calcium binding on Troponin C (TnC) triggers a series of conformational changes exposing a hydrophobic pocket in the N-domain of TnC (cNTnC), which leads to force generation. Mutations and acidic pH have been related to altering the sensitivity of TnC affecting the efficiency of the heart. Bepridil, identified as a calcium sensitizer to TnC, has been experimentally found to bind to the N-domain pocket of TnC but with negative cooperativity. Screening and de novo design were carried out using LUDI and AUTOLUDI programs in this work to identify and design potential ligands that can bind to the hydrophobic pocket of TnC. Two docking centers and multiple searching radii including 5 Å, 5.5 Å, 6 Å, 6.5 Å, 7.0 Å and 7.5 Å were used in LUDI to screen the ZINC database. Based on the LUDI docking results, 8 molecules were identified from the database with good potential to bind into the binding pocket and they were used as template molecules to generate a series of new molecules by AUTOLUDI design. Out of all the newly-designed molecules, 14 new ligands were recognized to be potential ligands that can bind and fit well into the binding pocket. These molecules can be used as starting molecules to develop TnC ligands. The binding stability and binding affinity of these molecules to the protein was further analyzed by molecular dynamics simulations. The results show that the binding energies, interactions and complex stabilities of 6 ligands are comparable to or better than bepridil.
Collapse
Affiliation(s)
- Jayson F Varguhese
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
| | | |
Collapse
|
37
|
Pai S, Das M, Banerjee R, Dasgupta D. Biphasic association of T7 RNA polymerase and a nucleotide analogue, cibacron blue as a model to understand the role of initiating nucleotide in the mechanism of enzyme action. J Biomol Struct Dyn 2011; 29:153-64. [PMID: 21696231 DOI: 10.1080/07391102.2011.10507380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
T7 RNA polymerase (T7 RNAP) is an enzyme that utilizes ribonucleotides to synthesize the nascent RNA chain in a template-dependent manner. Here we have studied the interaction of T7 RNAP with cibacron blue, an anthraquinone monochlorotriazine dye, its effect on the function of the enzyme and the probable mode of binding of the dye. We have used difference absorption spectroscopy and isothermal titration calorimetry to show that the dye binds T7 RNAP in a biphasic manner. The first phase of the binding is characterized by inactivation of the enzyme. The second binding site overlaps with the common substrate-binding site of the enzyme. We have carried out docking experiment to map the binding site of the dye in the promoter bound protein. Competitive displacement of the dye from the high affinity site by labeled GTP and isothermal titration calorimetry of high affinity GTP bound enzyme with the dye suggests a strong correlation between the high affinity dye binding and the high affinity GTP binding in T7 RNAP reported earlier from our laboratory.
Collapse
Affiliation(s)
- Sudipta Pai
- Biophysics Division, Saha Institute of Nuclear Physics, 1/AF Bidhan Nagar, Kolkata 700064, India
| | | | | | | |
Collapse
|
38
|
Dey R, Chen L. In search of allosteric modulators of a7-nAChR by solvent density guided virtual screening. J Biomol Struct Dyn 2011; 28:695-715. [PMID: 21294583 DOI: 10.1080/07391102.2011.10508600] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Nicotinic acetylcholine receptors (nAChR) are pentameric ligand gated ion channels whose activity can be modulated by endogenous neurotransmitters as well as by synthetic ligands that bind the same or distinct sites from the natural ligand. The subtype of α7 nAChR has been considered as a potenial therapeutic target for Alzheimer's disease, schizophrenia and other neurological and psychiatric disorders. Here we have developed a homology model of α7 nAChR based on two high resolution crystal structures with Brookhaven Protein Data Bank (PDB) codes 2QC1 and 2WN9 for threading on one monomer and then for building a pentamer, respectively. A number of small molecule binding sites are identified using Pocket Finder (J. An, M. Tortov, and R. Abagyan, Molecular & Cellular Proteomics, 4.6, 752-761 (2005)) of Internal Coordinate Mechanics (ICM). Remarkably, these computer-identified sites match perfectly with ordered solvent densities found in the high-resolution crystal structure of α1 nAChR, suggesting that the surface cavities in the α7 nAChR model are likely binding sites of small molecules. A high throughput virtual screening by flexible ligand docking of 5008 small molecule compounds was performed at three potential allosteric modulator (AM) binding sites of α7 nAChR using Molsoft ICM software (R. Abagyan, M. Tortov and D. Kuznetsov, J Comput Chem 15, 488-506, (1994)). Some experimentally verified allosteric modulators of α7 like CCMI comp-6, LY 7082101, 5-HI, TQS, PNU-120596, genistein, and NS-1738 ranked among top 100 compounds, while the rest of the compounds in the list could guide further search for new allosteric modulators.
Collapse
Affiliation(s)
- Raja Dey
- Molecular and Computational Biology, Department of Biological Sciences,University of Southern California, Los Angeles, CA 90089, USA.
| | | |
Collapse
|
39
|
Majumder R, Roy S, Thakur AR. Molecular Modeling and Molecular Dynamics Simulation Studies of Delta-Notch Complex. J Biomol Struct Dyn 2011; 29:297-310. [DOI: 10.1080/07391102.2011.10507386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
40
|
Li P, Tan JJ, Liu M, Zhang XY, Chen WZ, Wang CX. Insight into the Inhibitory Mechanism and Binding Mode Between D77 and HIV-1 Integrase by Molecular Modeling Methods. J Biomol Struct Dyn 2011; 29:311-23. [DOI: 10.1080/07391102.2011.10507387] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
41
|
Oliveira AA, Rennó MN, de Matos CAS, Bertuzzi MD, Ramalho TC, Fraga CA, França TCC. Molecular Modeling Studies ofYersinia pestisDihydrofolate Reductase. J Biomol Struct Dyn 2011; 29:351-67. [DOI: 10.1080/07391102.2011.10507390] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
42
|
Wang Y, Bian F, Deng S, Shi Q, Ge M, Wang S, Zhang X, Xu S. The key residues of active sites on the catalytic fragment for paclitaxel interacting with poly (ADP-ribose) polymerase. J Biomol Struct Dyn 2011; 28:881-93. [PMID: 21469749 DOI: 10.1080/07391102.2011.10508615] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Poly(ADP-ribose) polymerase (PARP) is regarded as a target protein for paclitaxel (PTX) to bind. An important issue is to identify the key residues as active sites for PTX interacting with PARP, which will help to understand the potential drug activity of PTX against cancer cells. Using docking method and MD simulation, we have constructed a refined structure of PTX docked on the catalytic function domain of PARP (PDB code: 1A26). The residues Glu327(988), Tyr246(907), Lys242(903), His165(826), Asp105(766), Gln102(763) and Gln98(759) in PARP are identified as potential sites involved in interaction with PTX according to binding energy (E(b)) between PTX and single residue calculated with B3LYP/6-31G(d,p). These residues form an active binding pocket located on the surface of the catalytic fragment, possibly interacting with the required groups of PTX leading to its activity against cancer cells. It is noted that most of the active sites make conatct with the "southern hemisphere" of PTX except for one residue, Tyr246(907), which interacts with the "northern hemisphere" of PTX. The conformation of PTX in complex with the catalytic fragment is observed as being T-shaped, similar to that complexed with β-tubulin. The total Eb of -269.9 kJ/mol represents the potent interaction between PTX and the catalytic fragment, implying that PTX can readily bind to the active pocket. The tight association of PTX with the catalytic fragment would inhibit PARP activation, suggesting a potential application of PTX as an effective antineoplastic agent.
Collapse
Affiliation(s)
- Yue Wang
- Key Laboratory of Education Ministry for Medicinal Chemistry of Natural Resource, College of Chemical Science and Technology, Yunnan University, Kunming 650091, PR China
| | | | | | | | | | | | | | | |
Collapse
|
43
|
Kim DS, Kim CM, Won CI, Kim JK, Ryu J, Cho Y, Lee C, Bhak J. BetaDock: Shape-Priority Docking Method Based on Beta-Complex. J Biomol Struct Dyn 2011; 29:219-42. [DOI: 10.1080/07391102.2011.10507384] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
44
|
Chang KW, Tsai TY, Chen KC, Yang SC, Huang HJ, Chang TT, Sun MF, Chen HY, Tsai FJ, Chen CYC. iSMART: An Integrated Cloud Computing Web Server for Traditional Chinese Medicine for Online Virtual Screening,de novoEvolution and Drug Design. J Biomol Struct Dyn 2011; 29:243-50. [DOI: 10.1080/073911011010524988] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
45
|
Omidvar Z, Parivar K, Sanee H, Amiri-Tehranizadeh Z, Baratian A, Saberi MR, Asoodeh A, Chamani J. Investigations with Spectroscopy, Zeta Potential and Molecular Modeling of the Non-Cooperative Behaviour Between Cyclophosphamide Hydrochloride and Aspirin upon Interaction with Human Serum Albumin: Binary and Ternary Systems from the View Point of Multi-Drug Therapy. J Biomol Struct Dyn 2011; 29:181-206. [DOI: 10.1080/07391102.2011.10507382] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
46
|
Xie HZ, Liu LY, Ren JX, Zhou JP, Zheng RL, Li LL, Yang SY. Pharmacophore Modeling and Hybrid Virtual Screening for the Discovery of Novel IκB Kinase 2 (IKK2) Inhibitors. J Biomol Struct Dyn 2011; 29:165-79. [DOI: 10.1080/07391102.2011.10507381] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
|
47
|
Cortopassi WA, Oliveira AA, Guimarães AP, Rennó MN, Krettli AU, França TC. Docking Studies on the Binding of Quinoline Derivatives and Hematin toPlasmodium FalciparumLactate Dehydrogenase. J Biomol Struct Dyn 2011; 29:207-18. [DOI: 10.1080/07391102.2011.10507383] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
48
|
Chang TT, Sun MF, Chen HY, Tsai FJ, Chen CYC. Drug design for hemagglutinin: Screening and molecular dynamics from traditional Chinese medicine database. J Taiwan Inst Chem Eng 2011. [DOI: 10.1016/j.jtice.2010.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
49
|
Ramalho TC, Caetano MS, Josa D, Luz GP, Freitas EA, da Cunha EFF. Molecular Modeling ofMycobacterium TuberculosisdUTpase: Docking and Catalytic Mechanism Studies. J Biomol Struct Dyn 2011; 28:907-17. [DOI: 10.1080/07391102.2011.10508617] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
50
|
Pankratov AN, Tsivileva OM, Drevko BI, Nikitina VE. Compounds of the 1,5-di(4-R-phenyl)-3-selenopentanediones-1,5 series interaction with the BasidiomyceteLentinula edodes, lectins: Computations and Experiment. J Biomol Struct Dyn 2011; 28:969-74. [DOI: 10.1080/07391102.2011.10508622] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|