1
|
Mora-Gamboa MPC, Ferrucho-Calle MC, Ardila-Leal LD, Rojas-Ojeda LM, Galindo JF, Poutou-Piñales RA, Pedroza-Rodríguez AM, Quevedo-Hidalgo BE. Statistical Improvement of rGILCC 1 and rPOXA 1B Laccases Activity Assay Conditions Supported by Molecular Dynamics. Molecules 2023; 28:7263. [PMID: 37959683 PMCID: PMC10648076 DOI: 10.3390/molecules28217263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 11/15/2023] Open
Abstract
Laccases (E.C. 1.10.3.2) are glycoproteins widely distributed in nature. Their structural conformation includes three copper sites in their catalytic center, which are responsible for facilitating substrate oxidation, leading to the generation of H2O instead of H2O2. The measurement of laccase activity (UL-1) results may vary depending on the type of laccase, buffer, redox mediators, and substrates employed. The aim was to select the best conditions for rGILCC 1 and rPOXA 1B laccases activity assay. After sequential statistical assays, the molecular dynamics proved to support this process, and we aimed to accumulate valuable insights into the potential application of these enzymes for the degradation of novel substrates with negative environmental implications. Citrate buffer treatment T2 (CB T2) (pH 3.0 ± 0.2; λ420nm, 2 mM ABTS) had the most favorable results, with 7.315 ± 0.131 UL-1 for rGILCC 1 and 5291.665 ± 45.83 UL-1 for rPOXA 1B. The use of citrate buffer increased the enzyme affinity for ABTS since lower Km values occurred for both enzymes (1.49 × 10-2 mM for rGILCC 1 and 3.72 × 10-2 mM for rPOXA 1B) compared to those obtained in acetate buffer (5.36 × 10-2 mM for rGILCC 1 and 1.72 mM for rPOXA 1B). The molecular dynamics of GILCC 1-ABTS and POXA 1B-ABTS showed stable behavior, with root mean square deviation (RMSD) values not exceeding 2.0 Å. Enzyme activities (rGILCC 1 and rPOXA 1B) and 3D model-ABTS interactions (GILCC 1-ABTS and POXA 1B-ABTS) were under the strong influence of pH, wavelength, ions, and ABTS concentration, supported by computational studies identifying the stabilizing residues and interactions. Integration of the experimental and computational approaches yielded a comprehensive understanding of enzyme-substrate interactions, offering potential applications in environmental substrate treatments.
Collapse
Affiliation(s)
- María P. C. Mora-Gamboa
- Laboratorio de Biotecnología Molecular, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia (M.C.F.-C.); (L.D.A.-L.)
| | - María C. Ferrucho-Calle
- Laboratorio de Biotecnología Molecular, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia (M.C.F.-C.); (L.D.A.-L.)
| | - Leidy D. Ardila-Leal
- Laboratorio de Biotecnología Molecular, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia (M.C.F.-C.); (L.D.A.-L.)
- Laboratorio de Biotecnología Vegetal, Grupo de Investigación en Asuntos Ambientales y Desarrollo Sostenible (MINDALA), Departamento de Ciencias Agrarias y del Ambiente, Universidad Francisco de Paula Santander, Ocaña 546552, Colombia
| | - Lina M. Rojas-Ojeda
- Departamento de Química, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Johan F. Galindo
- Departamento de Química, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Raúl A. Poutou-Piñales
- Laboratorio de Biotecnología Molecular, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia (M.C.F.-C.); (L.D.A.-L.)
| | - Aura M. Pedroza-Rodríguez
- Laboratorio de Microbiología Ambiental y Suelos, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Balkys E. Quevedo-Hidalgo
- Laboratorio de Biotecnología Aplicada, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia;
| |
Collapse
|
2
|
Li R, Li Q, Ji Q. Molecular targeted study in tumors: From western medicine to active ingredients of traditional Chinese medicine. Biomed Pharmacother 2020; 121:109624. [DOI: 10.1016/j.biopha.2019.109624] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/01/2019] [Accepted: 11/01/2019] [Indexed: 12/11/2022] Open
|
3
|
Li Z, Jiang S, Xie Y, Fang Z, Xiao Y, Fang W, Zhang X. Mechanism of the salt activation of laccase Lac15. Biochem Biophys Res Commun 2020; 521:997-1002. [DOI: 10.1016/j.bbrc.2019.11.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 11/03/2019] [Indexed: 01/08/2023]
|
4
|
Mukhopadhyay BP. Recognition dynamics of trinuclear copper cluster and associated histidine residues through conserved or semi-conserved water molecules in human Ceruloplasmin: The involvement of aspartic and glutamic acid gates. J Biomol Struct Dyn 2017; 36:3829-3842. [PMID: 29148316 DOI: 10.1080/07391102.2017.1401003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Human Ceruloplasmin belongs to the family of multi-copper oxidases and it is involved in different physiological processes, copper ion transport, iron metabolism, iron homeostasis, and biogenic amine metabolism. MD-simulation studies have indicated the higher hydrophilic susceptibility of the trinuclear copper cluster in native CP compared to its oxygen bound form. The copper (T2/T3) atom Cu3047 of the cluster, which is close to T1 copper center Cu3052 (~13 Å) has a higher affinity for water molecules compared to other copper centers. The water molecules of W3, W4, W5, W9, and W12 conserved water sites are coordinated to Cu3047, where W3, W9, and W12 centers are found to play some crucial role in the stabilization of native trinuclear copper cluster. The hydrogen bonding interaction of Asp169, Glu112, Asp995, and Glu1032 residues with the copper-bound conserved water molecules (W3, W4, W5, W10, and W11) in native CP is observed to be unique. The conformational flexibility of Asp169 and Glu112 and their association with the copper-bound water molecules, but the absence of such interaction in O2-bound simulated structure of the enzyme is indicating some plausible rational on the role of these acidic residues in the gating of O2 molecule in the native trinuclear Cu cluster of CP. The simulation results may shade some new light on the biochemistry/chemistry of CP, specially on the hydration dynamics of the trinuclear copper cluster.
Collapse
|
5
|
Sun J, Liu H, Yang W, Chen S, Fu S. Molecular Mechanisms Underlying Inhibitory Binding of Alkylimidazolium Ionic Liquids to Laccase. Molecules 2017; 22:E1353. [PMID: 28809813 PMCID: PMC6152407 DOI: 10.3390/molecules22081353] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 08/06/2017] [Accepted: 08/10/2017] [Indexed: 11/16/2022] Open
Abstract
Water-miscible alkylimidazolium ionic liquids (ILs) are "green" co-solvents for laccase catalysis, but generally inhibit enzyme activity. Here, we present novel insights into inhibition mechanisms by a combination of enzyme kinetics analysis and molecular simulation. Alkylimidazolium cations competitively bound to the TI Cu active pocket in the laccase through hydrophobic interactions. Cations with shorter alkyl chains (C₂~C₆) entered the channel inside the pocket, exhibiting a high compatibility with laccase (competitive inhibition constant Kic = 3.36~3.83 mM). Under the same conditions, [Omim]Cl (Kic = 2.15 mM) and [Dmim]Cl (Kic = 0.18 mM) with longer alkyl chains bound with Leu296 or Leu297 near the pocket edge and Leu429 around TI Cu, which resulted in stronger inhibition. Complexation with alkylimidazolium cations shifted the pH optima of laccase to the right by 0.5 unit, and might, thereby, lead to invalidation of the Hofmeister series of anions. EtSO₄- showed higher biocompatibility than did Ac- or Cl-, probably due to its binding near the TI Cu and its hindering the entry of alkylimidazolium cations. In addition, all tested ILs accelerated the scavenging of 2, 2'-azino-bis-(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) radicals, which, however, did not play a determining role in the inhibition of laccase.
Collapse
Affiliation(s)
- Jianliang Sun
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640, Guangdong, China.
| | - Hao Liu
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640, Guangdong, China.
| | - Wenping Yang
- School of Mathematics, South China University of Technology, Guangzhou 510640, Guangdong, China.
| | - Shicheng Chen
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.
| | - Shiyu Fu
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640, Guangdong, China.
| |
Collapse
|
6
|
Dellafiora L, Galaverna G, Reverberi M, Dall'Asta C. Degradation of Aflatoxins by Means of Laccases from Trametes versicolor: An In Silico Insight. Toxins (Basel) 2017; 9:toxins9010017. [PMID: 28045427 PMCID: PMC5308249 DOI: 10.3390/toxins9010017] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 12/16/2016] [Accepted: 12/26/2016] [Indexed: 12/26/2022] Open
Abstract
Mycotoxins are secondary metabolites of fungi that contaminate food and feed, and are involved in a series of foodborne illnesses and disorders in humans and animals. The mitigation of mycotoxin content via enzymatic degradation is a strategy to ensure safer food and feed, and to address the forthcoming issues in view of the global trade and sustainability. Nevertheless, the search for active enzymes is still challenging and time-consuming. The in silico analysis may strongly support the research by providing the evidence-based hierarchization of enzymes for a rational design of more effective experimental trials. The present work dealt with the degradation of aflatoxin B1 and M1 by laccase enzymes from Trametes versicolor. The enzymes–substrate interaction for various enzyme isoforms was investigated through 3D molecular modeling techniques. Structural differences among the isoforms have been pinpointed, which may cause different patterns of interaction between aflatoxin B1 and M1. The possible formation of different products of degradation can be argued accordingly. Moreover, the laccase gamma isoform was identified as the most suitable for protein engineering aimed at ameliorating the substrate specificity. Overall, 3D modeling proved to be an effective analytical tool to assess the enzyme–substrate interaction and provided a solid foothold for supporting the search of degrading enzyme at the early stage.
Collapse
Affiliation(s)
- Luca Dellafiora
- Department of Food Science, University of Parma, 43124 Parma, Italy.
| | - Gianni Galaverna
- Department of Food Science, University of Parma, 43124 Parma, Italy.
| | - Massimo Reverberi
- Department of Environmental Biology, Sapienza University, 00185 Rome, Italy.
| | - Chiara Dall'Asta
- Department of Food Science, University of Parma, 43124 Parma, Italy.
| |
Collapse
|
7
|
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
|
8
|
Ahmad A, Burns CS, Fink AL, Uversky VN. Peculiarities of copper binding to alpha-synuclein. J Biomol Struct Dyn 2016; 29:825-42. [PMID: 22208282 DOI: 10.1080/073911012010525023] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Heavy metals have been implicated as the causative agents for the pathogenesis of the most prevalent neurodegenerative disease. Various mechanisms have been proposed to explain the toxic effects of metals ranging from metal-induced oxidation of protein to metal-induced changes in the protein conformation. Aggregation of a-synuclein is implicated in Parkinson's disease (PD), and various metals, including copper, constitute a prominent group of alpha-synuclein aggregation enhancers. In this study, we have systematically characterized the a-synuclein-Cu21 binding sites and analyzed the possible role of metal binding in a-synuclein fibrillation using a set of biophysical techniques, such as electron paramagnetic resonance (EPR), electron spin-echo envelope modulation (ESEEM), circular dichroism (CD), and size exclusion chromatography (SEC). Our analyses indicated that a-synuclein possesses at least two binding sites for Cu21. We have been able to locate one of the binding sites in the N-terminal region. Furthermore, based on the EPR studies of model peptides and Beta-synuclein, we concluded that the suspected His residue did not appear to participate in strong Cu21 binding.
Collapse
Affiliation(s)
- Atta Ahmad
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California, USA.
| | | | | | | |
Collapse
|
9
|
Computational analysis and low-scale constitutive expression of laccases synthetic genes GlLCC1 from Ganoderma lucidum and POXA 1B from Pleurotus ostreatus in Pichia pastoris. PLoS One 2015; 10:e0116524. [PMID: 25611746 PMCID: PMC4303304 DOI: 10.1371/journal.pone.0116524] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 11/24/2014] [Indexed: 11/19/2022] Open
Abstract
Lacasses are multicopper oxidases that can catalyze aromatic and non-aromatic compounds concomitantly with reduction of molecular oxygen to water. Fungal laccases have generated a growing interest due to their biotechnological potential applications, such as lignocellulosic material delignification, biopulping and biobleaching, wastewater treatment, and transformation of toxic organic pollutants. In this work we selected fungal genes encoding for laccase enzymes GlLCC1 in Ganoderma lucidum and POXA 1B in Pleurotus ostreatus. These genes were optimized for codon use, GC content, and regions generating secondary structures. Laccase proposed computational models, and their interaction with ABTS [2, 2′-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid)] substrate was evaluated by molecular docking. Synthetic genes were cloned under the control of Pichia pastoris glyceraldehyde-3-phosphate dehydrogenase (GAP) constitutive promoter. P. pastoris X-33 was transformed with pGAPZαA-LaccGluc-Stop and pGAPZαA-LaccPost-Stop constructs. Optimization reduced GC content by 47 and 49% for LaccGluc-Stop and LaccPost-Stop genes, respectively. A codon adaptation index of 0.84 was obtained for both genes. 3D structure analysis using SuperPose revealed LaccGluc-Stop is similar to the laccase crystallographic structure 1GYC of Trametes versicolor. Interaction analysis of the 3D models validated through ABTS, demonstrated higher substrate affinity for LaccPost-Stop, in agreement with our experimental results with enzymatic activities of 451.08 ± 6.46 UL-1 compared to activities of 0.13 ± 0.028 UL-1 for LaccGluc-Stop. This study demonstrated that G. lucidum GlLCC1 and P. ostreatus POXA 1B gene optimization resulted in constitutive gene expression under GAP promoter and α-factor leader in P. pastoris. These are important findings in light of recombinant enzyme expression system utility for environmentally friendly designed expression systems, because of the wide range of substrates that laccases can transform. This contributes to a great gamut of products in diverse settings: industry, clinical and chemical use, and environmental applications.
Collapse
|
10
|
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
|
11
|
Laccase engineering by rational and evolutionary design. Cell Mol Life Sci 2015; 72:897-910. [PMID: 25586560 PMCID: PMC4323517 DOI: 10.1007/s00018-014-1824-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 12/30/2014] [Indexed: 11/27/2022]
Abstract
Laccases are considered as green catalysts of great biotechnological potential. This has attracted a great interest in designing laccases a la carte with enhanced stabilities or activities tailored to specific conditions for different fields of application. Over 20 years, numerous efforts have been taken to engineer these multicopper oxidases and to understand their reaction mechanisms by site-directed mutagenesis, and more recently, using computational calculations and directed evolution tools. In this work, we review the most relevant contributions made in the field of laccase engineering, from the comprehensive study of their structure–function relationships to the tailoring of outstanding biocatalysts.
Collapse
|
12
|
Chen M, Zeng G, Lai C, Li J, Xu P, Wu H. Molecular basis of laccase bound to lignin: insight from comparative studies on the interaction of Trametes versicolor laccase with various lignin model compounds. RSC Adv 2015. [DOI: 10.1039/c5ra07916k] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Binding orientation of lignin model compounds in laccase.
Collapse
Affiliation(s)
- Ming Chen
- College of Environmental Science and Engineering
- Hunan University
- Changsha 410082
- China
- Key Laboratory of Environmental Biology and Pollution Control
| | - Guangming Zeng
- College of Environmental Science and Engineering
- Hunan University
- Changsha 410082
- China
- Key Laboratory of Environmental Biology and Pollution Control
| | - Cui Lai
- College of Environmental Science and Engineering
- Hunan University
- Changsha 410082
- China
- Key Laboratory of Environmental Biology and Pollution Control
| | - Jian Li
- Department of River
- Yangtze River Scientific Research Institute
- Wuhan 430010
- China
| | - Piao Xu
- College of Environmental Science and Engineering
- Hunan University
- Changsha 410082
- China
- Key Laboratory of Environmental Biology and Pollution Control
| | - Haipeng Wu
- College of Environmental Science and Engineering
- Hunan University
- Changsha 410082
- China
- Key Laboratory of Environmental Biology and Pollution Control
| |
Collapse
|
13
|
Kinetic role of a histidine residue in the T1 copper site of the laccase from Rigidoporus lignosus. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2013.10.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
14
|
Sanchita, Chauhan R, Soni G, Sudhamalla B, Sharma A. Docking and molecular dynamics studies of peptide inhibitors of ornithine decarboxylase: a rate-limiting enzyme for the metabolism ofFusarium solani. J Biomol Struct Dyn 2013; 31:874-87. [DOI: 10.1080/07391102.2012.718526] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
15
|
Di Marino D, Achsel T, Lacoux C, Falconi M, Bagni C. Molecular dynamics simulations show how the FMRP Ile304Asn mutation destabilizes the KH2 domain structure and affects its function. J Biomol Struct Dyn 2013; 32:337-50. [PMID: 23527791 DOI: 10.1080/07391102.2013.768552] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mutations or deletions of FMRP, involved in the regulation of mRNA metabolism in brain, lead to the Fragile X syndrome (FXS), the most frequent form of inherited intellectual disability. A severe manifestation of the disease has been associated with the Ile304Asn mutation, located on the KH2 domain of the protein. Several hypotheses have been proposed to explain the possible molecular mechanism responsible for the drastic effect of this mutation in humans. Here, we performed a molecular dynamics simulation and show that the Ile304Asn mutation destabilizes the hydrophobic core producing a partial unfolding of two α-helices and a displacement of a third one. The affected regions show increased residue flexibility and motion. Molecular docking analysis revealed strongly reduced binding to a model single-stranded nucleic acid in agreement with known data that the two partially unfolded helices form the RNA-binding surface. The third helix, which we show here to be also affected, is involved in the PAK1 protein interaction. These two functional binding sites on the KH2 domain do not overlap spatially, and therefore, they can simultaneously bind their targets. Since the Ile304Asn mutation affects both binding sites, this may justify the severe clinical manifestation observed in the patient in which both mRNA metabolism activity and cytoskeleton remodeling would be affected.
Collapse
Affiliation(s)
- Daniele Di Marino
- a VIB Center for the Biology of Disease, Catholic University of Leuven , Herestraat 49, 3000 Leuven , Belgium
| | | | | | | | | |
Collapse
|
16
|
Hosainzadeh A, Gharanfoli M, Saberi M, Chamani J. Probing the interaction of human serum albumin with bilirubin in the presence of aspirin by multi-spectroscopic, molecular modeling and zeta potential techniques: insight on binary and ternary systems. J Biomol Struct Dyn 2012; 29:1013-50. [PMID: 22292958 DOI: 10.1080/073911012010525029] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Here, we report on the effect of aspirin (ASA), on the binding parameters with regard to bilirubin (BR) to human serum albumin (HSA). Two different classes of binding sites were detected. Binding to the first and second classes of the binding sites was dominated by hydrophobic forces in the case of HSA-BR, whereas in the case of the ternary system, binding to the first and second classes of the binding sites was achieved by electrostatic interaction. The binding constant (K(a)) and number of binding site (n) obtained were 1.6 × 10(6)M(-1) and 0.98, respectively, for the primary binding site in the case of HSA-BR, and 3.7 × 10(6)M(-1) and 0.84, respectively, in the presence of ASA (ternary complex) at λ(ex)= 280 nm. The progressive quenching of the protein fluorescence as the BR concentration increased indicated an arrangement of the domain IIA in HSA. Changes in the environment of the aromatic residues were also observed by synchronous fluorescence spectroscopy (SFS). Changes of the secondary structure of HSA involving a decrease of α-helical and β-sheet contents and increased amounts of turns and unordered conformations were mainly found at high concentrations of BR. For the first time, the relationship between the structural parameters of HSA-BR by RLS for determining the critical induced aggregation concentration (C(CIAC)) of BR in the absence and presence of ASA was investigated, and there was a more significant enhancement in the case of the ternary mixture as opposed to the binary one. Changes in the zeta potential of HSA and the HSA-ASA complex in the presence of BR demonstrated a hydrophobic adsorption of this anionic ligand onto the surface of HSA in the binary system as well as both electrostatic and hydrophobic adsorption in the case of the ternary complex. By performing docking experiments, it was found that the acting forces between BR and HSA were mainly hydrophobic > hydrogen bonding > electrostatic interactions, and consequently BR had a long storage time in blood plasma, especially in the presence of ASA. This was due to the electrostatic interaction force between the BR and HSA being stronger in (HSA-ASA) BR than in the HSA-BR complex. In addition, it was demonstrated that, in the presence of ASA, the first binding site of BR on HSA was altered, but the parameters of binding did not become significantly modified, and thus the affinity of BR barely changed with and without ASA.
Collapse
Affiliation(s)
- Akram Hosainzadeh
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | | | | | | |
Collapse
|
17
|
Chen KC, Chang SS, Huang HJ, Lin TL, Wu YJ, Chen CYC. Three-in-one agonists for PPAR-α, PPAR-γ, and PPAR-δ from traditional Chinese medicine. J Biomol Struct Dyn 2012; 30:662-83. [DOI: 10.1080/07391102.2012.689699] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
18
|
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]
|
19
|
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]
|
20
|
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
|
21
|
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
|
22
|
Cambria MT, Gullotto D, Garavaglia S, Cambria A. In silico study of structural determinants modulating the redox potential ofRigidoporus lignosusand other fungal laccases. J Biomol Struct Dyn 2012; 30:89-101. [DOI: 10.1080/07391102.2012.674275] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
23
|
Bruyneel F, Dive G, Marchand-Brynaert J. Non-symmetrically substituted phenoxazinones from laccase-mediated oxidative cross-coupling of aminophenols: an experimental and theoretical insight. Org Biomol Chem 2012; 10:1834-46. [PMID: 22257991 DOI: 10.1039/c1ob05795b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Oxidative cross-coupling reactions of substituted o-aminophenols were catalyzed by a commercial laccase to produce non-symmetrically substituted phenoxazinones for the first time. Identification by (1)H-, (13)C- and (31)P-NMR, and by HPLC-PDA and HPLC-MS/MS of exclusively two kinds of substituted phenoxazinones out of four potential heterocyclic frameworks was confirmed by a DFT study. The redox-properties of the substrates, their relative rates of conversion and the rigid docking of selected substrates led to a revisited mechanistic pathway for phenoxazinones biosynthesis. Our suggestions concern both the first formal two-electron oxidation by laccase and the first intermolecular 1,4-conjugated addition which secures the observed regioselectivity.
Collapse
Affiliation(s)
- Frédéric Bruyneel
- Institute of Condensed Matter and Nanosciences, Organic and Medicinal Chemistry, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | | | | |
Collapse
|
24
|
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
|
25
|
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
|
26
|
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
|
27
|
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
|
28
|
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]
|
29
|
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]
|
30
|
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
|
31
|
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]
|
32
|
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]
|
33
|
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]
|
34
|
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]
|
35
|
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]
|
36
|
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]
|
37
|
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]
|
38
|
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]
|
39
|
Atri MS, Saboury AA, Moosavi-Movahedi AA, Goliaei B, Sefidbakht Y, Alijanvand HH, Sharifzadeh A, Niasari-Naslaji A. Structure and Stability Analysis of Cytotoxic Complex of Camel α-Lactalbumin and Unsaturated Fatty Acids Produced at High Temperature. J Biomol Struct Dyn 2011; 28:919-28. [DOI: 10.1080/07391102.2011.10508618] [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]
|
40
|
Zhuohang M, Ji L, Hongwei Y. Modeling of Transition State by Molecular Dynamics. Prediction of Catalytic Efficiency of the Mutants of Mandelate Racemase. J Biomol Struct Dyn 2011; 28:871-9. [DOI: 10.1080/07391102.2011.10508614] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
41
|
Sun MF, Chang TT, Chang KW, Huang HJ, Chen HY, Tsai FJ, Lin JG, Chen CYC. Blocking the DNA Repair System by Traditional Chinese Medicine? J Biomol Struct Dyn 2011; 28:895-906. [DOI: 10.1080/07391102.2011.10508616] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|
42
|
Xu S, Chi S, Jin Y, Shi Q, Ge M, Wang S, Zhang X. Molecular dynamics simulation and density functional theory studies on the active pocket for the binding of paclitaxel to tubulin. J Mol Model 2011; 18:377-91. [PMID: 21537957 DOI: 10.1007/s00894-011-1083-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Accepted: 04/05/2011] [Indexed: 12/29/2022]
Abstract
Paclitaxel (PTX) is used to treat various cancers, but it also causes serious side effects and resistance. To better design similar compounds with less toxicity and more activity against drug-resistant tumors, it is important to clearly understand the PTX-binding pocket formed by the key residues of active sites on β-tubulin. Using a docking method, molecular dynamics (MD) simulation and density functional theory (DFT), we identified some residues (such as Arg278, Asp26, Asp226, Glu22, Glu27, His229, Arg369, Lys218, Ser277 and Thr276) on β-tubulin that are the active sites responsible for interaction with PTX. Another two residues, Leu371 and Gly279, also likely serve as active sites. Most of these sites contact with the "southern hemisphere" of PTX; only one key residue interacts with the "northern hemisphere" of PTX. These key residues can be divided into four groups, which serve as active compositions in the formation of an active pocket for PTX binding to β-tubulin. This active binding pocket enables a very strong interaction (the strength is predicted to be in the range of -327.8 to -365.7 kJ mol(-1)) between β-tubulin and PTX, with various orientated conformations. This strong interaction means that PTX possesses a high level of activity against cancer cells, a result that is in good agreement with the clinical mechanism of PTX. The described PTX pocket and key active residues will be applied to probe the mechanism of tumor cells resistant to PTX, and to design novel analogs with superior properties.
Collapse
Affiliation(s)
- Sichuan Xu
- Key Laboratory of Education Ministry for Medicinal Chemistry of Natural Resource, College of Chemical Science and Technology, Yunnan University, Kunming, People's Republic of China.
| | | | | | | | | | | | | |
Collapse
|
43
|
Lin CH, Chang TT, Sun MF, Chen HY, Tsai FJ, Chang KL, Fisher M, Chen CYC. Potent inhibitor design against H1N1 swine influenza: structure-based and molecular dynamics analysis for M2 inhibitors from traditional Chinese medicine database. J Biomol Struct Dyn 2011; 28:471-82. [PMID: 21142218 DOI: 10.1080/07391102.2011.10508589] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The rapid spread of influenza virus subtype H1N1 poses a great threat to million lives worldwide. To search for new anti-influenza compounds, we performed molecular docking and molecular dynamics simulation to identify potential traditional Chinese medicine (TCM) constituents that could block influenza M2 channel activity. Quinic acid, genipin, syringic acid, cucurbitine, fagarine, and methyl isoferulate all have extremely well docking results as compared to control amantadine. Further de novo drug design suggests that derivatives of genipin and methyl isoferulate could have enhanced binding affinity towards M2 channel. Selected molecular dynamics simulations of M2-derivative complexes show stable hydrogen bond interactions between the derivatives and M2 residues, Ser10 and Ala9. To our best knowledge, this is the first study on the anti-viral activity of the above listed TCM compounds.
Collapse
Affiliation(s)
- Chia-Hui Lin
- Department of Chinese Medicine, China Medical University Hospital, Taiwan
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Punetha A, Shanmugam K, Sundar D. Insight into the Enzyme-Inhibitor Interactions of the First Experimentally Determined Human Aromatase. J Biomol Struct Dyn 2011; 28:759-71. [DOI: 10.1080/07391102.2011.10508604] [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]
|
45
|
Guimarães AP, Oliveira AA, da Cunha EFF, Ramalho TC, França TCC. Design of New Chemotherapeutics Against the Deadly Anthrax Disease. Docking and Molecular Dynamics studies of Inhibitors Containing Pyrrolidine and Riboamidrazone Rings on Nucleoside Hydrolase fromBacillus anthracis. J Biomol Struct Dyn 2011; 28:455-69. [DOI: 10.1080/07391102.2011.10508588] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
46
|
Vahedian-Movahed H, Saberi MR, Chamani J. Comparison of Binding Interactions of Lomefloxacin to Serum Albumin and Serum Transferrin by Resonance Light Scattering and Fluorescence Quenching Methods. J Biomol Struct Dyn 2011; 28:483-502. [DOI: 10.1080/07391102.2011.10508590] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|