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In silico studies of semi-synthetic benzo[a]phenazines as inhibitors of dihydrofolate reductase from Plasmodium falciparum. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Devaurs D, Antunes DA, Hall-Swan S, Mitchell N, Moll M, Lizée G, Kavraki LE. Using parallelized incremental meta-docking can solve the conformational sampling issue when docking large ligands to proteins. BMC Mol Cell Biol 2019; 20:42. [PMID: 31488048 PMCID: PMC6729087 DOI: 10.1186/s12860-019-0218-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 08/08/2019] [Indexed: 02/04/2023] Open
Abstract
Background Docking large ligands, and especially peptides, to protein receptors is still considered a challenge in computational structural biology. Besides the issue of accurately scoring the binding modes of a protein-ligand complex produced by a molecular docking tool, the conformational sampling of a large ligand is also often considered a challenge because of its underlying combinatorial complexity. In this study, we evaluate the impact of using parallelized and incremental paradigms on the accuracy and performance of conformational sampling when docking large ligands. We use five datasets of protein-ligand complexes involving ligands that could not be accurately docked by classical protein-ligand docking tools in previous similar studies. Results Our computational evaluation shows that simply increasing the amount of conformational sampling performed by a protein-ligand docking tool, such as Vina, by running it for longer is rarely beneficial. Instead, it is more efficient and advantageous to run several short instances of this docking tool in parallel and group their results together, in a straightforward parallelized docking protocol. Even greater accuracy and efficiency are achieved by our parallelized incremental meta-docking tool, DINC, showing the additional benefits of its incremental paradigm. Using DINC, we could accurately reproduce the vast majority of the protein-ligand complexes we considered. Conclusions Our study suggests that, even when trying to dock large ligands to proteins, the conformational sampling of the ligand should no longer be considered an issue, as simple docking protocols using existing tools can solve it. Therefore, scoring should currently be regarded as the biggest unmet challenge in molecular docking.
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Affiliation(s)
- Didier Devaurs
- Department of Computer Science, Rice University, 6100 Main St, Houston, TX 77005, USA
| | - Dinler A Antunes
- Department of Computer Science, Rice University, 6100 Main St, Houston, TX 77005, USA
| | - Sarah Hall-Swan
- Department of Computer Science, Rice University, 6100 Main St, Houston, TX 77005, USA
| | - Nicole Mitchell
- Department of Computer Science, Rice University, 6100 Main St, Houston, TX 77005, USA
| | - Mark Moll
- Department of Computer Science, Rice University, 6100 Main St, Houston, TX 77005, USA
| | - Gregory Lizée
- Department of Melanoma Medical Oncology - Research, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Lydia E Kavraki
- Department of Computer Science, Rice University, 6100 Main St, Houston, TX 77005, USA.
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da Silva JAV, Nepovimova E, Ramalho TC, Kuca K, Costa França TC. Molecular modelling studies on the interactions of 7-methoxytacrine-4-pyridinealdoxime with VX-inhibited human acetylcholinesterase. A near attack approach to assess different spacer-lengths. Chem Biol Interact 2019; 307:195-205. [DOI: 10.1016/j.cbi.2019.05.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/18/2019] [Accepted: 05/13/2019] [Indexed: 10/26/2022]
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da Silva JAV, Nepovimova E, Ramalho TC, Kuca K, Celmar Costa França T. Molecular modeling studies on the interactions of 7-methoxytacrine-4-pyridinealdoxime, 4-PA, 2-PAM, and obidoxime with VX-inhibited human acetylcholinesterase: a near attack conformation approach. J Enzyme Inhib Med Chem 2019; 34:1018-1029. [PMID: 31074292 PMCID: PMC6522925 DOI: 10.1080/14756366.2019.1609953] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
7-methoxytacrine-4-pyridinealdoxime (7-MEOTA-4-PA, named hybrid 5C) is a compound formerly synthesized and evaluated in vitro, together with 4-pyridine aldoxime (4-PA) and commercial reactivators of acetylcholinesterase (AChE). This compound was designed with the purpose of being a prophylactic reactivator, capable of interacting with different subdomains of the active site of AChE. To investigate these interactions, theoretical results from docking were first compared with experimental data of hybrid 5C, 4-PA, and two commercial oximes, on the reactivation of human AChE (HssAChE) inhibited by VX. Then, further docking studies, molecular dynamics simulations, and molecular mechanics Poisson–Boltzmann surface area calculations, were carried out to investigate reactivation performances, considering the near attack conformation (NAC) approach, prior to the nucleophilic substitution mechanism. Our results helped to elucidate the interactions of such molecules with the different subdomains of the active site of HssAChE. Additionally, NAC poses of each oxime were suggested for further theoretical studies on the reactivation reaction.
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Affiliation(s)
- Jorge Alberto Valle da Silva
- a Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD), Department of Chemical Engineering , Military Institute of Engineering , Rio de Janeiro/RJ , Brazil
| | - Eugenie Nepovimova
- b Faculty of Science, Department of Chemistry , University of Hradec Kralove , Hradec Kralove , Czech Republic
| | - Teodorico Castro Ramalho
- b Faculty of Science, Department of Chemistry , University of Hradec Kralove , Hradec Kralove , Czech Republic.,c Laboratory of Molecular Modeling, Chemistry Department , Federal University of Lavras , Lavras , Brazil
| | - Kamil Kuca
- b Faculty of Science, Department of Chemistry , University of Hradec Kralove , Hradec Kralove , Czech Republic
| | - Tanos Celmar Costa França
- a Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD), Department of Chemical Engineering , Military Institute of Engineering , Rio de Janeiro/RJ , Brazil.,b Faculty of Science, Department of Chemistry , University of Hradec Kralove , Hradec Kralove , Czech Republic
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Schwertz G, Witschel MC, Rottmann M, Bonnert R, Leartsakulpanich U, Chitnumsub P, Jaruwat A, Ittarat W, Schäfer A, Aponte RA, Charman SA, White KL, Kundu A, Sadhukhan S, Lloyd M, Freiberg GM, Srikumaran M, Siggel M, Zwyssig A, Chaiyen P, Diederich F. Antimalarial Inhibitors Targeting Serine Hydroxymethyltransferase (SHMT) with in Vivo Efficacy and Analysis of their Binding Mode Based on X-ray Cocrystal Structures. J Med Chem 2017; 60:4840-4860. [DOI: 10.1021/acs.jmedchem.7b00008] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Geoffrey Schwertz
- Laboratorium für
Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | | | - Matthias Rottmann
- Swiss Tropical and Public Health Institute (SwissTPH), Socinstrasse
57, 4051 Basel, Switzerland
- Universität Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Roger Bonnert
- Medicines for Malaria Venture, Route de Pré-Bois 20, CH-1215 Geneva, Switzerland
| | - Ubolsree Leartsakulpanich
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Pathumthni 12120, Thailand
| | - Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Pathumthni 12120, Thailand
| | - Aritsara Jaruwat
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Pathumthni 12120, Thailand
| | - Wanwipa Ittarat
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Pathumthni 12120, Thailand
| | - Anja Schäfer
- Swiss Tropical and Public Health Institute (SwissTPH), Socinstrasse
57, 4051 Basel, Switzerland
- Universität Basel, Petersplatz 1, 4003 Basel, Switzerland
| | | | - Susan A. Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Karen L. White
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Abhijit Kundu
- TCG Lifesciences Private Limited, Block BN, Plot 7, Saltlake Electronics Complex, Sector V, Kolkata 700091, West Bengal India
| | - Surajit Sadhukhan
- TCG Lifesciences Private Limited, Block BN, Plot 7, Saltlake Electronics Complex, Sector V, Kolkata 700091, West Bengal India
| | - Mel Lloyd
- Covance Laboratories Ltd., Otley Road, Harrogate HG3 1PY, United Kingdom
| | - Gail M. Freiberg
- Molecular
Characterization, Department R4AE, AbbVie, 1 North Waukegan Road, North Chicago, Illinois 60064-6217, United States
| | - Myron Srikumaran
- Molecular
Characterization, Department R4AE, AbbVie, 1 North Waukegan Road, North Chicago, Illinois 60064-6217, United States
| | - Marc Siggel
- Laboratorium für
Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Adrian Zwyssig
- Laboratorium für
Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Pimchai Chaiyen
- Department of
Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science Mahidol University, 272 Rama VI Road, Bangkok 10400, Thailand
| | - François Diederich
- Laboratorium für
Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
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Bastos LDC, de Souza FR, Guimarães AP, Sirouspour M, Cuya Guizado TR, Forgione P, Ramalho TC, França TCC. Virtual screening, docking, and dynamics of potential new inhibitors of dihydrofolate reductase from Yersinia pestis. J Biomol Struct Dyn 2016; 34:2184-98. [DOI: 10.1080/07391102.2015.1110832] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Leonardo da Costa Bastos
- Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ 22290-270, Brazil
| | - Felipe Rodrigues de Souza
- Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ 22290-270, Brazil
| | - Ana Paula Guimarães
- Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ 22290-270, Brazil
- Department of Chemistry, Federal University of Viçosa, Viçosa, MG 36570-000 Brazil
| | - Mehdi Sirouspour
- Department of Chemistry & Biochemistry, Concordia University, Montreal, QC, Canada
| | - Teobaldo Ricardo Cuya Guizado
- Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ 22290-270, Brazil
- Faculty of Technology, University of the State of Rio de Janeiro, Resende, RJ 27.537-000, Brazil
| | - Pat Forgione
- Department of Chemistry & Biochemistry, Concordia University, Montreal, QC, Canada
| | - Teodorico Castro Ramalho
- Laboratory of Molecular Modeling, Chemistry Department, Federal University of Lavras, Lavras, MG, Brazil
- Faculty of Informatics and Management, Center for Basic and Applied Research, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Tanos Celmar Costa França
- Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ 22290-270, Brazil
- Department of Chemistry & Biochemistry, Concordia University, Montreal, QC, Canada
- Faculty of Informatics and Management, Center for Basic and Applied Research, University of Hradec Kralove, Hradec Kralove, Czech Republic
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Antunes DA, Devaurs D, Kavraki LE. Understanding the challenges of protein flexibility in drug design. Expert Opin Drug Discov 2015; 10:1301-13. [DOI: 10.1517/17460441.2015.1094458] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Folate metabolism in human malaria parasites—75 years on. Mol Biochem Parasitol 2013; 188:63-77. [DOI: 10.1016/j.molbiopara.2013.02.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 02/15/2013] [Accepted: 02/19/2013] [Indexed: 12/21/2022]
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Pornthanakasem W, Kongkasuriyachai D, Uthaipibull C, Yuthavong Y, Leartsakulpanich U. Plasmodium serine hydroxymethyltransferase: indispensability and display of distinct localization. Malar J 2012; 11:387. [PMID: 23173711 PMCID: PMC3521198 DOI: 10.1186/1475-2875-11-387] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 11/20/2012] [Indexed: 12/21/2022] Open
Abstract
Background Serine hydroxymethyltransferase (SHMT), a pyridoxal phosphate-dependent enzyme, plays a vital role in the de novo pyrimidine biosynthesis pathway in malaria parasites. Two genes have been identified in Plasmodium spp. encoding a cytosolic SHMT (cSHMT) and putative mitochondria SHMT (mSHMT), but their roles have not been fully investigated. Methods The presence of Plasmodium SHMT isoforms in the intra-erythrocytic stage was assessed based on their gene expression using reverse transcription PCR (RT-PCR). Localization studies of Plasmodium SHMT isoforms were performed by transfection of fluorescent-tagged gene constructs into P. falciparum and expressions of fluorescent fusion proteins in parasites were observed using a laser scanning confocal microscope. Genetic targeting through homologous recombination was used to study the essentiality of SHMT in Plasmodium spp. Results Semi-quantitative RT-PCR revealed the expression of these two genes throughout intra-erythrocytic development. Localization studies using P. falciparum expressing fluorescent-tagged SHMT showed that PfcSHMT-red fluorescent fusion protein (PfcSHMT-DsRed) is localized in the cytoplasm, while PfmSHMT-green fluorescent fusion protein (PfmSHMT-GFP) co-localized with Mitotracker™-labelled mitochondria as predicted. The essentiality of plasmodial cSHMT was inferred from transfection experiments where recovery of viable knock-out parasites was not achieved, unless complemented with a functional equivalent copy of shmt. Conclusions Distinct compartment localizations of PfSHMT were observed between cytoplasmic and mitochondrial isoforms, and evidence was provided for the indispensable role of plasmodial cSHMT indicating it as a valid target for development of novel anti-malarials.
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Affiliation(s)
- Wichai Pornthanakasem
- National Center for Genetic Engineering and Biotechnology, 113 Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
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Cortopassi WA, Feital RJC, Medeiros DDJ, Guizado TRC, França TCC, Pimentel AS. Docking and molecular dynamics studies of new potential inhibitors of the human epidermal receptor 2. MOLECULAR SIMULATION 2012. [DOI: 10.1080/08927022.2012.696113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Aguiar ACC, Rocha EMMD, Souza NBD, França TCC, Krettli AU. New approaches in antimalarial drug discovery and development: a review. Mem Inst Oswaldo Cruz 2012; 107:831-45. [DOI: 10.1590/s0074-02762012000700001] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Accepted: 08/16/2012] [Indexed: 01/22/2023] Open
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Da Rocha Pita SS, Batista PR, Albuquerque MG, Pascutti PG. Molecular Dynamics Simulations of Peptide Inhibitors Complexed WithTrypanosoma cruziTrypanothione Reductase. Chem Biol Drug Des 2012; 80:561-71. [DOI: 10.1111/j.1747-0285.2012.01429.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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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]
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Sun MF, Chang TT, Chen KC, Yang SC, Chang KW, Tsai TY, Chen HY, Tsai FJ, Lin JG, Chen CYC. Treat Alzheimer's disease by traditional Chinese medicine? MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2011.577074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Structural features of cytochrome P450 1A associated with the absence of EROD activity in liver of the loricariid catfish Pterygoplichthys sp. Gene 2011; 489:111-8. [PMID: 21840383 DOI: 10.1016/j.gene.2011.07.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Revised: 06/19/2011] [Accepted: 07/10/2011] [Indexed: 11/20/2022]
Abstract
The Amazon catfish genus Pterygoplichthys (Loricariidae, Siluriformes) is closely related to the loricariid genus Hypostomus, in which at least two species lack detectable ethoxyresorufin-O-deethylase (EROD) activity, typically catalyzed by cytochrome P450 1 (CYP1) enzymes. Pterygoplichthys sp. liver microsomes also lacked EROD, as well as activity with other substituted resorufins, but aryl hydrocarbon receptor agonists induced hepatic CYP1A mRNA and protein suggesting structural/functional differences in Pterygoplichthys CYP1s from those in other vertebrates. Comparing the sequences of CYP1As of Pterygoplichthys sp. and of two phylogenetically related siluriform species that do catalyze EROD (Ancistrus sp., Loricariidae and Corydoras sp., Callichthyidae) showed that these three proteins share amino acids at 17 positions that are not shared by any fish in a set of 24 other species. Pterygoplichthys and Ancistrus (the loricariids) have an additional 22 amino acid substitutions in common that are not shared by Corydoras or by other fish species. Pterygoplichthys has six exclusive amino acid substitutions. Molecular docking and dynamics simulations indicate that Pterygoplichthys CYP1A has a weak affinity for ER, which binds infrequently in a productive orientation, and in a less stable conformation than in CYP1As of species that catalyze EROD. ER also binds with the carbonyl moiety proximal to the heme iron. Pterygoplichthys CYP1A has amino acid substitutions that reduce the frequency of correctly oriented ER in the AS preventing the detection of EROD activity. The results indicate that loricariid CYP1As may have a peculiar substrate selectivity that differs from CYP1As of most vertebrate.
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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]
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Guimarães AP, Oliveira AA, da Cunha EFF, Ramalho TC, França TCC. Analysis of Bacillus anthracis nucleoside hydrolase via in silico docking with inhibitors and molecular dynamics simulation. J Mol Model 2011; 17:2939-51. [DOI: 10.1007/s00894-011-0968-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 01/11/2011] [Indexed: 10/18/2022]
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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]
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