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Structure Prediction and Docking Studies of Chorismate Synthase from Mycobacterium Tuberculosis [chapter]

Cláudia Lemelle Fernandes, Diógenes Santiago Santos, Luiz Augusto Basso, Osmar Norberto de Souza
2005 Lecture Notes in Computer Science  
The three-dimensional (3D) structure prediction of the enzyme was performed using the crystal structure (PDB ID: 1QX0) of CS from Streptococcus pneumoniae as template (≈ 42% identity), and the MODELLER6v2  ...  Chorismate Synthase (CS) catalyzes the last step of this pathway, the product of which is utilized in other enzymatic transformations like the biosynthesis of aromatic amino acids, folate, vitamin K and  ...  The three-dimensional (3D) structure prediction of the enzyme was performed using the crystal structure (PDB ID: 1QX0) of CS from Streptococcus pneumoniae as template (≈ 42% identity), and the MODELLER6v2  ... 
doi:10.1007/11532323_13 fatcat:bh7woka7ivbcxmoqktoyjogd2a

Homology modeling and Molecular docking studies of AS1 (Anthranilate synthase component I (TrpE)) model of Mycobacterium tuberculos

Naresh Kumar K, Suresh Kumar C, Subba Rao D
2011 INTERNATIONAL JOURNAL OF COMPUTERS & TECHNOLOGY  
In the present study three compounds Cannabigerolic acid, cannabinolic acid and adhumulone from Cannabis sativa have been used for insilio docking studies.  ...  The emergence of multi-drug resistant (MDR) strains of Mycobacterium tuberculosis is the main reason why tuberculosis (TB) continues to be a major health problem worldwide.  ...  INTRODUCTION Tuberculosis (TB), caused by Mycobacterium tuberculosis (M. tuberculosis), remains one of the most devastating global diseases.  ... 
doi:10.24297/ijct.v10i1.3326 fatcat:y2mt4nqwfzbnhpddhfn3f3eyam

Gut Microbiota Metabolite Indole Propionic Acid Targets Tryptophan Biosynthesis in Mycobacterium tuberculosis

Dereje Abate Negatu, Yoshiyuki Yamada, Yu Xi, Mei Lin Go, Matthew Zimmerman, Uday Ganapathy, Véronique Dartois, Martin Gengenbacher, Thomas Dick, Mary Jackson, Stefan H. E. Kaufmann
2019 mBio  
Indole propionic acid (IPA), produced by the gut microbiota, is active against Mycobacterium tuberculosis in vitro and in vivo. However, its mechanism of action is unknown.  ...  IPA is the deamination product of tryptophan (Trp) and thus a close structural analog of this essential aromatic amino acid.  ...  The crystal structure of anthranilate synthase component I (TrpE) from M. tuberculosis was retrieved from the Protein Data Bank (PDB no. 5CWA) (15) .  ... 
doi:10.1128/mbio.02781-18 fatcat:cerqz7osxvekdl4dbdne3wnfha

Protein-Drug Interaction Studies for Development of Drugs Against Plasmodium falciparum

Walter de Azevedo Jr., Rafael Caceres, Ivani Pauli, Luis Fernando Timmers, Guy Barcellos, Kelen Rocha, Milena Soares
2009 Current Drug Targets  
In addition, other key enzymes which play roles in biosynthetic pathways, such as enoyl reductase and chorismate synthase, can be valuable targets for drug development.  ...  The study of protein-drug interaction is of pivotal importance to understand the structural features essential for ligand affinity.  ...  together and derive a general model to predict affinity from the structures.  ... 
doi:10.2174/138945009787581104 pmid:19275563 fatcat:2czqemx4gfbw5kilhjj3rechcy

In Silico Investigation of Rv Hypothetical Proteins of Virulent Strain Mycobacterium tuberculosis H37Rv

Zahra M. Al-Khafaji
2013 Indian Journal of Pharmaceutical and Biological Research  
In Silico studies usually pave the way for more investigations of the real problem .On the other hand Mycobacterium tuberculosis does not lend itself for deep wet lab studies, therefore, In Silico studies  ...  In Silico studies were carried out using most virulent strain and a model of studies M. tuberculosis H37Rv to investigate some of the hypothetical proteins which compromised about 39% of the annotated  ...  Acknowledgments The author thanks Institute of Genetic Engineering and Biotechnology for Postgraduate Studies, University of Baghdad, Iraq.  ... 
doi:10.30750/ijpbr.1.4.15 fatcat:4dri3s34pzf7lbgo4rjwrwz3cm

Isolation and biochemical characterization of a metagenome-derived 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase gene from subtropical marine mangrove wetland sediments

Huaxian Zhao, Hua Gao, Kai Ji, Bing Yan, Quanwen Li, Shuming Mo, Minggang Zheng, Qian Ou, Bo Wu, Nan Li, Chengjian Jiang
2019 AMB Express  
Multiple sequence alignment, homologous modeling, and molecular docking showed that Aro1A had the typical (β/α)8 barrel-shaped catalytic structural domain of DAHPS.  ...  The gene encoded a polypeptide composed of 272 amino acids and had a maximum similarity of 52.4% to a known DAHPS at the amino acid level.  ...  Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.  ... 
doi:10.1186/s13568-019-0742-4 pmid:30715617 pmcid:PMC6362186 fatcat:4pq67g3fuzhnpheylxa5lcnopm

Discovery and development of novel salicylate synthase (MbtI) furanic inhibitors as antitubercular agents

Laurent R. Chiarelli, Matteo Mori, Daniela Barlocco, Giangiacomo Beretta, Arianna Gelain, Elena Pini, Marianna Porcino, Giorgia Mori, Giovanni Stelitano, Luca Costantino, Margherita Lapillo, Davide Bonanni (+4 others)
2018 European Journal of Medicinal Chemistry  
We report on the virtual screening, synthesis, and biological evaluation of new furan derivatives targeting Mycobacterium tuberculosis salicylate synthase (MbtI).  ...  Considering the most active compound I as starting point for the development of novel MbtI inhibitors, we obtained new derivatives based on the furan scaffold.  ...  Acknowledgments We acknowledge the University of Milan (Linea B) and the University of Pavia for the financial support. We thank Prof.  ... 
doi:10.1016/j.ejmech.2018.06.033 pmid:29940465 fatcat:esxmvxth45g25malbxujsu3noa

Interaction between DAHP synthase and chorismate mutase endows new regulation on DAHP synthase activity in Corynebacterium glutamicum

Pan-Pan Li, De-Feng Li, Di Liu, Yi-Ming Liu, Chang Liu, Shuang-Jiang Liu
2013 Applied Microbiology and Biotechnology  
Modeling based on the structure of the complex formed between DAHP synthase and chorismate mutase of Mycobacterium tuberculosis predicted the interaction surfaces of the putative DS Cg -CM Cg complex.  ...  In this study, we investigated the interaction by means of structure-guided mutation and enzymatic assays.  ...  Acknowledgments This work was supported by a grant from the Ministry of Science and Technology of China (973-project, grant no. 2012CB721104).  ... 
doi:10.1007/s00253-013-4806-0 pmid:23467831 fatcat:53y4b27nsreyrf56ustupvfmra

Structural analysis and molecular docking of potential ligands with chorismate synthase of Listeria monocytogenes: a novel antibacterial drug target

Md Musharaf Hossain, Pradip Kumar Roy, A T M Jannatul Mosnaz, Shahriar Kabir Shakil, Md Mehedi Hasan, Shamsul H Prodhan
2015 Indian Journal of Biochemistry & Biophysics  
The potency of binding was also checked with other structurally similar CS from Streptococcus pneumoniae (SpCS) and Mycobacterium tuberculosis (MtCS).  ...  Structure-based virtual screening and docking studies were performed using Autodock tools to retrieve potential candidates with high affinity binding against LmCS model from several ligand repositories  ...  Besides, we have also done comparative docking analysis of potential inhibitors with structurally similar CS from Streptococcus pneumoniae and Mycobacterium tuberculosis.  ... 
pmid:26040111 fatcat:fzh3wozsmfgypc6tw6o5v6ddja

Synergistic Allostery, a Sophisticated Regulatory Network for the Control of Aromatic Amino Acid Biosynthesis inMycobacterium tuberculosis

Celia J. Webby, Wanting Jiao, Richard D. Hutton, Nicola J. Blackmore, Heather M. Baker, Edward N. Baker, Geoffrey B. Jameson, Emily J. Parker
2010 Journal of Biological Chemistry  
The shikimate pathway, responsible for aromatic amino acid biosynthesis, is required for the growth of Mycobacterium tuberculosis and is a potential drug target.  ...  Whereas Mycobacterium tuberculosis DAH7PS (MtuDAH7PS) is not inhibited by the addition of Phe, Tyr, or Trp alone, combinations cause significant loss of enzyme activity.  ...  Recent gene disruption studies have shown that operation of the shikimate pathway is essential for the viability of Mycobacterium tuberculosis (5) , the causative agent of tuberculosis, a disease that  ... 
doi:10.1074/jbc.m110.111856 pmid:20667835 pmcid:PMC2945551 fatcat:c6ged2kcqbh3hfnzugzp4idx3m

New Chromane-Based Derivatives as Inhibitors of Mycobacterium tuberculosis Salicylate Synthase (MbtI): Preliminary Biological Evaluation and Molecular Modeling Studies

Elena Pini, Giulio Poli, Tiziano Tuccinardi, Laurent Chiarelli, Matteo Mori, Arianna Gelain, Luca Costantino, Stefania Villa, Fiorella Meneghetti, Daniela Barlocco
2018 Molecules  
Tuberculosis is the leading cause of death from a single infectious agent worldwide; therefore, the need for new antitubercular drugs is desperate.  ...  Molecular modeling studies were performed in order to evaluate the binding mode of 1 and rationalize the preliminary structure-activity relationships, thus providing crucial information to carry out further  ...  Acknowledgments: This work was funded by University of Milan (Linea B). Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/molecules23071506 pmid:29933627 fatcat:evaqtvo52zaa3eg326du5w2qem

Strategies and Challenges Involved in the Discovery of New Chemical Entities During Early-Stage Tuberculosis Drug Discovery

Geoffrey D. Coxon, Christopher B. Cooper, Stephen H. Gillespie, Timothy D. McHugh
2012 Journal of Infectious Diseases  
Because the development of a compound for treating tuberculosis is even longer than for treating other infection indications, the identification of selective, potent, and safe chemical entities early in  ...  of compound libraries, specific pharmacophores or chemical clusters, and natural products.  ...  Note Potential conflicts of interest. All authors: No reported conflicts. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest.  ... 
doi:10.1093/infdis/jis191 pmid:22448016 fatcat:mhw34agptndllhx6o6m6qzwth4

Alteration of the Route to Menaquinone towards Isochorismate-Derived Metabolites

Alexander Fries, Laura Mazzaferro, Björn Grüning, Philippe Bisel, Karin Stibal, Patrick Buchholz, Jürgen Pleiss, Georg Sprenger, Michael Müller
2019 ChemBioChem  
Chorismate and isochorismate constitute branch-point intermediates in the biosynthesis of many aromatic metabolites in microorganisms and plants.  ...  Unexpectedly, as the identified residues such as Arg107 are highly conserved (>94 %), some of the designed variations can be found in wild-type SEPHCHC synthases from other bacteria (Arg107Lys, 0.3 %).  ...  We thank Ursula Degner and Natalie Trachtmann (University of Stuttgart) for help with cloning strains F68 and F97, and Sascha Ferlaino and Lucia Robustini (University of Freiburg) for technical support  ... 
doi:10.1002/cbic.201900050 pmid:30866142 pmcid:PMC6618250 fatcat:oeldojw5rbbyrenp6he2mr4b7u

Molecular models of protein targets from Mycobacterium tuberculosis

Nelson José Freitas da Silveira, Hugo Brandão Uchôa, José Henrique Pereira, Fernanda Canduri, Luiz Augusto Basso, Mário Sérgio Palma, Diógenes Santiago Santos, Walter Filgueira de Azevedo
2005 Journal of Molecular Modeling  
There are currently more than 300 models for proteins from Mycobacterium tuberculosis genome in the database.  ...  DBMODEL-ING is a relational database, created to highlight the importance of methods of molecular modeling applied to the Mycobacterium tuberculosis genome with the aim of proposing protein-ligand docking  ...  Mycobacterium tuberculosis genome Mycobacterium tuberculosis Number of ORFs 3,924 Number of related structures 319 Number of solved protein structures 17 Number of modeled protein structures  ... 
doi:10.1007/s00894-005-0240-2 pmid:15759144 fatcat:lngpeimzbnahjcmp5dsbzrjyna

Reverse vaccinology and subtractive genomics approaches for identifying common therapeutics against Mycobacterium leprae and Mycobacterium lepromatosis

Arun Kumar Jaiswa Jaiswa, Sandeep Tiwari, Syed Babar Jamal, Letícia de Castro Oliveira, Helioswilton Sales-Campos, Leonardo Eurípedes Andrade-Silva, Carlo Jose Freire Oliveira, Preetam Ghosh, Debmalya Barh, Vasco Azevedo, Siomar C. Soares, Virmondes Rodrigues Junior (+1 others)
2021 Journal of Venomous Animals and Toxins including Tropical Diseases  
In this study, our contribution includes the prediction of vaccine targets and new putative drugs against leprosy, using reverse vaccinology and subtractive genomics.  ...  Mycobacterium leprae and Mycobacterium lepromatosis are gram-positive bacterial pathogens and the causative agents of leprosy in humans across the world.  ...  Acknowledgments The authors would like to thank the collaboration and assistance of the team members of all involved institutions. Availability of data and materials  ... 
doi:10.1590/1678-9199-jvatitd-2020-0027 pmid:33889182 pmcid:PMC8040911 fatcat:eyb2uhj5lvhw5nh2l23jhijk4y
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