scholarly journals Exhaustive reconstruction of the CRISPR locus in Mycobacterium tuberculosis complex using short reads

2019 ◽  
Author(s):  
Christophe Guyeux ◽  
Christophe Sola ◽  
Guislaine Refrégier
Keyword(s):  
Mycobacterium Tuberculosis ◽  
In Silico ◽  
Structural Characteristics ◽  
Computational Method ◽  
Direct Repeats ◽  
Crispr Locus ◽  
Short Read ◽  
General Rules ◽  
Genetic Mechanisms

AbstractSpoligotyping, a graphical partial display of the CRISPR locus that can be produced in vitro or in silico, is an important tool for analyzing the diversity of given Mycobacterium tuberculosis complex (MTC) isolates. As other CRISPR loci, this locus is made up of an alternation between direct repeats and spacers, and flanked by cas genes. Unveiling the genetic mechanisms of its evolution requires to have a fairly large amount of fully reconstructed loci among all MTC lineages.In this article, we point out and resolve the problem of CRISPR reconstruction based on short read sequences. We first show that more than 1/3 of the currently assembled genomes available for this complex contain a CRISPR locus erroneously reconstructed, and errors can be very significant. Second, we present a new computational method allowing this locus to be reconstructed extensively and reliably in silico using short read sequencing runs. Third, using this method, we describe new structural characteristics of CRISPR locus by lineages. We show how both the classical experimental in vitro approach and the basic in silico spoligotyping provided by existing analytic tools miss a whole diversity of this locus in MTC, by not capturing duplications, spacer and direct repeats variants, and IS6110 insertion locations. This description is extended in a second article that presents general rules for the evolution of the CRISPR locus in MTC.This work opens new perspectives for a larger exploration of CRISPR loci diversity and of mechanisms involved in its evolution and its functionality.

scholarly journals CRISPRbuilder-TB: “CRISPR-builder for tuberculosis”. Exhaustive reconstruction of the CRISPR locus in mycobacterium tuberculosis complex using SRA

2021 ◽  
Vol 17 (3) ◽  
pp. e1008500
Author(s):  
Christophe Guyeux ◽  
Christophe Sola ◽  
Camille Noûs ◽  
Guislaine Refrégier
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Bacterial Species ◽  
Direct Repeats ◽  
Crispr Locus ◽  
The Public ◽  
Whole Process ◽  
General Rules ◽  
Genetic Mechanisms ◽  
Set Up

Mycobacterium tuberculosis complex (MTC) CRISPR locus diversity has long been studied solely investigating the presence/absence of a known set of spacers. Unveiling the genetic mechanisms of its evolution requires a more exhaustive reconstruction in a large amount of representative strains. In this article, we point out and resolve, with a new pipeline, the problem of CRISPR reconstruction based directly on short read sequences in M. tuberculosis. We first show that the process we set up, that we coin as “CRISPRbuilder-TB” (https://github.com/cguyeux/CRISPRbuilder-TB), allows an efficient reconstruction of simulated or real CRISPRs, even when including complex evolutionary steps like the insertions of mobile elements. Compared to more generalist tools, the whole process is much more precise and robust, and requires only minimal manual investigation. Second, we show that more than 1/3 of the currently complete genomes available for this complex in the public databases contain largely erroneous CRISPR loci. Third, we highlight how both the classical experimental in vitro approach and the basic in silico spoligotyping provided by existing analytic tools miss a whole diversity of this locus in MTC, by not capturing duplications, spacer and direct repeats variants, and IS6110 insertion locations. This description is extended in a second article that describes MTC-CRISPR diversity and suggests general rules for its evolution. This work opens perspectives for an in-depth exploration of M. tuberculosis CRISPR loci diversity and of mechanisms involved in its evolution and its functionality, as well as its adaptation to other CRISPR locus-harboring bacterial species.

Arylquinolinecarboxamides: Synthesis, in vitro and in silico studies against Mycobacterium tuberculosis

2021 ◽  
Author(s):  
Fostino R. B. Bokosi ◽  
Richard M. Beteck ◽  
Audrey Jordaan ◽  
Ronnet Seldon ◽  
Digby F. Warner ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
In Silico ◽  
In Silico Studies

scholarly journals In silico discovery and in vitro activity of inhibitors against Mycobacterium tuberculosis 7,8-diaminopelargonic acid synthase (Mtb BioA)

2017 ◽  
Vol Volume11 ◽  
pp. 563-574 ◽  
Author(s):  
Junie Billones ◽  
Maria Constancia Carrillo ◽  
Voltaire Organo ◽  
Jamie Bernadette Sy ◽  
Nina Abigail Clavio ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
In Silico ◽  
Vitro Activity ◽  
In Vitro Activity

scholarly journals in Silico Docking and Molecular Dynamic Simulation of 3-Dehydroquinate Dehydratase from Mycobacterium Tuberculosis Through Virtual Screening and Pharmacokinetics Studies

2020 ◽  
Author(s):  
Mustafa Alhaji Isa ◽  
Muhammad M Ibrahim
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Virtual Screening ◽  
Molecular Dynamic ◽  
In Silico ◽  
Md Simulation ◽  
Binding Energies ◽  
In Silico Docking ◽  
Pharmacokinetic Properties

The 3-hydroquinate synthase (DHQase) is an enzyme that catalyzes the third step of the shikimate pathway in <i>Mycobacterium tuberculosis</i> (MTB), by converting 3-dehydroquinate into 3-dehydroshikimate. In this study, the novel inhibitors of DHQase from MTB was identified using in silico approach. The crystal structure of DHQase bound to 1,3,4-trihydroxy-5-(3-phenoxypropyl)-cyclohexane-1-carboxylic acid (CA) obtained from the Protein Data Bank (PDB ID: 3N76). The structure prepared through energy minimization and structure optimization. A total of 9699 compounds obtained from Zinc and PubChem databases capable of binding to DHQase and subjected to virtual screening through Lipinski’s rule of five and molecular docking analysis. Eight (8) compounds with good binding energies, ranged between ─8.99 to ─8.39kcal/mol were selected, better than the binding energy of ─4.93kcal/mol for CA and further filtered for pharmacokinetic properties (Absorption, Distribution, Metabolism, Excretion, and Toxicity or ADMET). Five compounds (ZINC14981770, ZINC14741224, ZINC14743698, ZINC13165465, and ZINC8442077) which had desirable pharmacokinetic properties selected for molecular dynamic (MD) simulation and molecular generalized born surface area (MM-GBSA) analyses. The results of the analyses showed that all the compounds formed stable and rigid complexes after the 50ns MD simulation and also had a lower binding as compared to CA. Therefore, these compounds considered as good inhibitors of MTB after in vitro and in vivo validation.”

scholarly journals BIOAKTIVITAS DAN STUDI IN SILICO SENYAWA TURUNAN N’-BENZOYLISONICOTINOHYDRAZIDE (4-methyl, 4-chloro dan 3,5-dinitro) PADA Mycobacterium Tuberculosis (H37RV) BAKTERI GRAM POSITIF SERTA BAKTERI GRAM NEGATIF

2019 ◽  
Vol 2 (1) ◽  
pp. 37-48
Author(s):  
Ruswanto Ruswanto
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Binding Affinity ◽  
In Silico ◽  
Tuberculosis H37rv ◽  
Mycobacterium Tuberculosis H37rv ◽  
Microtiter Assay

Isoniazid merupakan obat antituberkulosis yang memiliki aktivitas antimikobakterial yang baik yang bekerja secara aktif dengan menghambat biosintesis asam mikolat. Telah dilakukan pengujian In Vitro pada senyawa N’-(4-Methylbenzoyl) Isonicotinohydrazide N’-(4-Chlorobenzoyl) Isonicotinohydrazide dan N’-(3,5-Dinitrobenzoyl) Isonicotinohydrazide terhadap Mycobacterium tuberculosis H37Rv, bakteri gram positif serta bakteri gram negatif dengan menggunakan metode sumuran dan pada pengujian Mycobacterium tuberculosis H37Rv menggunakan metode REMA (Resazurin Microtiter Assay). Didapat nilai MIC terbaik pada senyawa N’-(3,5-Dinitrobenzoyl) Isonicotinohydrazide memiliki potensi tinggi sebagai antibakteri dengan nilai MIC 0,169 ppm terhadap bakteri e.colli. Ketiga senyawa yang diujikan pada  Mycobacterium tuberculosis H37Rv memiliki kemampuan sebagai anti tuberkulosis tetapi isoniazid lebih baik dari senyawa uji. Senyawa N’-(3,5-Dinitrobenzoyl) Isonicotinohydrazide di dockingkan pada reseptor 1KZN memiliki binding affinity yang lebih kecil dibandingkan senyawa pembanding yaitu isoniazid sebesar -6,89 kkal/mol.

scholarly journals in silico Design, ADME Prediction, Molecular Docking, Synthesis of Novel Triazoles, Indazoles & Aminopyridines and in vitro Evaluation of Antitubercular Activity

2020 ◽  
Vol 32 (11) ◽  
pp. 2713-2721
Author(s):  
S. Triveni ◽  
C. Naresh Babu ◽  
E. Bhargav ◽  
M. Vijaya Jyothi
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Molecular Docking ◽  
Drug Design ◽  
In Silico ◽  
Antitubercular Activity ◽  
Docking Studies ◽  
Luciferase Reporter ◽  
Assay Method ◽  
Adme Prediction

To design and synthesize novel triazoles, indazoles and aminopyridines from various (thiophene-2-yl)prop-2-en-1-one derivatives as antitubercular leads by in silico and in vitro methods. in silco Drug design, ADME prediction and molecular docking studies were performed to assess drug likeliness and antitubercular potential of all 30 novel triazoles, indazoles and aminopyridines. in silico Drug design studies revealed that the synthetic routes applied were appropriate according to the calculations of Swiss-ADME that measure synthetic accessibility. Most of the synthesized compounds found to have considerable binding score with enoyl ACP reductase enzyme of Mycobacterium tuberculosis. All the synthesized compounds were evaluated for antitubercular potential against Drug Resistant Mycobacterium tuberculosis H37Rv strain by Luciferase reporter assay method. Most of the synthesized compounds exhibited remarkable antitubercular potential against resistant strain.

scholarly journals In silico drug discovery strategies identified ADMET properties of decoquinate RMB041 and its potential drug targets against Mycobacterium Tuberculosis

2021 ◽  
Author(s):  
Kirsten Elke Knoll ◽  
Mietha M. van der Walt ◽  
Du toit Loots
Keyword(s):  
Mycobacterium Tuberculosis ◽  
In Silico ◽  
Drug Targets ◽  
Cellular Response ◽  
Molecular Mechanisms ◽  
Antimicrobial Agents ◽  
Screening Methods ◽  
Discovery Studio ◽  
Optimal Drug

The highly adaptive cellular response of Mycobacterium tuberculosis to various antibiotics and the high costs for clinical trials, hampers the development of novel antimicrobial agents with improved efficacy and safety. Subsequently, in silico drug screening methods are more commonly being used for the discovery and development of drugs, and have been proven useful for predicting the pharmacokinetics, toxicities, and targets, of prospective new antimicrobial agents. In this investigation, we used a reversed target fishing approach to determine potential hit targets and their possible interactions between M. tuberculosis and decoquinate RMB041, a propitious new antituberculosis compound. Two of the thirteen identified targets, Cyp130 and BlaI, were strongly proposed as optimal drug-targets for dormant M. tuberculosis, of which the first showed the highest comparative binding affinity to decoquinate RMB041. The metabolic pathways associated to the selected target proteins were compared to previously published molecular mechanisms of decoquinate RMB041 against M. tuberculosis, whereby we confirmed disrupted metabolism of proteins, cell wall components, and DNA. We also described the steps within these pathways that are inhibited and elaborated on decoquinate RMB041's activity against dormant M. tuberculosis. This compound has previously showed promising in vitro safety and good oral bioavailability, which were both supported by this in silico study. The pharmacokinetic properties and toxicity of this compound were predicted and investigated using the online tools pkCSM and SwissADME, and Discovery Studio software, which furthermore supports previous safety and bioavailability characteristics of decoquinate RMB041 for use as an antimycobacterial medication.

Indole chalcones: Design, synthesis, in vitro and in silico evaluation against Mycobacterium tuberculosis

2020 ◽  
Vol 198 ◽  
pp. 112358 ◽  
Author(s):  
Deepthi Ramesh ◽  
Annu Joji ◽  
Balaji Gowrivel Vijayakumar ◽  
Aiswarya Sethumadhavan ◽  
Maheswaran Mani ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
In Silico ◽  
Design Synthesis
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