scholarly journals Structural and molecular dynamics of Mycobacterium tuberculosis malic enzyme, a potential anti-TB drug target

2020 ◽  
Author(s):  
Kalistyn H. Burley ◽  
Bonnie J. Cuthbert ◽  
Piyali Basu ◽  
Jane Newcombe ◽  
Ervin M. Irimpan ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Cell Wall ◽  
Mycobacterium Tuberculosis ◽  
Malic Enzyme ◽  
Drug Targets ◽  
Reducing Power ◽  
Md Simulations ◽  
Oligomeric State ◽  
Effects Of Ph ◽  
Multiple Conformations

AbstractTuberculosis (TB) is the most lethal bacterial infectious disease worldwide. It is notoriously difficult to treat, requiring a cocktail of antibiotics administered over many months. The dense, waxy outer membrane of the TB-causing agent, Mycobacterium tuberculosis (Mtb), acts as a formidable barrier against uptake of antibiotics. Subsequently, enzymes involved in maintaining the integrity of the Mtb cell wall are promising drug targets. Recently, we demonstrated that Mtb lacking malic enzyme (MEZ) has altered cell wall lipid composition and attenuated uptake by macrophages. These results suggest that MEZ provides the required reducing power for lipid biosynthesis. Here, we present the X-ray crystal structure of MEZ to 3.6 Å resolution and compare it with known structures of prokaryotic and eukaryotic malic enzymes. We use biochemical assays to determine its oligomeric state and to evaluate the effects of pH and allosteric regulators on its kinetics and thermal stability. To assess the interactions between MEZ and its substrate malate and cofactors, Mn2+ and NAD(P)+, we ran a series of molecular dynamics (MD) simulations. First, the MD analysis corroborates our empirical observations that MEZ is unusually disordered, which persists even with the addition of substrate and cofactors. Second, the MD simulations reveal that MEZ subunits alternate between open and closed states and that MEZ can stably bind its NAD(P)+ cofactor in multiple conformations, including an inactive, compact NAD+ form. Together the structure of MEZ and insights from its dynamics can be harnessed to inform the design of MEZ inhibitors that target Mtb.

scholarly journals Molecular Investigation of Resistance to the Antituberculous Drug Ethionamide in Multidrug-Resistant Clinical Isolates ofMycobacterium tuberculosis

2010 ◽  
Vol 55 (1) ◽  
pp. 355-360 ◽  
Author(s):  
F. Brossier ◽  
N. Veziris ◽  
C. Truffot-Pernot ◽  
V. Jarlier ◽  
W. Sougakoff
Keyword(s):  
Cell Wall ◽  
Mycobacterium Tuberculosis ◽  
Drug Targets ◽  
Nadh Dehydrogenase ◽  
Multidrug Resistant ◽  
Clinical Isolates ◽  
Cell Wall Biosynthesis ◽  
Molecular Investigation ◽  
Antituberculous Drug ◽  
Resistant Cells

ABSTRACTEthionamide (ETH) needs to be activated by the mono-oxygenase EthA, which is regulated by EthR, in order to be active againstMycobacterium tuberculosis. The activated drug targets the enzyme InhA, which is involved in cell wall biosynthesis. Resistance to ETH has been reported to result from various mechanisms, including mutations altering EthA/EthR, InhA and its promoter, the NADH dehydrogenase encoded byndh, and the MshA enzyme, involved in mycothiol biosynthesis. We searched for such mutations in 87 clinical isolates: 47 ETH-resistant (ETHr) isolates, 24 ETH-susceptible (ETHs) isolates, and 16 isolates susceptible to ETH but displaying an intermediate proportion of resistant cells (ETHSip; defined as ≥1% but <10% resistant cells). In 81% (38/47) of the ETHrisolates, we found mutations inethA,ethR, orinhAor its promoter, which mostly corresponded to new alterations inethAandethR. The 9 ETHrisolates without a mutation in these three genes (9/47, 19%) had no mutation inndh, and a single isolate had a mutation inmshA. Of the 16 ETHSipisolates, 7 had a mutation inethA, 8 had no detectable mutation, and 1 had a mutation inmshA. Finally, of the 24 ETHsisolates, 23 had no mutation in the studied genes and 1 displayed a yet unknown mutation in theinhApromoter. Globally, the mechanism of resistance to ETH remained unknown for 19% of the ETHrisolates, highlighting the complexity of the mechanisms of ETH resistance inM. tuberculosis.

scholarly journals Data for Molecular Dynamics Simulations of Escherichia Coli Cytochrome Bd Oxidase with the Amber Force Field

2021 ◽  
Author(s):  
Surl-Hee Ahn ◽  
Christian Seitz ◽  
Vinicius Cruzeiro ◽  
James McCammon ◽  
Andreas Goetz
Keyword(s):  
Escherichia Coli ◽  
Molecular Dynamics ◽  
Force Field ◽  
Drug Targets ◽  
Food Poisoning ◽  
Md Simulations ◽  
Data Bank ◽  
Low Oxygen ◽  
Amber Force Field ◽  
E Coli

<div> <div> <div> <div> <p>Cytochrome <i>bd</i>-type quinol oxidase is an important metalloenzyme that allows many bacteria to survive in low oxygen conditions. Since bd oxidase is found in many prokaryotes but not in eukaryotes, it has emerged as a promising bacterial drug target. Examples of organisms containing bd oxidases include the <i>Mycobacterium tuberculosis (Mtb)</i> bacterium that causes tuberculosis (TB) in humans, the <i>Vibrio cholerae</i> bacterium that causes cholera, the <i>Pseudomonas aeruginosa</i> bacterium that contributes to antibiotic resistance and sepsis, and the <i>Campylobacter jejuni</i> bacterium that causes food poisoning. <i>Escherichia coli (E. coli)</i> is another organism exhibiting the cytochrome <i>bd</i> oxidase. Since it has the highest sequence identity to <i>Mtb</i> (36 %) and we are ultimately interested in finding drug targets for TB, we have built parameters for the <i>E. coli bd </i>oxidase (Protein Data Bank ID number: 6RKO) that are compatible with the all-atom Amber ff14SB force field for molecular dynamics (MD) simulations. Specifically, we built parameters for the three heme cofactors present in all species of bacterial cytochrome <i>bd</i>-type oxidases (heme b<sub>558</sub>, heme b<sub>595</sub>, and heme d) along with their axial ligands. This data report includes the parameter files that can be used with Amber's LEaP program to generate input files for MD simulations using the Amber software package. We also provide the PDB data files of the initial model both by itself and solvated with TIP3P water molecules and counterions. </p> </div> </div> </div> </div>

scholarly journals Molecular Docking, Dynamics Simulation, and Scanning Electron Microscopy (SEM) Examination of Clinically Isolated Mycobacterium tuberculosis by Ursolic Acid: A Pentacyclic Triterpenes

2019 ◽  
Vol 19 (2) ◽  
pp. 328
Author(s):  
Dian Ayu Eka Pitaloka ◽  
Sophi Damayanti ◽  
Aluicia Anita Artarini ◽  
Elin Yulinah Sukandar
Keyword(s):  
Electron Microscopy ◽  
Molecular Dynamics ◽  
Scanning Electron Microscopy ◽  
Cell Wall ◽  
Mycobacterium Tuberculosis ◽  
Ursolic Acid ◽  
Resistant Strain ◽  
Dynamics Simulation ◽  
Computational Docking ◽  
Scanning Electron

The purpose of this study was to analyze the inhibitory action of ursolic acid (UA) as an antitubercular agent by computational docking studies and molecular dynamics simulations. The effect of UA on the cell wall of Mycobacterium tuberculosis (MTB) was evaluated by using Scanning Electron Microscopy (SEM). UA was used as a ligand for molecular interaction and investigate its binding activities to a group of proteins involved in the growth of MTB and the biosynthesis of the cell wall. Computational docking analysis was performed by using autodock 4.2.6 based on scoring functions. UA binding was confirmed by 30 ns molecular dynamics simulation using gromacs 5.1.1. H37Rv sensitive strain and isoniazid-resistant strain were used in the SEM study. UA showed to have the optimum binding affinity to inhA (Two-trans-enoyl-ACP reductase enzyme involved in elongation of fatty acid) with the binding energy of -9.2 kcal/mol. The dynamic simulation showed that the UA-inhA complex relatively stable and found to establish hydrogen bond with Thr196 and Ile194. SEM analysis confirms that UA treatment in both sensitive strain and resistant strain affected the morphology cell wall of MTB. This result indicated that UA could be one of the potential ligands for the development of new antituberculosis drugs.

scholarly journals Multiple Mutations in Mycobacterium tuberculosis MmpL3 Increase Resistance to MmpL3 Inhibitors

mSphere ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Matthew B. McNeil ◽  
Theresa O’Malley ◽  
Devon Dennison ◽  
Catherine D. Shelton ◽  
Bjorn Sunde ◽  
...  
Keyword(s):  
Cell Wall ◽  
Mycobacterium Tuberculosis ◽  
Drug Targets ◽  
New Drugs ◽  
Content Type ◽  
Mechanism Of Resistance ◽  
Primary Mechanism ◽  
Resistant Mutants ◽  
Mycobacterial Cell Wall

ABSTRACT The Mycobacterium tuberculosis protein MmpL3 performs an essential role in cell wall synthesis, since it effects the transport of trehalose monomycolates across the inner membrane. Numerous structurally diverse pharmacophores have been identified as inhibitors of MmpL3 largely based on the identification of resistant isolates with mutations in MmpL3. For some compounds, it is possible there are different primary or secondary targets. Here, we have investigated resistance to the spiral amine class of compounds. Isolation and sequencing of resistant mutants demonstrated that all had mutations in MmpL3. We hypothesized that if additional targets of this pharmacophore existed, then successive rounds to generate resistant isolates might reveal mutations in other loci. Since compounds were still active against resistant isolates, albeit with reduced potency, we isolated resistant mutants in this background at higher concentrations. After a second round of isolation with the spiral amine, we found additional mutations in MmpL3. To increase our chance of finding alternative targets, we ran a third round of isolation using a different molecule scaffold (AU1235, an adamantyl urea). Surprisingly, we obtained further mutations in MmpL3. Multiple mutations in MmpL3 increased the level and spectrum of resistance to different pharmacophores but did not incur a fitness cost in vitro. These results support the hypothesis that MmpL3 is the primary mechanism of resistance and likely target for these pharmacophores. IMPORTANCE Mycobacterium tuberculosis is a major global human pathogen, and new drugs and new drug targets are urgently required. Cell wall biosynthesis is a major target of current tuberculosis drugs and of new agents under development. Several new classes of molecules appear to have the same target, MmpL3, which is involved in the export and synthesis of the mycobacterial cell wall. However, there is still debate over whether MmpL3 is the primary or only target for these classes. We wanted to confirm the mechanism of resistance for one series. We identified mutations in MmpL3 which led to resistance to the spiral amine series. High-level resistance to these compounds and two other series was conferred by multiple mutations in the same protein (MmpL3). These mutations did not reduce growth rate in culture. These results support the hypothesis that MmpL3 is the primary mechanism of resistance and likely target for these pharmacophores.

scholarly journals A Microbiological, Toxicological, and Biochemical Study of the Effects of Fucoxanthin, a Marine Carotenoid, on Mycobacterium tuberculosis and the Enzymes Implicated in Its Cell Wall: A Link Between Mycobacterial Infection and Autoimmune Diseases

Marine Drugs ◽  
2019 ◽  
Vol 17 (11) ◽  
pp. 641 ◽  
Author(s):  
Miroslava Šudomová ◽  
Mohammad Shariati ◽  
Javier Echeverría ◽  
Ioana Berindan-Neagoe ◽  
Seyed Nabavi ◽  
...  
Keyword(s):  
Cell Wall ◽  
Mycobacterium Tuberculosis ◽  
Autoimmune Diseases ◽  
Drug Targets ◽  
Bacterial Infections ◽  
Animal Studies ◽  
Biochemical Study ◽  
Mycobacterial Infection ◽  
Susceptible Host ◽  
Standard Drug

This study explored the antitubercular properties of fucoxanthin, a marine carotenoid, against clinical isolates of Mycobacterium tuberculosis (Mtb). Two vital enzymes involved in Mtb cell wall biosynthesis, UDP-galactopyranose mutase (UGM) and arylamine-N-acetyltransferase (TBNAT), were selected as drug targets to reveal the mechanism underlying the antitubercular effect of fucoxanthin. The obtained results showed that fucoxanthin showed a clear bacteriostatic action against the all Mtb strains tested, with minimum inhibitory concentrations (MIC) ranging from 2.8 to 4.1 µM, along with a good degree of selectivity index (ranging from 6.1 to 8.9) based on cellular toxicity evaluation compared with standard drug isoniazid (INH). The potent inhibitory actions of fucoxanthin and standard uridine-5’-diphosphate against UGM were recorded to be 98.2% and 99.2%, respectively. TBNAT was potently inactivated by fucoxanthin (half maximal inhibitory concentration (IC50) = 4.8 µM; 99.1% inhibition) as compared to INH (IC50 = 5.9 µM; 97.4% inhibition). Further, molecular docking approaches were achieved to endorse and rationalize the biological findings along with envisaging structure-activity relationships. Since the clinical evidence of the last decade has confirmed the correlation between bacterial infections and autoimmune diseases, in this study we have discussed the linkage between infection with Mtb and autoimmune diseases based on previous clinical observations and animal studies. In conclusion, we propose that fucoxanthin could demonstrate great therapeutic value for the treatment of tuberculosis by acting on multiple targets through a bacteriostatic effect as well as by inhibiting UGM and TBNAT. Such outcomes may lead to avoiding or decreasing the susceptibility to autoimmune diseases associated with Mtb infection in a genetically susceptible host.

scholarly journals Novel drug targets for Mycobacterium tuberculosis: 2-heterostyrylbenzimidazoles as inhibitors of cell wall protein synthesis

2017 ◽  
Vol 11 (1) ◽  
Author(s):  
Mohana Rao Anguru ◽  
Ashok Kumar Taduri ◽  
Rama Devi Bhoomireddy ◽  
Malathi Jojula ◽  
Shravan Kumar Gunda
Keyword(s):  
Cell Wall ◽  
Protein Synthesis ◽  
Mycobacterium Tuberculosis ◽  
Drug Targets ◽  
Cell Wall Protein ◽  
Novel Drug ◽  
Novel Drug Targets

scholarly journals Revealing Solvent-Dependent Folding Behavior of Mycolic Acids from Mycobacterium Tuberculosis by Advanced Simulation Analysis

2018 ◽  
Author(s):  
Wilma Groenewald ◽  
Ricardo Parra Cruz ◽  
Christof Jaeger ◽  
Anna Croft
Keyword(s):  
Cell Wall ◽  
Mycobacterium Tuberculosis ◽  
Functional Groups ◽  
Bacterial Cell ◽  
Simulation Analysis ◽  
Md Simulations ◽  
Bacterial Cell Wall ◽  
Mycolic Acids ◽  
Conformational Preferences ◽  
Cyclopropyl Group

<p>Mycobacterium tuberculosis remains a persistent pathogen, partly due to its lipid rich cell wall, of which mycolic acids (MAs) are a major component. The fluidity and conformational flexibilities of different MAs in the bacterial cell wall significantly influence its properties, function, and observed pathogenicity, thus a proper conformational description of different MAs in different environments (e.g. in vacuum, in solution, in monolayers) can inform about their potential role in the complex setup of the bacterial cell wall. Previously, we have shown that molecular-dynamics (MD) simulations of MA folding <i>in vacuo</i>can be used to characterise MA conformers in seven groupings relating to bending at the functional groups (W, U and Z-conformations). Providing a new OPLS-based forcefield parameterisation for the critical cyclopropyl group of MAs and extensive simulations in explicit solvents (TIP4P water, hexane) we now present a more complete picture of MA folding properties together with improved simulation analysis techniques. We show that the ‘WUZ’ distance-based analysis can be used pinpoint conformers with hairpin bends at the functional groups, with these conformers constituting only a fraction of accessible conformations. Applying principle component analysis (PCA) and refinement using free energy landscapes (FELs), we are able to discriminate a complete and unique set of conformational preferences for representative alpha-, methoxy-, and keto-MAs, with overall preference for folded conformations. A control backbone-MA without any mero-chain functional groups showed significantly less folding in the mero-chain, confirming the role of functionalisation in directing folding. Keto-MA showed the highest percentage of WUZ-type conformations and, in particular, a tendency to fold at its alpha-methyl trans-cyclopropane group, in agreement with results from Villeneuve <i>et al.</i>MAs demonstrate similar folding in vacuum and water, with a majority of folded conformations around the W-conformation, although the molecules are more flexible in vacuum than in water. Exchange between conformations, with a disperse distribution that includes unfolded conformers, is common in hexane for all MAs, although with more organisation for Keto-MA. Globular, folded conformations are newly defined and may be specifically relevant in biofilms.</p>

scholarly journals Insights from Molecular Dynamics Simulations for GPCR Drug Discovery

2019 ◽  
Author(s):  
Ye Zou ◽  
John Ewalt ◽  
Ho-Leung Ng
Keyword(s):  
Molecular Dynamics ◽  
Drug Discovery ◽  
G Protein ◽  
Drug Targets ◽  
Conformational Dynamics ◽  
Md Simulations ◽  
Protein Activation ◽  
Downstream Signaling ◽  
Dynamics Simulations ◽  
G Protein Coupled

G protein-coupled receptors (GPCRs) are critical drug targets. GPCRs convey signals from the extracellular to the intracellular environment through G proteins. There is evidence that some ligands that bind to the GPCRs activate different downstream signaling pathways. G protein activation or -arrestin biased signaling involves ligands binding to receptors and stabilizing conformations that trigger a specific pathway. Molecular dynamics (MD) simulations are especially valuable for obtaining detailed mechanistic information, including identification of allosteric sites and understanding modulators' interactions between receptors and ligands. Here, we highlight recent simulation studies and methods used to study biased G protein-coupled receptor signaling and their conformational dynamics. We also highlight applications of MD simulations to drug discovery.

scholarly journals Molecular Dynamics Reveals the Effects of Temperature on Critical SARS-CoV-2 Proteins

2021 ◽  
Author(s):  
Paul Morgan ◽  
Chih-Wen Shu
Keyword(s):  
Molecular Dynamics ◽  
Drug Targets ◽  
Rna Virus ◽  
Nonstructural Protein ◽  
Md Simulations ◽  
Effect Of Temperature ◽  
Temperature Variations ◽  
Serious Infection ◽  
Critical Residues ◽  
The Stability

ABSTRACTSevere Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a newly identified RNA virus that causes the serious infection Coronavirus Disease 2019 (COVID-19). The incidence of COVID-19 is still increasing worldwide despite the summer heat and cool winter. However, little is known about seasonal stability of SARS-CoV-2. Herein, we employ Molecular Dynamics (MD) simulations to explore the effect of temperature on four critical SARS-CoV-2 proteins. Our work demonstrates that the spike Receptor Binding Domain (RBD), Main protease (Mpro), and nonstructural protein 3 (macro X) possesses extreme thermos-stability when subjected to temperature variations rendering them attractive drug targets. Furthermore, our findings suggest that these four proteins are well adapted to habitable temperatures on earth and are largely insensitive to cold and warm climates. Furthermore, we report that the critical residues in SARS-CoV-2 RBD were less responsive to temperature variations as compared to the critical residues in SARS-CoV. As such, extreme summer and winter climates, and the transition between the two seasons, are expected to have a negligible effect on the stability of SARS-CoV-2 which will marginally suppress transmission rates until effective therapeutics are available world-wide.

Molecular Dynamics Simulations of Adenosine Receptors: Advances, Applications and Trends

2019 ◽  
Vol 25 (7) ◽  
pp. 783-816 ◽  
Author(s):  
Nizar A. Al-Shar'i ◽  
Qosay A. Al-Balas
Keyword(s):  
Molecular Dynamics ◽  
Adenosine Receptors ◽  
Drug Targets ◽  
Therapeutic Potential ◽  
Relevant Literature ◽  
Md Simulations ◽  
Structural Basis ◽  
Structural And Functional Properties ◽  
Starting Point ◽  
Dynamics Simulations

: Adenosine receptors (ARs) are transmembrane proteins that belong to the G protein-coupled receptors (GPCRs) superfamily and mediate the biological functions of adenosine. To date, four AR subtypes are known, namely A1, A2A, A2B and A3 that exhibit different signaling pathways, tissue localization, and mechanisms of activation. Moreover, the widespread ARs and their implication in numerous physiological and pathophysiological conditions had made them pivotal therapeutic targets for developing clinically effective agents. : The crystallographic success in identifying the 3D crystal structures of A2A and A1 ARs has dramatically enriched our understanding of their structural and functional properties such as ligand binding and signal transduction. This, in turn, has provided a structural basis for a larger contribution of computational methods, particularly molecular dynamics (MD) simulations, toward further investigation of their molecular properties and designing bioactive ligands with therapeutic potential. MD simulation has been proved to be an invaluable tool in investigating ARs and providing answers to some critical questions. For example, MD has been applied in studying ARs in terms of ligand-receptor interactions, molecular recognition, allosteric modulations, dimerization, and mechanisms of activation, collectively aiding in the design of subtype selective ligands. : In this review, we focused on the advances and different applications of MD simulations utilized to study the structural and functional aspects of ARs that can foster the structure-based design of drug candidates. In addition, relevant literature was briefly discussed which establishes a starting point for future advances in the field of drug discovery to this pivotal group of drug targets.

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