A fragment merging approach towards the development of small molecule inhibitors of Mycobacterium tuberculosis EthR for use as ethionamide boosters.

With the ever-increasing instances of resistance to frontline TB drugs there is the need to develop novel strategies to fight the worldwide TB epidemic. Boosting the effect of the existing second-line antibiotic ethionamide by inhibiting the mycobacterial transcriptional repressor protein EthR is an attractive therapeutic strategy. Herein we report the use of a fragment based drug discovery approach for the structure-guided systematic merging of two fragment molecules, each binding twice to the hydrophobic cavity of EthR from M. tuberculosis. These together fill the entire binding pocket of EthR. We elaborated these fragment hits and developed small molecule inhibitors which have a 100-fold improvement of potency in vitro over the initial fragments.We also thank the Bill and Melinda Gates Foundation and the EU FP7 MM4TB Grant n°260872, the ERC-STG INTRACELLTB Grant n°260901, the Agence Nationale de la Recherche (ANR-10-EQPX-04-01), the Feder (12001407 (D-AL) Equipex Imaginex BioMed) and the Région Nord Pas de Calais, France, for providing funding to support this work.This is the final version of the article. It first appeared from the Royal Society of Chemistry via http://dx.doi.org/10.1039/C5OB02630

Unconventional surface plasmon resonance signals reveal quantitative inhibition of transcriptional repressor EthR by synthetic ligands

International audienceEthR is a mycobacterial repressor that limits the bioactivation of ethionamide, a commonly used anti-tuberculosis second-line drug. Several efforts have been deployed to identify EthR inhibitors abolishing the DNA-binding activity of the repressor. This led to the demonstration that stimulating the bioactivation of ETH through EthR inhibition could be an alternative way to fight Mycobacterium tuberculosis. We propose a new SPR methodology to study the affinity between inhibitors and EthR. Interestingly, the binding between inhibitors and immobilized EthR produced a dose dependent negative SPR signal. We demonstrated that this signal reveals the affinity of the small molecules for the repressor. The affinity constants (KD) correlated with their capacity to inhibit the binding of EthR to DNA. We hypothesize that conformational changes of EthR during ligand interaction could be responsible for this SPR signal. Practically, this unconventional result open perspectives to the development of SPR assay that would at the same time tough on the structural changes of the target upon binding with an inhibitor and on the binding constant of this interaction

Structural activation of the transcriptional repressor EthR from Mycobacterium tuberculosis by single amino acid change mimicking natural and synthetic ligands

Ethionamide is an antituberculous drug for the treatment of multidrug-resistant Mycobacterium tuberculosis. This antibiotic requires activation by the monooxygenase EthA to exert its activity. Production of EthA is controlled by the transcriptional repressor EthR, a member of the TetR family. The sensitivity of M. tuberculosis to ethionamide can be artificially enhanced using synthetic ligands of EthR that allosterically inactivate its DNA-binding activity. Comparison of several structures of EthR co-crystallized with various ligands suggested that the structural reorganization of EthR resulting in its inactivation is controlled by a limited portion of the ligand-binding-pocket. In silico simulation predicted that mutation G106W may mimic ligands. X-ray crystallography of variant G106W indeed revealed a protein structurally similar to ligand-bound EthR. Surface plasmon resonance experiments established that this variant is unable to bind DNA, while thermal shift studies demonstrated that mutation G106W stabilizes EthR as strongly as ligands. Proton NMR of the methyl regions showed a lesser contribution of exchange broadening upon ligand binding, and the same quenched dynamics was observed in apo-variant G106W. Altogether, we here show that the area surrounding Gly106 constitutes the molecular switch involved in the conformational reorganization of EthR. These results also shed light on the mechanistic of ligand-induced allosterism controlling the DNA binding properties of TetR family repressors

Intrinsic antibacterial activity of nanoparticles made of β-cyclodextrins potentiates their effect as drug nanocarriers against tuberculosis

Multi-drug-resistant tuberculosis (TB) is a major public health problem, concerning about half a million cases each year. Patients hardly adhere to the current strict treatment consisting of more than 10 000 tablets over a 2-year period. There is a clear need for efficient and better formulated medications. We have previously shown that nanoparticles made of cross-linked poly-β-cyclodextrins (pβCD) are efficient vehicles for pulmonary delivery of powerful combinations of anti-TB drugs. Here, we report that in addition to being efficient drug carriers, pβCD nanoparticles are endowed with intrinsic antibacterial properties. Empty pβCD nanoparticles are able to impair Mycobacterium tuberculosis (Mtb) establishment after pulmonary administration in mice. pβCD hamper colonization of macrophages by Mtb by interfering with lipid rafts, without inducing toxicity. Moreover, pβCD provoke macrophage apoptosis, leading to depletion of infected cells, thus creating a lung microenvironment detrimental to Mtb persistence. Taken together, our results suggest that pβCD nanoparticles loaded or not with antibiotics have an antibacterial action on their own and could be used as a carrier in drug regimen formulations effective against TB.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis.

Background: Molecular diagnostics are considered the most promising route to achievement of rapid, universal drug susceptibility testing for Mycobacterium tuberculosis complex (MTBC). We aimed to generate a WHO-endorsed catalogue of mutations to serve as a global standard for interpreting molecular information for drug resistance prediction. Methods: In this systematic analysis, we used a candidate gene approach to identify mutations associated with resistance or consistent with susceptibility for 13 WHO-endorsed antituberculosis drugs. We collected existing worldwide MTBC whole-genome sequencing data and phenotypic data from academic groups and consortia, reference laboratories, public health organisations, and published literature. We categorised phenotypes as follows: methods and critical concentrations currently endorsed by WHO (category 1); critical concentrations previously endorsed by WHO for those methods (category 2); methods or critical concentrations not currently endorsed by WHO (category 3). For each mutation, we used a contingency table of binary phenotypes and presence or absence of the mutation to compute positive predictive value, and we used Fisher's exact tests to generate odds ratios and Benjamini-Hochberg corrected p values. Mutations were graded as associated with resistance if present in at least five isolates, if the odds ratio was more than 1 with a statistically significant corrected p value, and if the lower bound of the 95% CI on the positive predictive value for phenotypic resistance was greater than 25%. A series of expert rules were applied for final confidence grading of each mutation. Findings: We analysed 41 137 MTBC isolates with phenotypic and whole-genome sequencing data from 45 countries. 38 215 MTBC isolates passed quality control steps and were included in the final analysis. 15 667 associations were computed for 13 211 unique mutations linked to one or more drugs. 1149 (7·3%) of 15 667 mutations were classified as associated with phenotypic resistance and 107 (0·7%) were deemed consistent with susceptibility. For rifampicin, isoniazid, ethambutol, fluoroquinolones, and streptomycin, the mutations' pooled sensitivity was more than 80%. Specificity was over 95% for all drugs except ethionamide (91·4%), moxifloxacin (91·6%) and ethambutol (93·3%). Only two resistance mutations were identified for bedaquiline, delamanid, clofazimine, and linezolid as prevalence of phenotypic resistance was low for these drugs. Interpretation: We present the first WHO-endorsed catalogue of molecular targets for MTBC drug susceptibility testing, which is intended to provide a global standard for resistance interpretation. The existence of this catalogue should encourage the implementation of molecular diagnostics by national tuberculosis programmes. Funding: Unitaid, Wellcome Trust, UK Medical Research Council, and Bill and Melinda Gates Foundation

Création d'outils moléculaires pour le développement d'un BCG recombinant comme vecteur vaccinal polyvalent

Doctorat en sciences biologiques -- UCL, 199

Etude du contrôle de la bio-activation de l'éthionamide et applications thérapeutiques antituberculeuses

Mycobacterium tuberculosis est l agent étiologique de la tuberculose. En raison de l épidémie de SIDA et de l apparition de souches résistantes au traitement, la tuberculose est aujourd hui la première cause de mortalité dans le monde due à une infection bactérienne. L objectif de ce travail est l amélioration du traitement de la tuberculose par l éthionamide (ETH), un antituberculeux de seconde intention. Sur le terrain, l efficacité de cet antibiotique est lourdement contrebalancée par sa toxicité, ce qui entraîne trop souvent une faible compliance des patients face à leur traitement et favorise l émergence de bacilles résistants. L ETH est une drogue qui nécessite une étape d activation afin d exercer son effet bactéricide. Ce mécanisme enzymatique est lié à la monooxygénase mycobactérienne EthA. Le répresseur transcriptionnel EthR de M. tuberculosis a été identifié comme régulateur du gène ethA et donc, par conséquent, de la bio-activation de l ETH. Nous avons approfondi l étude de ces mécanismes de contrôle entamée par nos prédécesseurs et nous avons élaboré une stratégie chimiothérapique visant à dérégler ce système afin de rendre la bactérie hypersensible à l ETH. Deux structures cristallographiques d EthR ont révélé la présence de ligands fortuits capables d inhiber la fonction répressive de cette protéine. En s inspirant de ces études structurales, et en collaboration avec une équipe de chimistes médicinaux, nous avons développé une première famille d inhibiteurs drug-like de ce répresseur et nous avons montré qu ils permettent d augmenter l action de l ETH d un facteur dix in vitro et d un facteur trois dans un modèle murin de tuberculose. A l aide de plusieurs techniques de biophysique, nous avons d une part étudié les relations structureaffinité de cette famille de composés, et d autre part révélé l importance d acides aminés clés pour l interaction inhibiteur-régulateur. Enfin, nous avons identifié très précisément la zone d EthR qui perçoit la présence du ligand dans la poche et qui est donc à l origine du changement conformationnel menant à la forme inactive du répresseur. La fixation de quatre dimères d EthR sur un opérateur de 56 pb démuni de toute signature palindromique reste une originalité et une énigme. A l aide d un criblage génétique systématique, nous avons étudié l implication de chaque paire de bases de l opérateur dans la répression du gène ethA. Ces travaux ont permis de proposer un modèle de fixation coopérative inédit d EthR sur l ADN.LILLE2-BU Santé-Recherche (593502101) / SudocSudocFranceF

Direct measurement of hydrophobic forces on cell surfaces using AFM.

Although hydrophobic forces are of great relevance in biological systems, quantifying these forces on complex biosurfaces such as cell surfaces has been difficult owing to the lack of appropriate, ultrasensitive force probes. Here, chemical force microscopy (CFM) with hydrophobic tips was used to measure local hydrophobic forces on organic surfaces and on live bacteria. On organic surfaces, we found an excellent correlation between nanoscale CFM and macroscale wettability measurements, demonstrating the sensitivity of the method toward hydrophobicity and providing novel insight into the nature of hydrophobic forces. Then, we measured hydrophobic forces associated with mycolic acids on the surface of mycobacteria, supporting the notion that these hydrophobic compounds represent an important permeation barrier to drugs