Identification of gene targets against dormant phase Mycobacterium tuberculosis infections

<p>Abstract</p> <p>Background</p> <p><it>Mycobacterium tuberculosis</it>, the causative agent of tuberculosis (TB), infects approximately 2 billion people worldwide and is the leading cause of mortality due to infectious disease. Current TB therapy involves a regimen of four antibiotics taken over a six month period. Patient compliance, cost of drugs and increasing incidence of drug resistant <it>M. tuberculosis </it>strains have added urgency to the development of novel TB therapies. Eradication of TB is affected by the ability of the bacterium to survive up to decades in a dormant state primarily in hypoxic granulomas in the lung and to cause recurrent infections.</p> <p>Methods</p> <p>The availability of <it>M. tuberculosis </it>genome-wide DNA microarrays has lead to the publication of several gene expression studies under simulated dormancy conditions. However, no single model best replicates the conditions of human pathogenicity. In order to identify novel TB drug targets, we performed a meta-analysis of multiple published datasets from gene expression DNA microarray experiments that modeled infection leading to and including the dormant state, along with data from genome-wide insertional mutagenesis that examined gene essentiality.</p> <p>Results</p> <p>Based on the analysis of these data sets following normalization, several genome wide trends were identified and used to guide the selection of targets for therapeutic development. The trends included the significant up-regulation of genes controlled by <it>devR</it>, down-regulation of protein and ATP synthesis, and the adaptation of two-carbon metabolism to the hypoxic and nutrient limited environment of the granuloma. Promising targets for drug discovery were several regulatory elements (<it>devR/devS</it>, <it>relA</it>, <it>mprAB</it>), enzymes involved in redox balance and respiration, sulfur transport and fixation, pantothenate, isoprene, and NAD biosynthesis. The advantages and liabilities of each target are discussed in the context of enzymology, bacterial pathways, target tractability, and drug development.</p> <p>Conclusion</p> <p>Based on our bioinformatics analysis and additional discussion of in-depth biological rationale, several novel anti-TB targets have been proposed as potential opportunities to improve present therapeutic treatments for this disease.</p

The bacillary and macrophage response to hypoxia in tuberculosis and the consequences for T cell antigen recognition

M. tuberculosis is a facultative anaerobe and its characteristic pathological hallmark, the granuloma, exhibits hypoxia in humans and in most experimental models. Thus the host and bacillary adaptation to hypoxia is of central importance in understanding pathogenesis and thereby to derive new drug treatments and vaccines

Multi-omics technologies applied to tuberculosis drug discovery

Multi-omics strategies are indispensable tools in the search for new anti-tuberculosis drugs. Omics methodologies, where the ensemble of a class of biological molecules are measured and evaluated together, enable drug discovery programs to answer two fundamental questions. Firstly, in a discovery biology approach, to find new targets in druggable pathways for target-based investigation, advancing from target to lead compound. Secondly, in a discovery chemistry approach, to identify the mode of action of lead compounds derived from high-throughput screens, progressing from compound to target. The advantage of multi-omics methodologies in both of these settings is that omics approaches are unsupervised and unbiased to a priori hypotheses, making omics useful tools to confirm drug action, reveal new insights into compound activity, and discover new avenues for inquiry. This review summarizes the application of Mycobacterium tuberculosis omics technologies to the early stages of tuberculosis antimicrobial drug discovery

Characterization of mycobacterial enzymes as targets for potential antitubercular compounds.

Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis, an aerobic pathogen that establishes its infection mainly in lungs. Even if it was considered for a very long period an illness of the past, new hotspots arose at the beginning of ’90 and it is still today a global emergency. According to the 2019 WHO global report, tuberculosis is one of the top 10 causes of death worldwide.10 million new cases were estimated only in 2019 and 1.5 million people died for the disease in the same year, overall cause of the multi-drug resistant and extensively drug resistant strains. To fight back this emergency it is necessary to identify new therapeutic TB drug targets and to develop more effective drugs. In this thesis I show how it is possible to design multi-target molecules that may inhibits the M. tuberculosis salicylate synthase MbtI and the virulence factor protein phosphatase PtpB, two interesting mycobacterial druggable targets

Development and Investigation of a rabbit model of tuberculosis tissue destruction

Tuberculosis kills more people than any other bacterial disease. The characteristic tissue destruction that occurs during infection contributes to morbidity, mortality, and transmission. Tissue damage limits antibiotic effectiveness, and generates regions of immune privilege. Therefore, therapies that target tissue destruction may improve treatment outcomes. Currently, modelling tissue destruction in vivo requires the infection of large animals for prolonged periods. These models are highly variable in outcome. This makes experimentation challenging, and limits there use in testing therapeutic strategies, which in turn limits the progression of potential therapies to clinical trials. This thesis outlines the development of a highly consistent rabbit model of cavitary tuberculosis, in which novel therapies can be investigated, using small groups of animals. A method to assess pathology in vivo by breath-hold computed tomography was also developed. Matrix metalloproteinase-1 is confirmed as a potential mediator of tissue destruction, and cathepsin K is newly identified as a potential mediator of tissue destruction. These collagenases are targetable with the drugs Cipemastat and Odanacatib respectively, both of which are safe in man. This thesis provides a novel system for trialling treatments for tuberculosis in the context of human-like, tissue-destructive pathology. This may facilitate the selection of both antibiotic and non-antibiotic treatment strategies for tuberculosis. This model will allow for a better understanding of the physical, chemical, molecular, genetic and immunological characteristics and determinants of cavitary tuberculosis.Open Acces

Autophagy in the fight against tuberculosis.

Tuberculosis (TB), a chronic infectious disease mainly caused by the tubercle bacillus Mycobacterium tuberculosis, is one of the world's deadliest diseases that has afflicted humanity since ancient times. Although the number of people falling ill with TB each year is declining, its incidence in many developing countries is still a major cause of concern. Upon invading host cells by phagocytosis, M. tuberculosis can replicate within infected cells by arresting the maturation of the phagosome whose function is to target the pathogen for elimination. Host cells have mechanisms of controlling this evasion by inducing autophagy, an elaborate cellular process that targets bacteria for progressive elimination, decreasing bacterial loads within infected cells. In addition, autophagy activation also aids in the control of inflammation, contributing to a more efficient innate immune response against M. tuberculosis. Several innovative TB therapies have been envisaged based on autophagy manipulation, with some of them revealing high potential for future clinical trials and eventual implementation in healthcare systems. Thus, this review highlights the recent advances on the innate immune response regulation by autophagy upon M. tuberculosis infection and the promising new autophagy-based therapies for TB.This work was funded by Bill & Melinda Gates Foundation (subcontract on the production of high quality chemical hit series with defined, tractable targets as drug leads for tuberculosis grant awarded to the Foundation for the National Institutes of Health) (OPP1024021), Fundação para a Ciência e a Tecnologia and EU-FEDER-COMPETE for funding (FCOMP-01-0124-FEDER-028359; PTDC/BIAMIC/2779/2012). VM would like to acknowledge Fundação para a Ciência e a Tecnologia for a postdoctoral fellowship (SFRH/BPD/79531/2011).This is the accepted manuscript. The final published version is available from Mary Ann Liebert, Inc., publishers at http://dx.doi.org/10.1089/dna.2014.2745

Global analyses of TetR family transcriptional regulators in mycobacteria indicates conservation across species and diversity in regulated functions

BACKGROUND: Mycobacteria inhabit diverse niches and display high metabolic versatility. They can colonise both humans and animals and are also able to survive in the environment. In order to succeed, response to environmental cues via transcriptional regulation is required. In this study we focused on the TetR family of transcriptional regulators (TFTRs) in mycobacteria. RESULTS: We used InterPro to classify the entire complement of transcriptional regulators in 10 mycobacterial species and these analyses showed that TFTRs are the most abundant family of regulators in all species. We identified those TFTRs that are conserved across all species analysed and those that are unique to the pathogens included in the analysis. We examined genomic contexts of 663 of the conserved TFTRs and observed that the majority of TFTRs are separated by 200 bp or less from divergently oriented genes. Analyses of divergent genes indicated that the TFTRs control diverse biochemical functions not limited to efflux pumps. TFTRs typically bind to palindromic motifs and we identified 11 highly significant novel motifs in the upstream regions of divergently oriented TFTRs. The C-terminal ligand binding domain from the TFTR complement in M. tuberculosis showed great diversity in amino acid sequence but with an overall architecture common to other TFTRs. CONCLUSION: This study suggests that mycobacteria depend on TFTRs for the transcriptional control of a number of metabolic functions yet the physiological role of the majority of these regulators remain unknown. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1696-9) contains supplementary material, which is available to authorized users

Adjusting to a new home: Mycobacterium tuberculosis gene expression in response to an intracellular lifestyle.

Mycobacterium tuberculosis remains the most significant single species of bacteria causing disease in mankind. The ability of M. tuberculosis to survive and replicate within host macrophages is a pivotal step in its pathogenesis. Understanding the microenvironments that M. tuberculosis encounters within the macrophage and the adaptations that the bacterium undergoes to facilitate its survival will lead to insights into possible therapeutic targets for improved treatment of tuberculosis. This is urgently needed with the emergence of multi- and extensively drug resistant strains of M. tuberculosis. Significant advances have been made in understanding the macrophage response on encountering M. tuberculosis. Complementary information is also accumulating regarding the counter responses of M. tuberculosis during the various stages of its interactions with the host. As such, a picture is emerging delineating the gene expression of intracellular M. tuberculosis at different stages of the interaction with macrophages

Drug Repurposing

This book focuses on various aspects and applications of drug repurposing, the understanding of which is important for treating diseases. Due to the high costs and time associated with the new drug discovery process, the inclination toward drug repurposing is increasing for common as well as rare diseases. A major focus of this book is understanding the role of drug repurposing to develop drugs for infectious diseases, including antivirals, antibacterial and anticancer drugs, as well as immunotherapeutics