Molecular and biochemical characterisation of mycobacterial cell wall drug targets - Lipoarabinomannan

A recent surge in emergence of drug resistant strains of Mycobacterium tuberculosis, the etiological agent of tuberculosis has highlighted the importance of developing new therapeutics and devising novel strategies for effective management of this disease. The cell wall of M. tuberculosis is a major determinant of high level drug resistance demonstrated by this pathogen. Therefore pathways for the synthesis of its components and their regulation have remained an attractive drug target. In this study, the pathway for decaprenyl phosphate recycling emerges as a new target and illustrates a possible mechanism of resistance to the recently discovered anti-tubercular compounds, Benzothiazinones. Additionally, the newly identified Lac-I type transcriptional regulator IpsA, sheds light on an intricate regulatory network for synthesis of cell wall components, such as phosphatidyl inositol based lipoglycans. Since the pathway is critical for growth in members of Corynebacterineae, it provides for an untapped resource for designing novel inhibitors against the pathogenic species M. tuberculosis and Corynebacterium diphtheriae. This work also explores new approaches for design of anti-tubercular compounds against cell wall glycosyltransferases, such as ‘co-targeting’ of interacting transferases as revealed by protein-protein interaction studies and utilising the concept of ‘polar hydrophobicity’ in the design of ‘suicide inhibitors’ of transferase activity

A System for Identifying Named Entities in Biomedical Text: how Results From two Evaluations Reflect on Both the System and the Evaluations

We present a maximum entropy-based system for identifying named entities (NEs) in biomedical abstracts and present its performance in the only two biomedical named entity recognition (NER) comparative evaluations that have been held to date, namely BioCreative and Coling BioNLP. Our system obtained an exact match F-score of 83.2% in the BioCreative evaluation and 70.1% in the BioNLP evaluation. We discuss our system in detail, including its rich use of local features, attention to correct boundary identification, innovative use of external knowledge resources, including parsing and web searches, and rapid adaptation to new NE sets. We also discuss in depth problems with data annotation in the evaluations which caused the final performance to be lower than optimal

Exploring the boundaries: gene and protein identification in biomedical text

Background: Good automatic information extraction tools offer hope for automatic processing of the exploding biomedical literature, and successful named entity recognition is a key component for such tools. Methods: We present a maximum-entropy based system incorporating a diverse set of features for identifying gene and protein names in biomedical abstracts. Results: This system was entered in the BioCreative comparative evaluation and achieved a precision of 0.83 and recall of 0.84 in the “open ” evaluation and a precision of 0.78 and recall of 0.85 in the “closed ” evaluation. Conclusions: Central contributions are rich use of features derived from the training data at multiple levels of granularity, a focus on correctly identifying entity boundaries, and the innovative use of several external knowledge sources including full MEDLINE abstracts and web searches. Background The explosion of information in the biomedical domain and particularly in genetics has highlighted the need for automated text information extraction techniques. MEDLINE, the primary research database serving the biomedical community, currently contains over 14 million abstracts, with 60,000 new abstracts appearing each month. There is also an impressive number of molecular biological databases covering a

Two-Way Regulation of MmpL3 Expression Identifies and Validates Inhibitors of MmpL3 Function in Mycobacterium tuberculosis

MmpL3, an essential mycolate transporter in the inner membrane of Mycobacterium tuberculosis (Mtb), has been identified as a target of multiple, chemically diverse antitubercular drugs. However, several of these molecules seem to have secondary targets and inhibit bacterial growth by more than one mechanism. Here, we describe a cell-based assay that utilizes two-way regulation of MmpL3 expression to readily identify MmpL3-specific inhibitors. We successfully used this assay to identify a novel guanidine-based MmpL3 inhibitor from a library of 220 compounds that inhibit growth of Mtb by largely unknown mechanisms. We furthermore identified inhibitors of cytochrome bc1-aa3 oxidase as one class of off-target hits in whole-cell screens for MmpL3 inhibitors and report a novel sulfanylacetamide as a potential QcrB inhibitor

IpsA, a novel LacI-type regulator, is required for inositol-derived lipid formation in Corynebacteria and Mycobacteria

BACKGROUND: The development of new drugs against tuberculosis and diphtheria is focused on disrupting the biogenesis of the cell wall, the unique architecture of which confers resistance against current therapies. The enzymatic pathways involved in the synthesis of the cell wall by these pathogens are well understood, but the underlying regulatory mechanisms are largely unknown. RESULTS: Here, we characterize IpsA, a LacI-type transcriptional regulator conserved among Mycobacteria and Corynebacteria that plays a role in the regulation of cell wall biogenesis. IpsA triggers myo-inositol formation by activating ino1, which encodes inositol phosphate synthase. An ipsA deletion mutant of Corynebacterium glutamicum cultured on glucose displayed significantly impaired growth and presented an elongated cell morphology. Further studies revealed the absence of inositol-derived lipids in the cell wall and a complete loss of mycothiol biosynthesis. The phenotype of the C. glutamicum ipsA deletion mutant was complemented to different extend by homologs from Corynebacterium diphtheriae (dip1969) and Mycobacterium tuberculosis (rv3575), indicating the conserved function of IpsA in the pathogenic species. Additional targets of IpsA with putative functions in cell wall biogenesis were identified and IpsA was shown to bind to a conserved palindromic motif within the corresponding promoter regions. Myo-inositol was identified as an effector of IpsA, causing the dissociation of the IpsA-DNA complex in vitro. CONCLUSIONS: This characterization of IpsA function and of its regulon sheds light on the complex transcriptional control of cell wall biogenesis in the mycolata taxon and generates novel targets for drug development

Arabinogalactan and lipoarabinomannan biosynthesis: structure, biogenesis and their potential as drug targets.

Mycobacterium tuberculosis, the etiological agent of TB, remains the leading cause of mortality from a single infectious organism. The persistence of this human pathogen is associated with its distinctive lipid-rich cell wall structure that is highly impermeable to hydrophilic chemical drugs. This highly complex and unique structure is crucial for the growth, viability and virulence of M. tuberculosis, thus representing an attractive target for vaccine and drug development. It contains a large macromolecular structure known as the mycolyl–arabinogalactan–peptidoglycan complex, as well as phosphatidyl-myo-inositol derived glycolipids with potent immunomodulatory activity, notably lipomannan and lipoarabinomannan. These cell wall components are often the targets of effective chemotherapeutic agents against TB, such as ethambutol. This review focuses on the structural details and biosynthetic pathways of both arabinogalactan and lipoarabinomannan, as well as the effects of potent drugs on these important (lipo)polysaccharides. </jats:p

Genetics of Mycobacterial Arabinogalactan and Lipoarabinomannan Assembly

ABSTRACT The cell wall of Mycobacterium tuberculosis is unique in that it differs significantly from those of both Gram-negative and Gram-positive bacteria. The thick, carbohydrate- and lipid-rich cell wall with distinct lipoglycans enables mycobacteria to survive under hostile conditions such as shortage of nutrients and antimicrobial exposure. The key features of this highly complex cell wall are the mycolyl-arabinogalactan-peptidoglycan (mAGP)–based and phosphatidyl- myo -inositol–based macromolecular structures, with the latter possessing potent immunomodulatory properties. These structures are crucial for the growth, viability, and virulence of M. tuberculosis and therefore are often the targets of effective chemotherapeutic agents against tuberculosis. Over the past decade, sophisticated genomic and molecular tools have advanced our understanding of the primary structure and biosynthesis of these macromolecules. The availability of the full genome sequences of various mycobacterial species, including M. tuberculosis , Mycobacterium marinum , and Mycobacterium bovis BCG, have greatly facilitated the identification of large numbers of drug targets and antigens specific to tuberculosis. Techniques to manipulate mycobacteria have also improved extensively; the conditional expression-specialized transduction essentiality test (CESTET) is currently used to determine the essentiality of individual genes. Finally, various biosynthetic assays using either purified proteins or synthetic cell wall acceptors have been developed to study enzyme function. This article focuses on the recent advances in determining the structural details and biosynthesis of arabinogalactan, lipoarabinomannan, and related glycoconjugates. </jats:p

A system for identifying named entities in biomedical text: How results from two evaluations reflect on both the system and the evaluations. In The 2004 BioLink meeting at ISMB

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