SInCRe—structural interactome computational resource for Mycobacterium tuberculosis

We have developed an integrated database for Mycobacterium tuberculosis H37Rv (Mtb) that collates information on protein sequences, domain assignments, functional annotation and 3D structural information along with protein–protein and protein–small molecule interactions. SInCRe (Structural Interactome Computational Resource) is developed out of CamBan (Cambridge and Bangalore) collaboration. The motivation for development of this database is to provide an integrated platform to allow easily access and interpretation of data and results obtained by all the groups in CamBan in the field of Mtb informatics. In-house algorithms and databases developed independently by various academic groups in CamBan are used to generate Mtb-specific datasets and are integrated in this database to provide a structural dimension to studies on tuberculosis. The SInCRe database readily provides information on identification of functional domains, genome-scale modelling of structures of Mtb proteins and characterization of the small-molecule binding sites within Mtb. The resource also provides structure-based function annotation, information on small-molecule binders including FDA (Food and Drug Administration)-approved drugs, protein–protein interactions (PPIs) and natural compounds that bind to pathogen proteins potentially and result in weakening or elimination of host–pathogen protein–protein interactions. Together they provide prerequisites for identification of off-target binding

Web Resources on Tuberculosis: Information, Research, and Data Analysis

Since the first edition of this book in 2013, many new tools and databases have become publicly available, as well as several have been discontinued. Here, we present an updated version of web resources on tuberculosis, providing more detailed information on some key concepts. However, the purpose of this chapter is by no means to offer an exhaustive list of all the resources available on the Internet about TB, the topic of this book. This would be a massive and perhaps futile work since the evolution of the Internet occurs at a very fast pace. Rather, this chapter concentrates on a selection of the most important, relevant and stable websites with relevance to several aspects of TB, such as research, treatment, main institutions, funding, and specialized platforms. We think this should complement all the other information already presented in this book, offering the reader a more integrated view of the disease, as well as access to new platforms and systems specialized in the analysis of data generated by a series of new technologies such as DNA sequencing

TIBLE: a web-based, freely accessible resource for small-molecule binding data for mycobacterial species

TIBLE is a web-based resource that provides easy access to data on the minimal inhibitory concentrations for small molecules against several mycobacterial species, as well as the target binding and off-target predictions for Mycobacterium tuberculosis. The current version of the database holds the activity data for more than 19 000 distinct small molecules against 39 mycobacterial species, binding data for 106 Mycobacterium tuberculosis target proteins and predictions for their potential off-targets. The resource integrates disparate public data and methods to provide easy access to the minimum inhibitory concentration and binding data, facilitation of data sharing, and identification of small molecules and targets for development of anti-tuberculosis therapeutics.Wellcome Trust Seeding Drug Discovery (101134/Z/13/Z to A.P.H., T.L.B.); MRC Newton Award (RG78439 to S.M. and T.L.B.); Programme Grant (093167/Z/10/Z to T.L.B.); Cystic Fibrosis Trust Grant (RG 70975); Wellcome Trust Investigator Award (200814/Z/16/Z to T.L.B.)

A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis

Nucleoside tri-phosphates (NTP) form an important class of small molecule ligands that participate in, and are essential to a large number of biological processes. Here, we seek to identify the NTP binding proteome (NTPome) in M. tuberculosis (M.tb), a deadly pathogen. Identifying the NTPome is useful not only for gaining functional insights of the individual proteins but also for identifying useful drug targets. From an earlier study, we had structural models of M.tb at a proteome scale from which a set of 13,858 small molecule binding pockets were identified. We use a set of NTP binding sub-structural motifs derived from a previous study and scan the M.tb pocketome, and find that 1,768 proteins or 43% of the proteome can theoretically bind NTP ligands. Using an experimental proteomics approach involving dye-ligand affinity chromatography, we confirm NTP binding to 47 different proteins, of which 4 are hypothetical proteins. Our analysis also provides the precise list of binding site residues in each case, and the probable ligand binding pose. As the list includes a number of known and potential drug targets, the identification of NTP binding can directly facilitate structure-based drug design of these targets

Structural and functional analysis of thiaminephosphate and homoserine kinases from Mycobacterium tuberculosis

Thiamine-phosphate kinase (or ATP:thiamine-phosphate phosphotransferase, ThiL) and homoserine (ThrB) kinases are essential to metabolism in Mycobacterium tuberculosis (Mtb). ThiL and ThrB respectively phosphorylate thiamine monophosphate (TMP) to thiamine diphosphate (TDP), the active form of vitamin B1, and L-homoserine to Ophosphohomoserine, critical to aspartate biosynthesis. In this study, ThiL and ThrB from Mtb were characterised structurally and functionally by producing the proteins recombinantly in E. coli. Proteins were purified by affinity, anion exchange and size exclusion chromatographies and purity checked by SDS-PAGE. ThiL and ThrB enzyme activities were confirmed and reaction products verified by high pressure liquid chromatography (HPLC). The crystal structure of ThiL was solved by molecular replacement using X-ray diffraction data. Functionally active ThiL, 36 kDa, produced hexagonal crystals belonging to space group P6122 with one monomer per asymmetric unit. Structurally it is related to ThiL from other organisms with minor structural deviations. Enzymatically active ThrB, 33 kDa, was crystallised. However, crystals failed to diffract Xrays to a suitable resolution. ThiL and ThrB could act as possible anti-TB drug targets against Mtb.Dissertation (MSc)--University of Pretoria, 2017.BiochemistryMScUnrestricte

SInCRe-structural interactome computational resource for Mycobacterium tuberculosis

We have developed an integrated database for Mycobacterium tuberculosis H37Rv (Mtb) that collates information on protein sequences, domain assignments, functional annotation and 3D structural information along with protein-protein and protein-small molecule interactions. SInCRe (Structural Interactome Computational Resource) is developed out of CamBan (Cambridge and Bangalore) collaboration. The motivation for development of this database is to provide an integrated platform to allow easily access and interpretation of data and results obtained by all the groups in CamBan in the field of Mtb informatics. In-house algorithms and databases developed independently by various academic groups in CamBan are used to generate Mtb-specific datasets and are integrated in this database to provide a structural dimension to studies on tuberculosis. The SInCRe database readily provides information on identification of functional domains, genome-scale modelling of structures of Mtb proteins and characterization of the small-molecule binding sites within Mtb. The resource also provides structure-based function annotation, information on small-molecule binders including FDA (Food and Drug Administration)-approved drugs, protein-protein interactions (PPIs) and natural compounds that bind to pathogen proteins potentially and result in weakening or elimination of host-pathogen protein-protein interactions. Together they provide prerequisites for identification of off-target binding