Machine learning and docking models for Mycobacterium tuberculosis topoisomerase I

There is a shortage of compounds that are directed towards new targets apart from those targeted by the FDA approved drugs used against Mycobacterium tuberculosis. Topoisomerase I (Mttopo I) is an essential mycobacterial enzyme and a promising target in this regard. However, it suffers from a shortage of known inhibitors. We have previously used computational approaches such as homology modeling and docking to propose 38 FDA approved drugs for testing and identified several active molecules. To follow on from this, we now describe the in vitro testing of a library of 639 compounds. These data were used to create machine learning models for Mttopo I which were further validated. The combined Mttopo I Bayesian model had a 5 fold cross validation receiver operator characteristic of 0.74 and sensitivity, specificity and concordance values above 0.76 and was used to select commercially available compounds for testing in vitro. The recently described crystal structure of Mttopo I was also compared with the previously described homology model and then used to dock the Mttopo I actives norclomipramine and imipramine. In summary, we describe our efforts to identify small molecule inhibitors of Mttopo I using a combination of machine learning modeling and docking studies in conjunction with screening of the selected molecules for enzyme inhibition. We demonstrate the experimental inhibition of Mttopo I by small molecule inhibitors and show that the enzyme can be readily targeted for lead molecule development.

Seroprevalence and risk factors associated with Visna/Maedi virus in semi-intensive lamb-producing flocks in northwestern Spain

A cross-sectional study was carried out to determine Visna/Maedi virus (VMV) seroprevalence and risk factors in semi-intensive lamb-producing flocks as a prelude to establishing a monitoring program in northwestern (NW) Spain. A total of 15,155 serum samples were taken from 78 commercial flocks and were submitted to an indirect VMV ELISA. Association between potential risk factors and seroprevalence at the flock level was assessed using a multivariable logistic regression model. A Generalized Estimating Equations (GEE) model and Exhaustive Chi-squared Automatic Interaction Detector (CHAID) were used to determine the seropositivity against VMV at the individual animal level. Individual seropositivity was 24.8% while 52.6% of the flocks examined had a true seroprevalence ≥1%. Flock size and introduction of new animals in the flock were significantly associated with seropositivity at the flock level. Flock size, sheep-goat contact, type of housing of lambs prior to weaning and age were significantly associated with individual VMV seropositivity. Confinement of lambs in preweaning lamb groups and high sheep-goat contact, regardless of the low number of goats per flock, were risk factors associated with individual VMV seropositivity, suggesting that these two factors are crucial for VMV control in semi-intensive lamb-producing flocks. These factors should be considered for developing more efficient strategies that will reduce the rate of VMV transmission.

Imatinib-ULS-lysozyme: a proximal tubular cell-targeted conjugate of imatinib for the treatment of renal diseases

The anticancer drug imatinib is an inhibitor of the platelet-derived growth factor receptor (PDGFR) kinases, which are involved in the pathogenesis of fibrotic diseases. In the current study we investigated the delivery of imatinib to the proximal tubular cells of the kidneys and evaluated the potential antifibrotic effects of imatinib in tubulointerstitial fibrosis. Coupling of imatinib to the low molecular weight protein lysozyme via the platinum (II)-based linker ULS yielded a 0.8:1 drug-carrier conjugate that rapidly accumulated in the proximal tubular cells upon intravenous and intraperitoneal administration. The bioavailability of intraperitoneally administered imatinib-ULS-lysozyme was 100%. Renal imatinib levels persisted for up to 3 days after a single injection of imatinib-ULS-lysozyme. Compared with an equal dose imatinib mesylate, imatinib-ULS-lysozyme resulted in a 30- and 15-fold higher renal exposure of imatinib, for intravenous and intraperitoneal administration respectively. Imatinib-ULS-lysozyme could not be detected in the heart, which is the organ at risk for side-effects of prolonged treatment with imatinib. The efficacy of imatinib-ULS-lysozyme in the treatment of tubulointerstitial fibrosis was evaluated in the unilateral ureteral obstruction (UUO) model in mice. Three days UUO resulted in all signs of early fibrosis, i.e. an increased deposition of matrix and production of profibrotic factors. Although a moderately increased activity of PDGFR-β was observed, the profibrotic phenotype could not be inhibited with imatinib mesylate or with imatinib-ULS-lysozyme. Further evaluation of imatinib mesylate and imatinib-ULS-lysozyme is therefore warranted in an animal model of renal disease in which the activation of PDGFR-β is more pronounced.

Intracerebral implantation of hydrogel-coupled adhesion peptides: tissue reaction

Arg-Gly-Asp peptides (RGD) were synthesized and chemically coupled to the bulk of N-(2-hydroxypropyl) methacrylamide-based polymer hydrogels. Fourier Transform Infrared Spectroscopy (FTIR) and amino acid analysis confirmed the peptide coupling to the polymer. Activated and control (unmodified) polymer matrices were stereotaxically implanted in the striata of rat brains, and two months later the brains were processed for immunohistochemistry using antibodies for glial acidic fibrillary protein (GFAP), laminin and neurofilaments. RGD-containing polymer matrices promoted stronger adhesion to the host tissue than the unmodified polymer matrices. In addition, the RGD-grafted polymer implants promoted and supported the growth and spread of GFAP-positive glial tissue onto and into the hydrogels. Neurofilament-positive fibers were also seen running along the surface of the polymer and, in some instances, penetrating the matrix. These findings are discussed in the context of using bioactive polymers as a new approach for promoting tissue repair and axonal regeneration of damaged structures of the central nervous system.