A high content screening assay for discovery of antimycobacterial compounds based on primary human macrophages infected with virulent Mycobacterium tuberculosis

Prioritization of novel anti-infective stilbene derivatives by combining metabolomic data organization and a stringent 3R-infection model in a knowledge graph

The rising threat of multidrug-resistant tuberculosis, caused by Mycobacterium tuberculosis, underscores the urgent need for new therapeutic solutions to tackle the challenge of antibiotic resistance. The current study utilized an innovative 3R infection model featuring the amoeba Dictyostelium discoideum infected with Mycobacterium marinum, serving as stand-ins for macrophages and M. tuberculosis, respectively. This high-throughput phenotypic assay allowed for the evaluation of more specific anti-infective activities that may be less prone to resistance mechanisms. To discover novel anti-infective compounds, a diverse collection of 1600 plant NEs from the Pierre Fabre Library was screened using the latter assay. Concurrently, these NEs underwent untargeted UHPLC-HRMS/MS analysis. The biological screening flagged the NE from Stauntonia brunoniana as one of the anti-infective hit NEs. High-resolution HPLC micro-fractionation coupled with bioactivity profiling was employed to highlight the natural products driving this bioactivity. Stilbenes were eventually identified as the primary active compounds in the bioactive fractions. A knowledge graph was then used to leverage the heterogeneous data integrated into it to make a rational selection of stilbene-rich NEs. Using both CANOPUS chemical classes and Jaccard similarity indices to compare features within the metabolome of the 1600 plant NEs collection, 14 NEs rich in stilbenes were retrieved. Among those, the roots of Gnetum edule were flagged as possessing broader chemo-diversity in their stilbene content, along with the corresponding NE also being a strict anti-infective. Eventually, a total of 11 stilbene oligomers were isolated from G. edule and fully characterized by NMR with their absolute stereochemistry established through electronic circular dichroism. Six of these compounds are new since they possess a stereochemistry which was never described in the literature to the best of our knowledge. All of them were assessed for their anti-infective activity and (-)-gnetuhainin M was reported as having the highest anti-infective activity with an IC50 of 22.22 μM.

Exploiting cAMP signaling in Mycobacterium tuberculosis for drug discovery

Mycobacterium tuberculosis (Mtb) replicates within host macrophages by adapting to the stressful and nutritionally constrained environments in these cells. Exploiting these adaptations for drug discovery has revealed that perturbing cAMP signaling can restrict Mtb growth in macrophages. Specifically, compounds that agonize or stimulate the bacterial enzyme, Rv1625c/Cya, induce cAMP synthesis and this interferes with the ability of Mtb to metabolize cholesterol. In murine tuberculosis (TB) infection models, Rv1625c/Cya agonists contribute to reducing relapse and shortening combination treatments, highlighting the therapeutic potential for this class of compounds. More recently, cAMP signaling has been implicated in regulating fatty acid utilization by Mtb. Thus, a new model is beginning to emerge in which cAMP regulates the utilization of host lipids by Mtb during infection, and this could provide new targets for TB drug development. Here, we summarize the current understanding of cAMP signaling in Mtb with a focus on our understanding of how cAMP signaling impacts Mtb physiology during infection. We also discuss additional cAMP-related drug targets in Mtb and other bacterial pathogens that may have therapeutic potential.

Glycogen synthase kinase 3 inhibition controls Mycobacterium tuberculosis infection

Compounds targeting host control of infectious diseases provide an attractive alternative to antimicrobials. A phenotypic screen of a kinase library identified compounds targeting glycogen synthase kinase 3 as potent inhibitors of Mycobacterium tuberculosis (Mtb) intracellular growth in the human THP-1 cell line and primary human monocytes-derived macrophages (hMDM). CRISPR knockouts and siRNA silencing showed that GSK3 isoforms are needed for the growth of Mtb and that a selected compound, P-4423632 targets GSK3β. GSK3 inhibition was associated with macrophage apoptosis governed by the Mtb secreted protein tyrosine phosphatase A (PtpA). Phospho-proteome analysis of macrophages response to infection revealed a wide array of host signaling and apoptosis pathways controlled by GSK3 and targeted by P-4423632. P-4423632 was additionally found to be active against other intracellular pathogens. Our findings strengthen the notion that targeting host signaling to promote the infected cell's innate antimicrobial capacity is a feasible and attractive host-directed therapy approach.

Identification of Small Molecule Inhibitors against Mycobacteria in Activated Macrophages

Mycobacterial pathogens are intrinsically resistant to many available antibiotics, making treatment extremely challenging, especially in immunocompromised individuals and patients with underlying and chronic lung conditions. Even with lengthy therapy and the use of a combination of antibiotics, clinical success for non-tuberculous mycobacteria (NTM) is achieved in fewer than half of the cases. The need for novel antibiotics that are effective against NTM is urgent. To identify such new compounds, a whole cell high-throughput screen (HTS) was performed in this study. Compounds from the Chembridge DIVERSet library were tested for their ability to inhibit intracellular survival of M. avium subsp. hominissuis (MAH) expressing dtTomato protein, using fluorescence as a readout. Fifty-eight compounds were identified to significantly inhibit fluorescent readings of MAH. In subsequent assays, it was found that treatment of MAH-infected THP-1 macrophages with 27 of 58 hit compounds led to a significant reduction in intracellular viable bacteria, while 19 compounds decreased M. abscessus subsp. abscessus (Mab) survival rates within phagocytic cells. In addition, the hit compounds were tested in M. tuberculosis H37Ra (Mtb) and 14 compounds were found to exhibit activity in activated THP-1 cells. While the majority of compounds displayed inhibitory activity against both replicating (extracellular) and non-replicating (intracellular) forms of bacteria, a set of compounds appeared to be effective exclusively against intracellular bacteria. The efficacy of these compounds was examined in combination with current antibiotics and survival of both NTM and Mtb were evaluated within phagocytic cells. In time-kill dynamic studies, it was found that co-treatment promoted increased bacterial clearance when compared with the antibiotic or compound group alone. This study describes promising anti-NTM and anti-Mtb compounds with potential novel mechanisms of action that target intracellular bacteria in activated macrophages.