Knowledge Graphs for drug repurposing: a review of databases and methods.

Drug repurposing has emerged as a effective and efficient strategy to identify new treatments for a variety of diseases. One of the most effective approaches for discovering potential new drug candidates involves the utilization of Knowledge Graphs (KGs). This review comprehensively explores some of the most prominent KGs, detailing their structure, data sources, and how they facilitate the repurposing of drugs. In addition to KGs, this paper delves into various artificial intelligence techniques that enhance the process of drug repurposing. These methods not only accelerate the identification of viable drug candidates but also improve the precision of predictions by leveraging complex datasets and advanced algorithms. Furthermore, the importance of explainability in drug repurposing is emphasized. Explainability methods are crucial as they provide insights into the reasoning behind AI-generated predictions, thereby increasing the trustworthiness and transparency of the repurposing process. We will discuss several techniques that can be employed to validate these predictions, ensuring that they are both reliable and understandable.

Structural basis of positive allosteric modulation of metabotropic glutamate receptor activation and internalization.

The metabotropic glutamate receptors (mGluRs) are neuromodulatory family C G protein coupled receptors which assemble as dimers and allosterically couple extracellular ligand binding domains (LBDs) to transmembrane domains (TMDs) to drive intracellular signaling. Pharmacologically, mGluRs can be targeted at the LBDs by glutamate and synthetic orthosteric compounds or at the TMDs by allosteric modulators. Despite the potential of allosteric compounds as therapeutics, an understanding of the functional and structural basis of their effects is limited. Here we use multiple approaches to dissect the functional and structural effects of orthosteric versus allosteric ligands. We find, using electrophysiological and live cell imaging assays, that both agonists and positive allosteric modulators (PAMs) can drive activation and internalization of group II and III mGluRs. The effects of PAMs are pleiotropic, boosting the maximal response to orthosteric agonists and serving independently as internalization-biased agonists across mGluR subtypes. Motivated by this and intersubunit FRET analyses, we determine cryo-electron microscopy structures of mGluR3 in the presence of either an agonist or antagonist alone or in combination with a PAM. These structures reveal PAM-driven re-shaping of intra- and inter-subunit conformations and provide evidence for a rolling TMD dimer interface activation pathway that controls G protein and beta-arrestin coupling.

CD94+ natural killer cells potentiate pulmonary ischaemia-reperfusion injury.

BACKGROUND: Pulmonary ischaemia-reperfusion injury (IRI) is a major contributor to poor lung transplant outcomes. We recently demonstrated a central role of airway-centred natural killer (NK) cells in mediating IRI; however, there are no existing effective therapies for directly targeting NK cells in humans. METHODS: We hypothesised that a depleting anti-CD94 monoclonal antibody (mAb) would provide therapeutic benefit in mouse and human models of IRI based on high levels of KLRD1 (CD94) transcripts in bronchoalveolar lavage samples from lung transplant patients. RESULTS: We found that CD94 is highly expressed on mouse and human NK cells, with increased expression during IRI. Anti-mouse and anti-human mAbs against CD94 showed effective NK cell depletion in mouse and human models and blunted lung damage and airway epithelial killing, respectively. In two different allogeneic orthotopic lung transplant mouse models, anti-CD94 treatment during induction reduced early lung injury and chronic inflammation relative to control therapies. Anti-CD94 did not increase donor antigen-presenting cells that could alter long-term graft acceptance. CONCLUSIONS: Lung transplant induction regimens incorporating anti-CD94 treatment may safely improve early clinical outcomes.

Nonlinear comparative analysis of Greenland and Antarctica ice cores data.

We analyze the temperature time series of the EPICA Dome C ice cores in Antarctica and of the Greenland project, Summit, with durations of 800 000 and 248 000 years, respectively, with a recent mathematical tool defined through the Fourier phases of the series, known as the J-index. This data driven index can differentiate between purely random dynamics and dynamics with a deterministic component. It is sensitive to nonlinear components and robust to the presence of noise. Our J-index data analysis shows that both Greenland and Antarctica climatic fluctuations possess deterministic traits and suggests the presence of an underlying nonlinear dynamics. Furthermore, in both regions, it reveals the simultaneous occurrence of an important global event known as the "Pelukian transgression." For Antarctica, it also detects the marine isotopic stage 11. Additionally, our calculation of the time series Hurst exponents and our detrended fluctuation analysis show the presence of long-range persistent correlations for Antarctica and anti-persistent correlations for Greenland. For the latter case, our fractal dimension determinations are indicative of a more complex climatic dynamics in Greenland with respect to Antarctica. Our results are encouraging for further development of climate variability deterministic models for these regions.

Control of G protein-coupled receptor function via membrane-interacting intrinsically disordered C-terminal domains.

G protein-coupled receptors (GPCRs) control intracellular signaling cascades via agonist-dependent coupling to intracellular transducers including heterotrimeric G proteins, GPCR kinases (GRKs), and arrestins. In addition to their critical interactions with the transmembrane core of active GPCRs, all three classes of transducers have also been reported to interact with receptor C-terminal domains (CTDs). An underexplored aspect of GPCR CTDs is their possible role as lipid sensors given their proximity to the membrane. CTD-membrane interactions have the potential to control the accessibility of key regulatory CTD residues to downstream effectors and transducers. Here, we report that the CTDs of two closely related family C GPCRs, metabotropic glutamate receptor 2 (mGluR2) and mGluR3, bind to membranes and that this interaction can regulate receptor function. We first characterize CTD structure with NMR spectroscopy, revealing lipid composition-dependent modes of membrane binding. Using molecular dynamics simulations and structure-guided mutagenesis, we then identify key conserved residues and cancer-associated mutations that modulate CTD-membrane binding. Finally, we provide evidence that mGluR3 transducer coupling is controlled by CTD-membrane interactions in live cells, which may be subject to regulation by CTD phosphorylation and changes in membrane composition. This work reveals an additional mechanism of GPCR modulation, suggesting that CTD-membrane binding may be a general regulatory mode throughout the broad GPCR superfamily.

Antifungal capabilities of gut microbial communities of three dung beetle species (Scarabaeidae: Scarabaeinae).

Gut microbial communities are part of the regulatory array of various processes within their hosts, ranging from nutrition to pathogen control. Recent evidence shows that dung beetle's gut microbial communities release substances with antifungal activity. Because of the enormous diversity of gut microorganisms in dung beetles, there is a possibility of discovering novel compounds with antifungal properties. We tested the antifungal activity mediated by gut microbial communities of female dung beetles against nine phytopathogenic fungi strains (Colletotrichum asianum-339, C. asianum-340, C. asianum-1, C. kahawae-390, C. karstii-358, C. siamense-220, Fusarium oxysporum-ATCC338, Nectria pseudotrichia-232, Verticillium zaelandica-22). Our tests included the gut microbial communities of three species of dung beetles: Canthon cyanellus (roller beetle), Digitonthophagus gazella (burrower beetle), and Onthophagus batesi (burrower beetle), and we followed the dual confrontation protocol, i.e., we challenged each fungal strain with the microbial communities of each species of beetles in Petri dishes containing culture medium. Our results showed that gut microbial communities of the three dung beetle species exhibit antifungal activity against at least seven of the nine phytopathogenic fungal strains. The gut microbial communities of Onthophagus batesi significantly decreased the mycelial growth of the nine phytopathogenic fungi strains; the gut microbial communities of Canthon cyanellus and Digitonthophagus gazella significantly reduced the mycelial growth of seven strains. These results provide a basis for investigating novel antifungal substances within gut microbial communities of dung beetles.

Early safety and efficiency outcomes of a novel interdisciplinary laparoscopic resection rectopexy combined with sacrocolpopexy for women with obstructive defecation syndrome and pelvic organ prolapse: a single center study.

BACKGROUND: Obstructive defecation syndrome (ODS) defines a disturbed defecation process frequently associated with pelvic organ prolapse (POP) in women that substantially compromises quality of life. Conservative management offers limited relief and a surgical intervention may be required. This is characterized by individual approaches. AIM OF THE STUDY: This retrospective single center study evaluated the surgical and clinical short-term outcome of a novel interdisciplinary laparoscopic resection rectopexy (L-RRP) with mesh- sacrocolpopexy (L-SCP) for women suffering from ODS and POP. METHODS: The study participants underwent surgery in an interdisciplinary laparoscopic approach. Safety was the primary endpoint, assessed via postoperative morbidity classified by Clavien-Dindo scale. Secondary outcomes included evaluation of bowel function, fecal and urinary incontinence and pelvic organ prolapse status at 12 months follow-up. Additionally, a biological mesh (BM) was offered to women, who asked for an alternative to synthetic mesh material (SM). RESULTS: Of the 44 consecutive patients requiring surgery for ODS and POP, 36 patients underwent the interdisciplinary surgical approach; 28 patients with SM and 8 patients with BM. In total 5 complications occurred, four of them were classified as minor. One minor complication was observed in the BM group. One anastomotic leakage occurred in the SM group. The two ODS scores, the bowel dysfunction score, and the incontinence score improved significantly (p = 0.006, p = 0.003, p < 0.001, and p = 0.0035, respectively). Pelvic floor anatomy was fully restored (POP-Q 0) for 29 (80%) patients after surgery. 17 patients (47%) suffered from urinary incontinence before surgery, which was restored in 13 patients (76.5%). CONCLUSIONS: The interdisciplinary approach with L-RRP and L-SCP and the use of a BM in a small subgroup were technically feasible, safe, and effective in this single center setting. The study's retrospective design, the small sample size and the lack of comparators limit the generalizability of the findings requiring future randomized trials. TRIAL REGISTRATION: Retrospectively registered at clinicaltrials.gov, trial number NCT05910021, date of registration 06/10/2023.

Emerging modes of regulation of neuromodulatory G protein-coupled receptors.

In the nervous system, G protein-coupled receptors (GPCRs) control neuronal excitability, synaptic transmission, synaptic plasticity, and, ultimately, behavior through spatiotemporally precise initiation of a variety of signaling pathways. However, despite their critical importance, there is incomplete understanding of how these receptors are regulated to tune their signaling to specific neurophysiological contexts. A deeper mechanistic picture of neuromodulatory GPCR function is needed to fully decipher their biological roles and effectively harness them for the treatment of neurological and psychiatric disorders. In this review, we highlight recent progress in identifying novel modes of regulation of neuromodulatory GPCRs, including G protein- and receptor-targeting mechanisms, receptor-receptor crosstalk, and unique features that emerge in the context of chemical synapses. These emerging principles of neuromodulatory GPCR tuning raise critical questions to be tackled at the molecular, cellular, synaptic, and neural circuit levels in the future.

Deuteration as a General Strategy to Enhance Azobenzene-Based Photopharmacology.

Chemical photoswitches have become a widely used approach for the remote control of biological functions with spatiotemporal precision. Several molecular scaffolds have been implemented to improve photoswitch characteristics, ranging from the nature of the photoswitch itself (e.g. azobenzenes, dithienylethenes, hemithioindigo) to fine-tuning of aromatic units and substituents. Herein, we present deuterated azobenzene photoswitches as a general means of enhancing the performance of photopharmacological molecules. Deuteration can improve azobenzene performance in terms of light sensitivity (higher molar extinction coefficient), photoswitch efficiency (higher photoisomerization quantum yield), and photoswitch kinetics (faster macroscopic rate of photoisomerization) with minimal alteration to the underlying structure of the photopharmacological ligand. We report synthesized deuterated azobenzene-based ligands for the optimized optical control of ion channel and G protein-coupled receptor (GPCR) function in live cells, setting the stage for the straightforward, widespread adoption of this approach.

Seamless Fusion: Multi-Modal Localization for First Responders in Challenging Environments.

In dynamic and unpredictable environments, the precise localization of first responders and rescuers is crucial for effective incident response. This paper introduces a novel approach leveraging three complementary localization modalities: visual-based, Galileo-based, and inertial-based. Each modality contributes uniquely to the final Fusion tool, facilitating seamless indoor and outdoor localization, offering a robust and accurate localization solution without reliance on pre-existing infrastructure, essential for maintaining responder safety and optimizing operational effectiveness. The visual-based localization method utilizes an RGB camera coupled with a modified implementation of the ORB-SLAM2 method, enabling operation with or without prior area scanning. The Galileo-based localization method employs a lightweight prototype equipped with a high-accuracy GNSS receiver board, tailored to meet the specific needs of first responders. The inertial-based localization method utilizes sensor fusion, primarily leveraging smartphone inertial measurement units, to predict and adjust first responders' positions incrementally, compensating for the GPS signal attenuation indoors. A comprehensive validation test involving various environmental conditions was carried out to demonstrate the efficacy of the proposed fused localization tool. Our results show that our proposed solution always provides a location regardless of the conditions (indoors, outdoors, etc.), with an overall mean error of 1.73 m.