Henri Xhaard

We investigate the representation of atomic molecular environments as a list of the atoms neighboring an origin ranked by distance. We show that contact densities collected for origin-neighbor pairs of set types have regular and specific distributions when stratified by ranks. This is used to build a scoring function assessing the fitness of individual atoms with respect to their environment (FS, fitness score), as well as to characterize the contact preferences (CP) for pairs of atoms. Tested against the 3DRobot data set, the FS score was found to be highly discriminative of decoys vs native X-ray. The code is freely available on GitHub (https://github.com/DreanoLoic/Fitness_score.git).

In this study, we investigated the potential of diazaborine compounds for antibacterial drug development. Most promising diazaborines demonstrated activity against several Gram-negative pathogens including Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, and Salmonella enterica ser. Typhimurium. For a subset of diazaborines, we showed inhibitory activity against isolated FabI (enoyl-acyl carrier protein reductase) enzyme aligning with antimicrobial activity, suggesting a mechanism of action via the FabI enzyme and providing early information on structure–activity relationships. Optimized diazaborine scaffold 11 features an amino group in a meta-relative position to the sulfonamide group and exhibited the most favorable bioactivity profile, showing MIC of 6.25 μM against E. coli, low cytotoxicity, and high stability in human plasma. Furthermore, diazaborine 11 had synergistic effect with colistin (FICI 0.25) and preliminary data show that it may rescue Galleria mellonella larvae from lethal E. coli infection at the therapeutic dose of 1.13 and 2.81 mg/kg, demonstrating efficacy similar to ciprofloxacin.

EcoDrug PLUS (EcoDrug+; https://ecodrugplus.helsinki.fi/) is a freely available and publicly accessible database, established to facilitate environmental risk assessment of pharmaceuticals and other bioactive substances, including veterinary medicines and pesticides. EcoDrug+ advancements on the original ECODrug database include a more extensive and intuitive graphical user interface for investigating the potential for chemicals to interact with protein targets based on their conservation with human drug, veterinary, and pesticide targets across 180 phylogenetically diverse wildlife taxa. EcoDrug+ integrates genomic and chemoinformatic data from open-access sources for ~7200 pharmaceuticals, 34 000 agrochemicals, 61 000 human metabolites, and 5800 other bioactive chemicals. Advanced search capabilities of EcoDrug+ include the ability to interrogate the database via text queries, chemical structure drawings, target protein sequence BLAST, and/or specified mechanisms of action. Chemical compound data are organized into clusters to facilitate the exploration of similar groups using interactive knowledge graphs. The integration of effects-based knowledge informs on appropriate endpoints and susceptible species for the testing of drugs (and other bioactive chemicals). Georeferenced measured environmental concentrations (for n = 266 chemicals) furthermore provide relevant exposure data for testing and environmental risk analysis.

Membrane-bound pyrophosphatases (mPPases) are homodimeric proteins that hydrolyse pyrophosphate and pump H+/Na+ across membranes. They are crucial for the virulence of protist pathogens, making them attractive drug targets. In this study, we investigate the inhibitory effects of seven distinct bisphosphonates against Thermotoga maritima mPPase to explore their mode of action and assist in future small molecule inhibitor development. We solved two structures of mPPase bound to the inhibitors in the enzyme active sites and probed the conformational dynamics of mPPase under multiple inhibitors and functionally relevant conditions by double electron-electron resonance (DEER) spectroscopy. We found that mPPase adopts distinct conformational equilibria in solution in the presence of different inhibitors, including states consistent with asymmetric binding in the active site (closed-open), but a symmetric apo-like conformation on the periplasmic side (open-open). Combined with solid-supported membrane-based electrophysiology recordings, this revealed that during catalysis, one monomer of the dimer remains open, and Na+ can only be pumped in a closed state. These results further support symmetry-breaking across the membrane, consistent with half-of-the-sites-reactivity.

Membrane-bound pyrophosphatases (mPPases) are homodimeric proteins that hydrolyse pyrophosphate and pump H ⁺ /Na ⁺ across membranes. They are crucial for the virulence of protist pathogens, making them attractive drug targets. In this study, we investigate the inhibitory effects of seven distinct bisphosphonates against Thermotoga maritima mPPase to explore their mode of action and assist in future small molecule inhibitor development. We solved two structures of mPPase bound to the inhibitors in the enzyme active sites and probed the conformational dynamics of mPPase under multiple inhibitors and functionally relevant conditions by double electron-electron resonance (DEER) spectroscopy. We found that mPPase adopts distinct conformational equilibria in solution in the presence of different inhibitors, including states consistent with asymmetric binding in the active site (closed-open), but a symmetric apo-like conformation on the periplasmic side (open-open). Combined with solid-supported membrane-based electrophysiology recordings, this revealed that during catalysis, one monomer of the dimer remains open, and Na ⁺ can only be pumped in a closed state. These results further support symmetry-breaking across the membrane, consistent with half-of-the-sites-reactivity.

RepurposeDrugs (https://repurposedrugs.org/) is a comprehensive web-portal that combines a unique drug indication database with a machine learning (ML) predictor to discover new drug-indication associations for approved as well as investigational mono and combination therapies. The platform provides detailed information on treatment status, disease indications and clinical trials across 25 indication categories, including neoplasms and cardiovascular conditions. The current version comprises 4314 compounds (approved, terminated or investigational) and 161 drug combinations linked to 1756 indications/conditions, totaling 28 148 drug–disease pairs. By leveraging data on both approved and failed indications, RepurposeDrugs provides ML-based predictions for the approval potential of new drug–disease indications, both for mono- and combinatorial therapies, demonstrating high predictive accuracy in cross-validation. The validity of the ML predictor is validated through a number of real-world case studies, demonstrating its predictive power to accurately identify repurposing candidates with a high likelihood of future approval. To our knowledge, RepurposeDrugs web-portal is the first integrative database and ML-based predictor for interactive exploration and prediction of both single-drug and combination approval likelihood across indications. Given its broad coverage of indication areas and therapeutic options, we expect it accelerates many future drug repurposing projects.

Tunicates are evolutionary model organisms bridging the gap between vertebrates and invertebrates. A genomic sequence in Ciona intestinalis (CiOX) shows high similarity to vertebrate orexin receptors and protostome allatotropin receptors (ATR). Here, molecular phylogeny suggested that CiOX is divergent from ATRs and human orexin receptors (hOX_1/2). However, CiOX appears closer to hOX_1/2 than to ATR both in terms of sequence percent identity and in its modelled binding cavity, as suggested by molecular modelling. CiOX was heterologously expressed in a recombinant HEK293 cell system. Human orexins weakly but concentration-dependently activated its G_q signalling (Ca²⁺ elevation), and the responses were inhibited by the non-selective orexin receptor antagonists TCS 1102 and almorexant, but only weakly by the OX₁-selective antagonist SB-334867. Furthermore, the 5-/6-carboxytetramethylrhodamine (TAMRA)-labelled human orexin-A was able to bind to CiOX. Database mining was used to predict a potential endogenous C. intestinalis orexin peptide (Ci-orexin-A). Ci-orexin-A was able to displace TAMRA-orexin-A, but not to induce any calcium response at the CiOX. Consequently, we suggested that the orexin signalling system is conserved in Ciona intestinalis, although the relevant peptide-receptor interaction was not fully elucidated.

Cooperative molecular contacts play an important role in protein structure and ligand binding. Here, we constructed a PostgreSQL database that stores structural information in the form of atomic environments and allows flexible mining of molecular contacts. Taking the Ser‐His‐Asp/Glu catalytic triad as a first test case, we demonstrate that the presence of a carboxylate oxygen atom in the vicinity of a His is associated with shorter Ser‐OH..N‐His bond in the PDB30 subset. We prospectively mine catalytic triads in unannotated proteins, suggesting catalytic functions for unannotated proteins. As a second test case, we demonstrate that this database system can include ligand atoms, represented by Sybyl atom types, by evaluating the proportion of counter‐ions for ligand carboxylate oxygens.

Pharmaceutical proteins, compared to small molecular weight drugs, are relatively fragile molecules, thus necessitating monitoring protein unfolding and aggregation during production and post-marketing. Currently, many analytical techniques take offline measurements, which cannot directly assess protein folding during production and unfolding during processing and storage. In addition, several orthogonal techniques are needed during production and market surveillance. In this study, we introduce the use of time-gated Raman spectroscopy to identify molecular descriptors of protein unfolding. Raman spectroscopy can measure the unfolding of proteins in-line and in real-time without labels. Using K-means clustering and PCA analysis, we could correlate local unfolding events with traditional analytical methods. This is the first step toward predictive modeling of unfolding events of proteins during production and storage.