Docking rigid macrocycles using Convex-PL, AutoDock Vina, and RDKit in the D3R Grand Challenge 4

International audienceThe D3R Grand Challenge 4 provided a brilliant opportunity to test macrocyclic docking protocols on a diverse high-quality experimental data. We participated in both pose and affinity prediction exercises. Overall, we aimed to use an automated structure-based docking pipeline built around a set of tools developed in our team. This exercise again demonstrated a crucial importance of the correct local ligand geometry for the overall success of docking. Starting from the second part of the pose prediction stage, we developed a stable pipeline for sampling macrocycle conformers. This resulted in the subangstrom average precision of our pose predictions. In the affinity prediction exercise we obtained average results. However, we could improve these when using docking poses submitted by the best predictors. Our docking tools including the Convex-PL scoring function are available at https://team.inria.fr/nano-d/software/

Natural ligands of nuclear receptors. Isolation, design, synthesis, biochemical decodification and potential therapeutic applications.

Natural products have historically been a rich source of lead compounds in drug discovery. The biochemical investigation of marine organisms, through the deep collaboration between chemists and pharmacologists, focused on searching of new biologically active compounds, is a central issue of this kind of studies. My research work, described in this PhD thesis, has been developed in this research area and was addressed to the identification of new ligands of nuclear receptors, discovering potent and selective modulators of farnesoid-X-receptor (FXR) and pregnane-X-receptor (PXR), regulators of various processes including reproduction, development, and metabolism of xeno- and endobiotics. First, analysis of the polar extract of the sponge Theonella swinhoei afforded two new sulfated sterols, solomonsterols (SA and SB), the first example of marine PXR agonists. Both have been synthesized and characterized in animal models of inflammation. Administration of synthetic solomonsterol A effectively protects against development of clinical signs and symptoms of colitis; therefore SA holds promise in the treatment of inflammatory bowel deseases (IBDs). To overcome a limitation of SA in clinical settings, a small library of SA derivatives has been designed and prepared. Indeed, SA could be absorbed from the GIT causing severe systemic side effects resulting from the activation of PXR in the liver. This study disclosed cholestan disulfate (Coldisolf) as a new, simplified agonist of PXR, currently in pharmacological evaluation on animal models of liver fibrosis induced by HIV infection. Simultaneously, a wide family of 4-methylene steroids were isolated from the apolar extracts of Theonella swinhoei. These marine steroids are endowed with a potent agonistic activity on PXR while antagonize the effects of natural ligands for FXR. Among this rich family, we have identified theonellasterol as the first example of a sponge derived highly selective FXR antagonist demonstrating its pharmacological potential in the treatment of cholestasis. Using this compound as a novel FXR antagonist hit, we have prepared a series of semi-synthetic derivatives in order to gain insights into the structural requirements for exhibiting antagonistic activity. These molecules could be used for the pharmacological treatment of cholestasis but also in chemotherapy of carcinoma characterized by over-expression of FXR. In summary, Nature continues to be one of the best sources not only of potential chemotherapeutic agents but also of lead compounds that could represent an inspiration for the discovery of new therapeutic strategies

Solvated interaction energy: from small-molecule to antibody drug design

Scoring functions are ubiquitous in structure-based drug design as an aid to predicting binding modes and estimating binding affinities. Ideally, a scoring function should be broadly applicable, obviating the need to recalibrate and refit its parameters for every new target and class of ligands. Traditionally, drugs have been small molecules, but in recent years biologics, particularly antibodies, have become an increasingly important if not dominant class of therapeutics. This makes the goal of having a transferable scoring function, i.e., one that spans the range of small-molecule to protein ligands, even more challenging. One such broadly applicable scoring function is the Solvated Interaction Energy (SIE), which has been developed and applied in our lab for the last 15 years, leading to several important applications. This physics-based method arose from efforts to understand the physics governing binding events, with particular care given to the role played by solvation. SIE has been used by us and many independent labs worldwide for virtual screening and discovery of novel small-molecule binders or optimization of known drugs. Moreover, without any retraining, it is found to be transferrable to predictions of antibody-antigen relative binding affinities and as accurate as functions trained on protein-protein binding affinities. SIE has been incorporated in conjunction with other scoring functions into ADAPT (Assisted Design of Antibody and Protein Therapeutics), our platform for affinity modulation of antibodies. Application of ADAPT resulted in the optimization of several antibodies with 10-to-100-fold improvements in binding affinity. Further applications included broadening the specificity of a single-domain antibody to be cross-reactive with virus variants of both SARS-CoV-1 and SARS-CoV-2, and the design of safer antibodies by engineering of a pH switch to make them more selective towards acidic tumors while sparing normal tissues at physiological pH

SAMPL6: calculation of macroscopic pKa values from ab initio quantum mechanical free energies

International audienceMacroscopic pKa values were calculated for all compounds in the SAMPL6 blind prediction challenge, based on quantum chemical calculations with a continuum solvation model and a linear correction derived from a small training set. Microscopic pKa values were derived from the gas-phase free energy difference between protonated and deprotonated forms together with the Conductor-like Polarizable Continuum Solvation Model and the experimental solvation free energy of the proton. pH-dependent microstate free energies were obtained from the microscopic pKas with a maximum likelihood estimator and appropriately summed to yield macroscopic pKa values or microstate populations as function of pH. We assessed the accuracy of three approaches to calculate the microscopic pKas: direct use of the quantum mechanical free energy differences and correction of the direct values for short-comings in the QM solvation model with two different linear models that we independently derived from a small training set of 38 compounds with known pKa. The predictions that were corrected with the linear models had much better accuracy [root-mean-square error (RMSE) 2.04 and 1.95 pKa units] than the direct calculation (RMSE 3.74). Statistical measures indicate that some systematic errors remain, likely due to differences in the SAMPL6 data set and the small training set with respect to their interactions with water. Overall, the current approach provides a viable physics-based route to estimate macroscopic pKa values for novel compounds with reasonable accuracy

PPARs as Key Mediators of Metabolic and Inflammatory Regulation

Mounting evidence suggests a bidirectional relationship between metabolism and inflammation. Molecular crosstalk between these processes occurs at different levels with the participation of nuclear receptors, including peroxisome proliferator-activated receptors (PPARs). There are three PPAR isotypes, α, β/δ, and γ, which modulate metabolic and inflammatory pathways, making them key for the control of cellular, organ, and systemic processes. PPAR activity is governed by fatty acids and fatty acid derivatives, and by drugs used in clinics (glitazones and fibrates). The study of PPAR action, also modulated by post-translational modifications, has enabled extraordinary advances in the understanding of the multifaceted roles of these receptors in metabolism, energy homeostasis, and inflammation both in health and disease. This Special Issue of IJMS includes a broad range of basic and translational article, both original research and reviews, focused on the latest developments in the regulation of metabolic and/or inflammatory processes by PPARs in all organs and the microbiomes of different vertebrate species

ABC Transporters in Human Diseases

Mammalian ATP-binding cassette (ABC) transporters constitute a superfamily of proteins involved in many essential cellular processes. Most of these transporters are transmembrane proteins and allow the active transport of solutes, small molecules, and lipids across biological membranes. On the one hand, some of these transporters are involved in drug resistance (also referred to as MDR or multidrug resistance), a process known to be a major brake in most anticancer treatments, and the medical challenge is thus to specifically inhibit their function. On the other hand, molecular defects in some of these ABC transporters are correlated with several rare human diseases, the most well-documented of which being cystic fibrosis, which is caused by genetic variations in ABCC7/CFTR (cystic fibrosis transmembrane conductance regulator). In the latter case, the goal is to rescue the function of the deficient transporters using various means, such as targeted pharmacotherapies and cell or gene therapy. The aim of this Special Issue, “ABC Transporters in Human Diseases”, is to present, through original articles and reviews, the state-of-the-art of our current knowledge about the role of ABC transporters in human diseases and the proposed therapeutic options based on studies ranging from cell and animal models to patients

The role of the Kinin-Kallikrein System in chronic lymphocytic leukaemia

Background:Chronic lymphocytic leukaemia (CLL) is an incurable heterogeneous disease. The identification of reliable and cost effective biomarkers is therefore imperative. A comparative proteomic approach was previously employed to study protein expression changes associated with in vitro BCR ligation. Kininogen, a critical protein of Kinin-Kallikrein System (KKS) was found to be upregulated (p≥2) in 3/3 “high risk” clinical samples upon BCR stimulation. Both High and Low Molecular Weight Kininogens (HMWK and LMWK, respectively) serve as a substrate from which Plasma and Tissue Kallikreins liberate Kinins, which in turn act upon B1 and B2 kinin receptors. This project aimed to investigate the role of the KKS in CLL and to identify novel proteins which may have clinical relevance in this disease.Materials and Methods:KKS was investigated using CLL clinical samples and a range of methods such as immunoblotting, reverse transcription polymerase chain reaction (RT-PCR), enzyme-linked immunosorbent assay (ELISA) and flow cytometry as appropriate.Results:The up regulation of LMWK upon in vitro BCR stimulation was confirmed by immunoblotting in 3/3 CLL samples previously used in a discovery phase proteomics. In a pilot series of 52 unselected CLL samples, 71% demonstrated basal LMWK expression. A total of 18 of these samples were also analysed for LMWK transcript, which was not detected in any of these samples. The expression of Kallikrein 6 was confirmed in 25 CLL samples. The B1 and B2 receptors were identified in 15 and 3 CLL samples, respectively. An elevated Bradykinin level was demonstrated in 27/36 (75%) plasma samples from CLL patients and was found to be associated with untreated (p=0.039) stage A (p=0.03) CLL and increased Plasma Kallikrein (p=0.001).Discussion:It has been demonstrated for the first time that CLL cells express the components for KKS signalling pathway, which can be further investigated for clinical relevance

ASSESSING THE EFFECTS OF PERFLUOROALKYL SUBSTANCE EXPOSURE USING TRANSDISCIPLINARY SCIENCE

Per- and polyfluoroalkyl substances (PFAS) are ubiquitous drinking water contaminants of concern due to mounting evidence implicating adverse health outcomes associated with exposure, including reduced kidney function, metabolic syndrome, thyroid disruption, and adverse pregnancy outcomes. In an 18-year longitudinal repeated measures study of adult humans (N = 210), an interquartile (IQR) increase in serum perfluorononanoate (PFNA), perfluorohexane sulfonate (PFHxS), and perfluorodecanoate (PFDeA) was associated with a -1.62% (95% CI= -3.02, -0.23), -1.95% (95% CI= -3.41, -0.49), and -2.47% (95% CI= -4.48, -0.45) decrease in estimated glomerular filtration rate, respectively, and an IQR increase in serum perfluorooctanesulfonate (PFOS) was associated with a 10.21% increase in serum TSH (95% CI: 2.29, 18.74). Adverse pregnancy outcomes were studied in pregnant CD-1 mice exposed to perfluorooctanoic acid (PFOA: 0, 1, or 5 mg/kg/day) or a PFOA replacement (GenX: 0, 2, or 10 mg/kg/day) from embryonic day (E) 0.5 to E11.5 or E17.5. Generally, effects induced by GenX occurred with shorter latency or at lower internal concentrations than PFOA. Exposure to GenX or PFOA resulted in increased gestational weight gain. Embryo weight was 9.4% lower relative to controls after exposure to 5 mg/kg/day PFOA. Effect sizes for several outcomes were similar for higher doses (5 mg/kg/day PFOA and 10 mg/kg/day GenX) and lower doses (1 mg/kg/day PFOA and 2 mg/kg/day GenX), including higher maternal liver weights, abnormal liver histopathology, higher placental weights and embryo-placental weight ratios, and greater incidence of placental abnormalities relative to controls. Transcriptome-wide gene expression analysis of placentas revealed significant enrichment of pathways involved in cholesterol and lipid transport (e.g. liver X receptor activation), innate immune response/inflammation (e.g. acute phase response signaling), and hemostasis (e.g. atherosclerosis signaling). Human-derived placental trophoblasts were utilized in an in vitro high-throughput toxicity (HTTS) screen to evaluate the effect of 42 unique PFAS on trophoblast viability and function, and dose-response models were applied to determine EC50 values for viability (27/42, 66%), proliferation (28/42, 68%), and mitochondrial membrane potential (19/42, 45%). Collectively, these data highlight adverse health outcomes associated with PFAS exposure, demonstrate the placenta is a susceptible target tissue, and propose potential molecular mechanisms of placental toxicity.Doctor of Philosoph