Virtual screening of the SAMPL4 blinded HIV integrase inhibitors dataset

International audienceSeveral combinations of docking software and scoring functions were evaluated for their ability to predict the binding of a dataset of potential HIV integrase inhibitors. We found that different docking software were appropriate for each one of the three binding sites considered (LEDGF, Y3 and fragment sites), and the most suitable two docking protocols, involving Glide SP and Gold ChemScore, were selected using a training set of compounds identified from the structural data available. These protocols could successfully predict respectively 20.0% and 23.6% of the HIV integrase binders, all of them being present in the LEDGF site. When a different analysis of the results was carried out by removing all alternate isomers of binders from the set, our predictions were dramatically improved, with an overall ROC AUC of 0.73 and enrichment factor at 10% of 2.89 for the prediction obtained using Gold ChemScore. This study highlighted the ability of the selected docking protocols to correctly position in most cases the ortho-alkoxy-carboxylate core functional group of the ligands in the corresponding binding site, but also their difficulties to correctly rank the docking poses

Evaluation of docking performance in a blinded virtual screening of fragment-like trypsin inhibitors

International audienceIn this study, we have "blindly" assessed the ability of several combinations of docking software and scoring functions to predict the binding of a fragment-like library of bovine trypsine inhibitors. The most suitable protocols (involving Gold software and GoldScore scoring function, with or without rescoring) were selected for this purpose using a training set of compounds with known biological activities. The selected virtual screening protocols provided good results with the SAMPL3-VS dataset, showing enrichment factors of about 10 for Top 20 compounds. This methodology should be useful in difficult cases of docking, with a special emphasis on the fragment-based virtual screening campaigns

Prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with the OPLS-AA force field

International audienceAll-atom molecular dynamics computer simulations were used to blindly predict the hydration free energies of a range of chloro-organic compounds as part of the SAMPL3 challenge. All compounds were parameterized within the framework of the OPLS-AA force field, using an established protocol to compute the absolute hydration free energy via a windowed free energy perturbation approach and thermodynamic integration. Three different approaches to deriving partial charge parameters were pursued: (1) using existing OPLS-AA atom types and charges with minor adjustments of partial charges on equivalent connecting atoms; (2) calculation of quantum mechanical charges via geometry optimization, followed by electrostatic potential (ESP) fitting, using Jaguar at the LMP2/cc-pVTZ(-F) level; and (3) via geometry optimization and CHelpG charges (Gaussian03 at the HF/6-31G* level), followed by two-stage RESP fitting. Protocol 3 generated the most accurate predictions with a root mean square (RMS) error of 1.2 kcal·mol −1 for the entire data set. It was found that the deficiency of the standard OPLS-AA parameters, protocol 1 (RMS error 2.4 kcal·mol −1 overall), was mostly due to compounds with more than three chlorine substituents on an aromatic ring. For this latter subset, the RMS errors were 1.4 kcal·mol −1 (protocol 3) and 4.3 kcal·mol −1 (protocol 1), respectively. We propose new OPLS-AA atom types for aromatic carbon and chlorine atoms in rings with ≥ 4 Cl-substituents that perform better than the best QM-based approach, resulting in an RMS error of 1.2 kcal·mol −1 for these difficult compounds

Prediction of cyclohexane-water distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with the OPLS-AA force field

International audienceAll-atom molecular dynamics (MD) simulations were used to predict water-cyclohexane distribution coefficients D cw of a range of small molecules as part of the SAMPL5 blind prediction challenge. Molecules were parameterized with the trans-ferable all-atom OPLS-AA force field, which required the derivation of new parameters for sulfamides and heterocycles and validation of cyclohexane parameters as a solvent. The distribution coefficient was calculated from the solvation free energies of the compound in water and cyclohexane. Absolute solvation free energies were computed by an established protocol using windowed alchemical free energy perturbation with thermodynamic integration. This protocol resulted in an overall root mean square error (RMSE) in log D cw of almost 4 log units and an overall signed error of −3 compared to experimental data. There was no substantial overall difference in accuracy between simulating in NV T and NPT ensembles. The signed error suggests a systematic error but the experimental D cw data on their own are insufficient to Manuscript Click here to download Manuscript sampl5-manuscript.pdf Click here to view linked References 2 Ian M. Kenney et al. uncover the source of this error. Preliminary work suggests that the major source of error lies in the hydration free energy calculations

Ligandbook — an online repository for small and drug-like molecule force field parameters

International audienceLigandbook is a public database and archive for force field parameters of small and drug-like molecules. It is a repository for parameter sets that are part of published work but are not easily available to the community otherwise. Parameter sets can be downloaded and immediately used in molecular dynamics simulations. The sets of parameters are versioned with full histories and carry unique identifiers to facilitate reproducible research. Text-based search on rich metadata and chemical substructure search allow precise identification of desired compounds or functional groups. Ligandbook enables the rapid set up of reproducible molecular dynamics simulations of ligands and protein-ligand complexes. Availability and Implementation: Ligandbook is available online at https://ligandbook.org and supports all modern browsers. Parameters can be searched and downloaded without registration, including access through a programmatic RESTful API. Deposition of files requires free user registration. Ligandbook is implemented in the PHP Symfony2 framework with TCL scripts using the CACTVS toolkit

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

Morphological and Tribological Properties of PMMA/Halloysite Nanocomposites

From an environmental and cost-effective perspective, a number of research challenges can be found for electronics, household, but especially in the automotive polymer parts industry. Reducing synthesis steps, parts coating and painting, or other solvent-assisted processes, have been identified as major constrains for the existing technologies. Therefore, simple polymer processing routes (mixing, extrusion, injection moulding) were used for obtaining PMMA/HNT nanocomposites. By these techniques, an automotive-grade polymethylmethacrylate (PMMA) was modified with halloysite nanotubes (HNT) and an eco-friendly additive N,N′-ethylenebis(stearamide) (EBS) to improve nanomechanical properties involved in scratch resistance, mechanical properties (balance between tensile strength and impact resistance) without diminishing other properties. The relationship between morphological/structural (XRD, TEM, FTIR) and tribological (friction) properties of PMMA nanocomposites were investigated. A synergistic effect was found between HNT and EBS in the PMMA matrix. The synergy was attained by the phase distribution resulted from the selective interaction between partners and favourable processing conditions. Modification of HNT with EBS improved the dispersion of nanoparticles in the polymer matrix by increasing their interfacial compatibility through hydrogen bonding established by amide groups with aluminol groups. The increased interfacial adhesion further improved the nanocomposite scratch resistance. The PMMA/HNT-EBS nanocomposite had a lower coefficient of friction and lower scratch penetration depth than PMMA/HNT nanocomposite.Financial support by the EU Commission through Project H2020-686165-IZADINANO2INDUSTRY is gratefully acknowledged

Biochemical and Structural Characterization of OXA-405, an OXA-48 Variant with Extended-Spectrum β-Lactamase Activity

International audienceOXA-48-producing Enterobacterales have now widely disseminated globally. A sign of their extensive spread is the identification of an increasing number of OXA-48 variants. Among them, three are particularly interesting, OXA-163, OXA-247 and OXA-405, since they have lost carbapenem activities and gained expanded-spectrum cephalosporin hydrolytic activity subsequent to a four amino-acid (AA) deletion in the β5-β6 loop. We investigated the mechanisms responsible for substrate specificity of OXA-405. Kinetic parameters confirmed that OXA-405 has a hydrolytic profile compatible with an ESBL (hydrolysis of expanded spectrum cephalosporins and susceptibility to class A inhibitors). Molecular modeling techniques and 3D structure determination show that the overall dimeric structure of OXA-405 is very similar to that of OXA-48, except for the β5-β6 loop, which is shorter for OXA-405, suggesting that the length of the β5-β6 loop is critical for substrate specificity. Covalent docking with selected substrates and molecular dynamics simulations evidenced the structural changes induced by substrate binding, as well as the distribution of water molecules in the active site and their role in substrate hydrolysis. All this data may represent the structural basis for the design of new and efficient class D inhibitors