Systematic Approaches for the Encoding of Chemical Groups: A Case Study.

Regulatory authorities aim to organize substances into groups to facilitate prioritization within hazard and risk assessment processes. Often, such chemical groupings are not explicitly defined by structural rules or physicochemical property information. This is largely due to how these groupings are developed, namely, a manual expert curation process, which in turn makes updating and refining groupings, as new substances are evaluated, a practical challenge.

A non-clinical and clinical IUCLID database for 530 pharmaceuticals (part I): Methodological aspects of its development.

A new IUCLID database is provided containing results from non-clinical animal studies and human information for 530 approved drugs. The database was developed by extracting data from pharmacological reviews of repeat-dose, carcinogenicity, developmental, and reproductive toxicity studies. In the database, observed and no-observed effects are linked to the respective effect levels, including information on severity/incidence and transiency/reversibility.

Utility of In Vitro Bioactivity as a Lower Bound Estimate of In Vivo Adverse Effect Levels and in Risk-Based Prioritization.

Use of high-throughput, in vitro bioactivity data in setting a point-of-departure (POD) has the potential to accelerate the pace of human health safety evaluation by informing screening-level assessments. The primary objective of this work was to compare PODs based on high-throughput predictions of bioactivity, exposure predictions, and traditional hazard information for 448 chemicals. PODs derived from new approach methodologies (NAMs) were obtained for this comparison using the 50th (PODNAM, 50) and the 95th (PODNAM, 95) percentile credible interval estimates for the steady-state plasma concentration used in in vitro to in vivo extrapolation of administered equivalent doses.

The impact on classifications for carcinogenicity, mutagenicity, reproductive and specific target organ toxicity after repeated exposure in the first ten years of the REACH regulation.

The present study primarily aims at informing regulators and policy makers in Europe and examines the evolution of self-classifications and study availability for the endpoints of carcinogenicity, mutagenicity, reproductive toxicity (CMR) and specific target organ toxicity after repeated exposure (STOT RE) for the first ten years of the REACH legislation. Our knowledge on chemical safety keeps increasing due to the registration obligations under REACH, in combination with proactive actions by registrants and regulatory actions by Authorities, which jointly lead to new testing and critical reassessment of existing studies. The improvements become evident by the constant increase in the number of substances that are self-classified by the registrants for human health endpoints.

(Q)SARs as Adaptations to REACH Information Requirements.

REACH is a regulation of the European Union adopted to improve the safe use of chemicals with regard to human health and the environment. The safe use of chemicals can be achieved only if the hazard and the exposure of the substances are well characterized. Testing on animals has been traditionally the main tool for hazard assessment.

UVCB substances: methodology for structural description and application to fate and hazard assessment.

Substances of unknown or variable composition, complex reaction products, or biological materials (UVCBs) have been conventionally described in generic terms. Commonly used substance identifiers are generic names of chemical classes, generic structural formulas, reaction steps, physical-chemical properties, or spectral data. Lack of well-defined structural information has significantly restricted in silico fate and hazard assessment of UVCB substances.

Computer-aided molecular design of solvents for accelerated reaction kinetics.

Solvents can significantly alter the rates and selectivity of liquid-phase organic reactions, often hindering the development of new synthetic routes or, if chosen wisely, facilitating routes by improving rates and selectivities. To address this challenge, a systematic methodology is proposed that quickly identifies improved reaction solvents by combining quantum mechanical computations of the reaction rate constant in a few solvents with a computer-aided molecular design (CAMD) procedure. The approach allows the identification of a high-performance solvent within a very large set of possible molecules.

The polymorphs of ROY: application of a systematic crystal structure prediction technique.

We investigate the ability of current ab initio crystal structure prediction techniques to identify the polymorphs of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile, also known as ROY because of the red, orange and yellow colours of its polymorphs. We use a methodology combining the generation of a large number of structures based on a computationally inexpensive model using the CrystalPredictor global search algorithm, and the further minimization of the most promising of these structures using the CrystalOptimizer local minimization algorithm which employs an accurate, yet efficiently constructed, model based on isolated-molecule quantum-mechanical calculations. We demonstrate that this approach successfully predicts the seven experimentally resolved structures of ROY as lattice-energy minima, with five of these structures being within the 12 lowest energy structures predicted.

Towards crystal structure prediction of complex organic compounds--a report on the fifth blind test.

Following on from the success of the previous crystal structure prediction blind tests (CSP1999, CSP2001, CSP2004 and CSP2007), a fifth such collaborative project (CSP2010) was organized at the Cambridge Crystallographic Data Centre. A range of methodologies was used by the participating groups in order to evaluate the ability of the current computational methods to predict the crystal structures of the six organic molecules chosen as targets for this blind test. The first four targets, two rigid molecules, one semi-flexible molecule and a 1:1 salt, matched the criteria for the targets from CSP2007, while the last two targets belonged to two new challenging categories - a larger, much more flexible molecule and a hydrate with more than one polymorph.

Successful prediction of a model pharmaceutical in the fifth blind test of crystal structure prediction.

The range of target structures in the fifth international blind test of crystal structure prediction was extended to include a highly flexible molecule, (benzyl-(4-(4-methyl-5-(p-tolylsulfonyl)-1,3-thiazol-2-yl)phenyl)carbamate, as a challenge representative of modern pharmaceuticals. Two of the groups participating in the blind test independently predicted the correct structure. The methods they used are described and contrasted, and the implications of the capability to tackle molecules of this complexity are discussed.

Which, if any, hydrates will crystallise? Predicting hydrate formation of two dihydroxybenzoic acids.

A study of two dihydroxybenzoic acid isomers shows that computational methods can be used to predict hydrate formation, the compound:water ratio and hydrate crystal structures. The calculations also help identify a novel hydrate found in the solid form screening that validates this study.

Solid-State Forms of β-Resorcylic Acid: How Exhaustive Should a Polymorph Screen Be?

An extensive experimental screen, coupled with a computational study, revealed seven new solid-state forms of β-resorcylic acid. The known, stable polymorph II° shows a reversible phase transformation to the new, kinetically stable, probably disordered high temperature form I. The study provides a consistent picture of the solid-state of β-resorcylic acid.

Modelling organic crystal structures using distributed multipole and polarizability-based model intermolecular potentials.

Crystal structure prediction for organic molecules requires both the fast assessment of thousands to millions of crystal structures and the greatest possible accuracy in their relative energies. We describe a crystal lattice simulation program, DMACRYS, emphasizing the features that make it suitable for use in crystal structure prediction for pharmaceutical molecules using accurate anisotropic atom-atom model intermolecular potentials based on the theory of intermolecular forces. DMACRYS can optimize the lattice energy of a crystal, calculate the second derivative properties, and reduce the symmetry of the spacegroup to move away from a transition state.

The Use of Anisotropic Potentials in Modeling Water and Free Energies of Hydration.

We propose a novel, anisotropic rigid-body intermolecular potential model to predict the properties of water and the hydration free energies of neutral organic solutes. The electrostatic interactions of water and the solutes are modeled using atomic multipole moments up to hexadecapole; these are obtained from distributed multipole analysis of the quantum mechanically computed charge densities and include average polarization effects in solution. The repulsion-dispersion water-water interactions are modeled with a three-site, exp-6 model fitted to the experimental liquid water density and oxygen-oxygen radial distribution function at ambient conditions.

A computationally inspired investigation of the solid forms of (R)-1-phenylethylammonium-(S)-2-phenylbutyrate.

Following the computation of a lattice energy landscape which predicted that there should be more stable, denser forms of (R)-1-phenylethylammonium-(S)-2-phenylbutyrate, crystallizations from a range of solvents were performed to search for other polymorphs and investigate the possibility that the known P4(1) structure could be a hydrate. Extensive crystallization experiments from a wide range of solvents gave fine needles or microcrystalline samples. A redetermination of the P4(1) structure by powder X-ray diffraction located all protons, and in conjunction with other experimental and computational evidence showed that the structure was anhydrous.

Can the Formation of Pharmaceutical Cocrystals Be Computationally Predicted? 2. Crystal Structure Prediction.

We report a multistage lattice energy minimization methodology for generating stable packing arrangements of cocrystals containing flexible molecules. In the first approximation, the intermolecular electrostatic interactions are modeled with atomic charges and the molecular deformation energy is interpolated over a set of precomputed quantum mechanical values. At subsequent stages, the accuracy is improved by first using analytically rotated and then conformation-dependent multipole moments, computed from the isolated-molecule charge density, and "on-the-fly" quantum mechanical calculations to compute the intramolecular deformation energy.

Significant progress in predicting the crystal structures of small organic molecules--a report on the fourth blind test.

We report on the organization and outcome of the fourth blind test of crystal structure prediction, an international collaborative project organized to evaluate the present state in computational methods of predicting the crystal structures of small organic molecules. There were 14 research groups which took part, using a variety of methods to generate and rank the most likely crystal structures for four target systems: three single-component crystal structures and a 1:1 cocrystal. Participants were challenged to predict the crystal structures of the four systems, given only their molecular diagrams, while the recently determined but as-yet unpublished crystal structures were withheld by an independent referee.

Modeling the interplay of inter- and intramolecular hydrogen bonding in conformational polymorphs.

The predicted stability differences of the conformational polymorphs of oxalyl dihydrazide and ortho-acetamidobenzamide are unrealistically large when the modeling of intermolecular energies is solely based on the isolated-molecule charge density, neglecting charge density polarization. Ab initio calculated crystal electron densities showed qualitative differences depending on the spatial arrangement of molecules in the lattice with the greatest variations observed for polymorphs that differ in the extent of inter- and intramolecular hydrogen bonding. We show that accounting for induction dramatically alters the calculated stability order of the polymorphs and reduces their predicted stability differences to be in better agreement with experiment.

The thermal stability of lattice-energy minima of 5-fluorouracil: metadynamics as an aid to polymorph prediction.

This paper reports a novel methodology for the free-energy minimization of crystal structures exhibiting strong, anisotropic interactions due to hydrogen bonding. The geometry of the thermally expanded cell was calculated by exploiting the dependence of the free-energy derivatives with respect to cell lengths and angles on the average pressure tensor computed in short molecular dynamics simulations. All dynamic simulations were performed with an elaborate anisotropic potential based on a distributed multipole analysis of the isolated molecule charge density.

Is the Induction Energy Important for Modeling Organic Crystals?

We compare two methods for estimating the induction energy in organic molecular crystals by approximating the charge density polarization in the crystalline state. The first is a distributed atomic polarizability model combined with distributed multipole moments, derived from ab initio monomer properties. The second uses an ab initio calculation of the molecular charge density in a point-charge field.

The polymorphism of progesterone: stabilization of a 'disappearing' polymorph by co-crystallization.

Progesterone has been known to be polymorphic for over 70 years, and crystallization conditions for the production of both experimentally characterized polymorphs have been repeatedly reported in the literature up to 1975. Nevertheless, our attempts to produce crystals of the metastable form 2 suitable for single crystal X-ray diffraction failed until the structurally related molecule pregnenolone was introduced as an additive into the crystallization solution. Accurate low temperature crystal structures were obtained for forms 1 and 2, pregnenolone and a newly discovered pregnenolone-progesterone co-crystal, which appeared concomitantly with progesterone forms 1 and 2.

Toward the computational design of diastereomeric resolving agents: an experimental and computational study of 1-phenylethylammonium-2-phenylacetate derivatives.

The crystal structures, including two new polymorphs, of three diastereomerically related salt pairs formed by (R)-1-phenylethylammonium (1) with (S&R)-2-phenylpropanoate (2), (S&R)-2-phenylbutyrate (3), and (S&R)-mandelate (4) ions were characterized by low-temperature single crystal or powder X-ray diffraction. Thermal, solubility, and solution calorimetry measurements were used to determine the relative stabilities of the salt pairs and polymorphs. These were qualitatively predicted by lattice energy calculations combining realistic models for the dominant intermolecular electrostatic interactions and ab initio calculations for the ions' conformational energies due to the distortion of their geometries by the crystal packing forces.

Racemic progesterone: predicted in silico and produced in the solid state.

A computational prediction that mixing the synthetic mirror image of progesterone with its natural form would produce a specific racemic crystal structure was validated.