Free energy calculations have seen increased usage in structure-based drug design. Despite the rising interest, automation of the complex calculations and subsequent analysis of their results are still hampered by the restricted choice of available tools. In this work, an application for automated setup and processing of free energy calculations is presented. Several sanity checks for assessing the reliability of the calculations were implemented , constituting a distinct advantage over existing open-source tools. The underlying workflow is built on top of the software Sire, SOMD, BioSimSpace and OpenMM and uses the AMBER14SB and GAFF2.1

A general purpose force field such as MMFF94/MMFF94s, which can properly deal with a wide range of diverse structures, is very valuable in the context of a cheminformatics toolkit. Herein we present an open-source implementation of this force field within the RDKit. The new MMFF functionality can be accessed through a C++/C#/Python/Java application programming interface (API) developed along the lines of the one already available for UFF in the RDKit. Our implementation was fully validated against the official validation suite provided by the MMFF authors. All energies and gradients were correctly computed; moreover, atom type and force constants were correctly assigned for 3D molecules built from SMILES strings. To provide full flexibility, the available API provides direct access to include/exclude individual terms from the MMFF energy expression and to carry out constrained geometry optimizations. The availability of a MMFF-capable molecular mechanics engine coupled with the rest of the RDKit functionality and covered by the BSD license is appealing to researchers operating in both academia and industry.

An open-source, cross-platform software aimed at conformer generation and unsupervised rigid-body molecular alignment is presented. Different algorithms have been implemented to perform single and multi-conformation superimpositions on one or more templates. Alignments can be accomplished by matching pharmacophores, heavy atoms or a combination of the two. All methods have been successfully validated on eight comprehensive datasets previously gathered by Sutherland and co-workers. High computational performance has been attained through efficient parallelization of the code. The unsupervised nature of the alignment algorithms, together with its scriptable interface, make Open3DALIGN an ideal component of high-throughput, automated cheminformatics workflows.

Open3DQSAR is a freely available open-source program aimed at chemometric analysis of molecular interaction fields. MIFs can be imported from different sources (GRID, CoMFA/CoMSIA, quantum-mechanical electrostatic potential or electron density grids) or generated by Open3DQSAR itself. Much focus has been put on automation through the implementation of a scriptable interface, as well as on high computational performance achieved by algorithm parallelization. Flexibility and interoperability with existing molecular modeling software make Open3DQSAR a powerful tool in pharmacophore assessment and ligand-based drug design.

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A methodology that combines alchemical free energy calculations (FEP) with machine learning (ML) has been developed to compute accurate absolute hydration free energies. The hybrid FEP/ML methodology was trained on a subset of the Free-Solv database, and retrospectively shown to outperform most submissions from the SAMPL4 competition. Compared to pure machine-learning approaches, FEP/ML yields more precise estimates of free energies of hydration, and requires a fraction of the training set size to outperform standalone FEP calculations. The ML-derived correction terms are further shown to be transferable to a range of related FEP simulation protocols. The approach may be used to inexpensively improve the accuracy of FEP calculations, and to flag molecules which will benefit the most from bespoke forcefield parameterization efforts.

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A new series of polyvalent drugs obtained by joining edaravone with NO-donor moieties is described. All compounds display high antioxidant power together with NO-dependent vasodilator properties. The analysis of a number of molecular descriptors shows that the antioxidant activity, which is tightly linked to the presence of the edaravone substructure, is principally modulated by lipophilicity. These products are potentially useful in the treatment of cardiovascular disorders in which EDRF deficiency and ROS excess are involved.