David Alencar Araripe

NEQ ² introduces a non-equilibrium alchemical workflow in QligFEP that achieves accuracy comparable to equilibrium calculations with improved computational efficiency. Independent switching trajectories enable straightforward parallelization.

Computational blind challenges are essential for advancing drug discovery, especially in research areas with limited public data, such as absorption, distribution, metabolism, excretion, toxicity (ADMET) prediction. In this paper, we present the results of our latest community blind challenge, organized in collaboration with Expansion Therapeutics (ExpansionRx). Participants were tasked with predicting nine distinct ADMET endpoints routinely evaluated during lead optimization of compounds in drug discovery programs. Following unprecedented engagement from the global community, this challenge provided valuable insights into the state of the art in machine learning for ADMET modeling. Evaluating submissions against a realistic, challenging dataset from active ExpansionRx drug discovery programs revealed that message-passing neural networks and chemical foundation models dominated among the top performers. Furthermore, the results highlighted the power of proprietary industry datasets and a critical need to optimize predictive workflows for different endpoints independently via multitasking and task-affinity grouping. We also demonstrate how hosting our open-source blind challenge infrastructure on a flexible platform like Hugging Face was pivotal for driving community engagement and visibility. Ultimately, blind challenges supported by robust infrastructure, widespread dissemination, and rigorous post-challenge analysis are fundamental to maximizing the utility of public data releases. We anticipate that these community benchmarks will continue to drive the advancement of ADMET models, enabling their deployment in both early- and late-stage drug discovery.

Predicting how chemical modifications affect drug binding is central to rational drug design. Free energy perturbation (FEP) calculations provide accurate estimates of these binding affinity changes, but existing methods often require substantial computational resources and expert knowledge. Here, we present QligFEP v2.1.0, a flexible open-source workflow based on a graphical and command-line interface for calculating relative binding free energies using spherical boundary conditions, which dramatically reduces simulation system size by confining simulations to a focused region around the binding site. QligFEP features a configurable restraint algorithm that automatically handles diverse chemical transformations, streamlined setup procedures, and enhanced analysis tools. We validated the method using industry benchmarks comprising 16 protein targets and 639 ligand transformations. Statistical analysis demonstrates that QligFEP achieves comparable accuracy to established commercial and open-source alternatives while requiring only a fraction of the computational resources. The perturbation protocol simulates ∼6250 atoms per perturbation leg and completes transformation replicates in under 2 h on standard computational clusters. Unlike full-system simulations, QligFEP's modest computational requirements make FEP accessible for less than $1 on current AWS spot instances. The combination of accuracy, flexibility, and computational efficiency positions QligFEP as a practical solution for accelerating compound optimization in drug discovery, making rigorous binding affinity predictions accessible for large scale applications and to research groups with limited computational infrastructure.

Predicting how chemical modifications affect drug binding is central to rational drug design. Free Energy Perturbation (FEP) calculations provide accurate estimates of these binding affinity changes, but existing methods often require substantial computational resources and expert knowledge. Here we present QligFEP v2.1.0, an automated open-source platform for calculating relative binding free energies using spherical boundary conditions (SBC), which dramatically reduces computational cost by confining simulations to a focused region around the binding site. QligFEP features a configurable restraint algorithm that automatically handles diverse chemical transformations, streamlined setup procedures, and enhanced analysis tools. We validated the method using industry benchmarks comprising 16 protein targets and 639 ligand transformations. Statistical analysis demonstrates that QligFEP achieves comparable accuracy to established commercial and open-source alternatives, while requiring only a fraction of the computational resources. The perturbation protocol simulates ~6250 atoms per perturbation leg and completes transformation replicates in under 2 hours on standard computational clusters, which is substantially faster than traditional full-system simulations, and currently would cost less than $1 on current AWS spot instances. The combination of accuracy, automation, and computational efficiency positions QligFEP as a practical solution for accelerating compound optimization in drug discovery, making rigorous binding affinity predictions accessible for large scale applications and to research groups with limited computational infrastructure.

Building reliable and robust quantitative structure–property relationship (QSPR) models is a challenging task. First, the experimental data needs to be obtained, analyzed and curated. Second, the number of available methods is continuously growing and evaluating different algorithms and methodologies can be arduous. Finally, the last hurdle that researchers face is to ensure the reproducibility of their models and facilitate their transferability into practice. In this work, we introduce QSPRpred, a toolkit for analysis of bioactivity data sets and QSPR modelling, which attempts to address the aforementioned challenges. QSPRpred’s modular Python API enables users to intuitively describe different parts of a modelling workflow using a plethora of pre-implemented components, but also integrates customized implementations in a “plug-and-play” manner. QSPRpred data sets and models are directly serializable, which means they can be readily reproduced and put into operation after training as the models are saved with all required data pre-processing steps to make predictions on new compounds directly from SMILES strings. The general-purpose character of QSPRpred is also demonstrated by inclusion of support for multi-task and proteochemometric modelling. The package is extensively documented and comes with a large collection of tutorials to help new users. In this paper, we describe all of QSPRpred’s functionalities and also conduct a small benchmarking case study to illustrate how different components can be leveraged to compare a diverse set of models. QSPRpred is fully open-source and available at https://github.com/CDDLeiden/QSPRpred.Scientific ContributionQSPRpred aims to provide a complex, but comprehensive Python API to conduct all tasks encountered in QSPR modelling from data preparation and analysis to model creation and model deployment. In contrast to similar packages, QSPRpred offers a wider and more exhaustive range of capabilities and integrations with many popular packages that also go beyond QSPR modelling. A significant contribution of QSPRpred is also in its automated and highly standardized serialization scheme, which significantly improves reproducibility and transferability of models.

Building reliable and robust quantitative structure-property relationship (QSPR) models is a challenging task. First, the experimental data needs to be obtained, analyzed and curated. Second, the number of available methods is continuously growing and evaluating different algorithms and methodologies can be arduous. Finally, the last hurdle that researchers face is to ensure the reproducibility of their models and facilitate their transferability into practice. In this work, we introduce QSPRpred, a toolkit for analysis of bioactivity data sets and QSPR modelling, which attempts to address the aforementioned challenges. QSPRpred's modular Python API enables users to intuitively describe different parts of a modelling workflow using a plethora of pre-implemented components, but also integrate customized implementations in a "plug-and-play" manner. QSPRpred data sets and models are directly serializable, which means they can be readily reproduced and put into operation after training as the models are saved with all required data pre-processing steps to make predictions on new compounds directly from SMILES strings. The general-purpose character of QSPRpred is also demonstrated by inclusion of support for multi-task and proteochemometric modelling. The package is extensively documented and comes with a large collection of tutorials to help new users. In this paper, we describe all of QSPRpred's functionalities and also conduct a small benchmarking case study to illustrate how different components can be leveraged to compare a diverse set of models. QSPRpred is fully open-source and available at https://github.com/CDDLeiden/QSPRpred. Scientific Contribution QSPRpred aims to provide a complex, but comprehensive Python API to conduct all tasks encountered in QSPR modelling from data preparation and analysis to model creation and model deployment. In contrast to similar packages, QSPRpred offers a wider and more exhaustive range of capabilities and integrations with many popular packages that also go beyond QSPR modelling. A significant contribution of QSPRpred is also in its automated and highly standardized serialization scheme, which significantly improves reproducibility and transferability of models.

A series of 11 new substituted 1,5-dihydro-4,1-benzoxazepine derivatives was synthesised to study the influence of the methyl group in the 1-(benzenesulphonyl) moiety, the replacement of the purine by the benzotriazole bioisosteric analogue, and the introduction of a bulky substituent at position 6 of the purine, on the biological effects. Their inhibition against isolated HER2 was studied and the structure–activity relationships have been confirmed by molecular modelling studies. The most potent compound against isolated HER2 is 9a with an IC₅₀ of 7.31 µM. We have investigated the effects of the target compounds on cell proliferation. The most active compound (7c) against all the tumour cell lines studied (IC₅₀ 0.42–0.86 µM) does not produce any modification in the expression of pro-caspase 3, but increases the caspase 1 expression, and promotes pyroptosis. Graphical Abstract