Structure-based virtual screening utilizes molecular docking to explore and analyze ligand–macromolecule interactions, crucial for identifying and developing potential drug candidates. Although there is availability of several widely used docking programs, the accurate prediction of binding affinity and binding mode still presents challenges. In this study, we introduced a novel protocol that combines our in-house geometry optimization algorithm, the conjugate gradient with backtracking line search (CG-BS), which is capable of restraining and constraining rotatable torsional angles and other geometric parameters with a highly accurate machine learning potential, ANI-2x, renowned for its precise molecular energy predictions reassembling the wB97X/6-31G(d) model. By integrating this protocol with binding pose prediction using the Glide, we conducted additional structural optimization and potential energy prediction on 11 small molecule–macromolecule and 12 peptide–macromolecule systems. We observed that ANI-2x/CG-BS greatly improved the docking power, not only optimizing binding poses more effectively, particularly when the RMSD of the predicted binding pose by Glide exceeded around 5 Å, but also achieving a 26% higher success rate in identifying those native-like binding poses at the top rank compared to Glide docking. As for the scoring and ranking powers, ANI-2x/CG-BS demonstrated an enhanced performance in predicting and ranking hundreds or thousands of ligands over Glide docking. For example, Pearson’s and Spearman’s correlation coefficients remarkedly increased from 0.24 and 0.14 with Glide docking to 0.85 and 0.69, respectively, with the addition of ANI-2x/CG-BS for optimizing and ranking small molecules binding to the bacterial ribosomal aminoacyl-tRNA receptor. These results suggest that ANI-2x/CG-BS holds considerable potential for being integrated into virtual screening pipelines due to its enhanced docking performance.

The accurate prediction of protein-ligand binding poses and affinities is central to structure-based drug design. In this study, we first benchmarked three distinct pose generation strategies for data sets from the ASAP Antiviral Challenge 2025: molecular docking (Glide and AutoDock Vina), ligand-based superposition (FlexS), and deep learning-based modeling (AlphaFold3, Boltz-2, DiffDock and Gnina). We evaluated their performance on binding pose prediction for ligands targeting SARS-CoV-2 and MERS-CoV main protease (Mpro). For binding affinity estimation, we implemented a machine learning-based scoring approach called ligand-residue interaction profile scoring function (LRIP-SF), which integrates molecular mechanics generalized Born surface area (MM-GBSA) energy decomposition with machine learning algorithms. Our results showed that deep learning-based modeling with AlphaFold3 achieved the highest pose prediction accuracy with a success rate of 88.1% and an average ligand root-mean-square deviation (LRMSD) of 1.12 Å. Moreover, binding poses predicted by AlphaFold3 enabled the most accurate potency predictions by LRIP-SF, with the lowest mean absolute error (MAE) and root-mean-square error (RMSE) in pIC₅₀ units across both targets: the MAE and RMSE are 0.606 and 0.813, respectively, for MERS-CoV Mpro and 0.724 and 0.894 respectively for SARS-CoV-2 Mpro. Although ligand-based superposition method (FlexS) was less accurate in pose prediction, it offered competitive potency prediction performance with significantly lower computational cost. To interpret model predictions by LRIP-SF and identify critical binding determinants, we performed global sensitivity analysis (GSA), revealing key residues that contributed most significantly to ligand binding. These findings highlight the importance of pose quality and interaction profiling in affinity prediction and demonstrate the great potential of deep learning-based methods for drug discovery, especially in the absence of cocrystal structures.

The “Long-COVID syndrome” has posed significant challenges due to a lack of validated therapeutic options. We developed a novel multi-step virtual screening strategy to reliably identify inhibitors against 3-chymotrypsin-like protease of SARS-CoV-2 from abundant flavonoids, which represents a promising source of antiviral and immune-boosting nutrients. We identified 57 interacting residues as contributors to the protein-ligand binding pocket. Their energy interaction profiles constituted the input features for Machine Learning (ML) models. The consensus of 25 classifiers trained using various ML algorithms attained 93.9% accuracy and a 6.4% false-positive-rate. The consensus of 10 regression models for binding energy prediction also achieved a low root-mean-square error of 1.18 kcal/mol. We screened out 120 flavonoid hits first and retained 50 drug-like hits after predefined ADMET filtering to ensure bioavailability and safety profiles. Furthermore, molecular dynamics simulations prioritized nine bioactive flavonoids as promising anti-SARS-CoV-2 agents exhibiting both high structural stability (root-mean-square deviation < 5 Å for 218 ns) and low MM/PBSA binding free energy (<−6 kcal/mol). Among them, KB-2 (PubChem-CID, 14630497) and 9-O-Methylglyceofuran (PubChem-CID, 44257401) displayed excellent binding affinity and desirable pharmacokinetic capabilities. These compounds have great potential to serve as oral nutraceuticals with therapeutic and prophylactic properties as care strategies for patients with long-COVID syndrome.

Intranasal diamorphine (IND), approved for managing breakthrough pain in the UK, has been identified as an acceptable alternative offering effective, expedient, and less traumatic analgesia for children. However, the current dose regimen in pediatric populations relies on clinical expertise while the pharmacokinetics properties are poorly understood. This study aimed to develop diamorphine population pharmacokinetics (pop‐PK) models and simulate the IND dosing in virtual pediatric subjects. An integrated four‐compartment pop‐PK model with first‐order absorption and elimination provided an appropriate fit and characterized publicly available 385 concentration measurements of diamorphine, 6‐monoacetylmorphine, and morphine collected from adults. Body weight allometry and renal function maturation (age) were incorporated into the final model, serving as two covariates. The estimated IND relative bioavailability was around 52% compared with intramuscularly injected diamorphine. Using this final model, the morphine plasma concentrations, as the active metabolite for pain relief, were simulated in virtual subjects. The utility of model extrapolation was supported by external verification with acceptable average fold errors of 1.06 ± 0.30 and 0.83 ± 0.07 for morphine maximum concentration and exposures. Meanwhile, the simulated morphine concentration–time profiles could recover the PK profiles observed in children after a single dose of IND. The model‐based dosing simulations were therefore assessed in four children age groups to match the therapeutic window of morphine concentrations in steady state (10–20 μg/L). Our study demonstrates that the dose regimen of 0.3 mg/kg loading dose plus 0.1 mg/kg hourly maintenance dose is generally appropriate for multiple pediatric populations with breakthrough pain, in the view of PK.