{"title":"A computational perception of BBOX1-IP3R3 interaction uncovers inhibitors for dysregulated calcium signalling in triple negative breast cancer.","authors":"P Sangavi, G R Shri, S K Singh, K Langeswaran","doi":"10.1080/1062936X.2025.2497380","DOIUrl":"10.1080/1062936X.2025.2497380","url":null,"abstract":"<p><p>Triple Negative Breast Cancer (TNBC) is the most aggressive type of breast cancer unveiling negative expression on oestrogen receptors, progesterone receptors, and HER2. The anomalous activation of signalling pathways and specific types of mutations characterize the progression of TNBC. Protein-protein interaction in the tumour microenvironment plays a crucial role in tumour aggressiveness. Disrupting the signalling pathways that promote cell progression, migration, and survival opens up a promising avenue for targeting the aggressive form of TNBC. The present study emphasizes the molecular interaction mechanism driving the aggressive and recalcitrant TNBC between BBOX1-IP3R3. The BBOX1-IP3R3 complex destabilization was accomplished using compounds obtained from various databases through virtual screening, molecular, and essential dynamics. The interaction study revealed that the four hits bound at the interface and facilitated better binding affinity with the highest docking score and optimal binding free energy. In addition, the molecular dynamics simulation, PCA/FEL, and MM/PBSA analysis conclusively evaluate the binding potential of the compounds and unequivocally stabilize specific conformations or deception of the complexes in high-energy states. Thus, the identified compounds lead to the disruption of BBOX1-IP3R3 interaction, which aids in the therapeutic option of TNBC.</p>","PeriodicalId":21446,"journal":{"name":"SAR and QSAR in Environmental Research","volume":" ","pages":"305-332"},"PeriodicalIF":2.3,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143992722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A C de Faria, A P L de Mesquita, E F F da Cunha, M P Freitas
{"title":"In silico design of benzothiazole and phthalimide-derived hybrids as protoporphyrinogen IX oxidase inhibitors.","authors":"A C de Faria, A P L de Mesquita, E F F da Cunha, M P Freitas","doi":"10.1080/1062936X.2025.2496156","DOIUrl":"10.1080/1062936X.2025.2496156","url":null,"abstract":"<p><p>Protoporphyrinogen IX oxidase (PPO) inhibition is a critical strategy for weed control in crop production. This study employed a computational approach integrating QSAR modelling, docking studies, and molecular dynamics to investigate the inhibitory activities of benzothiazole- and phthalimide-derived compounds against PPO. The MIA-QSAR method modelled p<i>K</i>i values for 52 compounds, complemented by docking and molecular dynamics to analyse ligand-enzyme interactions and identify potential agrochemical candidates. QSAR analysis yielded predictive models with <i>r</i><sup>2</sup> = 0.77, <i>q</i><sup>2</sup> = 0.55, and <i>r</i><sup>2</sup> = 0.74. MIA plots guided the design of 12 derivatives, 5 of which showed promising p<i>K</i>i values (7.31-8.69). Docking and molecular dynamics revealed strong binding affinity and stability for these candidates. The presence of fluorine substituents and C=O and C=S bonds in tetrahydroisoindole moieties enhanced biological activity, leading to the proposition of effective PPO inhibitors. Synthetic routes for the top candidates were outlined for future development, aiming to improve agrochemical efficacy and address resistance issues in crop protection.</p>","PeriodicalId":21446,"journal":{"name":"SAR and QSAR in Environmental Research","volume":" ","pages":"287-303"},"PeriodicalIF":2.3,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143993943","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Targeting drug-resistant <i>Mycobacterium tuberculosis</i>: an integrated computational approach to identify DprE2 inhibitors.","authors":"S Saxena, A Banerjee, L Guruprasad","doi":"10.1080/1062936X.2025.2506055","DOIUrl":"https://doi.org/10.1080/1062936X.2025.2506055","url":null,"abstract":"<p><p><i>Mycobacterium tuberculosis</i> remains one of the leading causes of death from a single infectious agent, posing a major global health challenge. The rise of drug-resistant strains has intensified the need for novel therapeutic agents. Pretomanid and delamanid, two recently developed antitubercular drugs, are bicyclic nitroimidazoles that act as prodrugs, requiring activation by specific mycobacterial enzymes. However, the precise molecular targets of their active metabolites are not fully explained. Recent studies have identified DprE2, an essential enzyme in the biosynthesis of decaprenylphosphoryl-β-D-arabinofuranose (DPA) and arabinogalactan, as a potential target of delamanid. In this study, we applied structure-based pharmacophore modelling to identify potential inhibitors targeting DprE2. High-throughput virtual screening, followed by molecular docking, was used to evaluate binding affinities. ADMET predictions were incorporated to assess drug likeness and pharmacokinetic profiles. Nine promising hits were shortlisted, and their binding stability was further evaluated using 250 ns molecular dynamics simulations. Binding free energy calculations using the MM-GBSA method were then applied to refine the selection, identifying five potent lead molecules. These candidates show strong potential for further development as DprE2 inhibitors, offering a new path in the fight against drug-resistant tuberculosis.</p>","PeriodicalId":21446,"journal":{"name":"SAR and QSAR in Environmental Research","volume":"36 4","pages":"333-363"},"PeriodicalIF":2.3,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144174727","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Y K Zhang, J B Tong, M X Luo, J Y Zhao, Y L Yang, Y Sun, Z P Qing
{"title":"Identification, experimental validation, and computational evaluation of potential ALK inhibitors through hierarchical virtual screening.","authors":"Y K Zhang, J B Tong, M X Luo, J Y Zhao, Y L Yang, Y Sun, Z P Qing","doi":"10.1080/1062936X.2025.2496155","DOIUrl":"10.1080/1062936X.2025.2496155","url":null,"abstract":"<p><p>Anaplastic Lymphoma Kinase (ALK) plays a pivotal oncogenic role in the onset and progression of malignancies such as non-small cell lung cancer, lymphoma, and neuroblastoma. ALK gene mutations or rearrangements significantly enhance tumour cell proliferation and survival. However, the emergence of resistance to existing ALK inhibitors in clinical settings remains a major challenge. Consequently, the development of next-generation inhibitors targeting ALK-resistant mutations has become a central focus in the field of anticancer drug discovery. In this study, a hierarchical virtual screening strategy based on protein structure was utilized to screen 87,454 ligand conformations from 50,000 compounds in the Topscience drug-like database. Structural clustering analysis and ADMET drug-likeness predictions led to the identification of two potential ALK inhibitors, F6524-1593 and F2815-0802. Subsequent activity validation, molecular docking, and molecular dynamics simulations elucidated their potential binding modes and mechanisms of action. This study provides valuable theoretical insights for the development of novel ALK inhibitors targeting drug-resistant mutations and offers guidance for optimizing ALK-targeted therapeutic strategies.</p>","PeriodicalId":21446,"journal":{"name":"SAR and QSAR in Environmental Research","volume":" ","pages":"271-285"},"PeriodicalIF":2.3,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143978040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Computational design of PARP-1 inhibitors: QSAR, molecular docking, virtual screening, ADMET, and molecular dynamics simulations for targeted drug development.","authors":"N Najafi, M H Fatemi","doi":"10.1080/1062936X.2025.2480859","DOIUrl":"https://doi.org/10.1080/1062936X.2025.2480859","url":null,"abstract":"<p><p>Poly (ADP-ribose) polymerase-1 (PARP-1) inhibitors have shown promise in treating various cancers with homologous recombination repair deficiencies, particularly in breast and ovarian cancers harbouring BRCA1/2 mutations. This study aimed to identify and optimize novel PARP-1 inhibitors using the phthalazinone scaffold, known for forming strong and selective interactions with the active site of PARP-1. Through a combination of Quantitative Structure-Activity Relationship (QSAR) modelling, molecular docking simulations, and virtual screening, we discovered compounds with significant anticancer potential. Both the Multiple Linear Regression (MLR) and Support Vector Machines (SVM) models, utilizing four selected molecular descriptors, demonstrated high predictive efficiency for inhibitory activity (MLR: <i>r</i><sup>2</sup> = 0.944, <i>Q</i><sup>2</sup><sub>cv</sub> (cross-validated correlation coefficient) = 0.921, root mean square error (RMSE) = 0.249; SVM: <i>r</i><sup>2</sup> = 0.947, <i>Q</i><sup>2</sup><sub>cv</sub> = 0.887, RMSE = 0.245). Molecular docking studies revealed that several new compounds exhibited strong interactions with key amino acids GLY 227A, MET 229A, PHE 230A, and TYR 246A within the PARP-1 active site, similar to those observed in reference inhibitors Olaparib and AZD2461. Then, the top-ranked compound's (3a) ligand-protein complex underwent a 200 ns molecular dynamics (MD) simulation, confirming stable binding and revealing a robust set of intermolecular interactions maintained under physiological conditions.</p>","PeriodicalId":21446,"journal":{"name":"SAR and QSAR in Environmental Research","volume":"36 3","pages":"205-246"},"PeriodicalIF":2.3,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143994123","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Identification of potential inhibitors of hypoxanthine-guanine phosphoribosyl transferase for cancer treatment by molecular docking, dynamics simulation and in vitro studies.","authors":"O Afzal, A Altharawi, M A Alamri","doi":"10.1080/1062936X.2025.2478500","DOIUrl":"10.1080/1062936X.2025.2478500","url":null,"abstract":"<p><p>Hypoxanthine guanine phosphoribosyltransferase 1 (HPRT1) is a mutational biomarker and a housekeeping human reporter gene that is predominantly employed to assess mutation frequencies associated with cancer development. In this study, our purpose was to identify potential inhibitors against the human hypoxanthine guanine phosphoribosyltransferase (HPRT) protein encoded by HPRT1 gene by employing an integrated in silico approach. The library of 17,967 phytochemicals (IMPPAT 2.0 database) was screened for drug-like properties followed by molecular docking, resulting in the selection of top 20 phytochemicals. Further interaction profile revealed that IMPHY008718 (Gibberellin A34) and IMPHY011650 (Chasmanthin) binds at the GMP binding site of the HPRT1 protein. ADMET properties and biological function predictions of the selected compounds indicate their anticancer potential. Both IMPHY008718 and IMPHY011650 docked complexes were examined in 200 ns MD simulations. Comprehensive MD trajectory analysis was performed in addition to principal component, free energy and MM/PBSA analysis. Furthermore, in vitro human HPRT inhibition assay confirmed and revealed inhibitory potential for Gibberellin A34 (<i>K</i><sub>i</sub> 0.121 µM) and Chasmanthin (<i>K</i><sub>i</sub> 0.368 µM), as compared to standard inhibitor, HGPRT/TBrHGPRT1-IN-1 (<i>K</i><sub>i</sub> 0.032 µM). Overall, these results strongly recommend further experimental work concerning these plant-based molecules as human HPRT inhibitors for anticancer drug development.</p>","PeriodicalId":21446,"journal":{"name":"SAR and QSAR in Environmental Research","volume":" ","pages":"169-188"},"PeriodicalIF":2.3,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143692913","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Read-across-driven binary classification for the developmental and reproductive toxicity of organic compounds tested according to the OECD test guidelines 421/422.","authors":"M Chatterjee, S Pore, Z Szepesi, K Roy","doi":"10.1080/1062936X.2025.2483765","DOIUrl":"https://doi.org/10.1080/1062936X.2025.2483765","url":null,"abstract":"<p><p>Developmental and reproductive toxicity (DART) refers to the adverse effects on sexual function, fertility, and the development of offspring resulting from exposure to toxic substances or chemicals, which may occur at various stages of the reproductive cycle. In response to the increasing volume of chemicals, regulatory bodies advocate for implementing various new approach methodologies (NAMs) as alternatives to animal testing, enabling rapid assessments of the toxic potential of numerous chemical substances. In this study, in silico methodologies were utilized to assess the DART properties of various industrial chemicals. We employed a Read-Across (RA)-based binary classification approach to evaluate the DART potential of these chemicals. The data for the binary classification have been compiled from two distinct sources: eChemPortal (https://www.echemportal.org/echemportal/) and the National Institute of Health Sciences (NIHS) databases. The information gathered from these sources encompasses two types of toxicity data: No Observed Adverse Effect Level (NOAEL) and Low Observed Adverse Effect Level (LOAEL) tested as per the Organisation for Economic Co-operation and Development Test Guidelines 421 and 422, adopting the principles of Good Laboratory Practice (GLP). The data were utilized separately for safety assessment through a binary classification-based read-across prediction, demonstrating commendable classification capabilities for new chemicals (Accuracy<sub>test</sub> ~0.700).</p>","PeriodicalId":21446,"journal":{"name":"SAR and QSAR in Environmental Research","volume":"36 3","pages":"247-270"},"PeriodicalIF":2.3,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144046502","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Predicting acute toxicity of pesticides towards <i>Daphnia magna</i> with random forest algorithm.","authors":"S Xu","doi":"10.1080/1062936X.2025.2478510","DOIUrl":"https://doi.org/10.1080/1062936X.2025.2478510","url":null,"abstract":"<p><p>A large number of pesticides are released into the environment, resulting in serious threat for aquatic organisms. In this work, 15 quantum chemical descriptors were used to develop a quantitative structure-activity/toxicity relationship (QSAR/QSTR) model for toxicity pEC<sub>50</sub> of 745 pesticides towards <i>Daphnia magna</i>, by using random forest algorithm. The optimal QSTR model in this paper yielded a coefficient of determination of 0.828, root-mean-square error of 0.798, and mean absolute error of 0.628 for the test set of 149 pesticides, which are accurate values compared with those of QSTR models published recently. Research has revealed that increasing molecular size (or molar volume), the most positive atomic Mulliken (or APT) charge with hydrogens summed into heavy, and the highest occupied molecular orbital (HOMO) energy, can result in higher toxicity pEC<sub>50</sub>. Increasing the lowest unoccupied molecular orbital (LUMO) energy and the HOMO and LUMO energy gap can lead to lower toxicity pEC<sub>50</sub>.</p>","PeriodicalId":21446,"journal":{"name":"SAR and QSAR in Environmental Research","volume":"36 3","pages":"189-203"},"PeriodicalIF":2.3,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144031410","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
G Xu, W Zhang, J Du, J Cong, P Wang, X Li, X Si, B Wei
{"title":"Binding mechanism of inhibitors to DFG-in and DFG-out P38α deciphered using multiple independent Gaussian accelerated molecular dynamics simulations and deep learning.","authors":"G Xu, W Zhang, J Du, J Cong, P Wang, X Li, X Si, B Wei","doi":"10.1080/1062936X.2025.2475407","DOIUrl":"10.1080/1062936X.2025.2475407","url":null,"abstract":"<p><p>P38α has been identified as a key target for drug design to treat a wide range of diseases. In this study, multiple independent Gaussian accelerated molecular dynamics (GaMD) simulations, deep learning (DL), and the molecular mechanics generalized Born surface area (MM-GBSA) method were used to investigate the binding mechanism of inhibitors (SB2, SK8, and BMU) to DFG-in and DFG-out P38α and clarify the effect of conformational differences in P38α on inhibitor binding. GaMD trajectory-based DL effectively identified important functional domains, such as the A-loop and N-sheet. Post-processing analysis on GaMD trajectories showed that binding of the three inhibitors profoundly affected the structural flexibility and dynamical behaviour of P38α situated at the DFG-in and DFG-out states. The MM-GBSA calculations not only revealed that differences in the binding ability of inhibitors are affected by DFG-in and DFG-out conformations of P38α, but also confirmed that van der Waals interactions are the primary force driving inhibitor-P38α binding. Residue-based free energy estimation identifies hot spots of inhibitor-P38α binding across DFG-in and DFG-out conformations, providing potential target sites for drug design towards P38α. This work is expected to offer valuable theoretical support for the development of selective inhibitors of P38α family members.</p>","PeriodicalId":21446,"journal":{"name":"SAR and QSAR in Environmental Research","volume":" ","pages":"101-126"},"PeriodicalIF":2.3,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143664497","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A Awomuti, Z Yu, O Adesina, O W Samuel, A W Mumbi, D Yin
{"title":"Predictive modelling of peroxisome proliferator-activated receptor gamma (PPARγ) IC50 inhibition by emerging pollutants using light gradient boosting machine.","authors":"A Awomuti, Z Yu, O Adesina, O W Samuel, A W Mumbi, D Yin","doi":"10.1080/1062936X.2025.2478123","DOIUrl":"10.1080/1062936X.2025.2478123","url":null,"abstract":"<p><p>Peroxisome proliferator-activated receptor gamma (PPARγ), a critical nuclear receptor, plays a pivotal role in regulating metabolic and inflammatory processes. However, various environmental contaminants can disrupt PPARγ function, leading to adverse health effects. This study introduces a novel approach to predict the inhibitory activity (IC50 values) of 140 chemical compounds across 13 categories, including pesticides, organochlorines, dioxins, detergents, flame retardants, and preservatives, on PPARγ. The predictive model, based on the light-gradient boosting machine (LightGBM) algorithm, was trained on a dataset of 1804 molecules showed <i>r</i><sup>2</sup> values of 0.82 and 0.59, Mean Absolute Error (MAE) of 0.38 and 0.58, and Root Mean Square Error (RMSE) of 0.54 and 0.76 for the training and test sets, respectively. This study provides novel insights into the interactions between emerging contaminants and PPARγ, highlighting the potential hazards and risks these chemicals may pose to public health and the environment. The ability to predict PPARγ inhibition by these hazardous contaminants demonstrates the value of this approach in guiding enhanced environmental toxicology research and risk assessment.</p>","PeriodicalId":21446,"journal":{"name":"SAR and QSAR in Environmental Research","volume":" ","pages":"145-167"},"PeriodicalIF":2.3,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143692925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}