Molecular Diversity最新文献

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Multi-omics and genetic prioritization identify candidate molecular links between micro- and nanoplastics-associated signatures and chronic kidney disease. 多组学和遗传优先级确定微和纳米塑料相关特征与慢性肾脏疾病之间的候选分子联系。
IF 4.3 2区 化学
Molecular Diversity Pub Date : 2026-07-23 DOI: 10.1007/s11030-026-11671-7
Dianjie Zeng, Ze Cheng, Jiachen Liu, Yinhuai Wang, Fangzhi Chen
{"title":"Multi-omics and genetic prioritization identify candidate molecular links between micro- and nanoplastics-associated signatures and chronic kidney disease.","authors":"Dianjie Zeng, Ze Cheng, Jiachen Liu, Yinhuai Wang, Fangzhi Chen","doi":"10.1007/s11030-026-11671-7","DOIUrl":"https://doi.org/10.1007/s11030-026-11671-7","url":null,"abstract":"<p><p>Micro- and nanoplastics (MNPs) have been detected in human renal and urinary tissues and are increasingly recognized as potential environmental contributors to kidney injury and chronic kidney disease (CKD), but the molecular signatures connecting MNP-associated toxicogenomic signals with CKD remain poorly understood. In this study, we employed an integrative analytical framework combining toxicity prediction, toxicogenomic target analysis, transcriptomic analysis, machine learning, transcriptome-wide Mendelian randomization, single-nucleus RNA sequencing, and targeted in vitro expression validation to investigate candidate molecular links between MNP-associated toxicogenomic signatures and CKD. Among MNP monomers with available SMILES notations, PVC, PMMA, PP, and PS showed moderate predicted nephrotoxicity, whereas PE showed a borderline score and PET showed a lower predicted score. We identified 58 shared candidate genes between MNP-associated targets and CKD-related genes, which were mainly enriched in inflammatory and oxidative stress-related pathways. A machine learning model based on these features showed discriminative performance in training and external validation CKD datasets. Transcriptome-wide MR analyses prioritized several genes, including TGFB1, CTNNB1, PF4, and NR3C2, whose genetically predicted expression was associated with CKD risk, although colocalization evidence was limited. Single-nucleus analysis highlighted proximal tubular, endothelial, podocyte, and monocyte-lineage cells as CKD-relevant renal compartments. Exploratory molecular docking provided computational binding hypotheses between selected MNP monomeric units and candidate proteins. Targeted qRT-PCR validation further showed that PS-MP exposure increased the expression of profibrotic markers and altered the expression of selected candidate genes in proximal tubular epithelial cells. Overall, this study provides an integrative, systems-level characterization of candidate molecular links between MNP-associated toxicogenomic signatures and CKD. These findings highlight candidate genes, pathways, and CKD-relevant renal cell types, offering hypothesis-generating insights into environmentally related kidney injury and providing preliminary expression-level experimental support for selected prioritized genes.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148560449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
From structural features to mouse acute intraperitoneal toxicity prediction: a triple computational toxicology approach for safety assessment of flavonoids. 从结构特征到小鼠急性腹腔毒性预测:黄酮类化合物安全性评估的三重计算毒理学方法。
IF 4.3 2区 化学
Molecular Diversity Pub Date : 2026-07-23 DOI: 10.1007/s11030-026-11674-4
Yichen Yang, Na Zhang, Ting Ren, Lijiao Zhao, Rugang Zhong, Ning Lin, Guohui Sun
{"title":"From structural features to mouse acute intraperitoneal toxicity prediction: a triple computational toxicology approach for safety assessment of flavonoids.","authors":"Yichen Yang, Na Zhang, Ting Ren, Lijiao Zhao, Rugang Zhong, Ning Lin, Guohui Sun","doi":"10.1007/s11030-026-11674-4","DOIUrl":"https://doi.org/10.1007/s11030-026-11674-4","url":null,"abstract":"<p><p>Flavonoids, a ubiquitous class of plant polyphenolic compounds, are known for their wide spectrum of biological functions, exhibiting diverse physiological functions and possessing significant application value in pharmaceuticals, foods, and nutraceuticals. Thus, it is of great significance to conduct the toxicity assessment. However, it is impossible to perform the experimental testing for a vast number of flavonoid chemcials. In this case, in silico methods are promising to address this problem. In strict accordance with OECD principles, this study established quantitative structure-toxicity relationship (QSTR) models for predicting flavonoid acute intraperitoneal toxicity in mice by employing GA-MLR methodology. Read-Across (RA) methodology was employed to estimate the toxicity based on structural similarity. RASTR descriptors were then calculated and pooled together with QSTR descriptors to establish a q-RASTR model. Importantly, intelligent consensus modelling was implemented as another method to enhance model's stability and predictive performance. Finally, the optimal QSTR model satisfied rigorous internal and external validation benchmarks, with R<sup>2</sup> = 0.7887, [Formula: see text] = 0.7327, [Formula: see text] = 0.8521-0.8772, [Formula: see text] = 0.9299. Based on three computational toxicology methods (QSTR, RA, and consensus modeling), the optimal model was consensus model 0 (average predictions). This model was then applied to predict the toxicity of a real external dataset lacking toxicity values. A comparative analysis with the predictions from an open-source VEGA tool was conducted to verify the applicability and predictive reliability of our model. This work offers mechanistic insights into the toxicological behavior of flavonoids and provides a rapid toxicity prediction tool for evaluating the safety of flavonoid-based chemicals.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148560376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Synthesis, 131I-radioiodination, and biodistribution of a novel nicotinonitrile derivative with in vitro antimicrobial and DNA gyrase inhibitory activities. 具有体外抗菌和DNA旋切酶抑制活性的新型烟腈衍生物的合成、放射性碘化和生物分布。
IF 4.3 2区 化学
Molecular Diversity Pub Date : 2026-07-17 DOI: 10.1007/s11030-026-11661-9
Basant G Salib, Basma M Essa, Hesham A Shamsel-Din, Mohamed A Motaleb, M El-Tawoosy, Adli A Selim, Sameh Ahmed Rizk, Ahmed Hassan Ibrahim Faraag, Mohamed A Ali, Islam Yousif Mostafa, Reda Mansour, Salah S Elyan, Mohamed Salah Basiouny, Kurls E Anwer
{"title":"Synthesis, <sup>131</sup>I-radioiodination, and biodistribution of a novel nicotinonitrile derivative with in vitro antimicrobial and DNA gyrase inhibitory activities.","authors":"Basant G Salib, Basma M Essa, Hesham A Shamsel-Din, Mohamed A Motaleb, M El-Tawoosy, Adli A Selim, Sameh Ahmed Rizk, Ahmed Hassan Ibrahim Faraag, Mohamed A Ali, Islam Yousif Mostafa, Reda Mansour, Salah S Elyan, Mohamed Salah Basiouny, Kurls E Anwer","doi":"10.1007/s11030-026-11661-9","DOIUrl":"https://doi.org/10.1007/s11030-026-11661-9","url":null,"abstract":"<p><p>To address the rise of multidrug-resistant bacteria by developing novel antibacterial agents with integrated capabilities for targeted delivery and real-time tracking, and to evaluate their potential for infection theranostics. Novel enaminonitrile-based pyridine and pyran derivatives were sustainably synthesized. Among them, lead compound 5 was assessed for in vitro DNA gyrase inhibition. Compound 5 was then radiolabeled with iodine-131, and radiolabeling yield was measured. In vivo biodistribution and pharmacokinetic profile were evaluated using an inflammatory murine model, with target-to-muscle ratios calculated. Compound 5 showed potent DNA gyrase inhibition (IC<sub>50</sub> = 11.31 µg/mL). Radiolabeling produced [<sup>131</sup>I]I-5 with high radiolabeling yield (90.15%). In the murine model, the radiolabeled construct demonstrated rapid blood clearance and sustained, specific accumulation at the infection site, achieving a high target-to-muscle ratio of 5.18 at 1-h post-administration. This study introduces a new class of antibacterial agents and successfully translates a lead compound into a theranostic formulation. [<sup>131</sup>I]I-5 shows strong promise as a candidate for image-guided therapy and targeted treatment of infectious diseases.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148468144","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Fragment-based diffusion modeling and molecular dynamics simulation validation for the discovery of PD-L1 small-molecule inhibitors. 基于片段的扩散建模和分子动力学模拟验证PD-L1小分子抑制剂的发现。
IF 4.3 2区 化学
Molecular Diversity Pub Date : 2026-07-17 DOI: 10.1007/s11030-026-11642-y
Jun Liu, Yuxing Yi, Xiaoyan Wu, Jianhuai Liang, Boping Liu, Bingfeng Wang
{"title":"Fragment-based diffusion modeling and molecular dynamics simulation validation for the discovery of PD-L1 small-molecule inhibitors.","authors":"Jun Liu, Yuxing Yi, Xiaoyan Wu, Jianhuai Liang, Boping Liu, Bingfeng Wang","doi":"10.1007/s11030-026-11642-y","DOIUrl":"https://doi.org/10.1007/s11030-026-11642-y","url":null,"abstract":"<p><p>The programmed cell death-1/programmed cell death-ligand 1 (PD-1/PD-L1) pathway is a key target in cancer immunotherapy. Although monoclonal antibodies (mAbs) have demonstrated remarkable clinical efficacy, their application is limited by poor tissue penetration, high production costs, and the need for intravenous administration. Small-molecule inhibitors provide a promising complementary strategy, but designing them remains challenging due to the large, relatively flat PD-1/PD-L1 interface. In this study, we integrated fragment-based drug design (FBDD) with conditional diffusion modeling to overcome these obstacles. Core scaffolds consisting of key fragments identified through protein-ligand interaction analysis were used as conditional inputs. Considering the relatively conserved binding mode and limited pocket flexibility of reported PD-L1/small-molecule inhibitor complexes, seven representative co-crystal structures were selected to capture the major binding features and guide molecular generation. Structurally plausible candidate inhibitors were generated using diffusion modeling and screened by molecular docking. After 500 ns molecular dynamics (MD) simulations, we identified four candidates (bo1-bo4), which were selected for MD-based evaluation. The predicted binding free energy (BFE) values of three compounds (bo1, bo2, and bo3) were lower than - 40 kcal/mol, as calculated by the molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) method with interaction entropy (IE) correction, suggesting their potential to stabilize the PD-L1 dimer interface in silico and serve as computationally prioritized candidates for further experimental evaluation of PD-1/PD-L1 blockade. Overall, this work suggests that fragment-based diffusion modeling is an efficient and interpretable strategy for the discovery of computationally prioritized PD-L1 small-molecule candidate inhibitors and offers a promising framework for tackling challenging targets in cancer immunotherapy.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148468150","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Computational structural dynamics and immunoinformatic analysis of EIEC IpaH4.5 targeting immunoprophylaxis design against bacillary dysentery. EIEC IpaH4.5靶向细菌性痢疾免疫预防设计的计算结构动力学和免疫信息学分析。
IF 4.3 2区 化学
Molecular Diversity Pub Date : 2026-07-16 DOI: 10.1007/s11030-026-11667-3
Pinkan Sadhukhan, Nibedita Mahata
{"title":"Computational structural dynamics and immunoinformatic analysis of EIEC IpaH<sub>4.5</sub> targeting immunoprophylaxis design against bacillary dysentery.","authors":"Pinkan Sadhukhan, Nibedita Mahata","doi":"10.1007/s11030-026-11667-3","DOIUrl":"https://doi.org/10.1007/s11030-026-11667-3","url":null,"abstract":"<p><p>Bacillary dysentery continues as a latent global health challenge, mainly affecting infants in developing nations. The lack of a licensed vaccine and spread of antimicrobial resistance, underlines the need for an alternative immunoprophylactic management. The present study was to identify a nasal subunit vaccine candidate against bacillary dysentery. For this, the virulence-associated EIEC IpaH<sub>4.5</sub> protein, also conserved across pathogenic Shigella species, was selected as the antigenic source. A 29-mer protective antigenic peptide (PAP) (<sup>44</sup>TTTENRIQAVRLLKICLDTREPVLNLSLL<sup>72</sup>) was identified within its N-terminal region, consisted of overlapping two B-cell, one CTL, and seven HTL epitopes. Both, T-cell epitopes were screened for strong HLA-binding potential (IC<sub>50</sub> < 500 nM). Screened HTL epitopes positively induced IFN-γ, IL-4, and IL-10 and were non-homologous to human. Epitope clustering underscored the PAP region, having 99.68% world-wide population coverage. The 3D model of EIEC IpaH<sub>4.5</sub> was predicted using ab-initio method (c-score: 0.44). Whereas, homology modelling was utilized to model the extracellular human Toll-like receptors (TLR1/2/4/5/6) corresponding to pulmonary macrophages. A 100 ns molecular dynamics simulation revealed a stable RMSD (Backbone) plot with an average fluctuation of 0.92 ± 0.05 nm for IpaH<sub>4.5</sub> and TLR 4 complex. MM/PBSA analysis yielded an average ∆G: - 76.65 ± 8.12 kcal/mol, while MM/GBSA analysis produced a value of - 52.40 ± 6.45 kcal/mol, indicating an energetically favourable complex. In-silico immune titers of the IpaH<sub>4.5</sub>, was seen to activate both humoral and cellular immunity. Finally, in-silico cloning aided theoretical expression feasibility of the EIEC IpaH<sub>4.5</sub>. However, real-world experimental validation would be needed for evaluating its protective immunogenicity.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148468184","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Design, synthesis, and biological characterization of a hydrophobic tagging EGFR degrader for the treatment of non-small-cell lung cancer. 用于治疗非小细胞肺癌的疏水标记EGFR降解剂的设计、合成和生物学特性
IF 4.3 2区 化学
Molecular Diversity Pub Date : 2026-07-16 DOI: 10.1007/s11030-026-11669-1
Mo Li, Chengye Wang, Xingting Wang, Haotianyu Zhu, Yu Bai
{"title":"Design, synthesis, and biological characterization of a hydrophobic tagging EGFR degrader for the treatment of non-small-cell lung cancer.","authors":"Mo Li, Chengye Wang, Xingting Wang, Haotianyu Zhu, Yu Bai","doi":"10.1007/s11030-026-11669-1","DOIUrl":"https://doi.org/10.1007/s11030-026-11669-1","url":null,"abstract":"<p><p>EGFR is a validated therapeutic target for non-small cell lung cancer (NSCLC). Herein, we designed and synthesized a series of gefitinib-based hydrophobic tagging (Hyt) degraders to induce EGFR degradation. Among them, B3 was identified as an active degrader, with DC<sub>50</sub> values of 0.61 and 0.73 μM in the EGFR-del19 NSCLC cells HCC827 and PC9, respectively, and DT<sub>50</sub> values of 9.2 and 13.7 h. Mechanistic studies showed that B3 accelerated EGFR turnover and revealed a degradation process involving the ubiquitin-proteasome system and the autophagy-lysosome pathway. B3 also suppressed EGFR downstream signaling and inhibited the proliferation of HCC827 and PC9 cells, with IC<sub>50</sub> values of 0.17 and 0.25 μM, respectively. In an HCC827 xenograft model, B3 significantly inhibited tumor growth and reduced EGFR levels in tumor tissues without obvious toxicity. These results identify B3 as an active EGFR hydrophobic tag degrader and a useful compound for further investigation in NSCLC models harboring EGFR del19.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148468187","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
An acid-responsive rhodamine-based fluorescent probe for N-terminal protein labeling and aqueous Tsuji-Trost allylic alkylation. 用于n端蛋白标记和Tsuji-Trost烯丙基烷基化的酸反应性罗丹明荧光探针。
IF 4.3 2区 化学
Molecular Diversity Pub Date : 2026-07-16 DOI: 10.1007/s11030-026-11666-4
Yonghua Tan, Kaiyuan Hui, Raphaël Frédérick, Oliver Riant, Xiaodong Jiang
{"title":"An acid-responsive rhodamine-based fluorescent probe for N-terminal protein labeling and aqueous Tsuji-Trost allylic alkylation.","authors":"Yonghua Tan, Kaiyuan Hui, Raphaël Frédérick, Oliver Riant, Xiaodong Jiang","doi":"10.1007/s11030-026-11666-4","DOIUrl":"https://doi.org/10.1007/s11030-026-11666-4","url":null,"abstract":"<p><p>The development of acid-responsive fluorescent probes with additional chemical functionality remains of considerable interest in chemical biology. Herein, we report an acid-responsive rhodamine-based fluorescent probe, 2PCA-RhB, which exhibits a pronounced fluorescence \"turn-on\" response under acidic aqueous conditions through spirolactam ring opening. The probe displays favorable photophysical properties, good aqueous compatibility, and enables fluorescence imaging in living cells. Beyond its fluorescence response, 2PCA-RhB incorporates a 2-pyridinecarboxaldehyde (2PCA) moiety that enables N-terminal-selective protein labeling, while its allyl carbonate functionality is compatible with palladium-catalyzed Tsuji-Trost allylic alkylation under aqueous conditions. These studies establish 2PCA-RhB as an acid-responsive fluorescent probe with both N-terminal labeling capability and compatibility with aqueous transition-metal-mediated transformation. The present work provides a versatile molecular scaffold for the future development of fluorescent chemical tools for protein modification and bioorthogonal applications in complex biological environments.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148468205","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Copper-catalyzed desulfurative guanylation of amines using CS2 as a C1 synthon. 以CS2为C1合成物的铜催化胺的脱硫胍化反应。
IF 4.3 2区 化学
Molecular Diversity Pub Date : 2026-07-14 DOI: 10.1007/s11030-026-11660-w
Pinyong Zhong, Kangqiang Lu, Jin-Biao Liu
{"title":"Copper-catalyzed desulfurative guanylation of amines using CS<sub>2</sub> as a C1 synthon.","authors":"Pinyong Zhong, Kangqiang Lu, Jin-Biao Liu","doi":"10.1007/s11030-026-11660-w","DOIUrl":"10.1007/s11030-026-11660-w","url":null,"abstract":"<p><p>Guanidine compounds constitute a significant class of nitrogen-containing organic molecules with widespread applications in medicinal chemistry and synthetic science. Herein, we report a copper-catalyzed desulfurization strategy for the efficient synthesis of guanidine derivatives directly from amines and carbon disulfide. This transformation hinges on the in situ generation of a thiourea intermediate of a thiourea intermediate, followed by copper-catalyzed desulfurization to afford a highly reactive carbodiimide intermediate, with molecular oxygen serving as a green terminal oxidant in the catalytic cycle. In contrast to conventional methodologies relying on hypervalent iodine reagents, this protocol circumvents the use of strong oxidants and exhibits broad substrate scope and excellent functional group tolerance. Notably, this approach is amenable not only to the construction of structurally diverse and complex guanidine derivatives but also to the late-stage functionalization of drug-related molecules.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148434738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Deep learning-driven discovery of anti-metastatic phytochemicals targeting MMP-1 in breast cancer via advanced contrastive learning and structural attention. 通过先进的对比学习和结构注意,深度学习驱动的乳腺癌抗转移性植物化学物质靶向MMP-1的发现。
IF 4.3 2区 化学
Molecular Diversity Pub Date : 2026-07-14 DOI: 10.1007/s11030-026-11646-8
V Shunmuga Priya, S Mariaamalraj, S Asha, S Vanaja
{"title":"Deep learning-driven discovery of anti-metastatic phytochemicals targeting MMP-1 in breast cancer via advanced contrastive learning and structural attention.","authors":"V Shunmuga Priya, S Mariaamalraj, S Asha, S Vanaja","doi":"10.1007/s11030-026-11646-8","DOIUrl":"https://doi.org/10.1007/s11030-026-11646-8","url":null,"abstract":"<p><p>Matrix metalloproteinase-1 (MMP-1) is a key enzyme that drives extracellular matrix degradation and facilitates breast cancer progression, invasion, and metastasis. This abnormal MMP-1 activity is linked to worse patient outcomes and also improved progression of tumor, which promotes critical therapeutic target. However, recent deep learning approaches are utilized still unable to fully capture molecular structures, cross-domain molecular-protein interactions, and interpretable predictive features. These challenges are addressed by incorporating a novel Contrastive Learning-based Molecular-Protein Deep Kernel Learning (CLM-DKL) in this research to solve constraints during the high-throughput virtual screening of phytochemicals targeting MMP-1. This process is effectively fine-tuned via the Stellar Oscillation Optimizer (SOO). Moreover, the Structure-Enhanced Cross-Interaction Graph Attention Network (SECI-GAT) produces embeddings in a hierarchical manner that capture both intra-molecular structure and molecular-protein interactions. To improve the prediction of molecules with more structurally informative area-focused progress and the alignment of different representations of information, a Multi-View Contrastive Learning (MVCL) with both attentions, such as Structural Entropy Guided Attention (SEGA) and Encoder Attention Fusion (EAF), are utilized. The uncertainty-aware molecular-protein affinity prediction by CLM-DKL, and atom-residue-level contribution scores provided by the proposed Deep Learning Important FeaTures (DeepLIFT) for biological interpretability. Evaluation outcomes achieve ROC-AUC of 0.91, 0.88, 0.90, PR-AUC of 0.87, 0.84, 0.86, for ChEMBL, PubChem BioAssay, and BindingDB, respectively, and F1 scores up to 0.94, demonstrating strong predictive power, stability, and generalization. This integrated framework provides a robust, interpretable, and structurally informed pipeline for discovering potent MMP-1 inhibitors.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148434760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Synthesis and biological evaluation of bisspirooxindole-hexahydroindolizines as potential anticancer agent. 潜在抗癌剂双螺环吲哚-六氢吲哚嗪的合成及生物学评价。
IF 4.3 2区 化学
Molecular Diversity Pub Date : 2026-07-13 DOI: 10.1007/s11030-026-11657-5
Fereshteh Ahmadi, Mohammad Javadi, Naeimeh Shahrestani, Roshan Baharinia, Yasaman Tamaddon-Abibigloo, Hooman Aghamirza Moghim Aliabadi, Amir Kashtiaray, Behrouz Notash
{"title":"Synthesis and biological evaluation of bisspirooxindole-hexahydroindolizines as potential anticancer agent.","authors":"Fereshteh Ahmadi, Mohammad Javadi, Naeimeh Shahrestani, Roshan Baharinia, Yasaman Tamaddon-Abibigloo, Hooman Aghamirza Moghim Aliabadi, Amir Kashtiaray, Behrouz Notash","doi":"10.1007/s11030-026-11657-5","DOIUrl":"https://doi.org/10.1007/s11030-026-11657-5","url":null,"abstract":"<p><p>In this study, we report an efficient three-component domino reaction of isatin, pipecolic acid, and alkyl 2-(1-methyl-2-oxoindolin-3-ylidene) acetate that provided a simple and convenient route to synthesis of novel methyl-2,2″-dioxo-1',5',6',7',8',8a'-hexahydrodispiro[indoline-3,2'-indolizine-3',3″-indoline]-1'-carboxylate derivatives. This regio- and diastereoselective transformation presumably proceeds through a domino sequence involving azomethine ylide formation followed by a [3 + 2] cycloaddition reaction, leading to the construction of the bisspirooxindole scaffold in a one-pot operation. Preliminary biological evaluation revealed that the synthesized compounds exhibited significant cytotoxic activity against MCF-7 breast cancer cells. The docking study suggested that compound 3d can act as an estrogen receptor alpha (ER-α) modulator, and can be considered a promising lead compound.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148434793","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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