Molecular Diversity最新文献

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Structural bioinformatics insights into UDP-galactopyranose mutase (UGM) as a novel drug target for antifilarial therapy against human filarial parasite Brugia malayi. udp -半乳糖氨基葡萄糖突变酶(UGM)作为抗人马来布鲁氏丝虫病药物靶点的结构生物信息学研究。
IF 3.9 2区 化学
Molecular Diversity Pub Date : 2025-07-24 DOI: 10.1007/s11030-025-11304-5
Arasu Muneeshwari, Natarajan Sampath
{"title":"Structural bioinformatics insights into UDP-galactopyranose mutase (UGM) as a novel drug target for antifilarial therapy against human filarial parasite Brugia malayi.","authors":"Arasu Muneeshwari, Natarajan Sampath","doi":"10.1007/s11030-025-11304-5","DOIUrl":"https://doi.org/10.1007/s11030-025-11304-5","url":null,"abstract":"<p><p>A flavoenzyme, UDP-galactopyranose mutase (UGM), serves as a pivotal enzyme catalysing the conversion of UDP-galactopyranose (galP) into UDP-galactofuranose (galF), a metabolite exclusively present in pathogenic microorganisms, including filarial parasites. The galF plays a critical role in various pathogenic processes, like cell wall biosynthesis, virulence enhancement, and cuticle formation in filarial parasites. Notably, the absence of galF in humans renders, UGM an attractive and promising drug target for developing potent antifilarial therapeutics. In this study, we employed advanced bioinformatics approaches to identify effective antifilarial drug candidates. The UGM enzyme from Brugia malayi (BmUGM) was meticulously modelled and subsequently utilized for molecular docking studies against 20 triazolothiadiazine analogues using the AutoDock program. Among these, eight compounds exhibiting high binding affinities, ranging from - 8.7 to - 10.5 kcal/mol, were selected for further protein-ligand MD simulations. Post-simulation analyses, encompassing MM-PBSA and binding free energy decomposition, demonstrated that two triazolothiadiazine analogues, namely D4 and D8, exhibited exceptionally high binding free energies of - 29.76 kcal/mol and - 27.50 kcal/mol, respectively. These values exceeded the binding free energy of the natural substrate galP, which was calculated at - 20.01 kcal/mol. Furthermore, binding free energy decomposition analysis pinpointed critical binding site residues Tyr168, Trp184, Tyr326, Tyr335, Arg336, Tyr405, and Gln475 as essential mediators of the protein-ligand interactions. Additionally, ADMET and DFT quantum mechanical calculations confirmed that the triazolothiadiazine analogues exhibit low toxicity profiles and favourable chemical reactivity. Based on these findings, we propose that the identified ligand molecules hold potential as potent inhibitors of BmUGM, with broad-spectrum efficacy against all life stages of filarial parasites.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144697247","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
Deoxynojirimycin derivatives as potent α-glucosidase inhibitors: in silico ADMET evaluation, molecular dynamics and in vitro validation studies. 脱氧诺吉霉素衍生物作为有效的α-葡萄糖苷酶抑制剂:硅ADMET评价,分子动力学和体外验证研究。
IF 3.9 2区 化学
Molecular Diversity Pub Date : 2025-07-24 DOI: 10.1007/s11030-025-11307-2
Fariya Khan, Suhail Ahmad, Khwaja Osama, Alvina Farooqui, Ajay Kumar, Salman Akhtar
{"title":"Deoxynojirimycin derivatives as potent α-glucosidase inhibitors: in silico ADMET evaluation, molecular dynamics and in vitro validation studies.","authors":"Fariya Khan, Suhail Ahmad, Khwaja Osama, Alvina Farooqui, Ajay Kumar, Salman Akhtar","doi":"10.1007/s11030-025-11307-2","DOIUrl":"https://doi.org/10.1007/s11030-025-11307-2","url":null,"abstract":"<p><p>α-Glucosidase plays a critical role in digesting carbohydrates, leading to an increase in postprandial glucose levels, which contributes to the development and progression of diabetes. By inhibiting this enzyme, it is possible to manage postprandial hyperglycemia, thereby reducing the risk of developing or exacerbating diabetes. The primary aim of our study was to identify and evaluate potential α-glucosidase inhibitors from a series of deoxynojirimycin derivatives, using a combination of binding affinity analysis, simulation studies, and in vitro experiments. 371 deoxynojirimycin analogs were screened based on their compliance with Lipinski's Rule of Five and favorable absorption, distribution, metabolism, excretion, and toxicity (ADMET) parameters. Among these, compound MG257 (C<sub>10</sub>H<sub>21</sub>NO<sub>4</sub>) stood out due to its strong binding interactions with the active site residues of α-glucosidase, as demonstrated through virtual screening and docking studies. In our in vitro analysis, MG257 (C<sub>10</sub>H<sub>21</sub>NO<sub>4</sub>) demonstrated a notably potent α-glucosidase inhibitory activity with an IC<sub>50</sub> value of 0.44 ± 0.18 µM, surpassing the standard inhibitor miglitol, which exhibited an IC₅₀ of 0.64 ± 0.26 µM. Furthermore, molecular dynamics simulations conducted over 100 ns revealed that MG257 maintained excellent stability, further supporting its potential as a reliable inhibitor. Enzyme kinetics studies also confirmed that MG257 inhibits α-glucosidase competitively, reinforcing the findings from the molecular docking and simulation data. These comprehensive results, combining in silico and in vitro approaches, underscore the drug-likeness of MG257 and its promising pharmacokinetic profile. In conclusion, our findings suggest that MG257 (C<sub>10</sub>H<sub>21</sub>NO<sub>4</sub>) is a potent α-glucosidase inhibitor with significant potential as a novel therapeutic agent for the management of Type 2 diabetes, warranting further research and development.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144706026","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 antifungal evaluation of perillaldehyde derivatives as potential laccase inhibitors. 紫苏醛衍生物漆酶抑制剂的设计、合成及抑菌性评价。
IF 3.9 2区 化学
Molecular Diversity Pub Date : 2025-07-24 DOI: 10.1007/s11030-025-11299-z
Zhennan Cui, Yiming Zheng, Ning Ou, Ziyan Zhang, Boyu Lv, Jia Li, Wen Gu
{"title":"Design, synthesis and antifungal evaluation of perillaldehyde derivatives as potential laccase inhibitors.","authors":"Zhennan Cui, Yiming Zheng, Ning Ou, Ziyan Zhang, Boyu Lv, Jia Li, Wen Gu","doi":"10.1007/s11030-025-11299-z","DOIUrl":"https://doi.org/10.1007/s11030-025-11299-z","url":null,"abstract":"<p><p>The development of novel fungicides has still been a hot topic in the field of pesticide research. In this study, three series of new perillaldehyde hydrazide, amide and acylthiourea derivatives (3a-3n, 4a-4f, and 6a-6f) were designed and synthesized. The in vitro antifungal activity of the title compounds against seven plant pathogens was evaluated. The results displayed that several hydrazide derivatives showed significant antifungal activity. Especially, compound 3b exhibited the most potent inhibitory activity against Monilinia fructicola (EC<sub>50</sub> = 0.142 mg/L), outperforming the commercial fungicides bixafen and carbendazim. In vivo experiments further confirmed that 3b presented superior protective and curative effects on pear fruits infected by M. fructicola compared to bixafen. Mechanism studies revealed that 3b could damage the mycelial morphology and cell membrane integrity, increase cell membrane permeability, reduce mycelial dry weight and exocellular polysaccharide content, and increase intracellular ROS content of M. fructicola. Additionally, 3b exhibited significant laccase inhibitory activity (IC<sub>50</sub> = 4.87 μM), suggesting that laccase could be a key target for its antifungal action. Molecular docking studies further confirmed the strong binding affinity of 3b with the active sites of laccase. This study highlighted the potential of this perillaldehyde hydrazide derivative as a promising lead for the development of novel fungicides controlling the brown rot caused by M. fructicola.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144697345","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
PPGBioPred: a webserver for predicting the bioactivity of compounds against PPARγ involved in the negative regulation of the Wnt/β-catenin signaling pathway. PPGBioPred:用于预测化合物对参与Wnt/β-catenin信号通路负调控的PPARγ的生物活性的web服务器。
IF 3.9 2区 化学
Molecular Diversity Pub Date : 2025-07-22 DOI: 10.1007/s11030-025-11297-1
Mazumder Adhish, I Manjubala
{"title":"PPGBioPred: a webserver for predicting the bioactivity of compounds against PPARγ involved in the negative regulation of the Wnt/β-catenin signaling pathway.","authors":"Mazumder Adhish, I Manjubala","doi":"10.1007/s11030-025-11297-1","DOIUrl":"https://doi.org/10.1007/s11030-025-11297-1","url":null,"abstract":"<p><p>The Wnt/β-catenin signaling pathway is a key regulator of cellular activities and has implications for various diseases. This study explored the ability to predict the bioactivities of compounds against the peroxisome proliferator-activated receptor γ (PPARγ), paving the way to develop PPGBioPred, a user-friendly webserver to modulate this pathway. The research employs computational methodologies, particularly quantitative structure-activity relationship (QSAR) models, to understand the bioactivity of compounds. The study evaluated the efficacy of twelve categories of fingerprint descriptors for model development and used the Gini index to reveal the molecular features crucial for the studied bioactivity of PPARγ. The resulting high-performing models - achieving external R<sup>2</sup> values of 0.57 (IC<sub>50</sub>) and 0.62 (EC<sub>50</sub>), and classification MCCs of 0.74 (IC<sub>50</sub>) and 0.70 (EC<sub>50</sub>) - are deployed on PPGBioPred, providing a robust and translational tool for virtual screening. These models contribute significantly to the understanding of the structure‒activity relationship of PPARγ and the ability to predict the bioactivities of certain chemical compounds against the aforementioned target. This study underscores the potential of computational methodologies in supplementing experimental research in drug discovery. These findings pave the way for the development of effective drugs targeting PPARγ, highlighting the potential of these proteins in the treatment of diseases affecting multiple organs.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144688553","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
Advances in targeting p38 MAPK for cancer therapy: insights from molecular pharmacology and medicinal chemistry. 靶向p38 MAPK治疗癌症的进展:来自分子药理学和药物化学的见解。
IF 3.9 2区 化学
Molecular Diversity Pub Date : 2025-07-21 DOI: 10.1007/s11030-025-11291-7
Ritesh P Bhole, Nishigandha Kadam, Pawan N Karwa, Sonali D Labhade, Harshad S Kapare, Shailendra Gurav
{"title":"Advances in targeting p38 MAPK for cancer therapy: insights from molecular pharmacology and medicinal chemistry.","authors":"Ritesh P Bhole, Nishigandha Kadam, Pawan N Karwa, Sonali D Labhade, Harshad S Kapare, Shailendra Gurav","doi":"10.1007/s11030-025-11291-7","DOIUrl":"https://doi.org/10.1007/s11030-025-11291-7","url":null,"abstract":"<p><p>The p38 mitogen-activated protein kinase (MAPK) pathway plays a pivotal role in inflammatory responses, cell proliferation, differentiation, and cancer progression. Among its four isoforms (p38α, p38β, p38γ, and p38δ), p38α is the most widely studied and has been implicated in various malignancies, making it a compelling target for therapeutic intervention. This review systematically explores recent developments in both synthetic and natural small-molecule inhibitors of p38 MAPK with a focus on their relevance in cancer treatment. Two major classes of p38 inhibitors are highlighted: ATP-competitive inhibitors that block the kinase by targeting the ATP-binding pocket (e.g., SB203580, Ralimetinib), and allosteric inhibitors that interact with regulatory regions outside the active site, inducing conformational changes to suppress kinase activity (e.g., BIRB796). The manuscript further categorizes inhibitors based on chemical scaffolds and source, discusses structure-activity relationships (SAR), and outlines their mechanistic impact on the p38 MAPK signaling axis in various cancers. This review also emphasizes the therapeutic challenges, subtype selectivity, and opportunities for isoform-specific drug design. Ultimately, a comprehensive understanding of these mechanisms can support the rational development of p38 MAPK inhibitors with improved efficacy and selectivity in oncology.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144673681","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 integrated approach for novel PTP1B inhibitor screening: combining machine learning models, molecular docking, molecular and dynamics simulations. 新型PTP1B抑制剂筛选的综合方法:结合机器学习模型、分子对接、分子和动力学模拟。
IF 3.9 2区 化学
Molecular Diversity Pub Date : 2025-07-21 DOI: 10.1007/s11030-025-11292-6
Yihuan Zhao, Yujuan Chen, Xiaoli Tao, You Wang, Fushan Tang
{"title":"An integrated approach for novel PTP1B inhibitor screening: combining machine learning models, molecular docking, molecular and dynamics simulations.","authors":"Yihuan Zhao, Yujuan Chen, Xiaoli Tao, You Wang, Fushan Tang","doi":"10.1007/s11030-025-11292-6","DOIUrl":"https://doi.org/10.1007/s11030-025-11292-6","url":null,"abstract":"<p><p>Diabetes mellitus, particularly type 2 diabetes (T2DM), is a major global health challenge characterized by persistent hyperglycemia resulting from insulin resistance. Protein tyrosine phosphatase 1B (PTP1B) has emerged as a key enzyme involved in regulating insulin signaling, making it a promising target for therapeutic interventions aimed at improving insulin sensitivity. However, the development of effective PTP1B inhibitors has been hindered by issues such as poor bioavailability and off-target effects. This study presents an integrated approach combining machine learning (ML), molecular docking, and molecular dynamics (MD) simulations to identify novel PTP1B inhibitors. An ML-based predictive model was developed using a dataset of over 2183 known PTP1B inhibitors to guide the selection of compounds with high inhibitory potential. Molecular docking was applied to a compound database of 1.6 million molecules, identifying 1057 promising candidates, which were then refined using the ML model to select the top five compounds. Additionally, the same strategy was applied to a natural product-derived compound database containing 160,000 molecules, leading to the identification of two additional PTP1B inhibitors. This comprehensive approach, combining ML with computational predictions, accelerates the drug discovery process and enhances the reliability of the findings, offering a promising pathway for the development of novel treatments for T2DM and related metabolic disorders.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144673682","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 evaluation of aminopyrazine-based ATR/HDACs dual inhibitors. 氨基吡嗪类ATR/ hdac双抑制剂的设计、合成和生物学评价
IF 3.9 2区 化学
Molecular Diversity Pub Date : 2025-07-20 DOI: 10.1007/s11030-025-11282-8
Ying-Hui Yuan, Chen-Chen Wang, Ji-Long Duan, Peng-Peng Zhang, Meng-Lan He, Zhen Liu, Zi Hui, Xiang-Yang Ye
{"title":"Design, synthesis, and biological evaluation of aminopyrazine-based ATR/HDACs dual inhibitors.","authors":"Ying-Hui Yuan, Chen-Chen Wang, Ji-Long Duan, Peng-Peng Zhang, Meng-Lan He, Zhen Liu, Zi Hui, Xiang-Yang Ye","doi":"10.1007/s11030-025-11282-8","DOIUrl":"https://doi.org/10.1007/s11030-025-11282-8","url":null,"abstract":"<p><p>Ataxia telangiectasia mutated and rad3-related kinase (ATR) and histone deacetylases (HDACs) are important therapeutic targets for cancer. In this study, a series of novel ATR/HDACs dual inhibitors containing 2-aminopyrazine motifs were designed and synthesized for the first time. Compounds 18b and 18c not only exhibited good dual inhibition activity against ATR (IC<sub>50</sub> = 6 and 3 nM) and HDAC6 (IC<sub>50</sub> = 6 and 20 nM), but also showed good anti-proliferative activity against four cancer cell lines. Preliminary mechanistic studies showed that compared with 18b, compound 18c exhibited stronger inhibitory effect on tumor cell proliferation and more effective induction of cell death. 18c could induce an increase in the level of acetylated α-tubulin and reduce the phosphorylation levels of ATR (p-ATR) and CHK1 (p-CHK1). Additionally, 18c also demonstrated the ability to upregulate the expression level of γ-H2AX. This research firstly presents the design and synthesis of ATR/HDAC6 dual-target inhibitors. The mechanism of action of these inhibitors may involve the synergistic induction of tumor cell apoptosis by dual inhibition of the DNA damage repair pathway and tubulin deacetylation processes. Overall, the research findings in this paper lay a foundation for further exploiting ATR/HDACs dual inhibitors' therapeutic usefulness while addressing potential drug resistance and adverse effect issues caused by combination therapy in clinical practice.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144666813","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
Harnessing the synergistic potential of EGCG and camptothecin against skin melanoma: a computational and experimental approach. 利用EGCG和喜树碱对抗皮肤黑色素瘤的协同潜力:一种计算和实验方法。
IF 3.9 2区 化学
Molecular Diversity Pub Date : 2025-07-20 DOI: 10.1007/s11030-025-11296-2
Ansari Vikhar Danish Ahmad, Qazi Yasar, Syed Ayaz Ali, Subur W Khan, Mohd Mukhtar Khan
{"title":"Harnessing the synergistic potential of EGCG and camptothecin against skin melanoma: a computational and experimental approach.","authors":"Ansari Vikhar Danish Ahmad, Qazi Yasar, Syed Ayaz Ali, Subur W Khan, Mohd Mukhtar Khan","doi":"10.1007/s11030-025-11296-2","DOIUrl":"https://doi.org/10.1007/s11030-025-11296-2","url":null,"abstract":"<p><p>Skin melanoma remains a major global health concern, necessitating novel therapeutic strategies. Epigallocatechin gallate (EGCG), a predominant polyphenol in green tea, possesses potent antioxidant and anti-inflammatory properties that may suppress melanoma progression. Camptothecin (CPT), a topoisomerase I inhibitor, disrupts DNA replication in cancer cells, demonstrating promise in targeted melanoma therapy. This study employs a comprehensive integrative approach that combines network pharmacology (NP), molecular docking, molecular dynamics (MD) simulations, and in vitro experiments to investigate the potential synergistic anti-melanoma effects of EGCG and CPT. Network pharmacology analysis revealed a complex interaction network comprising 138 nodes and 145 edges, identifying key targets involved in melanoma pathophysiology. KEGG pathway enrichment analysis revealed significant involvement of the PI3K‒Akt signaling pathway in melanoma modulation. Molecular docking studies demonstrated strong binding affinities of camptothecin with EGFR (PDB: 3LZB), with binding energies ranging from - 8.6 to - 10.1 kcal/mol. Molecular dynamics simulations further confirmed the stability of these interactions, with minimal fluctuations observed. Experimental validation via the SRB assay in B16-F10 melanoma cells revealed potent inhibition of cell viability, particularly when EGCG and camptothecin were used in combination, indicating a potential synergistic effect. The observed synergism between EGCG and camptothecin suggests a multitargeted therapeutic approach, leveraging EGCG's antioxidant and anti-inflammatory effects alongside camptothecin's ability to inhibit DNA replication to enhance melanoma suppression. This integrative study highlights the promise of combination therapy using natural and chemotherapeutic agents, paving the way for the development of effective, targeted anticancer treatments for skin melanoma.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144666770","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 innovative machine learning-based QSAR approach for prediction and structural analysis of novel/repurposed acid ceramidase (ASAH1) inhibitors for glioblastoma therapy. 一种创新的基于机器学习的QSAR方法,用于预测和结构分析用于胶质母细胞瘤治疗的新型/重新用途的酸性神经酰胺酶(ASAH1)抑制剂。
IF 3.9 2区 化学
Molecular Diversity Pub Date : 2025-07-19 DOI: 10.1007/s11030-025-11281-9
Harshit Sajal, Seema Mishra
{"title":"An innovative machine learning-based QSAR approach for prediction and structural analysis of novel/repurposed acid ceramidase (ASAH1) inhibitors for glioblastoma therapy.","authors":"Harshit Sajal, Seema Mishra","doi":"10.1007/s11030-025-11281-9","DOIUrl":"https://doi.org/10.1007/s11030-025-11281-9","url":null,"abstract":"<p><p>Acid ceramidase (ASAH1), a lysosomal enzyme that regulates ceramide and sphingosine-1-phosphate balance, has emerged as a promising therapeutic target in Glioblastoma. Inhibiting ASAH1 by carmofur elevates ceramide levels, inducing apoptosis in Glioblastoma cells. However, its clinical application is limited by its instability & toxicological concerns, thereby necessitating the search for more effective inhibitors. We employed an innovative machine learning-quantitative structure-activity relationship (ML-QSAR) approach to investigate & identify related bioactive ASAH1 inhibitors. Herein, we report the results of ML-QSAR modeling utilizing a filtered dataset of 103 inhibitors from ChEMBL & 431 3D descriptors. Multiple algorithmic steps, incorporating top five ML models, were implemented. Among these, our tuned extra trees regressor (ETR) model achieved the highest predictive performance (R<sup>2</sup> = 0.867, RMSE = 0.248). Q<sup>2</sup>(LOO) & Q<sup>2</sup>(LMO) demonstrated 79.22% & 76.92% (Q<sup>2</sup> > 0.5) of inhibitors to be well-predicted, respectively. Descriptor ablation studies identified radial distribution function 20s (RDF20s) and SHAP analysis further demonstrated RDF20s, DPSA-1 & TDB2p as the key structural & pharmacological features. Utilizing this ML-QSAR model, a virtual screening identified 77 promising candidates with N-hexylsalicylamide as the top-most candidate in the ranked list, with superior ADME/T and pharmaco-kinetic characteristics. Notably, Cys143, the key active site residue essential for carmofur interaction, was also observed to be in contact with carbonyl group of N-hexylsalicylamide. MM/PBSA-derived BFE calculations from MD simulations showed that N-hexylsalicylamide had higher negative BFE than carmofur. Following SHAP analyses-based mechanistic interpretations, structural modifications of selected inhibitors led to the design of novel analogs for further testing.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144666812","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
Porphyrin/metalloporphyrin and their conjugates: a promising platform for drug delivery. 卟啉/金属卟啉及其偶联物:一个有前途的药物传递平台。
IF 3.9 2区 化学
Molecular Diversity Pub Date : 2025-07-15 DOI: 10.1007/s11030-025-11289-1
Dure Najaf Iqbal, Sohail Khaliq, Muhammad Zaeem Mehdi, Mohammed H Al Mughram, Mahmood Ahmed
{"title":"Porphyrin/metalloporphyrin and their conjugates: a promising platform for drug delivery.","authors":"Dure Najaf Iqbal, Sohail Khaliq, Muhammad Zaeem Mehdi, Mohammed H Al Mughram, Mahmood Ahmed","doi":"10.1007/s11030-025-11289-1","DOIUrl":"https://doi.org/10.1007/s11030-025-11289-1","url":null,"abstract":"<p><p>Porphyrins and metalloporphyrins are emerging as versatile platforms for advanced drug delivery due to their unique structural, photophysical, and coordination properties. These macrocyclic compounds, known for their chemical stability and capacity to chelate various metal ions, address critical challenges in drug delivery, including poor solubility, non-specific toxicity, and limited control over drug release. This review explores synthetic strategies for porphyrins and their metal complexes, including classical and green methods, and highlights their therapeutic applications through diverse nanocarrier systems, such as gold nanoparticles, cyclodextrin conjugates, mesoporous silica, liposomes, and metal-organic frameworks. These systems offer stimuli-responsive, targeted, and synergistic therapeutic functionalities-especially in cancer therapy-by combining chemotherapy with photodynamic or sonodynamic modalities. Despite their promise, limitations persist, including scalability issues, potential metal toxicity, and insufficient long-term biocompatibility data. The review outlines future directions, advocating for AI-driven design, sustainable synthesis, and expanded applications beyond oncology, emphasizing the need for systematic comparative studies and clinical translation efforts.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144635867","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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