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Identification of mycobacterial Thymidylate kinase inhibitors: a comprehensive pharmacophore, machine learning, molecular docking, and molecular dynamics simulation studies 鉴定分枝杆菌胸腺嘧啶激酶抑制剂:综合药理、机器学习、分子对接和分子动力学模拟研究。
IF 3.9 2区 化学
Molecular Diversity Pub Date : 2024-08-16 DOI: 10.1007/s11030-024-10967-w
Rupesh V. Chikhale, Surbhi Pravin Pawar, Mahima Sudhir Kolpe, Omkar Dilip Shinde, Kholood A. Dahlous, Saikh Mohammad, Pritee Chunarkar Patil, Shovonlal Bhowmick
{"title":"Identification of mycobacterial Thymidylate kinase inhibitors: a comprehensive pharmacophore, machine learning, molecular docking, and molecular dynamics simulation studies","authors":"Rupesh V. Chikhale,&nbsp;Surbhi Pravin Pawar,&nbsp;Mahima Sudhir Kolpe,&nbsp;Omkar Dilip Shinde,&nbsp;Kholood A. Dahlous,&nbsp;Saikh Mohammad,&nbsp;Pritee Chunarkar Patil,&nbsp;Shovonlal Bhowmick","doi":"10.1007/s11030-024-10967-w","DOIUrl":"10.1007/s11030-024-10967-w","url":null,"abstract":"<div><p>Thymidylate kinase (TMK) is a pivotal enzyme in Mycobacterium tuberculosis (Mtb), crucial for phosphorylating thymidine monophosphate (dTMP) to thymidine diphosphate (dTDP), thereby playing a critical role in DNA biosynthesis. Dysregulation or inhibition of TMK activity disrupts DNA replication and cell division, making it an attractive target for anti-tuberculosis drug development. In this study, the statistically validated pharmacophore mode was developed from a set of known TMK inhibitors. Further, the robust pharmacophore was considered for screening the Enamine database. The chemical space was reduced through multiple molecular docking approaches, pharmacokinetics, and absolute binding energy estimation. Two different molecular docking algorithms favor the strong binding affinity of the proposed molecules towards TMK. Machine learning-based absolute binding energy also showed the potentiality of the proposed molecules. The binding interactions analysis exposed the strong binding affinity between the proposed molecules and active site amino residues of TMK. Several statistical parameters from all atoms MD simulation explained the stability between proposed molecules and TMK in the dynamic states. The MM-GBSA approach also found a strong binding affinity for each proposed molecule. Therefore, the proposed molecules might be crucial TMK inhibitors for managing Mtb inhibition subjected to in vitro/in vivo validations.</p></div>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11449957/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141995079","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Gene network analysis combined with preclinical studies to identify and elucidate the mechanism of action of novel irreversible Keap1 inhibitor for Parkinson's disease. 基因网络分析与临床前研究相结合,确定并阐明治疗帕金森病的新型不可逆 Keap1 抑制剂的作用机制。
IF 3.9 2区 化学
Molecular Diversity Pub Date : 2024-08-15 DOI: 10.1007/s11030-024-10965-y
Monisha Arumugam, Ranjith Sanjeeve Pachamuthu, Emdormi Rymbai, Aditya Prakash Jha, Kalirajan Rajagopal, Ram Kothandan, Santhoshkumar Muthu, Divakar Selvaraj
{"title":"Gene network analysis combined with preclinical studies to identify and elucidate the mechanism of action of novel irreversible Keap1 inhibitor for Parkinson's disease.","authors":"Monisha Arumugam, Ranjith Sanjeeve Pachamuthu, Emdormi Rymbai, Aditya Prakash Jha, Kalirajan Rajagopal, Ram Kothandan, Santhoshkumar Muthu, Divakar Selvaraj","doi":"10.1007/s11030-024-10965-y","DOIUrl":"https://doi.org/10.1007/s11030-024-10965-y","url":null,"abstract":"<p><p>The cysteine residues of Keap1 such as C151, C273, and C288 are critical for its repressor activity on Nrf2. However, to date, no molecules have been identified to covalently modify all three cysteine residues for Nrf2 activation. Hence, in this study, our goal is to discover new Keap1 covalent inhibitors that can undergo a Michael addition with all three cysteine residues. The Keap1's intervening region was modeled using Modeller v10.4. Covalent docking and binding free energy were calculated using CovDock. Molecular dynamics (MD) was performed using Desmond. Various in-vitro assays were carried out to confirm the neuroprotective effects of the hit molecule in 6-OHDA-treated SH-SY5Y cells. Further, the best hit was evaluated in vivo for its ability to improve rotenone-induced postural instability and cognitive impairment in male rats. Finally, network pharmacology was used to summarize the complete molecular mechanism of the hit molecule. Chalcone and plumbagin were found to form the necessary covalent bonds with all three cysteine residues. However, MD analysis indicated that the binding of plumbagin is more stable than chalcone. Plumbagin displayed neuroprotective effects in 6-OHDA-treated SH-SY5Y cells at concentrations 0.01 and 0.1 μM. Plumbagin at 0.1 µM had positive effects on reactive oxygen species formation and glutathione levels. Plumbagin also improved postural instability and cognitive impairment in rotenone-treated male rats. Our network analysis indicated that plumbagin could also improve dopamine signaling. Additionally, plumbagin could exhibit anti-oxidant and anti-inflammatory activity through the activation of Nrf2. Cumulatively, our study suggests that plumbagin is a novel Keap1 covalent inhibitor for Nrf2-mediated neuroprotection in PD.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141981435","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
Multicomponent reaction for synthesis, molecular docking, and anti-inflammatory evaluation of novel indole-thiazole hybrid derivatives. 用于新型吲哚-噻唑混合衍生物的合成、分子对接和抗炎评估的多组分反应。
IF 3.9 2区 化学
Molecular Diversity Pub Date : 2024-08-15 DOI: 10.1007/s11030-024-10969-8
Faeza Alkorbi, Shareefa Ahmed Alshareef, Mahmoud A Abdelaziz, Noha Omer, Rasha Jame, Ibrahim Saleem Alatawi, Ali M Ali, Omran A Omran, Rania B Bakr
{"title":"Multicomponent reaction for synthesis, molecular docking, and anti-inflammatory evaluation of novel indole-thiazole hybrid derivatives.","authors":"Faeza Alkorbi, Shareefa Ahmed Alshareef, Mahmoud A Abdelaziz, Noha Omer, Rasha Jame, Ibrahim Saleem Alatawi, Ali M Ali, Omran A Omran, Rania B Bakr","doi":"10.1007/s11030-024-10969-8","DOIUrl":"https://doi.org/10.1007/s11030-024-10969-8","url":null,"abstract":"<p><p>In this article, novel thiazol-indolin-2-one derivatives 4a-f have been synthesized via treatment of thiosemicarbazide (1) with some isatin derivative 2a-f and N-(4-(2-bromoacetyl)phenyl)-4-tolyl-sulfonamide (3) under reflux in ethanol in the presence of triethyl amine (TEA). The structures of new products were elucidated by elemental and spectral analyses. Moreover, all compounds were investigated for their in vivo anti-inflammatory activity using celecoxib as a reference drug. The target compound 4b was the most active anti-inflammatory candidate and exhibited higher edema inhibition (EI = 38.50%) than that recorded by celecoxib (EI = 34.58%) after 3 h. Furthermore, the most active compounds 4b and 4f were subjected to a molecular docking study inside COX-2 enzyme to show their binding interactions. Both compounds 4b and 4f showed good fitting into COX-2 binding site with docking energy scores - 11.45 kcal/mol and - 10.48 kcal/mol, respectively which indicated that compound 4b revealed the most promising and effective anti-inflammatory potential.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141981437","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
Inhibition of monoamine oxidases and neuroprotective effects: chalcones vs. chromones. 抑制单胺氧化酶和神经保护作用:查尔酮与色酮。
IF 3.9 2区 化学
Molecular Diversity Pub Date : 2024-08-15 DOI: 10.1007/s11030-024-10959-w
Reshma Ipe, Jong Min Oh, Sunil Kumar, Iqrar Ahmad, Lekshmi R Nath, Sandeep Bindra, Harun Patel, Krishna Yallappa Kolachi, Prabitha Prabhakaran, Prashant Gahtori, Asad Syed, Abdallah M Elgorbanh, Hoon Kim, Bijo Mathew
{"title":"Inhibition of monoamine oxidases and neuroprotective effects: chalcones vs. chromones.","authors":"Reshma Ipe, Jong Min Oh, Sunil Kumar, Iqrar Ahmad, Lekshmi R Nath, Sandeep Bindra, Harun Patel, Krishna Yallappa Kolachi, Prabitha Prabhakaran, Prashant Gahtori, Asad Syed, Abdallah M Elgorbanh, Hoon Kim, Bijo Mathew","doi":"10.1007/s11030-024-10959-w","DOIUrl":"https://doi.org/10.1007/s11030-024-10959-w","url":null,"abstract":"<p><p>Eighteen compounds derived from two sub-series, (HC1-HC9) and (HF1-HF9), were synthesized and evaluated for their inhibitory activities against monoamine oxidase (MAO). HC (chalcone) series showed higher inhibitory activity against MAO-B than against MAO-A, whereas the HF (chromone) series showed reversed inhibitory activity. Compound HC4 most potently inhibited MAO-B with an IC<sub>50</sub> value of 0.040 μM, followed by HC3 (IC<sub>50</sub> = 0.049 μM), while compound HF4 most potently inhibited MAO-A (IC<sub>50</sub> = 0.046 μM), followed by HF2 (IC<sub>50</sub> = 0.075 μM). The selectivity index (SI) values of HC4 and HF4 were 50.40 and 0.59, respectively. Structurally, HC4 (4-OC<sub>2</sub>H<sub>5</sub> in B-ring) showed higher MAO-B inhibition than other derivatives, suggesting that the -OC<sub>2</sub>H<sub>5</sub> substitution of the 4-position in the B-ring contributes to the increase of MAO-B inhibition, especially -OC<sub>2</sub>H<sub>5</sub> (HC4) > -OCH<sub>3</sub> (HC3) > -F (HC7) > -CH<sub>3</sub> (HC2) > -Br (HC8) > -H (HC1) in order. In MAO-A inhibition, the substituent 4-OC<sub>2</sub>H<sub>5</sub> in the B-ring of HF4 contributed to an increase in inhibitory activity, followed by -CH<sub>3</sub> (HF2), -F (HF7), -Br (HF8), -OCH<sub>3</sub> (HF3), and-H (HF1). In the enzyme kinetics and reversibility study, the K<sub>i</sub> value of HC4 for MAO-B was 0.035 ± 0.005 μM, and that of HF4 for MAO-A was 0.035 ± 0.005 μM, and both were reversible competitive inhibitors. We confirmed that HC4 and HF4 significantly ameliorated rotenone-induced neurotoxicity, as evidenced by the reactive oxygen species and superoxide dismutase assays. This study also supports the significant effect of HC4 and HF4 on mitochondrial membrane potential in rotenone-induced toxicity. A lead molecule was used for molecular docking and dynamic simulation studies. These results show that HC4 is a potent selective MAO-B inhibitor and HF4 is a potent MAO-A inhibitor, suggesting that both compounds can be used as treatment agents for neurological disorders.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141981436","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
Defect-engineered indium-organic framework displays the higher CO2 adsorption and more excellent catalytic performance on the cycloaddition of CO2 with epoxides under mild conditions. 缺陷工程铟有机框架在温和条件下对二氧化碳与环氧化物的环化反应具有更高的吸附能力和更优异的催化性能。
IF 3.9 2区 化学
Molecular Diversity Pub Date : 2024-08-14 DOI: 10.1007/s11030-024-10956-z
Meiyu Ren, Bo Zhao, Chong Li, Yang Fei, Xiaotong Wang, Liming Fan, Tuoping Hu, Xiutang Zhang
{"title":"Defect-engineered indium-organic framework displays the higher CO<sub>2</sub> adsorption and more excellent catalytic performance on the cycloaddition of CO<sub>2</sub> with epoxides under mild conditions.","authors":"Meiyu Ren, Bo Zhao, Chong Li, Yang Fei, Xiaotong Wang, Liming Fan, Tuoping Hu, Xiutang Zhang","doi":"10.1007/s11030-024-10956-z","DOIUrl":"https://doi.org/10.1007/s11030-024-10956-z","url":null,"abstract":"<p><p>In order to achieve the high adsorption and catalytic performance of CO<sub>2</sub>, the direct self-assembly of robust defect-engineered MOFs is a scarcely reported and challenging proposition. Herein, a highly robust nanoporous indium(III)-organic framework of {[In<sub>2</sub>(CPPDA)(H<sub>2</sub>O)<sub>3</sub>](NO<sub>3</sub>)·2DMF·3H<sub>2</sub>O}<sub>n</sub> (NUC-107) consisting of two kinds of inorganic units of chain-shaped [In(COO)<sub>2</sub>(H<sub>2</sub>O)]<sub>n</sub> and watery binuclear [In<sub>2</sub>(COO)<sub>4</sub>(H<sub>2</sub>O)<sub>8</sub>] was generated by regulating the growth environment. It is worth mentioning that [In<sub>2</sub>(COO)<sub>4</sub>(H<sub>2</sub>O)<sub>8</sub>] is very rare in terms of its richer associated water molecules, implying that defect-enriched metal ions in the activated host framework can serve as strong Lewis acid. Compared to reported skeleton of [In<sub>4</sub>(CPPDA)<sub>2</sub>(μ<sub>3</sub>-OH)<sub>2</sub>(DMF)(H<sub>2</sub>O)<sub>2</sub>]<sub>n</sub> (NUC-66) with tetranuclear clusters of [In<sub>4</sub>(μ<sub>3</sub>-OH)<sub>2</sub>(COO)<sub>10</sub>(DMF)(H<sub>2</sub>O)<sub>2</sub>] as nodes, the void volume of NUC-107 (50.7%) is slightly lower than the one of NUC-66 (52.8%). However, each In<sup>3+</sup> ion in NUC-107 has an average of 1.5 coordinated small molecules (H<sub>2</sub>O), which far exceeds the average of 0.75 in NUC-66 (H<sub>2</sub>O and DMF). After thermal activation, NUC-107a characterizes the merits of unsaturated In<sup>3+</sup> sites, free pyridine moieties, solvent-free nanochannels (10.2 × 15.7 Å<sup>2</sup>). Adsorption tests prove that the host framework of NUC-107a has a higher CO<sub>2</sub> adsorption (113.2 cm<sup>3</sup>/g at 273 K and 64.8 cm<sup>3</sup>/g at 298 K) than NUC-66 (91.2 cm<sup>3</sup>/g at 273 K and 53.0 cm<sup>3</sup>/g at 298 K). Catalytic experiments confirmed that activated NUC-107a with the aid of n-Bu<sub>4</sub>NBr was capable of efficiently catalyzing the cycloaddition of CO<sub>2</sub> with epoxides into corresponding cyclic carbonates under the mild conditions. Under the similar conditions of 0.10 mol% MOFs, 0.5 mol% n-Bu<sub>4</sub>NBr, 0.5 MP CO<sub>2</sub>, 60 °C and 3 h, compared with NUC-66a, the conversion of SO to SC catalyzed by NUC-107a increased by 21%. Hence, this work offers a valuable perspective that the in situ creation of robust defect-engineered MOFs can be realized by regulating the growth environment.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141974832","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
Novel sulfonyl hydrazide based β-carboline derivatives as potential α-glucosidase inhibitors: design, synthesis, and biological evaluation. 新型磺酰肼基 β-咔啉衍生物作为潜在的 α-葡萄糖苷酶抑制剂:设计、合成和生物学评价。
IF 3.9 2区 化学
Molecular Diversity Pub Date : 2024-08-14 DOI: 10.1007/s11030-024-10943-4
Jinping Sun, Di Xiao, Ming Lang, Xuetao Xu
{"title":"Novel sulfonyl hydrazide based β-carboline derivatives as potential α-glucosidase inhibitors: design, synthesis, and biological evaluation.","authors":"Jinping Sun, Di Xiao, Ming Lang, Xuetao Xu","doi":"10.1007/s11030-024-10943-4","DOIUrl":"https://doi.org/10.1007/s11030-024-10943-4","url":null,"abstract":"<p><p>A series of novel sulfonyl hydrazide based β-carboline derivatives (SX1-SX32) were designed and synthesized, and their structures were characterized on NMR and HRMS. Their α-glucosidase inhibitory screening results found that compounds (SX1-SX32) presented potential α-glucosidase inhibitory: IC<sub>50</sub> values being 2.12 ± 0.33-19.37 ± 1.49 μM. Compound SX29 with a para-phenyl (IC<sub>50</sub>: 2.12 ± 0.33 μM) presented the strongest activity and was confirmed as a noncompetitive inhibitor. Fluorescence spectra, CD spectra and molecular docking were conducted to describe the inhibition mechanism of SX29 against α-glucosidase. Cells cytotoxicity indicated SX29 (0-32 μM) had no cytotoxicity on 293T cells. In particular, in vivo experiments revealed that oral administration of SX29 could regulate hyperglycemia and glucose tolerance of diabetic mice. These achieved findings indicated that sulfonyl hydrazide based β-carboline derivatives bore promising potential for discovering new α-glucosidase inhibitors with hypoglycemic activity.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141974833","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 drug repositioning for IL6 triggered JAK3 in rheumatoid arthritis using FDA database. 利用 FDA 数据库计算类风湿性关节炎中 IL6 触发 JAK3 的药物重新定位。
IF 3.9 2区 化学
Molecular Diversity Pub Date : 2024-08-14 DOI: 10.1007/s11030-024-10958-x
Kaushani Banerjee, Bavya Chandrasekar, Sruthy Sathish, Honglae Sohn, Thirumurthy Madhavan
{"title":"Computational drug repositioning for IL6 triggered JAK3 in rheumatoid arthritis using FDA database.","authors":"Kaushani Banerjee, Bavya Chandrasekar, Sruthy Sathish, Honglae Sohn, Thirumurthy Madhavan","doi":"10.1007/s11030-024-10958-x","DOIUrl":"https://doi.org/10.1007/s11030-024-10958-x","url":null,"abstract":"<p><p>Rheumatoid Arthritis (RA) is a persistent autoimmune disease affecting approximately 0.5-1 percent of the world population. RA prevalence is higher in woman aged between 35 and 50 years than in age matched men, though this difference is less evident among elderly patients. The profound immune specific effects of disrupted JAK 3 (Janus kinase 3) signaling highlight the possibility of therapeutic targeting of JAK3 as a highly specific mode of immune system suppression. To address the above problem which is unendurable to patients and in the hope to cater some respite to such suffering we have targeted JAK 3 protein and JAK/STAT signaling pathway with compounds downloaded from FDA database, and performed screening of all available compounds docked against JAK3 protein. The difference between the target protein and other proteins of the same family was studied using cross docking and the compounds having higher binding affinity to JAK3 protein also showed more selectivity towards the particular protein. Density functional theory and molecular dynamics simulation study was done to study the compounds at their atomic level to know more about their drug likeliness. At the end of the study and based on our analysis we have come up with three FDA approved drugs that can be proposed as a treatment option for Rheumatoid Arthritis.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141974831","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
Prediction of Mycobacterium tuberculosis cell wall permeability using machine learning methods 利用机器学习方法预测结核分枝杆菌细胞壁的渗透性。
IF 3.9 2区 化学
Molecular Diversity Pub Date : 2024-08-12 DOI: 10.1007/s11030-024-10952-3
Aritra Banerjee, Anju Sharma, Pradnya Kamble, Prabha Garg
{"title":"Prediction of Mycobacterium tuberculosis cell wall permeability using machine learning methods","authors":"Aritra Banerjee,&nbsp;Anju Sharma,&nbsp;Pradnya Kamble,&nbsp;Prabha Garg","doi":"10.1007/s11030-024-10952-3","DOIUrl":"10.1007/s11030-024-10952-3","url":null,"abstract":"<div><p>Tuberculosis (TB) caused by the bacteria <i>Mycobacterium tuberculosis</i> (<i>M. tb</i>), continues to pose a significant worldwide health threat. The advent of drug-resistant strains of the disease highlights the critical need for novel treatments. The unique cell wall of <i>M. tb</i> provides an extra layer of protection for the bacteria and hence only compounds that can penetrate this barrier can reach their targets within the bacterial cell wall. The creation of a reliable machine learning (ML) model to predict the mycobacterial cell wall permeability of small molecules is presented in this work and four ML algorithms, including Random Forest, Support Vector Machines (SVM), k-nearest Neighbour (k-NN) and Logistic Regression were trained on a dataset of 5368 compounds. RDKit and Mordred toolkits were used to calculate features. To determine the most effective model, various performance metrics were used such as accuracy, precision, recall, F1 score, and area under the receiver operating characteristic curve. The best-performing model was further refined with hyperparameter tuning and tenfold cross-validation. The SVM model with filtering outperformed the other machine learning models and demonstrated 80.26% and 81.13% accuracy on the test and validation datasets, respectively. The study also provided insights into the molecular descriptors that play the most important role in predicting the ability of a molecule to pass the <i>M. tb</i> cell wall, which could guide future compound design. The model is available at https://github.com/PGlab-NIPER/MTB_Permeability.</p></div>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141915828","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
Discovery of novel 4-trifluoromethyl-2-anilinoquinoline derivatives as potential anti-cancer agents targeting SGK1. 发现新型 4-三氟甲基-2-苯胺喹啉衍生物作为靶向 SGK1 的潜在抗癌剂。
IF 3.9 2区 化学
Molecular Diversity Pub Date : 2024-08-09 DOI: 10.1007/s11030-024-10951-4
Guangcan Xu, Lanlan Li, Mengfan Lv, Cheng Li, Jia Yu, Xiaoping Zeng, Xueling Meng, Gang Yu, Kun Liu, Sha Cheng, Heng Luo, Bixue Xu
{"title":"Discovery of novel 4-trifluoromethyl-2-anilinoquinoline derivatives as potential anti-cancer agents targeting SGK1.","authors":"Guangcan Xu, Lanlan Li, Mengfan Lv, Cheng Li, Jia Yu, Xiaoping Zeng, Xueling Meng, Gang Yu, Kun Liu, Sha Cheng, Heng Luo, Bixue Xu","doi":"10.1007/s11030-024-10951-4","DOIUrl":"https://doi.org/10.1007/s11030-024-10951-4","url":null,"abstract":"<p><p>Given the critical necessity for the development of more potent anti-cancer drugs, a series of novel compounds incorporating trifluoromethyl groups within the privileged 2-anilinoquinoline scaffold was designed, synthesized, and subjected to biological evaluation through a pharmacophore hybridization strategy. Upon evaluating the in vitro anti-cancer characteristics of the target compounds, it became clear that compound 8b, which contains a (4-(piperazin-1-yl)phenyl)amino substitution at the 2-position of the quinoline skeleton, displayed superior efficacy against four cancer cell lines by inducing apoptosis and cell cycle arrest. Following research conducted in a PC3 xenograft mouse model, it was found that compound 8b exhibited significant anti-cancer efficacy while demonstrating minimal toxicity. Additionally, the analysis of a 217-kinase panel pinpointed SGK1 as a potential target for this compound class with anti-cancer capabilities. This finding was further verified through molecular docking analysis and cellular thermal shift assays. To conclude, our results emphasize that compound 8b can be used as a lead compound for the development of anti-cancer drugs that target SGK1.</p>","PeriodicalId":708,"journal":{"name":"Molecular Diversity","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141905435","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
Green synthesis and cytotoxic activity of functionalized naphthyridine. 功能化萘啶的绿色合成和细胞毒性活性。
IF 3.9 2区 化学
Molecular Diversity Pub Date : 2024-08-08 DOI: 10.1007/s11030-024-10929-2
Somayeh Soleimani-Amiri, Mahsa Hojjati, Zinatossadat Hossaini
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