Journal of Biomolecular Structure & Dynamics最新文献_第5页

Decoding the structural integrity and multifunctional role of Era protein in the survival of Mycobacterium tuberculosis H₃₇Rv. 解码 Era 蛋白在结核分枝杆菌 H37Rv 存活过程中的结构完整性和多功能作用。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-07-01 Epub Date: 2024-02-06 DOI: 10.1080/07391102.2024.2309332

Preeti Agarwal, Ajit Kumar, Laxman S Meena

{"title":"Decoding the structural integrity and multifunctional role of Era protein in the survival of Mycobacterium tuberculosis H37Rv.","authors":"Preeti Agarwal, Ajit Kumar, Laxman S Meena","doi":"10.1080/07391102.2024.2309332","DOIUrl":"10.1080/07391102.2024.2309332","url":null,"abstract":"Era, a widely known GTP binding protein found in many organisms including prokaryotes and eukaryotes and plays a significant role in many fundamental cellular processes like cell growth, differentiation and signaling. In Mycobacterium tuberculosis (Mtb) H37Rv, Era protein had been proved as a GTPase protein but its structural and functional insights are still lacking. Through comparative analysis, structural modeling, docking and using various bioinformatic tools, a detailed investigation of Era was carried out to deduce the structure, function and residues involved in the activity of the protein. Intriguingly, docking results revealed high binding affinity of Era not only with GTP but also with ATP. Myristoylation modifications and phosphorylations on Era were predicted to possibly aid in regulating Era activity and localization; and also the role of Era in translation regulation was foreseen by showing its association with 16s rRNA. Moreover, point mutation of Era residues revealed the effect of W288G and K19G in highly destabilizing the protein structure and activity. Additionally, Era protein was docked with 25 GTPase/ATPase inhibitors, where, Dynasore inhibitor showed the highest affinity for the protein's GTP binding sites and can be used for further drug trials to inhibit growth of mycobacteria.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"5356-5371"},"PeriodicalIF":2.7,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139691882","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The in vitro and in vivo antiviral effects of IGF1R inhibitors against respiratory syncytial virus infection. IGF1R 抑制剂对呼吸道合胞病毒感染的体外和体内抗病毒作用。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-07-01 Epub Date: 2024-02-01 DOI: 10.1080/07391102.2024.2309643

Pinglang Ruan, Pei Dai, Yu Mao, Zhongxiang Tang, Hanlin He, Guojun Wu, Ling Qin, Yurong Tan

{"title":"The in vitro and in vivo antiviral effects of IGF1R inhibitors against respiratory syncytial virus infection.","authors":"Pinglang Ruan, Pei Dai, Yu Mao, Zhongxiang Tang, Hanlin He, Guojun Wu, Ling Qin, Yurong Tan","doi":"10.1080/07391102.2024.2309643","DOIUrl":"10.1080/07391102.2024.2309643","url":null,"abstract":"The insulin-like growth factor 1 receptor (IGF1R) was recognized as a pivotal receptor that facilitated the cellular entry of RSV. Small molecule inhibitors designed to target IGF1R exhibited potential as potent antiviral agents. Through virtual screening, we conducted a screening process involving small molecule compounds derived from natural products, aiming to target the IGF1R protein against respiratory syncytial virus infection. The molecular dynamics simulation analysis showed that tannic acid and daptomycin interacted with the IGF1R. The experimental results in vivo and in vitro showed that tannic acid and daptomycin had anti-RSV infection potential through reducing viral loads, inflammation, airway resistance and protecting alveolar integrity. The CC50 values of tannic acid and daptomycin were 6 nM and 0.45 μM, respectively. Novel small-molecule inhibitors targeting the IGF1R, tannic acid and daptomycin, may be effective anti-RSV therapy agents. This study may in future broaden the arsenal of therapeutics for use against RSV infection and lead to more effective care against the virus.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"5500-5511"},"PeriodicalIF":2.7,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139650830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

In silico screening of phytoconstituents as potential anti-inflammatory agents targeting NF-κB p65: an approach to promote burn wound healing. 以 NF-κB p65 为靶点的潜在抗炎剂植物成分的硅学筛选：促进烧伤伤口愈合的一种方法。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-07-01 Epub Date: 2024-01-29 DOI: 10.1080/07391102.2024.2306199

Saswati Pattnaik, Sneha Murmu, Bibhu Prasad Rath, Mahender Kumar Singh, Sunil Kumar, Chandana Mohanty

{"title":"In silico screening of phytoconstituents as potential anti-inflammatory agents targeting NF-κB p65: an approach to promote burn wound healing.","authors":"Saswati Pattnaik, Sneha Murmu, Bibhu Prasad Rath, Mahender Kumar Singh, Sunil Kumar, Chandana Mohanty","doi":"10.1080/07391102.2024.2306199","DOIUrl":"10.1080/07391102.2024.2306199","url":null,"abstract":"Chronic burn wounds are frequently characterised by a prolonged and dysregulated inflammatory phase that is mediated by over-activation of NF-κB p65. Synthetic wound healing drugs used for treatment of inflammation are primarily associated with several shortcomings which reduce their therapeutic index. In this scenario, phytoconstituents that exhibit multifaceted biological activities including anti-inflammatory effects have emerged as a promising therapeutic alternative. However, identification and isolation of phytoconstituents from medicinal herbs is a cumbersome method that is linked to profound uncertainty. Hence, present study aimed to identify prospective phytoconstituents as inhibitors of RHD of NF-κB p65 by utilizing in silico approach. Virtual screening of 2821 phytoconstituents was performed against protein model. Out of 2821 phytoconstituents, 162 phytoconstituents displayed a higher binding affinity (≤ -8.0 kcal/mol). These 162 phytoconstituents were subjected to ADMET predictions, and 15 of them were found to satisfy Lipinski's rule of five and showed favorable pharmacokinetic properties. Among these 15 phytoconstituents, 5 phytoconstituents with high docking scores i.e. silibinin, bismurrayaquinone A, withafastuosin B, yuccagenin, (+)-catechin 3-gallate were selected for molecular dynamics (MD) simulation analysis. Results of MD simulation indicated that withafastuosin B, (+)-catechin 3-gallate and yuccagenin produced a compact and stable complex with protein without significant variations in conformation. Relative binding energy analysis of best hit molecules indicate that withafastuosin B, and (+)-catechin 3-gallate exhibit high binding affinity with target protein among other lead molecules. Findings of study suggest that these phytoconstituents could serve as promising anti-inflammatory agents for treatment of burn wounds by inhibiting the RHD of NF-κB p65.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4956-4984"},"PeriodicalIF":2.7,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139575726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Binding order of substrate and cofactor in sulfonamide monooxygenase during sulfa drug degradation: in silico studies. 磺胺药物降解过程中磺胺单氧化酶中底物和辅助因子的结合顺序：硅学研究。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-07-01 Epub Date: 2024-01-23 DOI: 10.1080/07391102.2024.2306495

Amogh Desai, Ved Mahajan, Raghunath O Ramabhadran, Raju Mukherjee

{"title":"Binding order of substrate and cofactor in sulfonamide monooxygenase during sulfa drug degradation: in silico studies.","authors":"Amogh Desai, Ved Mahajan, Raghunath O Ramabhadran, Raju Mukherjee","doi":"10.1080/07391102.2024.2306495","DOIUrl":"10.1080/07391102.2024.2306495","url":null,"abstract":"For decades, sulfonamide antibiotics have been used across industries such as agriculture and animal husbandry. However, the use and inadvertent misuse of these antibiotics have resulted in the advent of sulfonamide-drug-resistant strains due to antibiotic pollution. Enzymatic bioremediation of antibiotics remains a potential emerging solution to combat antibiotic pollution. Here, we propose an enzymatic model for the degradation of sulfonamides by Microbacterium sp. We have employed a multi-pronged computational strategy involving - protein structure modelling, ligand docking and molecular dynamics simulations to decipher a plausible binding order for the enzymatic degradation of sulfonamides by the bacterial sulfonamide monooxygenase, SulX. Our results enable us to predict that this degradation is achieved through the sequential binding of the antibiotic sulfonamide followed by the reduced flavin cofactor FMNH2, thereby laying the computational foundation for further advancements in enzyme-mediated degradation of the antibiotic. We also provide a list of experiments which may be performed to verify and follow-up on our in-silico studies.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"5020-5034"},"PeriodicalIF":2.7,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139542642","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification of selective plant-derived natural carotenoid and flavonoids as the potential inhibitors of DHHC-mediated protein S-palmitoylation: an in silico study. 鉴定作为 DHHC 介导的蛋白质 S-棕榈酰化潜在抑制剂的选择性植物源天然类胡萝卜素和类黄酮：一项硅学研究。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-07-01 Epub Date: 2024-02-06 DOI: 10.1080/07391102.2024.2306502

Suchi Chaturvedi, Nirali Pandya, Sushabhan Sadhukhan, Avinash Sonawane

{"title":"Identification of selective plant-derived natural carotenoid and flavonoids as the potential inhibitors of DHHC-mediated protein S-palmitoylation: an in silico study.","authors":"Suchi Chaturvedi, Nirali Pandya, Sushabhan Sadhukhan, Avinash Sonawane","doi":"10.1080/07391102.2024.2306502","DOIUrl":"10.1080/07391102.2024.2306502","url":null,"abstract":"Protein S-palmitoylation mediated by DHHCs is recognized as a distinct and reversible form of lipid modification connected with several health perturbations, including neurodegenerative disorders, cancer, and autoimmune conditions. However, the pharmacological characteristics of current pan-DHHC inhibitors, particularly their toxicity and off-target effects, have hindered their in-depth cellular investigations. The therapeutic properties of the natural compounds, with minimal side effects, allowed us to evaluate them as DHHC-targeting inhibitors. Here, we performed an insilico screening of 115 phytochemicals to assess their interactions with the DHHC20 binding site. Among these compounds, lutein, 5-hydroxyflavone, and 6-hydroxyflavone exhibited higher binding energy (-9.2, -8.5, and -8.5 kcal/mol) in the DHHC20 groove compared to pan-DHHC inhibitor 2-BP (-7.0 kcal/mol). Furthermore, we conducted a 100 ns MD simulation to evaluate the stability of these complexes under physiological conditions. The MDsimulation results indicated that DHHC20 formed a more stable conformation with lutein compared to 5-hydroxyflavone and 6-hyroxyflavone via hydrophobic and H-bond interactions. Conclusively, these results could serve as a promising starting point for exploring the use of these natural molecules as DHHC20 inhibitors.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"5110-5123"},"PeriodicalIF":2.7,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139691887","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Association of cuproptosis-related signature with the prognosis of patients with head and neck squamous cell carcinoma. 杯突相关特征与头颈部鳞状细胞癌患者预后的关系

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-07-01 Epub Date: 2024-01-27 DOI: 10.1080/07391102.2024.2308776

Yunshan Li, Caidie Sun, Feihan Gu, Jiayuan Yue, Xu Huang, Bin Yuan, Yuanyin Wang, Ran Chen

{"title":"Association of cuproptosis-related signature with the prognosis of patients with head and neck squamous cell carcinoma.","authors":"Yunshan Li, Caidie Sun, Feihan Gu, Jiayuan Yue, Xu Huang, Bin Yuan, Yuanyin Wang, Ran Chen","doi":"10.1080/07391102.2024.2308776","DOIUrl":"10.1080/07391102.2024.2308776","url":null,"abstract":"Patients with head and neck squamous cell carcinoma (HNSCC) have a poor prognosis because of their high recurrence and metastasis rates. Cuproptosis is a novel type of copper-dependent cell death that differs from apoptosis, necroptosis, and cytosolic scorch death. We designed and validated an individualized cuproptosis-related gene (CRG) signature for risk evaluation and prognostic prediction in HNSCC patients. Ninety differentially expressed CRGs were found in HNSCC. Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analyses were performed to investigate the functional involvement of CRGs in the Cancer Genome Atlas (TCGA) HNSCC cohort. A CRG signature was created using 10 genes after univariate and multivariate analysis. Kaplan Meier (KM) analysis showed that the survival rate of the high-risk group was significantly lower than that of the low-risk group. Multivariate regression analysis identified risk scores based on prognostic characteristics as independent prognostic indicators of HNSCC. Moreover, risk models are related to tumor mutational burden (TMB), tumor-infiltrating immune cells (TICs), immune checkpoints, clinical characteristics, and antitumor drug susceptibility. Furthermore, we found that CuCl2 treatment promoted cuproptosis in HNSCC cells, and that the expression levels of cuproptosis-related genes were altered by different doses of CuCl2. In summary, understanding the detailed molecular mechanisms of cuproptosis and its impact on overall survival (OS), and identifying potential therapeutic targets for HNSCC will provide potential insights for treatment.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"5474-5485"},"PeriodicalIF":2.7,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139570011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Aspirin as a potential drug repurposing candidate targeting estrogen receptor alpha in breast cancer: a molecular dynamics and in-vitro study. 阿司匹林作为针对乳腺癌雌激素受体α的潜在候选药物再利用：分子动力学和体外研究。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-07-01 Epub Date: 2024-01-27 DOI: 10.1080/07391102.2024.2308780

Deepinder Kaur, Chinmayee Choudhury, Reena Yadav, Laxmi Kumari, Alka Bhatia

{"title":"Aspirin as a potential drug repurposing candidate targeting estrogen receptor alpha in breast cancer: a molecular dynamics and in-vitro study.","authors":"Deepinder Kaur, Chinmayee Choudhury, Reena Yadav, Laxmi Kumari, Alka Bhatia","doi":"10.1080/07391102.2024.2308780","DOIUrl":"10.1080/07391102.2024.2308780","url":null,"abstract":"Estrogen receptor alpha (ERα) is expressed by 70% of breast cancers (BCs). Any deregulation in ERα signaling is crucial for the initiation and progression of BC. Because of development of resistance to anti-estrogenic compounds, repurposing existing drugs is an apt strategy to avoid a long drug-discovery process. Substantial epidemiologic evidence suggests that Aspirin use reduces the risk of different cancers including BC, while its role as an adjuvant or a possible antineoplastic agent in cancer treatment is being investigated. In this study, we attempted to explore possibilities of ERα inhibition by Aspirin which may act through competitive binding to the ligand binding domain (LBD) of ERα. A list of 48 ERα-LBD crystal structures bound with agonists, antagonists, and selective ER modulators (SERMs) was thoroughly analysed to determine interaction patterns specific to each ligand category. Exhaustive docking and 500 ns molecular dynamics (MD) studies were performed on three ERα - Aspirin complexes generated using agonist, antagonist, and SERM-bound crystal structures. Besides, three ERα crystal structures bound to agonist, antagonist, and SERM respectively were also subjected to MD simulations. Aspirin showed good affinity to LBD of ERα. Comparative analyses of binding patterns, conformational changes and molecular interaction profiles from the docking results and MD trajectories suggests that Aspirin was most stable in complex generated using SERM bound crystal structure of ERα and showed interactions with Gly-521, Ala-350, Leu-525 and Thr-347 like SERMs. In addition, in-vitro assays, qPCR, and immunofluorescent assay demonstrated the decline in the expression of ERα in MCF-7 upon treatment with Aspirin. These preliminary bioinformatical and in-vitro findings may form the basis to consider Aspirin as a potential candidate for targeting ERα, especially in tamoxifen-resistant cancers.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"5268-5279"},"PeriodicalIF":2.7,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139570010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

In-vitro antimicrobial activity of AF-DP protein and in-silico approach of cell membrane disruption. AF-DP蛋白的体外抗菌活性和破坏细胞膜的硅学方法。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-07-01 Epub Date: 2024-02-06 DOI: 10.1080/07391102.2024.2308763

Fatemeh Velayatipour, Hossein Tarrahimofrad, Javad Zamani, Fatemeh Fotouhi, Saeed Aminzadeh

{"title":"In-vitro antimicrobial activity of AF-DP protein and in-silico approach of cell membrane disruption.","authors":"Fatemeh Velayatipour, Hossein Tarrahimofrad, Javad Zamani, Fatemeh Fotouhi, Saeed Aminzadeh","doi":"10.1080/07391102.2024.2308763","DOIUrl":"10.1080/07391102.2024.2308763","url":null,"abstract":"Microbial resistance against common antibiotics has become one of the most serious threats to human health. The increasing statistics on this problem show the necessity of finding a way to deal with it. In recent years, antimicrobial peptides with unique properties and the capability of targeting a wide range of pathogens, have been considered as a potential for replacing common antibiotics. A small chitin-binding protein with anticandidal activity was isolated from Moringa oleifera seeds by Neto and colleagues in 2017, which very much resembled antimicrobial peptides. In this study, the antimicrobial protein 'AF-DP' was identified and characterized. AF-DP was heterologously expressed, purified, and characterized, and its 3D structure was predicted. Six molecular dynamic simulations were performed to investigate how the protein interacts with Gram-negative inner and outer, Gram-positive, fungal, cancerous, and normal mammalian membranes. Also, its antimicrobial and anticancer activity was assessed in vitro via minimum inhibition concentration (MIC) and MTT assays, respectively. This protein with 111 amino acids and a total net charge (of 10.5) has been predicted to be mainly composed of alpha helix and random coils. Its MIC affecting the growth of Escherichia coli, Staphylococcus aureus, and Candida albicans was 30 µg/ml, 100 µg/ml, and 100 µg/ml, respectively; AF-DP showed anticancer activity against MCF-7 breast cancer cell line. Scanning electron microscopic analysis confirmed the creation of pores and scratches on the surface of the bacterial membrane. The results of this research show that AF-DP can be a candidate for the production of new drugs as an AMP with antimicrobial activity.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"5133-5150"},"PeriodicalIF":2.7,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139691880","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Comprehending interaction mechanism of natural actives of Colchicum autumnale L. for rheumatoid arthritis using integrative chemoinformatic approaches. 利用综合化学信息学方法了解秋水仙天然活性物质治疗类风湿性关节炎的相互作用机制。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-07-01 Epub Date: 2023-12-20 DOI: 10.1080/07391102.2023.2294177

Sowmya H S, Guruprasad V, Ningaraju T M, Anagha S Setlur, Chandrashekar K, Jitendra Kumar, Vidya Niranjan

{"title":"Comprehending interaction mechanism of natural actives of Colchicum autumnale L. for rheumatoid arthritis using integrative chemoinformatic approaches.","authors":"Sowmya H S, Guruprasad V, Ningaraju T M, Anagha S Setlur, Chandrashekar K, Jitendra Kumar, Vidya Niranjan","doi":"10.1080/07391102.2023.2294177","DOIUrl":"10.1080/07391102.2023.2294177","url":null,"abstract":"This research delves into the realm of therapeutic potential within natural compounds derived from Colchicum autumnale L., emphasizing a holistic perspective on medications used in human therapy. Rather than confining the study to their primary actions, the research endeavors to unveil molecular targets for these natural compounds, with a specific focus on their potential applicability in the treatment of rheumatoid arthritis (RA). The study focuses on understanding interactions between specific natural actives that target RA. Fifteen RA target proteins were identified from OMIM, GeneScan and PharmaGKB. Their structures were downloaded from RCSB PDB. Two active components of C. autumnale L. were chosen for mass spectrometry investigation. Ligand characteristics were determined using the ADMETlab and SwissADME software tools. Molecular docking was performed, and the top three complexes were simulated for 200 ns, along with identification of free binding energies. The compounds β-sitosterol-IL-10 (-6.50 kcal/mol), colchicine-IL-10 (-6.01 kcal/mol), linoleic acid-IL-10 (-7.22 kcal/mol) and linoleic acid-IL-10 (-7.22 kcal/mol) exhibited best binding energies. β-Sitosterol and colchicine showed the highest stability in simulations, confirmed by molecular mechanics free energy binding calculations. This work provides insights into the molecular interaction of natural compounds against RA targets, offering potential therapeutic anti-RA medications.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4865-4884"},"PeriodicalIF":2.7,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138803690","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exploring plant-derived small molecules as inhibitors of Marburg virus RNA binding protein activity. 探索作为马尔堡病毒 RNA 结合蛋白活性抑制剂的植物源小分子。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2025-07-01 Epub Date: 2024-01-25 DOI: 10.1080/07391102.2024.2306500

Leena Hussein Bajrai, Abdulrahman Abdullah Almalki, Amaresh Kumar Sahoo, Vivek Dhar Dwivedi, Esam Ibraheem Azhar

{"title":"Exploring plant-derived small molecules as inhibitors of Marburg virus RNA binding protein activity.","authors":"Leena Hussein Bajrai, Abdulrahman Abdullah Almalki, Amaresh Kumar Sahoo, Vivek Dhar Dwivedi, Esam Ibraheem Azhar","doi":"10.1080/07391102.2024.2306500","DOIUrl":"10.1080/07391102.2024.2306500","url":null,"abstract":"The search for antiviral medications is greatly influenced by the hunt for potent inhibitors of viral proteins. To find possible inhibitors of the RNA binding activity of the Marburg virus VP35 protein, we used a thorough in silico drug discovery approach in this investigation. A comprehensive virtual screening process, followed by a detailed MMGBSA analysis, led to the discovery of four potential inhibitory compounds viz. Kudzuisoflavone A, Miquelianin, Rutin, and Protopseudohypericin. They were identified from an extensive library of phytomolecules derived from three medicinal plants: Adiantum capillus-veneris, Hypericum perforatum, and Pueraria montana. In molecular dynamics (MD) simulations, all these compounds showed steady binding to the target protein and favourable interactions. Notably, the free binding energies of all the selected compounds were better than the myricetin, a well-known blocker of the VP35 protein of the Ebola virus. Overall, this investigation offers insightful information about the molecular interactions and binding dynamics of the identified inhibitors' binding to the VP35 protein of the Marburg virus. The findings highlight the potential of three particular medicinal plants as sources of key chemicals for the creation of brand-new Marburg virus antiviral drugs. More experimental validation and optimization of the identified inhibitors are necessary in order to transform these findings into effective medicines for treating Marburg virus infections.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"5086-5096"},"PeriodicalIF":2.7,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139546500","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0