Journal of Biomolecular Structure and Dynamics最新文献

Cheminformatics-enhanced discovery of therapeutic agents targeting isocitrate lyase in Mycobacterium tuberculosis infections. 通过化学信息学发现针对结核分枝杆菌感染中异柠檬酸酶的治疗药物。

Journal of Biomolecular Structure and Dynamics Pub Date : 2024-09-18 DOI: 10.1080/07391102.2024.2404145

Aftab Alam,Mohammed H Alqarni,Bader S Alotaibi,Farhan R Khan,Md Shamsher Alam,Faris F Aba Alkhayl,Ali A Alhafi,Turki M Almutairi,Zeyad M Alharbi,Faez Falah Alshehri

{"title":"Cheminformatics-enhanced discovery of therapeutic agents targeting isocitrate lyase in Mycobacterium tuberculosis infections.","authors":"Aftab Alam,Mohammed H Alqarni,Bader S Alotaibi,Farhan R Khan,Md Shamsher Alam,Faris F Aba Alkhayl,Ali A Alhafi,Turki M Almutairi,Zeyad M Alharbi,Faez Falah Alshehri","doi":"10.1080/07391102.2024.2404145","DOIUrl":"https://doi.org/10.1080/07391102.2024.2404145","url":null,"abstract":"Tuberculosis (TB) is a global health challenge; therefore, there is an urgent requirement to develop a novel and more effective anti-TB therapeutic. This study targeted the isocitrate lyase (ICL) protein due to its pivotal role in the pathogenicity of Mycobacterium tuberculosis (Mtb). Virtual screening of 8752 bioactive compounds used an ML-based QSAR model and molecular docking. ADMET testing was performed on the top three hits to identify the compound most closely mimicking a drug molecule. The top hits, 648 and 2785758, showed high binding affinity towards ICL with -7.3 and -7 kcal/mol, comparable to the control. These molecules also showed strong binding with the residue Asp108, which plays a vital role in ICL activity. Molecular dynamics simulations showed stability for 648 and 2785758, comparable to the control compound used in this study. It was found that 648 bound to the protein maintained the RMSD constant and consistent at 0.3 nm for a complete 100 ns simulation. 2785758 showed a comparable RMSD trend to the control. Both 648 and 2785758 showed high RMSF for critical residue Asp108. Further, PCA and FEL confirmed the formation of a stable complex. MM/GBSA estimations of binding free energy indicated that compounds 648 had an elevated level of stability (ΔGTOTAL = -28.11 kcal/mol) and 2785758 (ΔGTOTAL = -21.05 kcal/mol). This study suggests that compounds 648 and 2785758 can potentially affect the activity of ICL, leading to its inactivation and ultimately preventing the progression of tuberculosis.Communicated by Ramaswamy H. Sarma.","PeriodicalId":15085,"journal":{"name":"Journal of Biomolecular Structure and Dynamics","volume":"28 1","pages":"1-18"},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142267551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Molecular interaction studies of L-proline in water and ethanol at different temperatures using dielectric relaxation, refractive index and DFT methods. 利用介电弛豫、折射率和 DFT 方法研究不同温度下 L-脯氨酸在水和乙醇中的分子相互作用。

Journal of Biomolecular Structure and Dynamics Pub Date : 2024-09-13 DOI: 10.1080/07391102.2024.2402692

K Aiswarya,T Vishwam,T Vamshi Prasad,C Thirmal,K C James Raju

{"title":"Molecular interaction studies of L-proline in water and ethanol at different temperatures using dielectric relaxation, refractive index and DFT methods.","authors":"K Aiswarya,T Vishwam,T Vamshi Prasad,C Thirmal,K C James Raju","doi":"10.1080/07391102.2024.2402692","DOIUrl":"https://doi.org/10.1080/07391102.2024.2402692","url":null,"abstract":"The complex dielectric permittivity of L-Proline in water and ethanol solutions with molar concentrations ranging from 0.025 M to 0.15 M was measured by open-ended coaxial probe technique. The measurements were carried out across a frequency span of 0.02 < ν/GHz < 20 and temperatures varying from 298.15 K to 323.15 K. The densities (ρ) and refractive index (nD) of the L-proline in aqueous and ethanol solutions were also determined to provide insights into the solute-solvent interactions in the system. The Havriliak-Negami equation was employed to compute the dielectric relaxation time of the mixtures. The relaxation time of L-Proline in an ethanol medium was found to be higher than that of L-Proline in an aqueous medium due to the greater degree of self-association of ethanol molecules. Additionally, the relaxation time of the mixtures lengthened with rising molar concentration, which is attributed to the presence of hydrogen bonds among L-Proline and aqueous/ethanol molecules. The strength of the hydrogen bond interaction of L-Proline in both mediums was calculated using single-point energy calculations employing IEFPCM/PCM solvation models through DFT/B3LYP and MP2 approaches with a 6-311 G ++ (d, p) basis set. The results were correlated with the hydrogen bond strength, Gibbs' free energy of activation parameter, and dipole-dipole interactions.Communicated by Ramaswamy H. Sarma.","PeriodicalId":15085,"journal":{"name":"Journal of Biomolecular Structure and Dynamics","volume":"21 1","pages":"1-13"},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142269652","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Kaempferol as a novel inhibitor of SARS-CoV-2 RNA-dependent RNA polymerase. 山奈酚是一种新型的 SARS-CoV-2 RNA 依赖性 RNA 聚合酶抑制剂。

Journal of Biomolecular Structure and Dynamics Pub Date : 2024-09-11 DOI: 10.1080/07391102.2024.2402695

Alessandro Medoro,Francesca Benedetti,Mariano Intrieri,Tassadaq Hussain Jafar,Sawan Ali,Truong Tan Trung,Daniela Passarella,Saba Ismail,Davide Zella,Giovanni Scapagnini,Sergio Davinelli

{"title":"Kaempferol as a novel inhibitor of SARS-CoV-2 RNA-dependent RNA polymerase.","authors":"Alessandro Medoro,Francesca Benedetti,Mariano Intrieri,Tassadaq Hussain Jafar,Sawan Ali,Truong Tan Trung,Daniela Passarella,Saba Ismail,Davide Zella,Giovanni Scapagnini,Sergio Davinelli","doi":"10.1080/07391102.2024.2402695","DOIUrl":"https://doi.org/10.1080/07391102.2024.2402695","url":null,"abstract":"Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has quickly become a global health pandemic. Among the viral proteins, RNA-dependent RNA polymerase (RdRp) is responsible for viral genome replication and has emerged as a promising target against SARS-CoV-2 infection. Dietary bioactive compounds represent an important source of evolutionarily optimized molecules with antiviral properties against SARS-CoV-2 RdRp. We investigated the inhibitory potential effects of different phytochemicals against SARS-CoV-2 RdRp, including andrographolide, kaempferol, resveratrol, and silibinin. Unlike the other investigated compounds, kaempferol exhibited a significant dose-dependent in vitro inhibition of SARS-CoV-2 RdRp activity. To assess the binding interactions and stability of the SARS-CoV-2 RdRp-kaempferol complex, we performed in silico techniques, including molecular docking, quantum chemical calculation, and molecular dynamics simulations. We found strong binding affinities and stability between kaempferol and SARS-CoV-2 RdRp variants (Wuhan and Omicron). These findings provide valuable insights into the antiviral properties of kaempferol as a stable inhibitor of SARS-CoV-2 RdRp.Communicated by Ramaswamy H. Sarma.","PeriodicalId":15085,"journal":{"name":"Journal of Biomolecular Structure and Dynamics","volume":"181 1","pages":"1-10"},"PeriodicalIF":0.0,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142217345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Book of Abstracts. The 1st Next Generation Conversations: Albany at Ruston 2024 (The 21st Albany Conversation) 摘要集。第一届下一代对话：2024 年拉斯顿的奥尔巴尼（第 21 届奥尔巴尼对话）

Journal of Biomolecular Structure and Dynamics Pub Date : 2024-08-28 DOI: 10.1080/07391102.2024.2384693

引用次数: 0

Antifungal drug discovery for targeting Candida albicans morphogenesis through structural dynamics study 通过结构动力学研究发现针对白色念珠菌形态发生的抗真菌药物

Journal of Biomolecular Structure and Dynamics Pub Date : 2024-04-18 DOI: 10.1080/07391102.2024.2332507

Ali A. Rabaan, Wadha A. Alfouzan, Mohammed Garout, Muhammad A. Halwani, Nouf Alotaibi, Mubarak Alfaresi, Nawal A. Al Kaabi, Zainab H. Almansour, Ahmed S. Bueid, Amjad A. Yousuf, Hamza M. A. Eid, Mohammed Alissa

引用次数: 0

Detection of intrinsic transcription termination sites in bacteria: consensus from hairpin detection approaches 细菌内在转录终止位点的检测：发夹检测方法的共识

Journal of Biomolecular Structure and Dynamics Pub Date : 2024-04-11 DOI: 10.1080/07391102.2024.2325107

Swati Gupta, Debnath Pal

引用次数: 0

Prediction of deleterious non-synonymous SNPs of TMPRSS2 protein combined with Molecular Dynamics Simulations and free energy analysis to identify the potential peptide substrates against SARS-CoV-2 预测 TMPRSS2 蛋白的有害非同义 SNPs，结合分子动力学模拟和自由能分析，确定抗 SARS-CoV-2 的潜在多肽底物

Journal of Biomolecular Structure and Dynamics Pub Date : 2024-04-09 DOI: 10.1080/07391102.2024.2330710

Balajee Ramachandran, Ahmed Nadeem, Aruchamy Mohanprasanth, Muthupandian Saravanan

引用次数: 0

In silico screening of potential agonists of a glucagon-like peptide-1 receptor among female sex hormone derivatives 雌性激素衍生物中胰高血糖素样肽-1 受体潜在激动剂的硅学筛选

Journal of Biomolecular Structure and Dynamics Pub Date : 2024-04-08 DOI: 10.1080/07391102.2024.2330714

Miroslava Nedyalkova, Ralitsa Robeva, Julia Romanova, Kirila Yovcheva, Marco Lattuada, Vasil Simeonov

引用次数: 0

Synthesis, topology, molecular docking and dynamics studies of o-phenylenediamine derivative 邻苯二胺衍生物的合成、拓扑结构、分子对接和动力学研究

Journal of Biomolecular Structure and Dynamics Pub Date : 2024-04-05 DOI: 10.1080/07391102.2024.2317981

T. Sankar Ganesan, N. Elangovan, Munusamy Thirumavalavan, Shanthi Seenan, S. Sowrirajan, S. Chandrasekar, Natarajan Arumugam, Abdulrahman I. Almansour, Sakkarapalayam M. Mahalingam, Datta Darshan V M, Subbarao Kanchi, Venketesh Sivaramakrishnan

引用次数: 0

Describing the ligandin properties of Plasmodium falciparum and vivax glutathione transferase towards bromosulfophthalein from empirical and computational modelling viewpoints 从经验和计算模型的角度描述恶性疟原虫和间日疟原虫谷胱甘肽转移酶对溴磺酞的配位性质

Journal of Biomolecular Structure and Dynamics Pub Date : 2024-03-20 DOI: 10.1080/07391102.2024.2329291

Olalekan Onisuru, Ikechukwu Achilonu

引用次数: 0