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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。
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
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.
结核病(TB)是一项全球健康挑战;因此,迫切需要开发一种新型、更有效的抗结核疗法。由于异柠檬酸酯裂解酶(ICL)蛋白在结核分枝杆菌(Mtb)的致病性中起着关键作用,因此本研究以该蛋白为目标。利用基于 ML 的 QSAR 模型和分子对接对 8752 种生物活性化合物进行了虚拟筛选。对前三个命中化合物进行了 ADMET 测试,以确定最接近药物分子的化合物。前三名化合物 648 和 2785758 与 ICL 的结合亲和力分别为 -7.3 和 -7 kcal/mol,与对照组相当。这些分子还显示出与 Asp108 残基的强结合力,而 Asp108 残基在 ICL 活性中起着至关重要的作用。分子动力学模拟显示,648 和 2785758 的稳定性与本研究中使用的对照化合物相当。研究发现,648 与蛋白质结合后,在 100 毫微秒的模拟过程中,RMSD 始终保持在 0.3 毫微米。2785758 的 RMSD 变化趋势与对照化合物相当。648 和 2785758 对关键残基 Asp108 都显示出较高的 RMSF。此外,PCA 和 FEL 证实了稳定复合物的形成。MM/GBSA 结合自由能估算结果表明,化合物 648 和 2785758 的稳定性较高(ΔGTOTAL = -28.11 kcal/mol),ΔGTOTAL = -21.05 kcal/mol。这项研究表明,化合物 648 和 2785758 有可能影响 ICL 的活性,导致其失活,最终阻止结核病的发展。
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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。
Pub Date : 2024-09-13 DOI: 10.1080/07391102.2024.2402692
K Aiswarya,T Vishwam,T Vamshi Prasad,C Thirmal,K C James Raju
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.
采用开口同轴探针技术测量了 L-脯氨酸在摩尔浓度为 0.025 M 至 0.15 M 的水和乙醇溶液中的复介电常数。测量的频率跨度为 0.02 < ν/GHz < 20,温度范围为 298.15 K 至 323.15 K。此外,还测定了 L-脯氨酸在水溶液和乙醇溶液中的密度 (ρ)和折射率 (nD),以便深入了解体系中溶质与溶剂之间的相互作用。计算混合物的介电弛豫时间时采用了 Havriliak-Negami 方程。结果发现,由于乙醇分子的自结合程度较高,L-脯氨酸在乙醇介质中的弛豫时间高于 L-脯氨酸在水介质中的弛豫时间。此外,混合物的弛豫时间随着摩尔浓度的增加而延长,这是因为 L-脯氨酸和水/乙醇分子之间存在氢键。通过 DFT/B3LYP 和 MP2 方法,采用 6-311 G ++ (d, p) 基集,利用 IEFPCM/PCM 溶解模型进行单点能量计算,计算了两种介质中 L-脯氨酸氢键相互作用的强度。计算结果与氢键强度、吉布斯活化自由能参数和偶极-偶极相互作用相关。
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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。
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
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.
严重急性呼吸系统综合征冠状病毒 2(SARS-CoV-2)已迅速成为一种全球流行病。在病毒蛋白中,RNA依赖性RNA聚合酶(RdRp)负责病毒基因组的复制,已成为抗击SARS-CoV-2感染的一个有希望的靶点。膳食生物活性化合物是具有抗 SARS-CoV-2 RdRp 病毒特性的进化优化分子的重要来源。我们研究了不同植物化学物质对 SARS-CoV-2 RdRp 的潜在抑制作用,包括穿心莲内酯、山柰酚、白藜芦醇和丝核苷。与其他研究化合物不同的是,山奈酚对 SARS-CoV-2 RdRp 的体外活性具有显著的剂量依赖性抑制作用。为了评估 SARS-CoV-2 RdRp 与山奈酚复合物的结合相互作用和稳定性,我们采用了分子对接、量子化学计算和分子动力学模拟等硅学技术。我们发现山奈酚与 SARS-CoV-2 RdRp 变体(武汉和 Omicron)之间具有很强的结合亲和力和稳定性。这些发现为山奈酚作为 SARS-CoV-2 RdRp 的稳定抑制剂的抗病毒特性提供了宝贵的见解。
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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)
Pub Date : 2024-08-28 DOI: 10.1080/07391102.2024.2384693
Published in Journal of Biomolecular Structure and Dynamics (Vol. 42, No. sup1, 2024)
发表于《生物分子结构与动力学杂志》(第 42 卷,第 sup1 期,2024 年)
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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
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
In response to the escalating threat of drug-resistant fungi to human health, there is an urgent need for innovative strategies. Our focus is on addressing this challenge by exploring a previously ...
为应对耐药真菌对人类健康不断升级的威胁,迫切需要创新的策略。我们的重点是通过探索一种以前...
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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
Pub Date : 2024-04-11 DOI: 10.1080/07391102.2024.2325107
Swati Gupta, Debnath Pal
We compare the WebGeSTer and INtrinsic transcription TERmination hairPIN (INTERPIN) databases used for intrinsic transcription termination (ITT) site prediction in bacteria. The former deploys inve...
我们比较了用于预测细菌内在转录终止位点的 WebGeSTer 和内在转录终止发平(INTERPIN)数据库。WebGeSTer和INtrinsic transcription TERmining hairPIN(INTERPIN)数据库用于预测细菌的内在转录终止位点。
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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
Pub Date : 2024-04-09 DOI: 10.1080/07391102.2024.2330710
Balajee Ramachandran, Ahmed Nadeem, Aruchamy Mohanprasanth, Muthupandian Saravanan
Globally the SARS-CoV-2 viral infection demands for the new drugs, the TMPRSS2 target plays a vital role in facilitating the virus entry. The aim of the present study is to identify the potential p...
全球范围内的 SARS-CoV-2 病毒感染都需要新的药物,而 TMPRSS2 靶点在促进病毒进入方面起着至关重要的作用。本研究的目的是找出潜在的TMPRSS2靶点,并对其进行研究。
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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
Pub Date : 2024-04-08 DOI: 10.1080/07391102.2024.2330714
Miroslava Nedyalkova, Ralitsa Robeva, Julia Romanova, Kirila Yovcheva, Marco Lattuada, Vasil Simeonov
Glucagon-like peptide-1 (GLP-1) is an intestinal hormone that exerts its pleiotropic effects through a specific GLP-1 receptor (GLP-1R). The hormone–receptor complex might regulate glucose-dependen...
胰高血糖素样肽-1(GLP-1)是一种肠道激素,通过特定的GLP-1受体(GLP-1R)发挥其多效应。这种激素-受体复合物可能会调节葡萄糖依赖性,从而导致血糖升高。
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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
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
The N, N’-(1,2-phenylene) bis (1- (4- chlorophenyl) methanimine) (CS4) was synthesized and characterized by infrared (IR), absorption (UV-vis) and NMR (1H and 13C) spectral analyses. The structural...
合成了 N,N'-(1,2-亚苯基)双(1-(4-氯苯基)甲亚胺)(CS4),并通过红外(IR)、吸收(UV-vis)和核磁共振(1H 和 13C)光谱分析对其进行了表征。其结构...
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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
Pub Date : 2024-03-20 DOI: 10.1080/07391102.2024.2329291
Olalekan Onisuru, Ikechukwu Achilonu
Research has spotlighted glutathione transferase (GST) as a promising target for antimalarial drug development due to its pivotal role in cellular processes, including metabolizing toxins and manag...
由于谷胱甘肽转移酶(GST)在细胞过程(包括代谢毒素和管理毒素)中的关键作用,研究人员已将其作为抗疟疾药物开发的一个有前途的靶点。
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引用次数: 0
期刊
Journal of Biomolecular Structure and Dynamics
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