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Development of a novel CYP3A4 classifier model via site of metabolism (SOM)-based molecular docking, multivariate analysis and molecular dynamics of known substrates and inhibitors 通过基于代谢位点(SOM)的分子对接、多变量分析和已知底物和抑制剂的分子动力学,建立新的CYP3A4分类模型
4区 化学 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2023-10-27 DOI: 10.1142/s2737416523500618
Mohamad Jemain Mohamad Ridhwan, Nurul Azmir Amir Hashim, Noraini Kasim, Nor Nadirah Abdullah, Nurul Alam Inayatsyah, Nor Hadiani Ismail, Syahrul Imran
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引用次数: 0
Novel specific SARS-CoV-2 miRNAs Targeting Human Genes involved in COVID-19 Infection and their Regulation by Bemcentinib and Zavegepant: A Promising Evidence for RNA-Based Repurposing Therapeutic Strategy 靶向人类COVID-19感染相关基因的新型特异性SARS-CoV-2 miRNAs及其在百森替尼和扎维吉坦中的调控作用:基于rna的靶向治疗策略的有希望证据
4区 化学 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2023-10-27 DOI: 10.1142/s273741652350062x
Jitender Singh, Pramod K Avti, Krishan L Khanduja, Radhika Dhawan, Namrata Sangwan, Arushi Chauhan
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引用次数: 0
A Graph Deep Learning-Based Framework for Drug-Disease Association Identification with Chemical Structure Similarities 基于图深度学习的化学结构相似性药物-疾病关联识别框架
4区 化学 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2023-10-20 DOI: 10.1142/s2737416523410053
Bo-Wei Zhao, Xiao-Rui Su, Dong-Xu Li, Guo-Dong Li, Peng-Wei Hu, Yong-Gang Zhao, Lun Hu
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引用次数: 0
In silico molecular docking approach and in vitro antioxidant and antimicrobial activity of Physalis angulata L. extract 角Physalis l.l .的硅分子对接方法及体外抗氧化和抗菌活性研究
4区 化学 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2023-10-20 DOI: 10.1142/s2737416523500564
Riuh Wardhani, Cici Darsih, Ade Chandra Iwansyah, Ashri Indriati, Hazrulrizawati Abdul Hamid, Dirayah Rauf Husain
The biological properties of Physalis angulata L. include antibacterial, and antioxidant activity, anticancer and anti-inflammatory. The main goal of the research was to determine, using in silico methods, if some of the bioactive substances found in P. angulata L. extract were able to bind and inhibit the important protein/receptor. The Physalis angulata L. extract yielded significant in vitro-free radical scavenging activity against 2,2-diphenyl-1-picrylhydrazyl (DPPH) with IC[Formula: see text] value of 1.14 mg/ml, total phenolic content (TPC) value 133.96 ± 2.35 mg of gallic acid equivalent (GAE/g) and TFC value 47.6 ± 5.08 mg of quercetin equivalent (QE/g), respectively. The antibacterial activity was modest when compared with antibiotics controls. The extract was more effective on gram-positive Staphylococcus aureus than gram Escherichia coli yielding 11.367 ± 0.9 (mm) and 7.102 ± 0.5 (mm), respectively, at a 1 mg/mL concentration. The LC-HRMS analysis of the plant extract showed the most responsive compounds (30) that were present were selected to get the hit compound(s) on all target proteins viz., lipoxygenase-3, cytochrome P450, DNA gyrase topoisomerase II and histone acetyltransferase. Computational approaches revealed the low binding affinity of (+)-gallocatechin among 30 identified compounds on all target proteins. All identified compounds have good pharmacokinetic characteristics on ADMET parameters. Based on this study, P. angulata L. extract is a promising source of biological activity with great potential therapeutic use as an antibacterial and antioxidant.
角Physalis angulata L.具有抗菌、抗氧化、抗癌、抗炎等生物学特性。本研究的主要目的是利用计算机方法,确定棘叶提取物中发现的一些生物活性物质是否能够结合和抑制重要的蛋白质/受体。该提取物对2,2-二苯基-1-苦酰肼(DPPH)具有明显的体外自由基清除活性,IC值为1.14 mg/ml,总酚含量(TPC)为133.96±2.35 mg没食子酸当量(GAE/g), TFC值为47.6±5.08 mg槲皮素当量(QE/g)。与抗生素对照相比,抗菌活性一般。在1 mg/mL浓度下,该提取物对革兰氏阳性金黄色葡萄球菌的抑制效果优于革兰氏大肠杆菌,分别为11.367±0.9 (mm)和7.102±0.5 (mm)。植物提取物的LC-HRMS分析显示,选择了最有效的化合物(30)来获得所有靶蛋白的命中化合物,即脂氧合酶-3,细胞色素P450, DNA旋切酶拓扑异构酶II和组蛋白乙酰转移酶。计算方法显示(+)-没食子儿茶素在30种已鉴定化合物中对所有靶蛋白的结合亲和力较低。所有化合物在ADMET参数上均具有良好的药动学特征。本研究表明,马齿苋提取物具有良好的生物活性,具有抗菌和抗氧化的潜在治疗价值。
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引用次数: 0
Sequence-based Mechanistic Resolution of Amino Acid Replacement and Impact on the Activities of Peptide-Based Derivatives Targeting CXCR4 for the Treatment of Waldenstrom's Macroglobulinemia 基于序列的氨基酸替代机制解析及其对CXCR4肽基衍生物治疗华氏大球蛋白血症活性的影响
4区 化学 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2023-10-20 DOI: 10.1142/s273741652350059x
Ghazi Elamin, Opeyemi S. Soremekun, Shaban R. M. Sayed, Peter A. Sidhom, Mahmoud A. A. Ibrahim, Muhammad Naeem Ahmed, Mahmoud E.S. Soliman
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引用次数: 0
Computational Design, Combinatorial Screening and Experimental Analysis of Lung Cancer EGFRVIII-binding Peptides 肺癌egfrviii结合肽的计算设计、组合筛选和实验分析
4区 化学 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2023-10-19 DOI: 10.1142/s2737416523500576
Dongyun Gao, Jun Yao, Xuefeng Zhou, Xia Zhang, Linlin Zhou, Qiangrong Wang, Shan Li, Xi Ding
Human epidermal growth factor receptor mutation variant III (EGFR[Formula: see text] is a cancer-specific cell surface oncogenic marker and has been observed to be widely involved in the formation, progression and metastasis of lung cancer and some other tumors. Previously, a massive quantity of EGFR[Formula: see text]-binding peptides were enriched via random phage display (RPD) targeted against the protein. In this study, we reported rational discovery of 12-mer peptides with high affinity to EGFR[Formula: see text] and strong selectivity for EGFR[Formula: see text] over wild-type EGFR (EGFR[Formula: see text]. A combinatorial peptide library was designed to target EGFR[Formula: see text] based on over ten thousands of known EGFR[Formula: see text] binders enriched from RPD analysis, and a virtual high-throughput screening protocol was then systematically performed against the library to derive those potential candidates, which were further examined rigorously at structural and energetic levels to identify few promising hits. Anisotropy binding assays were carried out to substantiate the computational findings. Consequently, eight 12-mer peptides were designed as effective binders that can target the EGFR[Formula: see text] extracellular subdomain 3 (SD3). In particular, two potent peptides (T1: FLHRYEIVTSYF and T3: FLQKYEWNTSYW) were found to have a high affinity to EGFR[Formula: see text] and a good selectivity for EGFR[Formula: see text] over EGFR WT . Structural analysis revealed that the peptide-binding site can be divided into hydrophobic, polar and mixed regions, which correspond to the nonpolar [Formula: see text]-terminal section, polar/charged middle section and hybrid C-terminal section of the peptide. The peptide selectivity originated from the middle section, which can form a different hydrogen bond network between the two proteins upon the mutating perturbation, whereas the N- and C-terminal sections are primarily responsible for the peptide stability but not specificity.
人表皮生长因子受体突变型III (epidermal growth factor receptor mutation variant III, EGFR)是一种癌症特异性的细胞表面致癌标志物,已被观察到广泛参与肺癌和其他一些肿瘤的形成、进展和转移。以前,通过针对蛋白质的随机噬菌体展示(RPD)富集大量的EGFR结合肽。在这项研究中,我们报告了对EGFR高亲和力的12聚肽的合理发现[公式:见文本],以及对EGFR的强选择性[公式:见文本]优于野生型EGFR(公式:见文本)。基于从RPD分析中富集的超过一万种已知EGFR结合物,设计了一个针对EGFR的组合肽文库[公式:见文本],然后系统地针对该文库执行虚拟高通量筛选协议,以获得这些潜在的候选物,并在结构和能量水平上进一步严格检查,以确定少数有希望的命中。进行了各向异性结合试验来证实计算结果。因此,八种12聚肽被设计为有效的结合物,可以靶向EGFR[公式:见文本]细胞外亚结构域3 (SD3)。特别是,两种有效的肽(T1: FLHRYEIVTSYF和T3: FLQKYEWNTSYW)被发现对EGFR具有高亲和力[公式:见文本],并且对EGFR具有良好的选择性[公式:见文本]。结构分析表明,肽结合位点可分为疏水区、极性区和混合区,分别对应于肽的非极性[公式:见文]-末端区、极性/带电中间区和杂化c末端区。肽的选择性源于中间部分,在突变扰动下,中间部分在两种蛋白质之间形成不同的氢键网络,而N端和c端部分主要负责肽的稳定性,而不是特异性。
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引用次数: 0
Computational Study on D-π-A-based Electron Donating and Withdrawing Effect of Metal-Free Organic Dye Sensitizers for Efficient Dye-Sensitized Solar Cells 高效染料敏化太阳能电池中无金属有机染料敏化剂D-π基给电子和吸电子效应的计算研究
4区 化学 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2023-10-19 DOI: 10.1142/s2737416523420139
A Arunkumar
A new generation of metal-free organic dyes with a range of donor (D1) and acceptors (A1-A3) were designed and examined for dye-sensitized solar cells (DSSCs) based on (3a) dye as a literature. Triphenylamine (TPA), thiophene ([Formula: see text] and 2-cyanoacrylic acid groups each perform the roles of an acceptor (A), donor (D) and spacer in order to produce a D-[Formula: see text]-A system. To investigate the intramolecular charge transfer (ICT), electronic distribution, ultra-violet visible (UV–Vis) absorption wavelengths, molecular electrostatic potential (MEP) and photovoltaic (PV) parameters of the D1 and A1–A3 molecules, density functional theory (DFT) and time-dependent DFT (TD-DFT) were used. The classification of the tunable donor D1 and A1–A3 determines the PV performance of the dye molecules. Results show that the A2 dye replacement group increases the performance of PV cells via red-shifting absorption spectra. Also, when compared to 3a, A2 dye have lower energy gap ([Formula: see text] and superior UV–Vis spectra that cover the full visible range. These results demonstrate the viability of molecular tailoring as an approach to improve D-[Formula: see text]-A sensitizer proposal for efficient DSSCs fabrication.
以染料敏化太阳能电池(DSSCs)为材料,设计了新一代的无金属有机染料,并对其供体(D1)和受体(A1-A3)进行了研究。三苯胺(TPA)、噻吩([分子式:见文])和2-氰丙烯酸基团各自扮演受体(A)、给体(D)和间隔基团的角色,从而生成D-[分子式:见文]-A体系。为了研究D1和A1-A3分子的分子内电荷转移(ICT)、电子分布、紫外可见(UV-Vis)吸收波长、分子静电势(MEP)和光伏(PV)参数,采用密度泛函理论(DFT)和时变DFT (TD-DFT)。可调谐供体D1和A1-A3的分类决定了染料分子的PV性能。结果表明,A2染料替代基团通过红移吸收光谱提高了光伏电池的性能。此外,与3a相比,A2染料具有更低的能隙([公式:见文])和优越的紫外可见光谱,覆盖了整个可见范围。这些结果表明,分子裁剪作为一种改善D-[公式:见文本]- a增敏剂方案的可行性,可以有效地制造DSSCs。
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引用次数: 0
An ensemble approach for prioritizing antivirals against COVID-19 via heterogeneous network inference-based inductive matrix completion 基于异构网络推理的归纳矩阵补全的COVID-19抗病毒药物优先排序集成方法
4区 化学 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2023-10-19 DOI: 10.1142/s2737416523410041
A S Aruna, K R Remesh Babu, K Deepthi
The global spread of COVID-19 caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originated in Wuhan in December 2019, created a massive health crisis, and disrupted the world economy. Much research has been conducted to discover drugs, develop vaccines, and find repurposable drugs against the disease. Computational drug repurposing, the process of determining new uses for approved drugs through computational techniques, becomes an effective solution to fight the COVID-19 pandemic. This study aims to investigate and prioritize potential drugs against SARS-CoV-2 through an integrated network-based approach. We propose an ensemble approach based on network inference and inductive matrix completion (NIMCVDA) for virus–drug association prediction to identify antivirals against COVID-19. We constructed a heterogeneous drug–virus network using intra-similarities of virus genomic sequences and drug chemical structures and existing associations between viruses and drugs. A network inference method is used to infer missing drug–virus edges. Based on this, existing drug–virus association matrix is reconstructed. Finally, more accurate association scores between drugs and viruses are computed using the inductive matrix completion algorithm. The proposed method achieved an AUC of 0.9020 on five-fold cross-validation and 0.8786 on leave-one-out cross-validation. We compared the performance of the model with related approaches. In addition, we carried out case studies on the top-predicted drugs and implemented our model with other datasets to verify prediction performance. Our work prioritized repurposable drugs to battle with COVID-19 epidemic. The cross-validation results and case studies illustrate that the top-predicted drugs are strong candidates for further biological tests.
2019年12月,由严重急性呼吸综合征冠状病毒2型(SARS-CoV-2)引起的新型冠状病毒肺炎(COVID-19)在全球传播,起源于武汉,造成了大规模的健康危机,扰乱了世界经济。已经进行了大量研究,以发现药物,开发疫苗,并找到可重复使用的药物来对抗这种疾病。计算药物再利用,即通过计算技术确定已批准药物的新用途的过程,成为抗击COVID-19大流行的有效解决方案。本研究旨在通过基于综合网络的方法研究和优先考虑潜在的抗SARS-CoV-2药物。我们提出了一种基于网络推理和归纳矩阵补全(NIMCVDA)的病毒-药物关联预测集成方法,以识别针对COVID-19的抗病毒药物。我们利用病毒基因组序列和药物化学结构的相似性以及病毒和药物之间存在的关联,构建了一个异质药物-病毒网络。采用网络推理方法对缺失的药物病毒边缘进行推断。在此基础上,重构现有药物-病毒关联矩阵。最后,利用感应矩阵补全算法计算出更准确的药物与病毒之间的关联分数。五重交叉验证的AUC为0.9020,留一交叉验证的AUC为0.8786。我们将该模型的性能与相关方法进行了比较。此外,我们对预测最高的药物进行了案例研究,并在其他数据集上实现了我们的模型,以验证预测性能。我们的工作重点是使用可重复使用的药物来抗击COVID-19流行病。交叉验证结果和案例研究表明,预测最高的药物是进一步生物学试验的有力候选者。
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引用次数: 0
Discovery of Potential Natural STAT3 Inhibitors: An in silico Molecular Docking and Molecular Dynamics Study 发现潜在的天然 STAT3 抑制剂:硅学分子对接和分子动力学研究
IF 2.2 4区 化学 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2023-10-06 DOI: 10.1142/s2737416523500588
Sameena Gul, Shabbir Muhammad, Muhammad Irfan, Tareg M Belali, A. R. Chaudhry, Muhammad Khan
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引用次数: 0
In silico studies of (Z)-3-(2-chloro-4-nitrophenyl)-5-(4-nitrobenzylidene)-2-thioxothiazolidin-4-one derivatives as PPAR-α agonist: Design, Molecular Docking, MM-GBSA Assay, Toxicity Predictions, DFT Calculations and MD Simulation Studies PPAR-α激动剂(Z)-3-(2-氯-4-硝基苯基)-5-(4-硝基亚苄基)-2-硫杂噻唑啉-4-酮衍生物的计算机研究:设计、分子对接、MM-GBSA测定、毒性预测、DFT计算和MD模拟研究
IF 2.2 4区 化学 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2023-09-04 DOI: 10.1142/s2737416523500540
Mahendra Gowdru Srinivasa, Shivakumar, Udaya Kumar, C. Mehta, U. Nayak, B. C. Revanasiddappa
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引用次数: 0
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Journal of Computational Biophysics and Chemistry
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