Targeted inhibition of the PTEN/PI3K/AKT pathway by YSV induces cell cycle arrest and apoptosis in oral squamous cell carcinoma by Lin Qiu, Qian Gao, Yiheng Liao, Xinxin Li, Cuiying Li

“…RNA sequencing (RNA-seq), molecular docking, and western blotting were employed to investigate the molecular mechanisms. …”
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Unveiling the prognostic value of ARID3A in breast cancer through bioinformatic analysis by Wen-Run Cai, Xu-Gang Sun, Yue Yu, Xin Wang, Xu-Chen Cao, Xiao-Feng Liu

“…Protein-protein interactions (PPI) were established using GeneMANIA and STRING, with validation through molecular docking using Cluspro. Results: Elevated ARID3A expression was associated with poor prognosis in breast cancer, particularly in Luminal and HER2-positive subtypes. …”
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Identification of therapeutic target genes for age-related hearing loss through systematic genome-wide mendelian randomization of druggable genes by Kun Zhang, Bo Hou, Tao Yan, Ruru Qiao, Peng Qu, Xinbo Xu, Hanbing Zhang

“…Additionally, we conducted phenome-wide research, enrichment analysis, protein network construction, drug prediction, and molecular docking to help develop more effective and targeted therapeutic treatments. …”
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Identification and validation of diagnostic genes IFI44 and IRF9 in insomnia-associated autoimmune uveitis by Chao Wu, Hui Feng, Meng Tian, Baorui Chu, Xianyang Liu, Shuhao Zeng, Yakun Wang, Hong Wang, Shengping Hou, Qingfeng Liang

“…Finally, two compounds were selected based on docking scores of less than −7 kcal/mol.ConclusionOur study demonstrated involvement of the viral response in both insomnia and AU and identified the diagnostic significance of IFI44 and IRF9 in these conditions. …”
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The Development Trend of China’s Agricultural Product Cold Chain Logistics from the Perspective of Big Data by Shenxiang Wang

“…Using big data technology can improve the efficiency of information docking, improve the stickiness of enterprise customers, and speed up the value-added of cold chain logistics data. …”
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Rational Design, Synthesis, In Vitro, and In Silico Studies of Dihydropyrimidinone Derivatives as β-Glucuronidase Inhibitors by Somaye Karimian, Yasaman Moghdani, Mahsima Khoshneviszadeh, Somayeh Pirhadi, Aida Iraji, Mehdi Khoshneviszadeh

“…In vitro biological evaluations revealed that 4i as the most potent compound in this series has an IC50 value of 31.52 ± 2.54 μM compared to the standard D-saccharic acid 1,4-lactone (IC50 = 41.32 ± 1.82 µM). Also, molecular docking and dynamics studies of the most potent compound are performed to evaluate interactions between the active compound and binding site.…”
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Design and synthesis of phenylthiophosphoryl dichloride derivatives and evaluation of their antitumour and anti-inflammatory activities by Chunyun Xu, Na Yang, Haichun Yu, Xiaojing Wang

“…We predicted its potential anticancer targets based on network pharmacology and then verified the inhibitory effect of the active compound S11 on the pathway PI3K/AKT by enzyme inhibition and molecular docking assay. In addition, compound S11 exhibited a potent anti-inflammatory effect on macrophages, effectively reducing the levels of inflammatory mediators TNF-α, IL-10 and HO-1. …”
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Identification of Novel LCN2 Inhibitors Based on Construction of Pharmacophore Models and Screening of Marine Compound Libraries by Fragment Design by Ningying Zheng, Xuan Li, Nan Zhou, Lianxiang Luo

“…Six compounds were optimized for protein binding after being docked against the positive control Compound A. Two compounds showed promising results in ADMET screening. …”
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Salicylanilide Diethyl Phosphates as Potential Inhibitors of Some Mycobacterial Enzymes by Martin Krátký, Eva Novotná, Shalini Saxena, Perumal Yogeeswari, Dharmarajan Sriram, Markéta Švarcová, Jarmila Vinšová

“…The most active MtAlaDH inhibitor, 5-chloro-2-[(3-chlorophenyl)carbamoyl]phenyl diethyl phosphate, has an IC50 of 4.96 µM and the best docking results. Other mycobacterial enzymes were mostly inhibited by some derivatives but at higher concentrations; isocitrate lyase showed the highest resistance to salicylanilide diethyl phosphates.…”
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Network pharmacology and experimental verification to investigate the mechanism of isoliquiritigenin for the treatment of Alzheimer’s disease by Waimao Gao, Guang Yang, Xinjuan Liu, Kaifan Hu, Jie Pan, Xingyu Wang, Yan Zhao, Ying Xu

“…The protein-protein interaction (PPI) network was constructed and clusters were obtained using the Molecular Complex Detection (MCODE) and the Cytohubba plugins. Further, molecular docking study was performed for these core targets. …”
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In Silico Identification of New Anti-SARS-CoV-2 Main Protease (Mpro) Molecules with Pharmacokinetic Properties from Natural Sources Using Molecular Dynamics (MD) Simulations and Hi... by Harrison Onyango, Patrick Odhiambo, David Angwenyi, Patrick Okoth

“…The root means square deviation (RMSD) values of the potential drug candidates informed the selection of some of them, which were docked with SARS-CoV-2 Mpro to comprehend their interactions. …”
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Puerarin Ameliorates the Ferroptosis in Diabetic Liver Injure Through the JAK2/STAT3 Pathway Inhibition Based on Network Pharmacology and Experimental Validation by Fan X, Liu S, Yu J, Hua J, Feng Y, Wang Z, Shen Y, Lan W, Wang J

“…Protein-protein interaction (PPI) network and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were used to predict key targets and pathways. Molecular docking was used to predict the interactions between Puerarin and core targets. …”
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Computational insights into Sitahe (Leuconotis eugenifolia) bioactive compounds: A promising approach for radioprotection through p53 inhibition by Dian Pribadi Perkasa, Iin Kurnia, Taufik Muhammad Fakih, Teja Kisnanto, Dwi Ramadhani, Harry Nugroho Eko Surniyantoro, Boky Jeanne Tuasikal, Alfian Mahardika Forentin, Mukh Syaifudin

“…In this study, in silico docking simulations were conducted to systematically assess the ability of key phytochemicals from Sitahe to modulate p53 activity, a critical gene in DNA repair and cancer therapy. …”
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Understanding the Molecular Mechanisms of Incomptine A in Treating Non-Hodgkin Lymphoma Associated with U-937 Cells: Bioinformatics Approaches, Part I by Fernando Calzada, Normand García-Hernández, Elihú Bautista, José Manuel Sánchez-López, Miguel Valdes, Claudia Velázquez, Elizabeth Barbosa

“…<b>Methods</b>: Five approaches, including Tandem Mass Tag (TMT), Gene ontology (GO), Reactome, KEGG pathway analysis, and molecular docking, were used. <b>Results</b>: TMT showed that 74 proteins were differentially expressed, out of which 12 presented overexpression (FC ≥ 1.5) and 62 were under expressed (FC ≤ 0.67). …”
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Adaptive Finite-Time Control on SE(3) for Spacecraft Final Proximity Maneuvers with Input Quantization by Sai Zhang, Zhen Yang

“…In this paper, a bounded finite-time control strategy is developed for the final proximity maneuver of spacecraft rendezvous and docking exposed to external disturbance and input quantization. …”
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Molecular Basis of Inhibitory Activities of Berberine against Pathogenic Enzymes in Alzheimer's Disease by Hong-Fang Ji, Liang Shen

“…In the present study, docking simulations were performed to gain deeper insights into the molecular basis of berberine's inhibitory effects against the important pathogenic enzymes of AD, that is, acetylcholinesterase, butyrylcholinesterase, and two isoforms of monoamine oxidase. …”
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Characterization of phenolic compounds and evaluation of anti-diabetic potential in Cannabis sativa L. seeds: In vivo, in vitro, and in silico studies by El-Mernissi Rafik, El Menyiy Naoual, Metouekel Amira, Zouhri Aziz, El-Mernissi Yahya, Siddique Farhan, Nadeem Sumaira, Amhamdi Hassan, Abboussi Oualid, Alsahli Abdulaziz Abdullah, Bourhia Mohammed, Dauelbait Musaab, Shazly Gamal A., Hajji Lhoussain

“…In vivo studies in diabetic rats demonstrated significant hypoglycemic, hypolipidemic, hepatoprotective, and nephroprotective effects. Molecular docking studies further supported these findings, revealing strong interactions between identified phenolic and the α-amylase enzyme. …”
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An insight into the therapeutic impact of quinoxaline derivatives: Recent advances in biological activities (2020–2024) by Aly M. Waseem, Ranya Mohammed Elmagzoub, Mervat Mohammed Mazhar Abdelgadir, Areej Al Bahir, N.S. Abd EL-Gawaad, Ahmed S. Abdel-Samea, Devendra Pratap Rao, Konstantinos Kossenas, Stefan Bräse, Hamada Hashem

“…Advanced studies, including molecular docking and ADMET analyses, have further clarified their pharmacological profiles, optimizing their drug-like properties and bioavailability. …”
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Response Suppression of Multiple Hinged Floating Structures by Using Rubber Cushion by Ye Lu, Qijia Shi, Yuchao Chen, Wenhui Zheng, Ye Zhou

“…A brand-new rubber cushion is proposed in this paper, which is installed between hinged floating modules in order to reduce the relative motion of the pitch; meanwhile, the cushion can be used as a fender for anti-impact in the docking process. Using the linear wave potential method, the structural dynamic model is formulated where the equivalent stiffness matrix for the rubber cushion is obtained by an integrating method employing linear assumption in addition to considering the heterogeneity of rubber. …”
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Assessing the efficacy of iso-mukaadial acetate and betulinic acid against selected Plasmodium falciparum glycolytic pathway proteins: in silico and in vitro studies by Lindiwe Khumbuzile Zuma, Ofentse Jacob Pooe, Nonduduzo Hlengiwe Mabaso, John Alake, Vincent A. Obakachi, Sinethemba Yakobi, Nothando Gasa, Rajshekhar Karpoormath, Mthokozisi Simelane

“…Molecular docking reported a binding score of − 1.155 kcal/mol for the PfLDH-BA complex and a binding score of − 3.200 kcal/mol for PfLDH-IMA. …”
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