Examining Prenylated Xanthones as Potential Inhibitors Against Ketohexokinase C Isoform for the Treatment of Fructose-Driven Metabolic Disorders: An Integrated Computational Approa... by Tilal Elsaman, Magdi Awadalla Mohamed

“…<b>Methods:</b> A library of 1383 analogs was compiled from chemical databases and the literature. Molecular docking, binding free energy calculations, pharmacokinetic assessments, molecular dynamics simulations, and quantum mechani–cal analyses were used to screen and evaluate the compounds. α-Mangostin’s binding affinity (37.34 kcal/mol) served as the benchmark. …”
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Toll-like receptor 4 pathway evolutionary trajectory and functional emergence by Shailya Verma, Ramanathan Sowdhamini, Ramanathan Sowdhamini, Ramanathan Sowdhamini

“…Our previous work on pan-genome-wide survey, indicates Callorhincus milli to be the ancestral organism with both TRAM and TRIF proteins.MethodsTo gain a deeper insight into the protein function and to compare them with Homo sapiens adaptor proteins, we modeled the docking of the TRAM–TRIF complex of representative organisms across various taxa. …”
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Discovery of amino acid substitutions in penicillin-binding proteins associated with adaptation to D-Ala-D-Lac in vancomycin-resistant Enterococcus faecalis by Nese Caglayan, Banu Sancak, Zeynep Kanlidere, Tanil Kocagoz, Tanil Kocagoz

“…We then applied homology modeling to assess structural impacts of these changes on PBPs and conducted docking studies to investigate ligand-binding interactions. …”
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Deodorization of Egg White Powder by Ozone Treatment and Underlying Mechanism by XIN Xiaojuan, LIU Ying, MA Lulu, HUO Jiaying, GAO Ying, DONG Shijian, LIU Liya, WANG Fengzhong, LI Shugang

“…In addition, fluorescence quenching and molecular docking showed that the major binding force between egg white protein and off-flavor substances was hydrophobic interaction, and their main binding sites were in a hydrophobic cavity composed of amino acids such as Leu66, Lys69, Glu87E, Ala87F, Cys87H, Glu129, Tyr130, Cys133, and Gly320. …”
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To Probe Full and Partial Activation of Human Peroxisome Proliferator-Activated Receptors by Pan-Agonist Chiglitazar Using Molecular Dynamics Simulations by Holli-Joi Sullivan, Xiaoyan Wang, Shaina Nogle, Siyan Liao, Chun Wu

“…Yet, it has no high-resolution complex structure with PPARs and its detailed interactions and activation mechanism remain unclear. In this study, we docked chiglitazar into three experimentally resolved crystal structures of hPPAR subtypes, PPARα, PPARβ/δ, and PPARγ, followed by 3 μs molecular dynamics simulations for each system. …”
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Golgin Subfamily A Member 5 Is Essential for Production of Extracellular Matrix Proteins during TGF-β1-Induced Periodontal Ligament-Fibroblastic Differentiation by Hyun-Jin Kim, Seong-Min Kim, Min-Jeong Choi, Young-Joo Jang

“…GOLGA5 plays a role in vesicle tethering and docking between the endoplasmic reticulum and the Golgi apparatus. siRNA-mediated depletion of endogenous GOLGA5 upregulated in TGF-β1-induced PDL-fibroblastic progenitors resulted in downregulation of representative PDL-fibroblastic markers and upregulation of osteoblast markers. …”
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Management of intraocular pressure and inflammation using febuxostat film: in vitro - in vivo correlation by Mouli Das, Sk Habibullah, Tanisha Das, Rakesh Swain, Subrata Mallick

“…Disappearance of ocular inflammation was also observed in the test animals after 2.5 h of film application, whereas acute inflammation was continued in the group without treatment for more than 4 h. Docking study revealed good binding interaction of drug and NLRP3, A2A, and TLR4 receptor. …”
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Antibacterial and Antioxidant Activities of Triterpenoids and Cyclic 1,7-Diarylheptanoids from the Stem Bark of Myrica salicifolia: A Combined Experimental and Computational Study by Abraham Dilnesa Gashaw, Kibrom Gebreheiwot Bedane, Taye B. Demissie, Japheth O. Ombito, Estifanos Ele Yaya, Mekonnen Abebayehu Desta

“…Compounds 2, 3, and 7 were assessed for their in silico molecular docking analysis. The lowest binding affinity for compound 7 was found to be −7.26 to −10.35 kcal/mol against PqsA protein of P. aeruginosa, pyruvate kinase (PK) enzyme of S. aureus, LuxS protein of S. pyogenes, and DNA gyrase B of E. coli, which showed better binding affinity compared to the standard drug ampicillin (−7.36 to −8.03 kcal/mol) and ciprofloxacin (−6.19 to −6.83 kcal/mol). …”
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Terminalia catappa Extract Palliates Redox Imbalance and Inflammation in Diabetic Rats by Upregulating Nrf-2 Gene by Franklyn Nonso Iheagwam, Gaber El-Saber Batiha, Olubanke Olujoke Ogunlana, Shalom Nwodo Chinedu

“…Hepatic relative expressions of tumour necrosis factor-alpha (TNF-α), interleukin-six (IL-6), and nuclear factor-erythroid 2 related factor 2 (Nrf-2) were also assessed. Molecular docking and prediction of major TCA phytoconstituents’ biological activity related to T2DM-induced oxidative stress were evaluated in silico. …”
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Do antibody CDR loops change conformation upon binding? by Chu’nan Liu, Lilian M. Denzler, Oliver E.C. Hood, Andrew C.R. Martin

“…In future, our results will contribute to developing insights into antibodies and new methods for modeling and docking.…”
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Studying the impact of chitosan salicylaldehyde/schiff base/CuFe2O4 in PC3 cells via theoretical studies and inhibition of PI3K/AKT/mTOR signalling by Ghada H. Elsayed, Asmaa M. Fahim

“…The mRNA expression levels of PI3K, AKT, mTOR, and CCND1 were examined in PC3-treated cells by using QRT-PCR, and the results demonstrated that, by down-regulating the expression levels of these genes, chitosan salicylaldehyde/CuFe2O4 significantly affected prostate cancer cell proliferation, progression, and autophagy more than chitosan salicylaldehyde. Furthermore, the docking stimulation of the chitosan derivatives with different proteins showed the presence of CuFe2O4 particles effect on the interaction inside their pockets and increased the activities, and it’s related to biological evaluation. …”
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NIPAL1 as a prognostic biomarker associated with pancreatic adenocarcinoma progression and immune infiltration by Youlong Zhu, Zongze Qi, Shaoqi Zu, Fangchao Yang, Yanming Wang, Lei Zhu, Xintong Li, Ruixue Li, Hong Zhu

“…Subsequently, we predicted five small-molecule drugs targeted at NIPAL1 using molecular docking. Finally, high expression of NIPAL1 in tumor tissues was validated through immunohistochemistry. …”
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Lyophilized and Oven-Dried <i>Manilkara zapota</i> Extracts: Characterization and <i>In Vitro</i>, <i>In Vivo</i>, and <i>In Silico</i> Analyses by María Fernanda Rivas-Gastélum, Patricia Ariadna Galindo-Castillo, Juan Esparza-Sánchez, Miriam Irene Jiménez-Pérez, Yocanxóchitl Perfecto-Avalos, Luis Eduardo Garcia-Amezquita, Diego E. Navarro-López, Edgar R. López-Mena, Eugenio Sánchez-Arreola, Juan Pablo Tamayo-Martínez, Humberto L. Mendoza-Figueroa, María Magdalena Crosby-Galván, Elsa Margarita Crosby-Galván, Jorge L. Mejía-Méndez, Angélica Lizeth Sánchez-López

“…The phytochemical content of fruits was assessed by gas chromatography flame ionization detector (GC-FID), and their biological performance was studied using <i>in vitro</i> antibacterial and antioxidant assays (DPPH and ABTS) and <i>in vivo</i> toxicity models. Molecular docking was implemented to evaluate the interaction between polar compounds from chicozapote fruits with receptors involved in the pathogenesis of bacterial strains. …”
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Glutathione reductase plays a role in the metabolism of methylmercury degradation in Rhodotorula mucilaginosa by Yi Guo, Wenlong Deng, Qigui Mo, You Yu, Zhenwang Zhang, Mingjie Wei, Ruiling Tang, Surui Lu, Yanting Su

“…Structural domain analysis and molecular docking experiments suggest that the glutathione reductase of R. mucilaginosa has the potential to directly or indirectly participate in methylmercury degradation metabolism. …”
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Cooperative mechanisms of LexA and HtpG in the regulation of virulence gene expression in Pseudomonas plecoglossicida by Rongchao He, Yanfei Zuo, Qiu Li, Qingpi Yan, Lixing Huang

“…We employed an array of methods including molecular dynamics simulations, molecular docking, ChIP-seq, RNA-seq, mass spectrometry, gene mutagenesis, LacZ reporter assays, electrophoretic mobility shift assays, co-immunoprecipitation, and in vitro LexA degradation experiments. …”
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Impact of sodium alginate hydrogel containing bacteriophage peptides that specifically bind to the EtCab protein on the inhibition of Eimeria tenella infection by Hang Chen, Wenjing Zhi, Bingrong Bai, Faisal R. Anjum, Zhipeng Jia, Rui Kong, Qiuju Liu, Biao Wang, Chunli Ma, Dexing Ma

“…Additionally, oral administration of the encapsulated phages Y and G provided a higher level of protection against Eimeria infection compared to encapsulated phage V and the unencapsulated phages. Molecular docking studies revealed that three peptides, particularly Y and G, efficiently bind to the EtCab protein through hydrogen bonds. …”
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Multiscale Adaptively Spatial Feature Fusion Network for Spacecraft Component Recognition by Wuxia Zhang, Xiaoxiao Shao, Chao Mei, Xiaoying Pan, Xiaoqiang Lu

“…Spacecraft component recognition is crucial for tasks such as on-orbit maintenance and space docking, aiming to identify and categorize different parts of a spacecraft. …”
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Molecular mechanisms of cis-oxygen bridge neonicotinoids to Apis mellifera Linnaeus chemosensory protein: Surface plasmon resonance, multiple spectroscopy techniques, and molecular... by Xiangshuai Li, Shiyu Li, Yang Liu, Li Cui, Daibin Yang, Shuning Chen, Xusheng Shao, Huizhu Yuan, Xiaojing Yan

“…The findings revealed that hydrogen bonding and hydrophobic interactions serve as the primary forces driving the binding process, with fluorescence quenching mechanisms involving both dynamic and static interactions. Molecular docking and dynamics simulations further illustrated the stability of these interactions within the active site of the protein. …”
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Exploring precision therapeutics: computational design of antisense oligonucleotides targeting AXL gene transcripts in multiple sclerosis treatment management by Bhargav Shreevatsa, Bhargav Shreevatsa, Abhigna Nagaraj, Chandan Dharmashekar, Anisha Jain, Bhavana Harendra, Siddesh V. Siddalingegowda, Haneen A. Al-Mazroua, Sheikh F. Ahmad, Shashanka K. Prasad, Chandrashekar Srinivasa, Chandan Shivamallu, Shiva Prasad Kollur

“…To investigate ASO-mRNA interactions and gauge their ability to alter AXL expression, Molecular Docking was performed. Our analyses showed that A1, A2, and A3 had substantial interactions with AXL mRNA, with binding affinities of −9.5 kcal/mol, −10.8 kcal/mol, and −10.6 kcal/mol, respectively. …”
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Lucidin from <i>Rubia cordifolia</i> Outperforms FDA-Approved Lapatinib as a Potential Multitargeted Candidate for Breast Cancer Signalling Proteins by Akram Ahmed Aloqbi, Hadil Alahdal, Amany I. Alqosaibi, Mashael M. Alnamshan, Ibtesam S. Al-Dhuayan, Ahood A. Al-Eidan, Hind A. S. Alzahrani, Nouf K. ALaqeel, Fatmah Hazza Alsharif, Abeer Al Tuwaijri

“…<b>Methods:</b> We performed multitargeted molecular docking studies on key breast cancer proteins using a natural compound library from ZINC. …”
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