Comprehensive Assessment of Biomolecular Interactions of Morpholine-Based Mixed Ligand Cu(II) and Zn(II) Complexes of 2,2′-Bipyridine as Potential Anticancer and SARS-CoV-2 Agents:... by Karunganathan Sakthikumar, Rui Werner Maçedo Krause, Bienfait Kabuyaya Isamura

“…Density FunctionalTheory (DFT) and molecular docking calculations were relied on to unveil the electronic structure, reactivity, and interacting capability of all substances with DNA, BSA, and SARS-CoV-2 main protease (Mpro). …”
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Synthesis, In Silico, and Biological Applications of Novel Heteroleptic Copper (II) Complex of Natural Product-Based Semicarbazone Ligands by Fekadu Muleta, Tegene Desalegn

“…The [Cu(L1) (L2)] complex also shows better antiradical potential (63.7%). Furthermore, the docking result of prepared compounds on S. aureus gyrase confirms the ligands (L1 and L2) and the complex potential molecules possess the smallest binding potential of −8.0 to −8.4 kcal/mol. …”
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Anti-proliferative and photodynamic activities of Senna didymobotrya (Fresen.) leaf alkaloid-rich extracts against breast cancer cells by Kolawole A. Olofinsan, Heidi Abrahamse, Blassan P. George

“…Moreover, the molecular docking analysis revealed the involvement of only hydrophobic bonds in the interactions of the plant’s alkaloid-derived phytoconstituents’ with selected cancer protein biomarkers. …”
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Wedelolactone Mitigates Alcoholic Steatohepatitis via Modulating the TLR4/MyD88/NF-κB Pathway by Tao Jiang, Bingde Hu, Yongxia Li, Shuihong Yu

“…Network pharmacology analysis identified the toll-like receptor 4 (TLR4) pathway as the primary target of WEL in treating ASH. Molecular docking simulations demonstrated WEL’s strong binding affinity with TLR4. …”
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Identification of Flavonoid C-Glycosides as Promising Antidiabetics Targeting Protein Tyrosine Phosphatase 1B by Athika Rampadarath, Fatai Oladunni Balogun, Charlene Pillay, Saheed Sabiu

“…Of the seven flavonoid C-glycosides docked against the enzyme, three compounds (apigenin, vitexin, and orientin) had the best affinity for the enzyme with a binding score of –7.3 kcal/mol each, relative to –7.4 kcal/mol for the reference standard, ursolic acid. …”
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Evaluation of Anti-HIV-1 Integrase and Anti-Inflammatory Activities of Compounds from Betula alnoides Buch-Ham by Prapaporn Chaniad, Teeratad Sudsai, Abdi Wira Septama, Arnon Chukaew, Supinya Tewtrakul

“…Potential interactions of compounds with IN active sites were investigated using computational docking. The results indicated that active compounds interacted with Asp64, a residue participating in 3′-processing, and Thr66, His67, and Lys159, residues participating in strand-transfer reactions of the integration process. …”
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Hyperinsulinemia Induced Altered Insulin Signaling Pathway in Muscle of High Fat- and Carbohydrate-Fed Rats: Effect of Exercise by Anu Joseph, S. Parvathy, Koyikkal Karthikeya Varma

“…Exercise significantly upregulated phosphoinositide 3 kinase (PI3K) docking site phosphorylation and downregulated the negative IRS1 phosphorylations thereby increasing the glucose transporter (GLUT) expressions and reducing the lactate accumulation. …”
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Investigating the mechanisms of resveratrol in the treatment of gouty arthritis through the integration of network pharmacology and metabolics by Xiaomin Xu, Donghua Yu, Yu Wang, Xin Jiang, Fang Lu, Shumin Liu

“…ObjectiveThis study integrates network pharmacology and metabolomics techniques to explore the potential regulatory mechanisms of Res on gouty arthritis (GA).MethodsNetwork pharmacology was used to predict the mechanism of Res in regulating GA, and methods such as HE staining, ELISA, immunohistochemistry, Real-time PCR, Western blot, and molecular docking were used to verify the role of NF-κB, MAPK, and JAK/STAT inflammatory signaling pathways in the MSU-induced GA rat model. …”
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Design, synthesis, and in vitro, in vivo, and in silico evaluation of novel substituted 1,3,4-thiadiazole derivatives as anticonvulsant agents by Tulika Anthwal, Swati Pant, Preeti Rana, Sumitra Nain

“…Finally, compound 6d was docked against CA-II and CA-IX (PDB-ID-5SZ5 and 5AML) receptors. …”
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In Silico Design of a Trans-Amplifying RNA-Based Vaccine against SARS-CoV-2 Structural Proteins by Fatemeh Nafian, Ghazal Soleymani, Zahra Pourmanouchehri, Mahnaz Kiyanjam, Simin Nafian, Sayed Mohammad Mohammadi, Hanie Jeyroudi, Sharareh Berenji Jalaei, Fatemeh Sabzpoushan

“…Construct 1 showed better structural properties and interactions with toll-like receptor 2 (TLR-2), TLR-3, and TLR-4 during molecular docking and dynamic simulation. A 50S ribosomal L7/L12 adjuvant was added to its N-terminus to improve stability and immunogenicity. …”
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Neuropharmacological profile of new thiazepinone and thiazolidinone compounds designed by virtual screening by Juan Sebastian Carrero-Sandoval, Paola Andrea Cuervo-Prado, Fabian Orozco-Lopez, Christian Alonso Becerra-Rivas, Estefany Arias-Quiroz, Mario Francisco Guerrero-Pabón

“…From a library of 240 pyrazolo[1,4]thiazepin-3-ones and 39 pyrimidinyl thiazolidin-4-ones, two molecular prototypes of each series were selected by virtual screening using the rank consensus molecular docking approach, based on the GABA-A/BZD site. These compounds, coded as cpTP-0, cpTP-1, TAP-2 and cpTAP-2, were synthesised by multicomponent reactions and evaluated by neuropharmacological screening in CD1 mice (100 mg/kg, p.o.). …”
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A Novel Nitrite Reductase from <i>Acinetobacter haemolyticus</i> for Efficient Degradation of Nitrite by Xiao-Yan Yin, Emmanuel Mintah Bonku, Jian-Feng Yuan, Zhong-Hua Yang

“…Structural analysis of <i>Ah</i>NiR revealed the presence of [Fe-S] clusters, with molecular docking studies identifying Tyr-282 and Ala-289 as key catalytic sites. …”
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Genetic Variant of C-5434T REN Enhancer on Serum Renin Levels and Binding Pattern of Signal Transducers and Activators Transcription 3 by Imama Maslahah, Mohammad Saifur Rohman, Nashi Widodo, Agustina Tri Endharti, Didik Utomo

“…Here, we also present a docking approach for predicting interaction between genetic variant -5434C/T and STAT3 (Signal Transducers and Activators Transcription 3), the predicted transcription factor that regulates renin gene enhancer. …”
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Ginsenoside Rk2 alleviates hepatic ischemia/reperfusion injury by enhancing AKT membrane translocation and activation by Hong Shen, Jiajun Fu, Jiayue Liu, Toujun Zou, Kun Wang, Xiao‐Jing Zhang, Jian‐Bo Wan

“…Integrated approaches, including network pharmacology, molecular docking, transcriptome analysis, and isothermal titration calorimetry, along with experimental validation, indicated that Rk2 protects against hepatic IRI by targeting and activating the AKT (RAC serine/threonine protein kinase) signaling pathway. …”
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Isovitexin targets SIRT3 to prevent steroid-induced osteonecrosis of the femoral head by modulating mitophagy-mediated ferroptosis by Yinuo Fan, Zhiwen Chen, Haixing Wang, Mengyu Jiang, Hongduo Lu, Yangwenxiang Wei, Yunhao Hu, Liang Mo, Yuhao Liu, Chi Zhou, Wei He, Zhenqiu Chen

“…Furthermore, molecular docking and co-immunoprecipitation confirmed the strong interaction between SIRT3 and BNIP3. …”
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Pharmacophore-based approach for the identification of prospective UDP-2,3-diacylglucosamine hydrolase (LpxH) inhibitor from natural product database against Salmonella Typhi by Divyapriya Karthikeyan, Sanjit Kumar, NS Jayaprakash

“…Further, virtual screening, molecular docking, and MD simulation (100 ns) studies identified two lead compounds, 1615 and 1553. …”
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Fragmenstein: predicting protein–ligand structures of compounds derived from known crystallographic fragment hits using a strict conserved-binding–based methodology by Matteo P. Ferla, Rubén Sánchez-García, Rachael E. Skyner, Stefan Gahbauer, Jenny C. Taylor, Frank von Delft, Brian D. Marsden, Charlotte M. Deane

“…We show that an algorithmic approach (Fragmenstein) that ‘stitches’ the ligand atoms from this structural information together can provide more accurate and reliable predictions for protein–ligand complex conformation than general methods such as pharmacophore-constrained docking. This approach works under the assumption of conserved binding: when a larger molecule is designed containing the initial fragment hit, the common substructure between the two will adopt the same binding mode. …”
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Gallic acid protects intervertebral disc cells from ferroptosis and alleviates intervertebral disc degeneration by regulating key factors of oxidative stress by Zaishi Zhu, Zeling Huang, Chaofeng Zhang, Bo Xu, Hua Chen, Shuai Pei, Baofei Zhang, Lishi Jie, Xiaoqing Shi, Yujiang Liu, Yuwei Li, Yuwei Li, Xiaofeng Shen, Xiaofeng Shen

“…However, the role of GA in IDD ferroptosis remains unclear.MethodsThis study explored the pathological mechanism of GA in IDD in relation to ferroptosis: (1) to identify ferroptosis-related targets for GA treatment of IDD using network pharmacology and molecular docking technology, (2) to evaluate the therapeutic effect of GA in an IDD rat model and changes in ferroptosis-related targets, (3) to investigate the changes of oxidative stress and lipid peroxidation products in NP cells after GA intervention, and (4) to study the changes of ferroptosis-related proteins and iron ions in cells and mitochondria after GA intervention.ResultsExperimental results confirmed that GA can treat IDD by reducing the degradation of extracellular matrix (ECM) and pathological changes in IDD. …”
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Co-Localized in Amyloid Plaques Cathepsin B as a Source of Peptide Analogs Potential Drug Candidates for Alzheimer’s Disease by Marilena K. Theodoropoulou, Konstantina D. Vraila, Nikos C. Papandreou, Georgia I. Nasi, Vassiliki A. Iconomidou

“…In silico studies on the complexes of the oligomeric state of A<i>β</i> and Cathepsin B peptide analogs were performed utilizing molecular docking and molecular dynamics simulations, revealing that these analogs disrupt the <i>β</i>-sheet-rich core of A<i>β</i> oligomers, a critical structural feature of their stability. …”
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Ultrasonication-assisted lipase-catalyzed esterification of chlorogenic acid: A comparative study using fatty alcohol and acids in solvent and solvent-free conditions by Chia-Hung Kuo, Parushi Nargotra, Tsung-Han Lin, Chwen-Jen Shieh, Yung-Chuan Liu

“…Despite optimization of factors including molar ratio, enzyme dosage, and reaction time, the highest conversion rate achieved was of only 36.8 %. Moreover, molecular docking results revealed that the lowest binding energy was between lipase and octanol. …”
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