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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Core-genome guided novel therapeutic targets identification and chimeric vaccine designing against Rickettsia rickettsii by Fizza Arshad, Asifa Sarfraz, Muhammad Shehroz, Umar Nishan, Asia Perveen, Riaz Ullah, Mohamed A. Ibrahim, Mohibullah Shah

“…Using conserved antigenic peptides, two chimeric vaccine constructs were developed and assessed using molecular docking, molecular dynamics simulations, principal component analysis, MM-GBSA binding free energy, and dynamic cross-correlation matrix studies. …”
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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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Characterization and enhanced antibiofilm activity of Annona muricata extract in combination with fluconazole against Candida albicans by Abhay Mishra, Masande Yalo, Jennifer Nambooze, Carolina H. Pohl, Gabré Kemp, Lekgoana K. Setsiba, Motlalepula G. Matsabisa

“…Methods: Phytochemicals in the methanol extract were analyzed using LC-MS, biofilm metabolic activity was assessed with the XTT assay, and morphological changes were examined via scanning electron microscopy (SEM). Molecular docking evaluated the binding of compounds in the A. muricata extract to the Sap3 receptor (PDB: 2H6T). …”
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Reduction of the oxidative damage to H2O2-induced HepG2 cells via the Nrf2 signalling pathway by plant flavonoids Quercetin and Hyperoside by Meijing Zhang, Gaoshuai Zhang, Xiangxing Meng, Xinxin Wang, Jiao Xie, Shaoshu Wang, Biao Wang, Jilite Wang, Suwen Liu, Qun Huang, Xu Yang, Jing Li, Hao Wang

“…Furthermore, molecular docking and dynamics simulations demonstrated that the quercetin- Kelch-like ECH-associated protein 1 (Keap1) complex was more stable than the hyperoside-Keap1 complex. …”
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Polydatin enhances oxaliplatin-induced cell death by activating NOX5-ROS-mediated DNA damage and ER stress in colon cancer cells by Qi Zhao, Qi Zhao, Qi Zhao, Yan Zhang, Yan Zhang, Jieyu Liu, Peipei Chen, Annabeth Onga, Namki Cho, Ri Cui, Chenguo Zheng

“…The relative gene and protein expressions were analyzed by quantitative real time-PCR (qRT-PCR) and Western blot assays. Molecular docking analysis predicted the interaction between PD and potential targets.ResultsWe found that PD exerted anti-CRC activity by promoting Nicotinamide Adenine Dinucleotide Phosphate (NADPH) oxidase 5 (NOX5)-mediated ROS production, activating the endoplasmic reticulum (ER) stress, and inducing DNA damage. …”
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Mitochondrial ROS modulate presynaptic plasticity in the drosophila neuromuscular junction by Irina Stavrovskaya, Bethany Kristi Morin, Stephen Madamba, Cliyahnelle Alexander, Alexis Romano, Samia Alam, Lucas Pavlov, Erna Mitaishvili, Pablo M. Peixoto

“…However, in existing boutons we observed an increase in the active zone (AZ) marker Brp/Erc1, which serves as docking site for the neurotransmitter vesicle release pool. …”
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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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Novel Antibacterial 4-Piperazinylquinoline Hybrid Derivatives Against <i>Staphylococcus aureus</i>: Design, Synthesis, and In Vitro and In Silico Insights by Gabriele La Monica, Annamaria Gallo, Alessia Bono, Federica Alamia, Antonino Lauria, Rosa Alduina, Annamaria Martorana

“…On the other hand, no significant activity was observed against <i>P. aeruginosa</i>. Further in silico docking and molecular dynamics studies highlighted strong interactions of <b>5k</b> with bacterial enzymes, such as tyrosyl-tRNA synthetase, pyruvate kinase, and DNA gyrase B, suggesting potential modes of action. …”
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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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Design and synthesis of antiproliferative 2-oxoindolin-3-ylidenes incorporating urea function with potential VEGFR-2 inhibitory properties by Dalia R. Aboshouk, M. Adel Youssef, Siva S. Panda, Benson M. Kariuki, Mohamed S. Bekheit, Ahmed R. Hamed, Walid Fayad, Ahmed A. F. Soliman, Adel S. Girgis

“…Compound 12b (R = 4-NHCONHPh, R′ = H; % inhibition = 87.2) is the most promising/potent anti-VEGFR-2 agent synthesized with activity close to that of sunitinib (% inhibition = 89.4) at 10 μM. Molecular docking studies (PDB: 3WZE and 3AGD) support the antiproliferation effects against cancer cell lines tested with VEGFR-2 inhibitory properties. …”
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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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