Network pharmacology analysis of Lanatoside C: molecular targets and mechanisms in the treatment of ulcerative colitis by Wenjing Zhu, Zhengjie Zhang, Xinyuan Wang

“…Molecular docking simulations revealed favorable binding interaction between LanC and KDR, STAT3, ABCB1, CYP3A5, and CYP2B6. …”
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Wet-spun Ag/PEDOT: PSS composite fibers for high-sensitive SERS sensing and high electrical conducting by Fan Wu, Haoyu Shi, Yulong Gao, Lin Cheng, Tongkai Gu, Tong Liu, Ziyun Chen, Wei Fan

“…Abstract Nanometal-based composite fibers have been widely explored in flexible sensors due to their outstanding optical and electrical properties. However, the weak binding force between metallic nanomaterial and fiber greatly limits the real application. …”
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A cyclophilin homology domain-independent role for Nup358 in HIV-1 infection. by Anne M Meehan, Dyana T Saenz, Rebekah Guevera, James H Morrison, Mary Peretz, Hind J Fadel, Masakazu Hamada, Jan van Deursen, Eric M Poeschla

“…The 164 C-terminal amino acids of this 3,224 amino acid protein are a cyclophilin homology domain (Nup358Cyp), which has potential to bind the HIV-1 capsid and regulate viral progress to integration. …”
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De novo genome hybrid assembly and annotation of the endangered and euryhaline fish Aphanius iberus (Valenciennes, 1846) with identification of genes potentially involved in salini... by Alfonso López-Solano, Ignacio Doadrio, Tessa Lynn Nester, Silvia Perea

“…GO Term annotation revealed, among others, categories related with salinity regulation processes (ion transport, transmembrane transport, membrane related terms or calcium ion binding). Conclusions The integration of genomic data with predicted genes presents future research opportunities across multiple disciplines, such as physiology, reproduction, disease, and opens up new avenues for future studies in comparative genomic studies. …”
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Exploring the Structural Diversity and Biotechnological Potential of the Rhodophyte Phycolectome by Éllen F. Rodrigues, Flavia Alves Verza, Felipe Garcia Nishimura, Renê Oliveira Beleboni, Cedric Hermans, Kaat Janssens, Maarten Lieven De Mol, Paco Hulpiau, Mozart Marins

“…Lectins are non-covalent glycan-binding proteins found in all living organisms, binding specifically to carbohydrates through glycan-binding domains. …”
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Unveiling the Solvent Effect: DMSO Interaction with Human Nerve Growth Factor and Its Implications for Drug Discovery by Francesca Paoletti, Tjaša Goričan, Alberto Cassetta, Jože Grdadolnik, Mykola Toporash, Doriano Lamba, Simona Golič Grdadolnik, Sonia Covaceuszach

“…This study investigates whether DMSO directly interacts with hNGF and affects its receptor-binding properties. <b>Methods:</b> Integrative/hybrid computational and experimental biophysical approaches were used to assess DMSO-NGF interaction by combining machine-learning tools and Nuclear Magnetic Resonance (NMR), Fourier Transform Infrared (FT-IR) spectroscopy, Differential Scanning Fluorimetry (DSF) and Grating-Coupled Interferometry (GCI). …”
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Essential oil-derived compounds target core fatigue-related genes: A network pharmacology and molecular Docking approach. by Gyaltsen Dakpa, Yu-Ting Chiang, Li-Yin Lin, Nai-Wen Tsao, Chung-Hsuan Wang, Horacio Pérez-Sánchez, Jorge Ricardo Alonso Fernández, Sheng-Yang Wang

“…Molecular docking exhibits strong binding affinity between key compounds such as Calamenene, T-cadinol, and Bornyl acetate and core targets, suggesting their potential antifatigue effects. …”
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In-silico study of approved drugs as potential inhibitors against 3CLpro and other viral proteins of CoVID-19. by Imra Aqeel, Abdul Majid, Tahani Jaser Alahmadi, Areej Althubaity

“…The highest ranked compounds possessed good binding affinities (-12.6 to -19.7 kcal/mol) and favorable pharmacokinetics. …”
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Structure-based identification of bioactive compounds as trace amine-associated receptor 1 agonists for the therapeutic management of major depressive disorder. by Abdelbaset Mohamed Elasbali, Ahmed S Ali, Mohd Adnan, Taj Mohammad, Anas Shamsi, Md Imtaiyaz Hassan

“…The initial filtering was done on the compounds based on Lipinski's rule of five, which was followed by molecular docking, PAINS screening, pharmacokinetic evaluation, and bioactivity predictions. Through this integrative screening approach, we discovered two promising phytochemicals, Bianthraquinone and Peimisine, demonstrating strong binding affinities and favorable drug-like properties. …”
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The C-terminal domain of the MutL homolog from Neisseria gonorrhoeae forms an inverted homodimer. by Sivakumar Namadurai, Deepti Jain, Dhananjay S Kulkarni, Chaitanya R Tabib, Peter Friedhoff, Desirazu N Rao, Deepak T Nair

“…This activity is dependent on the integrity of a conserved metal binding motif. Unlike their eukaryotic counterparts, MutL in bacteria like Neisseria exist in the form of a homodimer. …”
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Identification of Potential Inhibitors of Histone Deacetylase 6 Through Virtual Screening and Molecular Dynamics Simulation Approach: Implications in Neurodegenerative Diseases by Anas Shamsi, Moyad Shahwan, Azna Zuberi, Nojood Altwaijry

“…The docking results indicate that penfluridol and pimozide share the same binding site as the reference inhibitor with HDAC6. …”
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Unveiling the role of the PhoP master regulator in arsenite resistance through ackA downregulation in Lacticaseibacillus paracasei by Daniela Corrales, Cristina Alcántara, Dinoraz Vélez, Vicenta Devesa, Vicente Monedero, Manuel Zúñiga

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Relative sparing of dopaminergic terminals in the caudate nucleus is a feature of rest tremor in Parkinson’s disease by Marcelo D. Mendonça, Pedro C. Ferreira, Francisco Oliveira, Raquel Barbosa, Bruna Meira, Durval C. Costa, Albino J. Oliveira-Maia, Joaquim Alves da Silva

“…We analysed data from 432 subjects from the Parkinson’s Progression Markers Initiative, 57 additional PD patients and controls and 86 subjects referred for dopamine transporter single-photon emission computed tomography (DaT-SPECT). Caudate binding ratio (CBR), but not putamen binding ratio, was higher in RT patients. …”
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Autoregulation of the real-time kinetics of the human mitochondrial replicative helicase by Ismael Plaza-G A, María Ortiz-Rodríguez, Seth P. Buchanan, Samuel Miguez-Amil, Kateryna M. Lemishko, Fernando Moreno-Herrero, Rafael Fernandez-Leiro, Grzegorz L. Ciesielski, Borja Ibarra

“…Abstract The human mitochondrial helicase Twinkle is essential for mitochondrial DNA (mtDNA) replication and integrity. Using biochemical and single-molecule techniques, we investigated Twinkle’s real-time kinetics, including DNA loading, unwinding, and rewinding, and their regulation by its N-terminal Zinc-binding domain (ZBD), C-terminal tail, and mitochondrial SSB protein (mtSSB). …”
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Computational exploration of Eucommia ulmoides flavonoids as potential RANKL inhibitors via molecular docking and dynamics simulations by Xiaofei Zhang, Lixia Zhang, Dan Li, Qi Wang, Libin Wang, Ziqi Zheng, Yun Xie

“…Here, we investigated six EU-derived flavonoids (cyrtominetin, quercetin, syringetin, genistein, ombuin, and kaempferol) targeting RANKL using integrated computational approaches. Molecular docking revealed strong binding affinities (Total_Score > 4.0) for all compounds, with cyrtominetin exhibiting the highest affinity (-50.205 kJ/mol via MM-PBSA), primarily through hydrogen bonds with Gly178, His180, Lys181, and Asn295. …”
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Decoding phospho-regulation and flanking regions in autophagy-associated short linear motifs by Mattia Utichi, Oana N. Antonescu, Valentina Sora, Henri-Baptiste Marjault, Matteo Tiberti, Emiliano Maiani, Matteo Lambrughi, Elena Papaleo

“…Abstract Short Linear Motifs (SLiMs) play a pivotal role in the interactions between intrinsically disordered proteins and their binding partners. SLiMs can undergo regulation through post-translational modifications, including phosphorylation. …”
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Heme bound to the bacterial transcription factor SqrR/YgaV catalyzes oxygen-dependent conversion of hydrogen sulfide to polysulfide for regulated gene expression by Ryoma Iwata, Shinji Masuda

“…In contrast, heme binding suppresses cysteine reactivity toward polysulfides under anaerobic conditions in both proteins, with this suppression modulated by the redox state of the heme iron. …”
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Components of SurA required for outer membrane biogenesis in uropathogenic Escherichia coli. by Kristin M Watts, David A Hunstad

“…FimD is a SurA-dependent, integral outer membrane protein through which heteropolymeric type 1 pili, which confer bladder epithelial binding and invasion capacity upon uropathogenic E. coli, are assembled and extruded. …”
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TFAP2 paralogs facilitate chromatin access for MITF at pigmentation and cell proliferation genes. by Colin Kenny, Ramile Dilshat, Hannah E Seberg, Eric Van Otterloo, Gregory Bonde, Annika Helverson, Christopher M Franke, Eiríkur Steingrímsson, Robert A Cornell

“…We then assessed gene expression, chromatin accessibility, binding of TFAP2A and of MITF, and the chromatin marks H3K27Ac and H3K27Me3 which are characteristic of active enhancers and silenced chromatin, respectively. …”
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In-cell NMR reveals the first direct observation of endogenous interaction between HIV Tat protein and Tat RNA aptamer in human cells by Omar Eladl

“…In-cell NMR spectra exhibited characteristic chemical shift perturbations and nuclear Overhauser effect (NOE) signatures indicative of specific RNA–protein binding under physiological conditions. Comparison directly with in vitro spectra confirmed structural integrity and binding specificity in the intracellular environment. …”
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