Interpretable deep learning to uncover the molecular binding patterns determining TCR–epitope interaction predictions by Ceder Dens, Wout Bittremieux, Fabio Affaticati, Kris Laukens, Pieter Meysman

“…We demonstrate how interpretable AI techniques can be linked to the three-dimensional structure of molecules to offer novel insights into the factors that determine TCR affinity on a molecular level. Additionally, our results show the importance of using interpretability techniques to verify the predictions of machine learning models for challenging molecular biology problems where small hard-to-detect problems can accumulate to inaccurate results.…”
Get full text

Therapeutic potential of T-cell receptor targeting the HLA-A*11:01-restricted KRASG12V neoantigen without cross-recognition of the self-antigen RAB7B in solid tumors by Wang Wang, Jingjing Huang, Yanan Hao, Lin Zou, Xiaxia Han, Tong Chen, Meiying Shen, Bozhi Wang, Luo Li, Siyin Chen, Shengchun Liu, Xiaojian Han, Aishun Jin

“…This study evaluates the human leukocyte antigen (HLA) binding properties of T-cell epitopes derived from these public neoantigens to identify optimal T-cell target and further develops T-cell receptor (TCR)-based therapeutics.Methods The binding properties of public neoantigens to HLA-I molecules were evaluated using peptide-HLA binding affinity and stability assays. Naive T-cell repertoires were used to expand and detect neoantigen-specific TCRs. …”
Get full text

Multi-Target Mechanism of Compound Qingdai Capsule for Treatment of Psoriasis: Multi-Omics Analysis and Experimental Verification by Qiao Y, Li C, Chen C, Wu P, Yang Y, Xie M, Liu N, Gu J

“…The ingredients of CQC were detected by UPLC-MS/MS, and target prediction was performed by systems pharmacology. …”
Get full text

Gingerols and Shogaols of Zingiber officinale var. sunti Valeton as Potential Allosteric Agonists of Human GABAA Receptor by in silico Pharmacology Approach by Kuswandani F, Wilar G, Wahyuni IS, Megantara S, Pitaloka DAE, Levita J, Jiranusornkul S

“…The UPLC analysis was performed to detect and quantify gingerol and shogaol in EEZO.Results: The best pre-ADMET prediction was shown by 6-gingerol, whereas the molecular docking simulations revealed that the best binding affinity and stability were shown by 6-gingerol (− 7.41 kcal/mol) and 10-shogaol (− 8.24 kcal/mol), which are comparable to that of diazepam. …”
Get full text

In vivo Polycystin-1 interactome using a novel Pkd1 knock-in mouse model. by Cheng-Chao Lin, Luis F Menezes, Jiahe Qiu, Elisabeth Pearson, Fang Zhou, Yu Ishimoto, D Eric Anderson, Gregory G Germino

“…Using this model, we sought to visualize endogenous PC1-eGFP and performed affinity-purification mass spectrometry (AP-MS) and network analyses. …”
Get full text

Measuring emergent mechanical changes in cytoskeletal ensembles in vitro using QCM-D by Victoria N. Amari, Emily M. Kerivan, Dana N. Reinemann, Dana N. Reinemann

“…Our results demonstrate that QCM-D is capable of detecting viscoelastic changes in actomyosin bundles in response to molecular-scale perturbations, including variations in concentration, nucleotide state, and actin-binding affinity. …”
Get full text

Poly-β-hydroxybutyrate (PHB) Depolymerase from Fusarium solani Thom by Srividya Shivakumar

“…Optimum enzyme activity was detected at pH 7.0 and 55°C. The enzyme was stable at pH 7.0 and 55°C for 24 h with a residual activity of almost 85%. …”
Get full text

Quantification of Folded and Misfolded Proinsulin Forms Using Nonreducing SDS-PAGE and Proinsulin-Specific Immunoblotting by Anoop Arunagiri, Insook Jang, Pamela Itkin-Ansari, Randal Kaufman, Peter Arvan

“…By proinsulin immunoblotting after nonreducing SDS-PAGE, the signal for disulfide-linked complexes can exceed the total proinsulin signal detected after reducing SDS-PAGE (i.e., overestimating the abundance of misfolded species due to antibody affinity differences). …”
Get full text

Degradation of catecholate, hydroxamate, and carboxylate model siderophores by extracellular enzymes. by Chinazam Emmanuel Chukwuma, Owen William Duckworth, Oliver Baars

“…Siderophores are low-molecular weight biomolecules with a high affinity for ferric iron (FeIII) that can impact plant and microbial growth. …”
Get full text

Organic Sunscreens—Is Their Placenta Permeability the Only Issue Associated with Exposure During Pregnancy? In Silico Studies of Sunscreens’ Placenta Permeability and Interactions... by Anna W. Sobańska, Andrzej M. Sobański

“…Many organic sunscreens are known to cross biological barriers—they are detected in mother’s milk, semen, umbilical cord blood or placental tissues. …”
Get full text

Imaging Comparison between 18F-FDG-PET/CT and 18F-Flouroethyl Choline PET/CT in Rare Case of Thymus Carcinoma Exhibiting a Positive Choline Uptake by Mustafa Takesh, Stefan Adams

“…In particular, it is known that the lymphocytes express high affinity of choline transporter and enzymes involving its metabolism. …”
Get full text

In-Silico Exploration of Plant Metabolites as Potential Remedies of Norovirus by Zenifer Alam, Md. Nazmul Islam Bappy, Abida Sultana, Fayeza Sadia Laskar, Kawsar Miah, Kazi Md. Ali Zinnah, Sudeb Saha

“…According to the analysis of the toxicity pattern, no detectable tumorigenic, mutagenic, irritating, or reproductive effects of the compounds were discovered. …”
Get full text

Discovery of <i>N</i>-(6-Methoxypyridin-3-yl)quinoline-2-amine Derivatives for Imaging Aggregated α-Synuclein in Parkinson’s Disease with Positron Emission Tomography by Haiyang Zhao, Tianyu Huang, Dhruva D. Dhavale, Jennifer Y. O’Shea, Zsofia Lengyel-Zhand, Dinahlee Saturnino Guarino, Jiwei Gu, Xuyi Yue, Ying-Hwey Nai, Hao Jiang, Marshall G. Lougee, Vinayak V. Pagar, Hee Jong Kim, Benjamin A. Garcia, E. James Petersson, Chester A. Mathis, Paul T. Kotzbauer, Joel S. Perlmutter, Robert H. Mach, Zhude Tu

“…The design and synthesis of 43 new <i>N</i>-(6-methoxypyridin-3-yl)quinolin-2-amine derivatives and an evaluation of their α-synuclein binding affinity is reported here. Compounds <b>7f</b>, <b>7j</b>, and <b>8i</b> exhibited high affinity for α-synuclein and were selected for ¹¹C, ¹⁸F, ¹²⁵I, or ³H radiolabeling. …”
Get full text

Expression of acyl-CoA-binding protein 5 from Rhodnius prolixus and its inhibition by RNA interference. by Muriel G M D Almeida, Daniela S Arêdes, David Majerowicz, Nils J Færgeman, Jens Knudsen, Katia C Gondim

“…However, the amount of protein, which was only detected in this organ, did not change during digestion. …”
Get full text

Remimazolam attenuates intestinal ischemia-reperfusion injury in mice by regulating ferroptosis through CX43 by KONG Lingguo, KONG Lingguo, LENG Yufang, LENG Yufang, MA Xiaojie

“…Methods‍　‍Molecular docking was applied to predict the binding affinity of remimazolam to CX43. A total of 72 SPF-grade adult male C57BL/6J mice (6~8 weeks old, weighing 20~25 g) were subjected. …”
Get full text

Correlation between IL-36α and IL-17 and Activity of the Disease in Selected Autoimmune Blistering Diseases by Agnieszka Żebrowska, Anna Woźniacka, Katarzyna Juczyńska, Kamila Ociepa, Elżbieta Waszczykowska, Izabela Szymczak, Rafał Pawliczak

“…While cytokines are crucial for the affinity and activation of different leukocyte cells in the inflammation and blister formation, there are no studies concerning a role of IL-36. …”
Get full text

Effects of a single intravitreal injection of aflibercept and ranibizumab on glomeruli of monkeys. by Alexander Tschulakow, Sarah Christner, Sylvie Julien, Maximilian Ludinsky, Markus van der Giet, Ulrich Schraermeyer

“…Whether intravitreal drugs can be detected within the glomeruli or affect VEGF in glomerular podocytes is not known. …”
Get full text

A novel anxiety-associated SNP identified in LYNX2 (LYPD1) is associated with decreased protein binding to nicotinic acetylcholine receptors by Kristin R. Anderson, Wenpeng Cao, Hui Sun Lee, Mark A. Crenshaw, Talulla B. Palumbo, Ethan Fisher-Perez, Amanda DeGraaf, Peter Rogu, Maria A. Beatty, Gabrielle M. Gracias, Gabrielle M. Gracias, Avani V. Pisapati, Katie Hoffman, Krystle J. McLaughlin, Almut Hupbach, Wonpil Im, Wonpil Im, X. Frank Zhang, Julie M. Miwa

“…In the future, this work may lead to the development of a biomarker for anxiety or a diagnostic tool for the early detection of individuals with susceptibility to anxiety.…”
Get full text

High-throughput screening of monoclonal antibodies against carbapenemases using a multiplex protein microarray platform by Sascha D. Braun, Sascha D. Braun, Martin Reinicke, Martin Reinicke, Celia Diezel, Celia Diezel, Elke Müller, Elke Müller, Katrin Frankenfeld, Thomas Schumacher, Hugo Arends, Stefan Monecke, Stefan Monecke, Ralf Ehricht, Ralf Ehricht, Ralf Ehricht

“…Given the urgent clinical need for rapid diagnostics, immunochromatographic assays represent a promising and urgently needed approach for economic and available point-of-care detection. However, the development of such assays is often hindered by the time-consuming process of identifying high-affinity antibody pairs.MethodsTo accelerate this process, we evaluated a protein microarray platform as a high-throughput screening tool to identify optimal monoclonal antibody (mAb) pairs targeting the most clinically relevant carbapenemases. …”
Get full text

Bioinformatics analysis combined with experimental validation reveals the novel mechanisms of multi-targets of dapagliflozin attenuating diabetic liver injury by Pengyu Wang, Pengyu Wang, Zhen Sun, Qing Lan, Qing Lan, Qing Lan, Shuo Zhang, Shuo Zhang, Yan Song, Yan Song, Leiming Yang, Leiming Yang, Mi Chen, Jianfen Shen, Qi Huang, Qi Huang, Youzhi Zhang, Youzhi Zhang

“…Moreover, the expression of inflammatory and apoptosis-related factors was detected using western blotting (WB) and quantitative polymerase chain reaction (qPCR). …”
Get full text