7,829 results match your criteria ligands analyzed

Transcription factor NF-κB as target for SARS-CoV-2 drug discovery efforts using inflammation-based QSAR screening model.

J Mol Graph Model 2021 Jun 23;108:107968. Epub 2021 Jun 23.

Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey; Neuroscience Program, Institute of Health Sciences, Bahcesehir University, Istanbul, Turkey. Electronic address:

NF-κB is a central regulator of immunity and inflammation. It is suggested that the inflammatory response mediated by SARS-CoV-2 is predominated by NF-κB activation. Thus, NF-κB inhibition is considered a potential therapeutic strategy for COVID-19. Read More

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Disruption of protein rhamnosylation affects the host interaction.

Cell Surf 2021 Dec 26;7:100058. Epub 2021 Jun 26.

Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n, col. Noria Alta, C.P. 36050 Guanajuato, Gto., Mexico.

Sporotrichosis is a fungal disease caused by the members of the pathogenic clade, and one of the etiological agents is The cell wall of this organism has been previously analyzed and thus far is known to contain an inner layer composed of chitin and β -glucans, and an outer layer of glycoproteins, which are decorated with mannose and rhamnose-containing oligosaccharides. The L-rhamnose biosynthesis pathway is common in bacteria but rare in members of the Fungi kingdom. Therefore, in this study, we aimed to disrupt this metabolic route to assess the contribution of rhamnose during the -host interaction. Read More

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December 2021

Somatostatin Receptors and Chemokine Receptor CXCR4 in Lymphomas: A Histopathological Review of Six Lymphoma Subtypes.

Front Oncol 2021 8;11:710900. Epub 2021 Jul 8.

Department of Oncology and Radiotherapy, Turku University Hospital, University of Turku, Turku, Finland.

Background: Somatostatin receptors (SSTR) and chemokine receptor CXCR4 are expressed in lymphomas, while the abundance is known to be heterogeneous in different subtypes of lymphomas. Targeting tumor cells expressing these receptors might add to therapeutic opportunities while radiolabeled ligands for both imaging and therapy have been developed. The aim of this study was to establish SSTR subtype 2, 3 and 5 and also CXCR4 status immunohistochemically in six different lymphoma subtypes: diffuse large B-cell lymphoma (DLBCL), follicular lymphoma (FL), mantle cell lymphoma (MCL), mucosa-associated marginal B-cell lymphoma (MALT), Hodgkin lymphoma (HL) and peripheral T-cell lymphoma (PTCL). Read More

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Is Hypoxia a Factor Influencing PSMA-Directed Radioligand Therapy?-An In Silico Study on the Role of Chronic Hypoxia in Prostate Cancer.

Cancers (Basel) 2021 Jul 8;13(14). Epub 2021 Jul 8.

Department of Nuclear Medicine, Inselspital, University of Bern, 3010 Bern, Switzerland.

Radioligand therapy (RLT) targeting prostate specific-membrane antigen (PSMA) is an emerging treatment for metastatic castration-resistant prostate cancer (mCRPC). It administrates 225Ac- or 177Lu-labeled ligands for the targeted killing of tumor cells. Differently from X- or γ-ray, for the emitted α or β particles the ionization of the DNA molecule is less dependent on the tissue oxygenation status. Read More

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Temperature effects on RNA polymerase initiation kinetics reveal which open complex initiates and that bubble collapse is stepwise.

Proc Natl Acad Sci U S A 2021 Jul;118(30)

Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706;

Transcription initiation is highly regulated by promoter sequence, transcription factors, and ligands. All known transcription inhibitors, an important class of antibiotics, act in initiation. To understand regulation and inhibition, the biophysical mechanisms of formation and stabilization of the "open" promoter complex (OC), of synthesis of a short RNA-DNA hybrid upon nucleotide addition, and of escape of RNA polymerase (RNAP) from the promoter must be understood. Read More

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Structures of the TetR-like transcription regulator RcdA alone and in complexes with ligands.

Proteins 2021 Jul 20. Epub 2021 Jul 20.

Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland.

RcdA is a helix-turn-helix (HTH) transcriptional regulator belonging to the TetR family. The protein regulates the transcription of curlin subunit gene D, the master regulator of biofilm formation. Moreover, it was predicted that it might be involved in the regulation of up to 27 different genes. Read More

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Complexation of -Functionalized Cyclams with Copper(II) and Zinc(II): Similarities and Changes When Compared to Parent Cyclam Analogues.

Inorg Chem 2021 Jul 21. Epub 2021 Jul 21.

University Brest, UMR CNRS 6521 CEMCA, 6 avenue Victor le Gorgeu, 29238 Brest, France.

Herein, we report a comprehensive coordination study of the previously reported ligands , , , , and and of their -functional analogues, , , , , and . This group of ligands includes , cross-bridged , their di- or tetramethylated derivatives, and the analogues bearing an additional hydroxyethyl group on one β-N position of the ring. The Cu(II) and Zn(II) complexes of these macrocycles have been highlighted previously for the biological interest, but the details of their structures in the solid state and in solution remained largely unexplored. Read More

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The Role of ApoE Expression and Variability of Its Glycosylation in Human Reproductive Health in the Light of Current Information.

Int J Mol Sci 2021 Jul 4;22(13). Epub 2021 Jul 4.

Department of Laboratory Diagnostics, Division of Laboratory Diagnostics, Faculty of Pharmacy, Wroclaw Medical University, Borowska Street 211A, 50-556 Wroclaw, Poland.

Apolipoprotein E (ApoE), a 34-kDa glycoprotein, as part of the high-density lipoprotein (HDL), has antioxidant, anti-inflammatory and antiatherogenic properties. The variability of ApoE expression in the course of some female fertility disorders (endometriosis, POCS), and other gynecological pathologies such as breast cancer, choriocarcinoma, endometrial adenocarcinoma/hyperplasia and ovarian cancer confirm the multidirectional biological function of ApoE, but the mechanisms of its action are not fully understood. It is also worth taking a closer look at the associations between ApoE expression, the type of its genotype and male fertility disorders. Read More

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Ag(I) Pyridine-Amidoxime Complex as the Catalysis Activity Domain for the Rapid Hydrolysis of Organothiophosphate-Based Nerve Agents: Mechanistic Evaluation and Application.

ACS Appl Mater Interfaces 2021 Jul 19. Epub 2021 Jul 19.

Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, College of Chemistry and Frontier Science Center for the Creation of New Organic Substances, Nankai University, Tianjin 300071, China.

Two novel Ag(I) complexes containing synergistic pyridine and amidoxime ligands (Ag-DPAAO and Ag-PAAO) were first designed as complex monomers. Taking advantage of the molecular imprinting technique and solvothermal method, molecular imprinted porous cross-linked polymers (MIPCPs) were developed as a robust platform for the first time to incorporate Ag-PAAO into a polymer material as a recyclable catalyst. Advantageously, the observed pseudo first-order rate constant () of MIPCP-Ag-PAAO-20% for ethyl-parathion () hydrolysis is about 1. Read More

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Neuropilin-1: A Key Protein to Consider in the Progression of Pediatric Brain Tumors.

Front Oncol 2021 1;11:665634. Epub 2021 Jul 1.

Université de Lorraine, CNRS, CRAN, Nancy, France.

Neuropilins are transmembrane glycoproteins that play important roles in cardiovascular and neuronal development, as well as in immunological system regulations. NRP1 functions as a co-receptor, binding numerous ligands, such as SEMA 3 or VEGF and, by doing so, reinforcing their signaling pathways and can also interface with the cytoplasmic protein synectin. NRP1 is expressed in many cancers, such as brain cancers, and is associated with poor prognosis. Read More

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Current noise of a protein-selective biological nanopore.

Proteomics 2021 Jul 18:e2100077. Epub 2021 Jul 18.

Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York, 13244-1130, USA.

1/f current noise is ubiquitous in protein pores, porins, and channels. We have previously shown that a protein-selective biological nanopore with an external protein receptor can function as a 1/f noise generator when a high-affinity protein ligand is reversibly captured by the receptor. Here, we demonstrate that the binding affinity and concentration of the ligand are key determinants for the nature of current noise. Read More

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Differential sensitivity of inflammatory macrophages and alternatively activated macrophages to ferroptosis.

Eur J Immunol 2021 Jul 17. Epub 2021 Jul 17.

Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Zurich, Switzerland.

Acumulation of oxidized membrane lipids ultimately results in ferroptotic cell death, which can be prevented by the selenoenzyme glutathione peroxidase 4 (Gpx4). In vivo conditions promoting ferroptosis and susceptible cell types are still poorly defined. In this study, we analyzed the conditional deletion of Gpx4 in mice specifically in the myeloid cell lineages. Read More

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Effects of dopamine D1-like receptor ligands on food-cocaine choice in socially housed male cynomolgus monkeys.

J Pharmacol Exp Ther 2021 Jul 16. Epub 2021 Jul 16.

Department of Physiology & Pharmacology, Wake Forest University School of Medicine, United States.

Although dopamine is known to play a prominent role in mediating the abuse-related effects of cocaine, the specific roles of dopamine receptor subtypes are not fully understood. Whereas the effects of drugs acting at dopamine D2-like receptors (D2R) have been characterized, less is known about dopamine D1-like receptors (D1R). The present experiments examined the effect of drugs with varying intrinsic efficacy at D1R on the relative reinforcing strength of cocaine in male cynomolgus monkeys. Read More

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Ultrafast Excited-State Dynamics of Photoluminescent Pt(II) Dimers Probed by a Coherent Vibrational Wavepacket.

J Phys Chem Lett 2021 Jul 16:6794-6803. Epub 2021 Jul 16.

Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States.

Intricate potential energy surfaces (PESs) of some transition metal complexes (TMCs) pose challenges in mapping out initial excited-state pathways that could influence photochemical outcomes. Ultrafast intersystem crossing (ISC) dynamics of four structurally related platinum(II) dimer complexes were examined by detecting their coherent vibrational wavepacket (CVWP) motions of Pt-Pt stretching mode in the metal-metal-to-ligand-charge-transfer excited states. Structurally dependent CVWP behaviors (frequency, dephasing time, and oscillation amplitudes) were captured by femtosecond transient absorption spectroscopy, analyzed by short-time Fourier transformation, and rationalized by quantum mechanical calculations, revealing dual ISC pathways. Read More

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Expression levels of chemokine (C-X-C motif) ligands CXCL1 and CXCL3 as prognostic biomarkers in rectal adenocarcinoma: evidence from Gene Expression Omnibus (GEO) analyses.

Bioengineered 2021 Dec;12(1):3711-3725

Department of Radiotherapy, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.

Rectal cancer is a life‑threatening disease worldwide. Chemotherapy resistance is common in rectal adenocarcinoma patients and has unfavorable survival outcomes; however, its related molecular mechanisms remain unknown. To identify genes related to the initiation and progression of rectal adenocarcinoma, three datasets were obtained from the Gene Expression Omnibus database. Read More

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December 2021

Decision-support for treatment with Lu-PSMA: machine learning predicts response with high accuracy based on PSMA-PET/CT and clinical parameters.

Ann Transl Med 2021 May;9(9):818

Department of Nuclear Medicine, University Hospital Bonn, Bonn, Germany.

Background: Treatment with radiolabeled ligands to prostate-specific membrane antigen (PSMA) is gaining importance in the treatment of patients with advanced prostate carcinoma. Previous imaging with positron emission tomography/computed tomography (PET/CT) is mandatory. The aim of this study was to investigate the role of radiomics features in PSMA-PET/CT scans and clinical parameters to predict response to Lu-PSMA treatment given just baseline PSMA scans using state-of-the-art machine learning (ML) methods. Read More

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Immune-Based Prediction of COVID-19 Severity and Chronicity Decoded Using Machine Learning.

Front Immunol 2021;12:700782. Epub 2021 Jun 28.

Lab of Tumor Chemosensitivity, CIET/DC Lab, Faculty of Microbiology, Universidad de Costa Rica, San Jose, Costa Rica.

Expression of CCR5 and its cognate ligands have been implicated in COVID-19 pathogenesis, consequently therapeutics directed against CCR5 are being investigated. Here, we explored the role of CCR5 and its ligands across the immunologic spectrum of COVID-19. We used a bioinformatics approach to predict and model the immunologic phases of COVID so that effective treatment strategies can be devised and monitored. Read More

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Phase II Randomized Study of CMB305 and Atezolizumab Compared With Atezolizumab Alone in Soft-Tissue Sarcomas Expressing NY-ESO-1.

J Clin Oncol 2021 Jul 14:JCO2003452. Epub 2021 Jul 14.

Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.

Purpose: CMB305 is a heterologous prime-boost vaccination regimen created to prime NY-ESO-1-specific CD8 T-cell populations and then activate the immune response with a potent TLR-4 agonist. This open-label randomized phase II trial was designed to investigate the efficacy and safety of adding the CMB305 regimen to atezolizumab (anti-programmed death ligand-1 therapy) in comparison with atezolizumab alone in patients with synovial sarcoma or myxoid liposarcoma.

Patients And Methods: Patients with locally advanced, relapsed, or metastatic synovial sarcoma or myxoid liposarcoma (any grade) were randomly assigned to receive CMB305 with atezolizumab (experimental arm) or atezolizumab alone (control arm). Read More

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Georgian Med News 2021 May(314):179-184

Sechenov First Moscow State Medical University, Russian Federation.

The development study was a continuation research of the action mechanism of the developed innovative pharmaceutical substance based on the 3,7-diazabicyclo[3.3.1]nonane derivative, which belongs to the class of AMPA receptor modulators. Read More

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Initial Stages of Spontaneous Binding of Folate-Based Vectors to Folate Receptor-α Observed by Unbiased Molecular Dynamics.

J Phys Chem B 2021 Jul 12;125(28):7598-7612. Epub 2021 Jul 12.

Laboratory of Quantum and Computational Chemistry, Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1 James Bourchier boulevard, Sofia 1164, Bulgaria.

Active targeting is a prospective strategy for controlled drug delivery to malignant tumor tissues. One of the approaches relies on recognition of a bioactive ligand by a receptor expressed abundantly on the surface of cancer cell membranes. A promising ligand-receptor pair is folic acid (or its dianionic form, folate) combined with the folate receptor-α (FRα). Read More

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Bioinformatics analysis of the role of CXC ligands in the microenvironment of head and neck tumor.

Aging (Albany NY) 2021 07 11;13(13):17789-17817. Epub 2021 Jul 11.

Department of Dental Implant Center, Stomatologic Hospital and College, Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province, Hefei 230032, China.

Chemokines play a significant role in cancer. CXC-motif chemokine ligands (CXCLs) are associated with the tumorigenesis and progression of head and neck squamous cell carcinoma (HNSC); however, their specific functions in the tumor microenvironment remain unclear. Here, we analyzed the molecular networks and transcriptional data of HNSC patients from the Oncomine, GEPIA, String, cBioPortal, Metascape, TISCH, and TIMER databases. Read More

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Dissecting activation steps in P2X7 receptors.

Biochem Biophys Res Commun 2021 Jul 6;569:112-117. Epub 2021 Jul 6.

Institute of Physiology II, Jena University Hospital, Friedrich Schiller University Jena, 07743, Jena, Germany. Electronic address:

P2X7 receptors are trimeric ion channels activated by extracellular ATP. Upon activation, they trigger cytolysis and apoptosis but also control cell proliferation. To shed more light on channel gating and the underlying function of the individual subunits, receptors of concatenated subunits were built containing a defined number of functional binding sites. Read More

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The sequenced genomes of non-flowering land plants reveal the innovative evolutionary history of peptide signaling.

Plant Cell 2021 Jul 7. Epub 2021 Jul 7.

Section for Evolutionary Biology and Genetics, Department of Biosciences, University of Oslo, Norway.

An understanding of land plant evolution is a prerequisite for in-depth knowledge of plant biology. Here we extract and explore information hidden in the increasing number of sequenced plant genomes, from bryophytes to angiosperms, to elucidate a specific biological question - how peptide signaling evolved. To conquer land and cope with changing environmental conditions, plants have gone through transformations that must have required innovations in cell-to-cell communication. Read More

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Immune infiltration-related N6-methyladenosine RNA methylation regulators influence the malignancy and prognosis of endometrial cancer.

Aging (Albany NY) 2021 06 16;13(12):16287-16315. Epub 2021 Jun 16.

Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110004, China.

N6-methyladenosine (m6A) RNA methylation is associated with malignant tumor progression and is modulated by various m6A RNA methylation regulator proteins. However, its role in endometrial cancer is unclear. In this work, we analyzed sequence, copy number variation, and clinical data obtained from the TCGA database. Read More

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Interactions of Ozone-Functionalized Activated Charcoal with SARS-Cov-2 Proteases Using Molecular Docking and Dynamics.

J Nanosci Nanotechnol 2021 12;21(12):6060-6072

Laboratory of Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, C. P. 479, 66075-110, Belem, PA, Brazil.

The high contamination by the SARS-Cov-2 virus has led to the search for ways to minimize contagion. Masks are used as part of a strategy of measures to suppress transmission and save lives. However, they are not sufficient to provide an adequate level of protection against COVID-19. Read More

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December 2021

Inflammatory Environment Promotes the Adhesion of Tumor Cells to Brain Microvascular Endothelial Cells.

Front Oncol 2021 16;11:691771. Epub 2021 Jun 16.

State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.

Cancer patients usually suffer from unfavorable prognosis, particularly with the occurrence of brain metastasis of lung cancer. The key incident of brain metastasis initiation is crossing of blood-brain barrier (BBB) by cancer cells. Although preventing brain metastasis is a principal goal of cancer therapy, the cellular mechanisms and molecular regulators controlling the transmigration of cancer cells into the brain are still not clearly illustrated. Read More

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Directed evolution of orthogonal RNA-RBP pairs through library-vs-library in vitro selection.

Nucleic Acids Res 2021 Jul 5. Epub 2021 Jul 5.

Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan.

RNA-binding proteins (RBPs) and their RNA ligands play many critical roles in gene regulation and RNA processing in cells. They are also useful for various applications in cell biology and synthetic biology. However, re-engineering novel and orthogonal RNA-RBP pairs from natural components remains challenging while such synthetic RNA-RBP pairs could significantly expand the RNA-RBP toolbox for various applications. Read More

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Non-invasive determination of ionizable ligand group density on high internal phase emulsion derived polymer.

J Chromatogr A 2021 Mar 18;1652:462077. Epub 2021 Mar 18.

Faculty for Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia; COBIK, 5270 Ajdovščina, Slovenia. Electronic address:

Stepwise change between low and high salt concentration buffers of the same pH results in pH transition, the length of which was demonstrated to be proportional to the quantity of ion-exchange groups present on the matrix. In this work, we analyzed the effect of the ligand type, density, and buffer concentration on the pH transition shape for typical ion-exchange groups (QA, DEAE, SO3, and COOH) and ligands acting as metal-chelators, such as IDA, TAEA, and EDA. It was demonstrated that pH transition can occur either as a chromatographic or flat-top peak. Read More

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Cross-Linking Effects Dictate the Preference of Galectins to Bind LacNAc-Decorated HPMA Copolymers.

Int J Mol Sci 2021 Jun 1;22(11). Epub 2021 Jun 1.

CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, 48162 Derio, Bizkaia, Spain.

The interaction of multi-LacNAc (Galβ1-4GlcNAc)-containing -(2-hydroxypropyl) methacrylamide (HPMA) copolymers with human galectin-1 (Gal-1) and the carbohydrate recognition domain (CRD) of human galectin-3 (Gal-3) was analyzed using NMR methods in addition to cryo-electron-microscopy and dynamic light scattering (DLS) experiments. The interaction with individual LacNAc-containing components of the polymer was studied for comparison purposes. For Gal-3 CRD, the NMR data suggest a canonical interaction of the individual small-molecule bi- and trivalent ligands with the lectin binding site and better affinity for the trivalent arrangement due to statistical effects. Read More

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Activin-A Induces Early Differential Gene Expression Exclusively in Periodontal Ligament Fibroblasts from Patients.

Biomedicines 2021 Jun 1;9(6). Epub 2021 Jun 1.

Department of Periodontology, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and Vrije Universiteit, 1012 Amsterdam, The Netherlands.

(FOP) is a rare genetic disease characterized by heterotopic ossification (HO). It is caused by mutations in the Activin receptor type 1 () gene, resulting in enhanced responsiveness to ligands, specifically to Activin-A. Though it has been shown that capturing Activin-A protects against heterotopic ossification in animal models, the exact underlying mechanisms at the gene expression level causing ACVR1 R206H-mediated ossifications and progression are thus far unknown. Read More

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