Abstract SY26-01: Targeting natural ligands for TCR engineering

2021 ◽  
Author(s):  
Stephen P. Schoenberger
Keyword(s):  
Natural Ligands

Withdrawal Notice: Lead Optimization from Natural Ligands by In-Silico Approach for Discovering Potential Monoamine Oxidasesinhibitors (MAOIs)

2020 ◽  
Vol 21 ◽  
Author(s):  
Priyanka Dhiman ◽  
Neelam Malik ◽  
Anurag Khatkar
Keyword(s):  
Drug Metabolism ◽  
In Silico ◽  
Editorial Policy ◽  
Lead Optimization ◽  
Editorial Policies ◽  
Current Drug ◽  
Natural Ligands ◽  
Copyright Permission ◽  
Legal Right

The article has been withdrawn at the request of the authors and editor of the journal Current Drug Metabolism. Bentham Science apologizes to the readers of the journal for any inconvenience this may have caused. The Bentham Editorial Policy on Article Withdrawal can be found at https://benthamscience.com/editorial-policies-main.php BENTHAM SCIENCE DISCLAIMER: It is a condition of publication that manuscripts submitted to this journal have not been published and will not be simultaneously submitted or published elsewhere. Furthermore, any data, illustration, structure or table that has been published elsewhere must be reported, and copyright permission for reproduction must be obtained. Plagiarism is strictly forbidden, and by submitting the article for publication the authors agree that the publishers have the legal right to take appropriate action against the authors, if plagiarism or fabricated information is discovered. By submitting a manuscript, the authors agree that the copyright of their article is transferred to the publishers if and when the article is accepted for publication.

scholarly journals Chimeric non-antigen receptors in T cell-based cancer therapy

2021 ◽  
Vol 9 (8) ◽  
pp. e002628
Author(s):  
Jitao Guo ◽  
Andrew Kent ◽  
Eduardo Davila
Keyword(s):  
T Cells ◽  
T Cell ◽  
Cancer Therapy ◽  
Tumor Antigen ◽  
Cell Function ◽  
Antigen Recognition ◽  
Cancer Therapies ◽  
Antigen Receptors ◽  
Natural Ligands ◽  
And Function

Adoptively transferred T cell-based cancer therapies have shown incredible promise in treatment of various cancers. So far therapeutic strategies using T cells have focused on manipulation of the antigen-recognition machinery itself, such as through selective expression of tumor-antigen specific T cell receptors or engineered antigen-recognition chimeric antigen receptors (CARs). While several CARs have been approved for treatment of hematopoietic malignancies, this kind of therapy has been less successful in the treatment of solid tumors, in part due to lack of suitable tumor-specific targets, the immunosuppressive tumor microenvironment, and the inability of adoptively transferred cells to maintain their therapeutic potentials. It is critical for therapeutic T cells to overcome immunosuppressive environmental triggers, mediating balanced antitumor immunity without causing unwanted inflammation or autoimmunity. To address these hurdles, chimeric receptors with distinct signaling properties are being engineered to function as allies of tumor antigen-specific receptors, modulating unique aspects of T cell function without directly binding to antigen themselves. In this review, we focus on the design and function of these chimeric non-antigen receptors, which fall into three broad categories: ‘inhibitory-to-stimulatory’ switch receptors that bind natural ligands, enhanced stimulatory receptors that interact with natural ligands, and synthetic receptor-ligand pairs. Our intent is to offer detailed descriptions that will help readers to understand the structure and function of these receptors, as well as inspire development of additional novel synthetic receptors to improve T cell-based cancer therapy.

Simulations of the Estrogen Receptor Ligand-Binding Domain:  Affinity of Natural Ligands and Xenoestrogens

2000 ◽  
Vol 43 (24) ◽  
pp. 4594-4605 ◽  
Author(s):  
B. Chris Oostenbrink ◽  
Jed W. Pitera ◽  
Marola M. H. van Lipzig ◽  
John H. N. Meerman ◽  
Wilfred F. van Gunsteren
Keyword(s):  
Estrogen Receptor ◽  
Ligand Binding ◽  
Binding Domain ◽  
Ligand Binding Domain ◽  
Receptor Ligand ◽  
Natural Ligands ◽  
Estrogen Receptor Ligand

Comparison of moonlighting guanylate cyclases: roles in signal direction?

2014 ◽  
Vol 42 (6) ◽  
pp. 1773-1779 ◽  
Author(s):  
Lubna Freihat ◽  
Victor Muleya ◽  
David T. Manallack ◽  
Janet I. Wheeler ◽  
Helen R. Irving
Keyword(s):  
Interleukin 1 ◽  
Structural Features ◽  
Kinase Domain ◽  
The Novel ◽  
Natural Ligands ◽  
Signalling Cascades ◽  
A Minor ◽  
Mammalian Protein ◽  
Homology Models

Over 30 receptor-like kinases contain a guanylate cyclase (GC) catalytic centre embedded within the C-terminal region of their kinase domain in the model plant Arabidopsis. A number of the kinase GCs contain both functional kinase and GC activity in vitro and the natural ligands of these receptors stimulate increases in cGMP within isolated protoplasts. The GC activity could be described as a minor or moonlighting activity. We have also identified mammalian proteins that contain the novel GC centre embedded within kinase domains. One example is the interleukin 1 receptor-associated kinase 3 (IRAK3). We compare the GC functionality of the mammalian protein IRAK3 with the cytoplasmic domain of the plant prototype molecule, the phytosulfokine receptor 1 (PSKR1). We have developed homology models of these molecules and have undertaken in vitro experiments to compare their functionality and structural features. Recombinant IRAK3 produces cGMP at levels comparable to those produced by PSKR1, suggesting that IRAK3 contains GC activity. Our findings raise the possibility that kinase-GCs may switch between downstream kinase-mediated or cGMP-mediated signalling cascades to elicit desired outputs to particular stimuli. The challenge now lies in understanding the interaction between the GC and kinase domains and how these molecules utilize their dual functionality within cells.

Minireview: Orphan Receptors and their Natural Ligands

1997 ◽  
Vol 17 (1-3) ◽  
pp. 545-550 ◽  
Author(s):  
O. Civelli ◽  
H. P. Nothacker ◽  
A. Bourson ◽  
A. Ardati ◽  
F. Monsma ◽  
...  
Keyword(s):  
Orphan Receptors ◽  
Natural Ligands

scholarly journals In Silico Screening for Natural Ligands to Non-Structural Nsp7 Conformers of Coronaviruses

2020 ◽  
Author(s):  
Rafael Blasco ◽  
Julio Coll
Keyword(s):  
In Silico ◽  
Chemical Properties ◽  
Structural Similarity ◽  
Binding Pocket ◽  
Binding Affinities ◽  
Structural Protein ◽  
Autodock Vina ◽  
Natural Ligands ◽  
Final Optimization

<p>The non-structural protein 7 (nsp7) of Severe Acute Respiratory Syndrome (SARS) coronaviruses was selected as a new target to potentially interfere with viral replication. The nsp7s are one of the most conserved, unique and small coronavirus proteins having a critical, yet intriguing participation on the replication of the long viral RNA genome after complexing with nsp8 and nsp12. Despite the difficulties of having no previous binding pocket, two high-throughput virtual blind screening of 158240 natural compounds > 400 Da by AutoDock Vina against nsp7.1ysy identified 655 leads displaying predicted binding affinities between 10 to 1100 nM. The leads were then screened against 14 available conformations of nsp7 by both AutoDock Vina and seeSAR programs employing different binding score algorithms, to identify 20 consensus top-leads. Further <i>in silico</i> predictive analysis of physiological and toxicity ADMET criteria (chemical properties, adsorption, metabolism, toxicity) narrowed top-leads to a few drug-like ligands many of them showing steroid-like structures. A final optimization by search for structural similarity to the top drug-like ligand that were also commercially available, yielded a collection of predicted novel ligands with ~100-fold higher-affinity whose antiviral activity may be experimentally validated. Additionally, these novel nsp7-interacting ligands and/or their further optimized derivatives, may offer new tools to investigate the intriguing role of nsp7 on replication of coronaviruses.</p>

scholarly journals Protein-observed 19F NMR of LecA from Pseudomonas aeruginosa

Glycobiology ◽  
2020 ◽  
Author(s):  
Elena Shanina ◽  
Eike Siebs ◽  
Hengxi Zhang ◽  
Daniel Varón Silva ◽  
Ines Joachim ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis ◽  
Carbohydrate Binding ◽  
Binding Region ◽  
Chronic Infections ◽  
Nmr Titration ◽  
Affinity Ligands ◽  
Natural Ligands ◽  
Future Drug

Abstract The carbohydrate-binding protein LecA (PA-IL) from Pseudomonas aeruginosa plays an important role in the formation of biofilms in chronic infections. Development of inhibitors to disrupt LecA-mediated biofilms is desired but it is limited to carbohydrate-based ligands. Moreover, discovery of drug-like ligands for LecA is challenging because of its weak affinities. Therefore, we established a protein-observed 19F (PrOF) nuclear magnetic resonance (NMR) to probe ligand binding to LecA. LecA was labeled with 5-fluoroindole to incorporate 5-fluorotryptophanes and the resonances were assigned by site-directed mutagenesis. This incorporation did not disrupt LecA preference for natural ligands, Ca2+ and d-galactose. Following NMR perturbation of W42, which is located in the carbohydrate-binding region of LecA, allowed to monitor binding of low-affinity ligands such as N-acetyl d-galactosamine (d-GalNAc, Kd = 780 ± 97 μM). Moreover, PrOF NMR titration with glycomimetic of LecA p-nitrophenyl β-d-galactoside (pNPGal, Kd = 54 ± 6 μM) demonstrated a 6-fold improved binding of d-Gal proving this approach to be valuable for ligand design in future drug discovery campaigns that aim to generate inhibitors of LecA.

scholarly journals Computational redesign of the Escherichia coli ribose-binding protein ligand binding pocket for 1,3-cyclohexanediol and cyclohexanol

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Diogo Tavares ◽  
Artur Reimer ◽  
Shantanu Roy ◽  
Aurélie Joublin ◽  
Vladimir Sentchilo ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Ligand Binding ◽  
Binding Proteins ◽  
Binding Pocket ◽  
Wild Type ◽  
Ligand Binding Pocket ◽  
Mutant Proteins ◽  
Periplasmic Binding Proteins ◽  
Natural Ligands ◽  
Ribose Binding Protein

AbstractBacterial periplasmic-binding proteins have been acclaimed as general biosensing platform, but their range of natural ligands is too limited for optimal development of chemical compound detection. Computational redesign of the ligand-binding pocket of periplasmic-binding proteins may yield variants with new properties, but, despite earlier claims, genuine changes of specificity to non-natural ligands have so far not been achieved. In order to better understand the reasons of such limited success, we revisited here the Escherichia coli RbsB ribose-binding protein, aiming to achieve perceptible transition from ribose to structurally related chemical ligands 1,3-cyclohexanediol and cyclohexanol. Combinations of mutations were computationally predicted for nine residues in the RbsB binding pocket, then synthesized and tested in an E. coli reporter chassis. Two million variants were screened in a microcolony-in-bead fluorescence-assisted sorting procedure, which yielded six mutants no longer responsive to ribose but with 1.2–1.5 times induction in presence of 1 mM 1,3-cyclohexanediol, one of which responded to cyclohexanol as well. Isothermal microcalorimetry confirmed 1,3-cyclohexanediol binding, although only two mutant proteins were sufficiently stable upon purification. Circular dichroism spectroscopy indicated discernable structural differences between these two mutant proteins and wild-type RbsB. This and further quantification of periplasmic-space abundance suggested most mutants to be prone to misfolding and/or with defects in translocation compared to wild-type. Our results thus affirm that computational design and library screening can yield RbsB mutants with recognition of non-natural but structurally similar ligands. The inherent arisal of protein instability or misfolding concomitant with designed altered ligand-binding pockets should be overcome by new experimental strategies or by improved future protein design algorithms.

Production of human lactoferrin in animal milk1This article is part of a Special Issue entitled Lactoferrin and has undergone the Journal's usual peer review process.

2012 ◽  
Vol 90 (3) ◽  
pp. 513-519 ◽  
Author(s):  
I.L. Goldman ◽  
S.G. Georgieva ◽  
Ya.G. Gurskiy ◽  
A.N. Krasnov ◽  
A.V. Deykin ◽  
...  
Keyword(s):  
Peer Review Process ◽  
Micrococcus Luteus ◽  
Chemical Properties ◽  
Human Lactoferrin ◽  
Natural Ligands ◽  
Terminal Amino ◽  
Transgenic Goats ◽  
Genetic Constructs ◽  
Physical And Chemical ◽  
Circular Dichroic

Genetic constructs containing the human lactoferrin (hLf) gene were created within a joint program of Russian and Belorussian scientists. Using these constructs, transgenic mice were bred (the maximum hLf concentration in their milk was 160 g/L), and transgenic goats were also generated (up to 10 g/L hLf in their milk). Experimental goatherds that produced hLf in their milk were also bred, and the recombinant hLf was found to be identical to the natural protein in its physical and chemical properties. These properties included electrophoretic mobility, isoelectric point, recognition by polyclonal and monoclonal antibodies, circular dichroic spectra, interaction with natural ligands (DNA, lipopolysaccharides, and heparin), the binding of iron ions, the sequence of the 7 terminal amino acids, and its biological activity. The latter was assessed by the agglutination of Micrococcus luteus protoplasts, bactericidal activity against Escherichia coli and Listeria monocytogenes , and fungicidal activity against Candida albicans . We also demonstrated a significant increase in the activity of antibiotics when used in combination with Lf.

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