Identification of A Novel Small-Molecule Binding Site of the Fat Mass and Obesity Associated Protein (FTO)

2015 ◽  
Vol 58 (18) ◽  
pp. 7341-7348 ◽  
Author(s):  
Wu He ◽  
Bin Zhou ◽  
Weijia Liu ◽  
Meizi Zhang ◽  
Zhenhua Shen ◽  
...  
Keyword(s):  
Binding Site ◽  
Small Molecule ◽  
Fat Mass

scholarly journals Structural Insight into the Two-Step Mechanism of PAI-1 Inhibition by Small Molecule TM5484

2021 ◽  
Vol 22 (3) ◽  
pp. 1482 ◽  
Author(s):  
Machteld Sillen ◽  
Toshio Miyata ◽  
Douglas E. Vaughan ◽  
Sergei V. Strelkov ◽  
Paul J. Declerck
Keyword(s):  
Binding Site ◽  
Small Molecule ◽  
Intracellular Signaling ◽  
Plasminogen Activator Inhibitor ◽  
Plasminogen Activator Inhibitor 1 ◽  
Joint Region ◽  
Flexible Joint ◽  
Step Mechanism ◽  
Pai 1

Plasminogen activator inhibitor-1 (PAI-1), a key regulator of the fibrinolytic system, is the main physiological inhibitor of plasminogen activators. By interacting with matrix components, including vitronectin (Vn), PAI-1 plays a regulatory role in tissue remodeling, cell migration, and intracellular signaling. Emerging evidence points to a role for PAI-1 in various pathological conditions, including cardiovascular diseases, cancer, and fibrosis. Targeting PAI-1 is therefore a promising therapeutic strategy in PAI-1-related pathologies. A class of small molecule inhibitors including TM5441 and TM5484, designed to bind the cleft in the central β-sheet A of PAI-1, showed to be potent PAI-1 inhibitors in vivo. However, their binding site has not yet been confirmed. Here, we report two X-ray crystallographic structures of PAI-1 in complex with TM5484. The structures revealed a binding site at the flexible joint region, which is distinct from the presumed binding site. Based on the structural analysis and biochemical data we propose a mechanism for the observed dose-dependent two-step mechanism of PAI-1 inhibition. By binding to the flexible joint region in PAI-1, TM5484 might restrict the structural flexibility of this region, thereby inducing a substrate form of PAI-1 followed by a conversion to an inert form.

scholarly journals Dual Labeling of the CBP/p300 KIX Domain for19F NMR Leads to Identification of a New Small-Molecule Binding Site

ChemBioChem ◽  
2018 ◽  
Vol 19 (9) ◽  
pp. 963-969 ◽  
Author(s):  
Clifford T. Gee ◽  
Keith E. Arntson ◽  
Edward J. Koleski ◽  
Rachel Lynn Staebell ◽  
William C. K. Pomerantz
Keyword(s):  
Binding Site ◽  
Small Molecule ◽  
Kix Domain

scholarly journals High resolution structure of human apolipoprotein (a) kringle IV type 2: beyond the lysine binding site

2020 ◽  
Vol 61 (12) ◽  
pp. 1687-1696
Author(s):  
Alice Santonastaso ◽  
Maristella Maggi ◽  
Hugo De Jonge ◽  
Claudia Scotti
Keyword(s):  
High Resolution ◽  
Binding Site ◽  
Small Molecule ◽  
Aminocaproic Acid ◽  
Variable Number ◽  
Crystallographic Structure ◽  
Heparin Binding ◽  
Human Apolipoprotein ◽  
Unique Shape

Lipoprotein (a) [Lp(a)] is characterized by an LDL-like composition in terms of lipids and apoB100, and by one copy of a unique glycoprotein, apo(a). The apo(a) structure is mainly based on the repetition of tandem kringle domains with high homology to plasminogen kringles 4 and 5. Among them, kringle IV type 2 (KIV-2) is present in a highly variable number of genetically encoded repeats, whose length is inversely related to Lp(a) plasma concentration and cardiovascular risk. Despite it being the major component of apo(a), the actual function of KIV-2 is still unclear. Here, we describe the first high-resolution crystallographic structure of this domain. It shows a general fold very similar to other KIV domains with high and intermediate affinity for the lysine analog, ε-aminocaproic acid. Interestingly, KIV-2 presents a lysine binding site (LBS) with a unique shape and charge distribution. KIV-2 affinity for predicted small molecule binders was found to be negligible in surface plasmon resonance experiments; and with the LBS being nonfunctional, we propose to rename it “pseudo-LBS”. Further investigation of the protein by computational small-molecule docking allowed us to identify a possible heparin-binding site away from the LBS, which was confirmed by specific reverse charge mutations abolishing heparin binding. This study opens new possibilities to define the pathogenesis of Lp(a)-related diseases and to facilitate the design of specific therapeutic drugs.

scholarly journals Discovery and Design of Novel Small Molecule GSK-3 Inhibitors Targeting the Substrate Binding Site

2020 ◽  
Vol 21 (22) ◽  
pp. 8709
Author(s):  
Ido Rippin ◽  
Netaly Khazanov ◽  
Shirley Ben Joseph ◽  
Tania Kudinov ◽  
Eva Berent ◽  
...  
Keyword(s):  
Binding Site ◽  
Small Molecule ◽  
Substrate Binding ◽  
Pharmacophore Model ◽  
Drug Induced ◽  
Substrate Binding Site ◽  
Zinc Database ◽  
Competitive Inhibitors ◽  
Ic50 Values ◽  
Critical Binding

The serine/threonine kinase, GSK-3, is a promising drug discovery target for treating multiple pathological disorders. Most GSK-3 inhibitors that were developed function as ATP competitive inhibitors, with typical limitations in specificity, safety and drug-induced resistance. In contrast, substrate competitive inhibitors (SCIs), are considered highly selective, and more suitable for clinical practice. The development of SCIs has been largely neglected in the past because the ambiguous, undefined nature of the substrate-binding site makes them difficult to design. In this study, we used our previously described structural models of GSK-3 bound to SCI peptides, to design a pharmacophore model and to virtually screen the “drug-like” Zinc database (~6.3 million compounds). We identified leading hits that interact with critical binding elements in the GSK-3 substrate binding site and are chemically distinct from known GSK-3 inhibitors. Accordingly, novel GSK-3 SCI compounds were designed and synthesized with IC50 values of~1–4 μM. Biological activity of the SCI compound was confirmed in cells and in primary neurons that showed increased β-catenin levels and reduced tau phosphorylation in response to compound treatment. We have generated a new type of small molecule GSK-3 inhibitors and propose to use this strategy to further develop SCIs for other protein kinases.

scholarly journals Allosteric “beta-blocker” isolated from a DNA-encoded small molecule library

2017 ◽  
Vol 114 (7) ◽  
pp. 1708-1713 ◽  
Author(s):  
Seungkirl Ahn ◽  
Alem W. Kahsai ◽  
Biswaranjan Pani ◽  
Qin-Ting Wang ◽  
Shuai Zhao ◽  
...  
Keyword(s):  
Binding Site ◽  
G Protein ◽  
Small Molecule ◽  
Adrenergic Receptor ◽  
Camp Production ◽  
Small Molecule Library ◽  
Small Molecule Libraries ◽  
Negative Allosteric Modulator ◽  
G Protein Coupled ◽  
Small Molecule Ligand

The β2-adrenergic receptor (β2AR) has been a model system for understanding regulatory mechanisms of G-protein–coupled receptor (GPCR) actions and plays a significant role in cardiovascular and pulmonary diseases. Because all known β-adrenergic receptor drugs target the orthosteric binding site of the receptor, we set out to isolate allosteric ligands for this receptor by panning DNA-encoded small-molecule libraries comprising 190 million distinct compounds against purified human β2AR. Here, we report the discovery of a small-molecule negative allosteric modulator (antagonist), compound 15 [([4-((2S)-3-(((S)-3-(3-bromophenyl)-1-(methylamino)-1-oxopropan-2-yl)amino)-2-(2-cyclohexyl-2-phenylacetamido)-3-oxopropyl)benzamide], exhibiting a unique chemotype and low micromolar affinity for the β2AR. Binding of 15 to the receptor cooperatively enhances orthosteric inverse agonist binding while negatively modulating binding of orthosteric agonists. Studies with a specific antibody that binds to an intracellular region of the β2AR suggest that 15 binds in proximity to the G-protein binding site on the cytosolic surface of the β2AR. In cell-signaling studies, 15 inhibits cAMP production through the β2AR, but not that mediated by other Gs-coupled receptors. Compound 15 also similarly inhibits β-arrestin recruitment to the activated β2AR. This study presents an allosteric small-molecule ligand for the β2AR and introduces a broadly applicable method for screening DNA-encoded small-molecule libraries against purified GPCR targets. Importantly, such an approach could facilitate the discovery of GPCR drugs with tailored allosteric effects.

Discovery of a novel small molecule binding site of human survivin

2007 ◽  
Vol 17 (11) ◽  
pp. 3122-3129 ◽  
Author(s):  
Michael D. Wendt ◽  
Chaohong Sun ◽  
Aaron Kunzer ◽  
Daryl Sauer ◽  
Kathy Sarris ◽  
...  
Keyword(s):  
Binding Site ◽  
Small Molecule

scholarly journals Antibody purification via affinity membrane chromatography method utilizing nucleotide binding site targeting with a small molecule

The Analyst ◽  
2016 ◽  
Vol 141 (24) ◽  
pp. 6571-6582 ◽  
Author(s):  
Nur Mustafaoglu ◽  
Tanyel Kiziltepe ◽  
Basar Bilgicer
Keyword(s):  
Affinity Chromatography ◽  
Binding Site ◽  
Small Molecule ◽  
Nucleotide Binding ◽  
Nucleotide Binding Site ◽  
Chromatography Method ◽  
Antibody Purification ◽  
Membrane Affinity ◽  
Affinity Membrane ◽  
Site Targeting

m-NBST is a small-molecule based membrane affinity chromatography system that utilizes the NBS, providing high levels of antibody recovery and purity.

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