Binding site hotspot map of PI3Kα and mTOR in the presence of selective and dual ATP-competitive inhibitors

2021 ◽  
pp. 1-13
Author(s):  
Francisca Fernanda Nunes Azevedo ◽  
Francisca Joseli Freitas de Sousa ◽  
Francisco Lucas Santos de Oliveira ◽  
Jaqueline Vieira Carletti ◽  
Geancarlo Zanatta
Keyword(s):  
Binding Site ◽  
Competitive Inhibitors

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.

Putrescine or spermidine binding site of aminopropyltransferases and competitive inhibitors

1991 ◽  
Vol 41 (2) ◽  
pp. 205-212 ◽  
Author(s):  
Akira Shirahata ◽  
Toru Morohohi ◽  
Masayo Fukai ◽  
Sakae Akatsu ◽  
Keijiro Samejima
Keyword(s):  
Binding Site ◽  
Competitive Inhibitors

scholarly journals Identification and Mechanistic Characterization of a Peptide Inhibitor of Glycogen Synthase Kinase (GSK3β) Derived from the Disrupted in Schizophrenia 1 (DISC1) Protein

2020 ◽  
Author(s):  
Stephanie Saundh ◽  
Debasis Patnaik ◽  
Steve Gagné ◽  
Josh Bishop ◽  
Sean Lipsit ◽  
...  
Keyword(s):  
Binding Site ◽  
Glycogen Synthase ◽  
Specific Binding ◽  
Direct Interaction ◽  
Glycogen Synthase Kinase ◽  
Atp Binding Site ◽  
Inhibitory Region ◽  
Competitive Inhibitors ◽  
Cellular Pathways

ABSTRACTGlycogen Synthase Kinase 3-beta (GSK3β) is a critical regulator of several cellular pathways involved in neuroplasticity and is a potential target for neurotherapeutic development in the treatment of neuropsychiatric and neurodegenerative diseases. The majority of efforts to develop inhibitors of GSK3β have been focused on developing small molecule inhibitors that compete with ATP through direct interaction with the ATP binding site. This strategy has presented selectivity challenges due to the evolutionary conservation of this domain within the kinome. The Disrupted in Schizophrenia (DISC1) protein, has previously been shown to bind and inhibit GSK3β activity. Here, we report the characterization of a 44-mer peptide derived from human DISC1 (hDISCtide) that is sufficient to both bind and inhibit GSK3β in a non-competitive mode that is distinct from classical ATP competitive inhibitors. Based on multiple independent biochemical and biophysical assays, we propose that hDISCtide interacts at two distinct regions of GSK3β: an inhibitory region that partially overlaps with the binding site of FRATide, a well-known GSK3β binding peptide, and a specific binding region that is unique to hDISCtide. Taken together, our findings present a novel avenue for developing a peptide-based selective inhibitor of GSK3β.

scholarly journals Binding of NAD+ by cholera toxin

1987 ◽  
Vol 244 (1) ◽  
pp. 225-230 ◽  
Author(s):  
T S Galloway ◽  
S van Heyningen
Keyword(s):  
Binding Site ◽  
Dissociation Constant ◽  
Cholera Toxin ◽  
Equilibrium Dialysis ◽  
Accurate Determination ◽  
Polyacrylamide Gel ◽  
Nad Glycohydrolase ◽  
Competitive Inhibitors ◽  
Dissociation Constant Kd

1. The Km for NAD+ of cholera toxin working as an NAD+ glycohydrolase is 4 mM, and this is increased to about 50 mM in the presence of low-Mr ADP-ribose acceptors. Only molecules having both the adenine and nicotinamide moieties of NAD+ with minor alterations in the nicotinamide ring can be competitive inhibitors of this reaction. 2. This high Km for NAD+ is also reflected in the dissociation constant, Kd, which was determined by a variety of methods. 3. Results from equilibrium dialysis were subject to high error, but showed one binding site and a Kd of about 3 mM. 4. The A1 peptide of the toxin is digested by trypsin, and this digestion is completely prevented by concentrations of NAD+ above 50 mM. Measurement (by densitometric scanning of polyacrylamide-gel electrophoretograms) of the rate of tryptic digestion at different concentrations of NAD+ allowed a more accurate determination of Kd = 4.0 +/- 0.4 mM. Some analogues of NAD+ that are competitive inhibitors of the glycohydrolase reaction also prevented digestion.

scholarly journals Evidence that enzyme-generated aromatic Michael acceptors covalently modify the nucleotide-binding site of 3α-hydroxysteroid dehydrogenase

1990 ◽  
Vol 269 (3) ◽  
pp. 749-755 ◽  
Author(s):  
J W Ricigliano ◽  
T M Penning
Keyword(s):  
Binding Site ◽  
Kinetic Scheme ◽  
Hydroxysteroid Dehydrogenase ◽  
Enzyme Inactivation ◽  
Affinity Column ◽  
Compound I ◽  
Unsaturated Ketones ◽  
Competitive Inhibitors ◽  
Michael Acceptors ◽  
Steroid Binding

The non-steroidal allylic and acetylenic alcohols 1-(4′-nitrophenyl)prop-2-en-1-ol (I) and 1-(4′-nitrophenyl)prop-2-yn-1-ol (II) are oxidized by homogeneous 3 alpha-hydroxysteroid dehydrogenase to the corresponding alpha β-unsaturated ketones 1-(4′-nitrophenyl)prop-2-en-1-one (III) and 1-(4′-nitrophenyl)prop-2-yn-1-one (IV), which then inactivate the enzyme selectively with high affinity; low effective partition ratios are observed for the parent alcohols [Ricigliano & Penning (1989) Biochem. J. 262, 139-149]. Inactivation of 3 alpha-hydroxysteroid dehydrogenase by compound (I) displays an NAD+ concentration optimum. Scavenging experiments indicate that the enzyme-generated inactivators (III) and (IV) alkylate the enzyme via a release-and-return mechanism. Several lines of evidence suggest that compounds (III) and (IV) covalently modify the NAD(P)(+)-binding site. First, micromolar concentrations of NAD(P)H offer substantial protection against enzyme inactivation mediated by Michael acceptors (III) and (IV). In these protection studies Kd measurements for NAD(P)H approached those measured by fluorescence titration of free enzyme. Secondly, under initial-velocity conditions compounds (III) and (IV) act essentially as competitive inhibitors of NAD+ binding, and as mixed competitive or non-competitive inhibitors against androsterone binding. Thirdly, enzyme inactivated with either compound (III) or compound (IV) fails to bind to NAD+ affinity columns (e.g. Affi-gel Blue). Under the same conditions of chromatography native enzyme and enzyme affinity-labelled at the steroid-binding site with 17 β-bromoacetoxy-5 alpha-dihydrotestosterone is retained on the affinity column. A kinetic scheme that represents the inactivation of the homogeneous dehydrogenase by the enzyme-generated alkylators (III) and (IV) is presented.

Inhibition of bacterial D-3-hydroxybutyrate dehydrogenase by substrates and substrate analogues

1981 ◽  
Vol 59 (10) ◽  
pp. 810-815 ◽  
Author(s):  
Ronald Kluger ◽  
Wing-Cheong Tsui
Keyword(s):  
Hydrogen Bond ◽  
Kinetic Analysis ◽  
Binding Site ◽  
Substrate Inhibition ◽  
Secondary Site ◽  
Hydrogen Bond Donor ◽  
Structural Requirements ◽  
Substrate Analogues ◽  
Competitive Inhibitors ◽  
To Receive

D-3-Hydroxybutyrate dehydrogenase (Pseudomonas lemoignei, EC 1.1.1.30) is subject to substrate inhibition by acetoacetate at concentrations above 5 mM but not by D-3-hydroxybutyrate at concentrations up to 50 mM. NADH causes substrate inhibition at concentrations over 0.1 mM as does NAD. Kinetic analysis suggests that substrate inhibition by acetoacetate is due to its binding to enzyme lacking NADH, a consequence of the ordered bibi mechanism. Substrate inhibition by NADH and NAD arises from binding of these species to a secondary site. This is confirmed by kinetics which indicate that ADP and ATP compete with NAD and NADH at both sites.New analogues of acetoacetate were synthesized to test the specificity requirements of the acetoacetate binding site which has been proposed to contain a hydrogen bond donor and a cation spaced to receive acetoacetate. Both dimethoxyphosphinylacetate and methyl 2-methoxyphosphinylacetate fulfill the structural requirements and are effective. They thus join methyl acetonylphosphonate as the only known competitive inhibitors for the acetoacetate site, confirming the proposed structure.

scholarly journals Structure Activity Relationships of Flavonoids as Potent α-Amylase Inhibitors

2014 ◽  
Vol 9 (8) ◽  
pp. 1934578X1400900 ◽  
Author(s):  
Erdong Yuan ◽  
Benguo Liu ◽  
Qingyi Wei ◽  
Jiguo Yang ◽  
Lei Chen ◽  
...  
Keyword(s):  
Fluorescence Quenching ◽  
Fluorescence Spectroscopy ◽  
Binding Site ◽  
Hydroxyl Group ◽  
Binding Affinities ◽  
Binding Force ◽  
Structure Activity ◽  
Competitive Inhibitors ◽  
Quenching Process ◽  
Amylase Inhibitors

The effects of three flavonoids (quercetin, luteolin, diosmetin) on α-amylase were examined by enzymatic kinetics and fluorescence spectroscopy. The three test flavonoids were non-competitive inhibitors of the enzyme. Addition of flavonoids led to fluorescence quenching of α-amylase. The quenching was initiated from the formation of a complex between the flavonoids and the enzyme, corresponding to a static quenching process. An α-amylase molecule provides a binding site for the test flavonoid. The main binding force was hydrophobic. The decreasing order of inhibition of α-amylase by flavonoids and the binding force was luteolin, diosmetin, and quercetin. It is demonstrated that hydroxylation in ring C and methylation of the hydroxyl group in ring B of flavonoids may weaken the binding affinities to α-amylase.

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