Quinacrine Noncompetitive Inhibitor Binding Site Localized on theTorpedoAcetylcholine Receptor in the Open State†

Biochemistry ◽  
1996 ◽  
Vol 35 (20) ◽  
pp. 6330-6336 ◽  
Author(s):  
David A. Johnson ◽  
Scott Ayres
Keyword(s):  
Binding Site ◽  
Inhibitor Binding ◽  
Noncompetitive Inhibitor

scholarly journals Crystallographic Identification of a Noncompetitive Inhibitor Binding Site on the Hepatitis C Virus NS5B RNA Polymerase Enzyme

2003 ◽  
Vol 77 (13) ◽  
pp. 7575-7581 ◽  
Author(s):  
Robert A. Love ◽  
Hans E. Parge ◽  
Xiu Yu ◽  
Michael J. Hickey ◽  
Wade Diehl ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Rna Polymerase ◽  
Binding Site ◽  
Rna Binding ◽  
Nonstructural Protein ◽  
Inhibitor Binding ◽  
Catalytic Center ◽  
Molecule Inhibitor ◽  
Noncompetitive Inhibitor

ABSTRACT The virus-encoded nonstructural protein 5B (NS5B) of hepatitis C virus (HCV) is an RNA-dependent RNA polymerase and is absolutely required for replication of the virus. NS5B exhibits significant differences from cellular polymerases and therefore has become an attractive target for anti-HCV therapy. Using a high-throughput screen, we discovered a novel NS5B inhibitor that binds to the enzyme noncompetitively with respect to nucleotide substrates. Here we report the crystal structure of NS5B complexed with this small molecule inhibitor. Unexpectedly, the inhibitor is bound within a narrow cleft on the protein's surface in the “thumb” domain, about 30 Å from the enzyme's catalytic center. The interaction between this inhibitor and NS5B occurs without dramatic changes to the structure of the protein, and sequence analysis suggests that the binding site is conserved across known HCV genotypes. Possible mechanisms of inhibition include perturbation of protein dynamics, interference with RNA binding, and disruption of enzyme oligomerization.

scholarly journals Crystallographic Identification of a Noncompetitive Inhibitor Binding Site on the Hepatitis C Virus NS5B RNA Polymerase Enzyme

2003 ◽  
Vol 77 (18) ◽  
pp. 10176-10176
Author(s):  
Robert A. Love ◽  
Hans E. Parge ◽  
Xiu Yu ◽  
Michael J. Hickey ◽  
Wade Diehl ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Rna Polymerase ◽  
Binding Site ◽  
Inhibitor Binding ◽  
Noncompetitive Inhibitor

scholarly journals Structural elements of a pH-sensitive inhibitor binding site in NMDA receptors

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Michael C. Regan ◽  
Zongjian Zhu ◽  
Hongjie Yuan ◽  
Scott J. Myers ◽  
Dave S. Menaldino ◽  
...  
Keyword(s):  
Nmda Receptors ◽  
Binding Site ◽  
Ph Sensitive ◽  
Structural Elements ◽  
Inhibitor Binding

scholarly journals Identification of Small Molecule Inhibitors of the Deubiquitinating Activity of the SARS-CoV-2 Papain-Like Protease: in silico Molecular Docking Studies and in vitro Enzymatic Activity Assay

2020 ◽  
Vol 8 ◽  
Author(s):  
Eleni Pitsillou ◽  
Julia Liang ◽  
Katherine Ververis ◽  
Kah Wai Lim ◽  
Andrew Hung ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Enzymatic Activity ◽  
Small Molecules ◽  
Binding Site ◽  
Protein Docking ◽  
Activity Assay ◽  
Epicatechin Gallate ◽  
Inhibitor Binding ◽  
Enzymatic Activity Assay

COVID-19 is an ongoing pandemic caused by the SARS-CoV-2 virus with important political, socio-economic, and public health consequences. Inhibiting replication represents an important antiviral approach, and in this context two viral proteases, the SARS-CoV-2 main and papain-like proteases (PLpro), which cleave pp1a and pp1ab polypeptides, are critical. Along with protease activity, the PLpro possesses deubiquitinating activity, which is important in immune regulation. Naphthalene-based inhibitors, such as the well-investigated GRL-0617 compound, have been shown to possess dual effects, inhibiting both protease and deubiquitinating activity of the PLpro. Rather than binding to the canonical catalytic triad, these type of non-covalent inhibitors target an adjacent pocket, the naphthalene-inhibitor binding site. Using a high-throughput screen, we have previously identified the dietary hypericin, rutin, and cyanidin-3-O-glucoside compounds as potential protease inhibitors targeting the naphthalene-inhibitor binding site. Here, our aim was to investigate the binding characteristics of these compounds to the PLpro, and to evaluate deubiquitinating activity, by analyzing seven different PLpro crystal structures. Molecular docking highlighted the relatively high affinity of GRL-0617 and dietary compounds. In contrast binding of the small molecules was abolished in the presence of ubiquitin in the palm subdomain of the PLpro. Further, docking the small molecules in the naphthalene-inhibitor binding site, followed by protein-protein docking revealed displacement of ubiquitin in a conformation inconsistent with functional activity. Finally, the deubiquitinating activity was validated in vitro using an enzymatic activity assay. The findings indicated that the dietary compounds inhibited deubiquitinase activity in the micromolar range with an order of activity of GRL-0167, hypericin >> rutin, cyanidin-3-O-glucoside > epigallocatechin gallate, epicatechin gallate, and cefotaxime. Our findings are in accordance with mechanisms and potential antiviral effects of the naphthalene-based, GRL-0617 inhibitor, which is currently progressing in preclinical trials. Further, our findings indicate that in particular hypericin, rutin, and cyanidin-3-O-glucoside, represent suitable candidates for subsequent evaluation as PLpro inhibitors.

scholarly journals The Noncompetitive Inhibitor Ww781 Senses Changes in Erythrocyte Anion Exchanger (Ae1) Transport Site Conformation and Substrate Binding

2000 ◽  
Vol 115 (2) ◽  
pp. 159-174 ◽  
Author(s):  
Philip A. Knauf ◽  
Nancy Mendoza Raha ◽  
Laurie J. Spinelli
Keyword(s):  
Free Energy ◽  
Binding Site ◽  
Magnetic Resonance Data ◽  
Ping Pong ◽  
Asymmetric Distributions ◽  
Disulfonic Stilbene ◽  
Noncompetitive Inhibitor ◽  
Relationship Of ◽  
Asymmetrically Distributed ◽  
Transport Site

WW781 binds reversibly to red blood cell AE1 and inhibits anion exchange by a two-step mechanism, in which an initial complex (complex 1) is rapidly formed, and then there is a slower equilibration to form a second complex (complex 2) with a lower free energy. According to the ping-pong kinetic model, AE1 can exist in forms with the anion transport site facing either inward or outward, and the transition between these forms is greatly facilitated by binding of a transportable substrate such as Cl−. Both the rapid initial binding of WW781 and the formation of complex 2 are strongly affected by the conformation of AE1, such that the forms with the transport site facing outward have higher affinity than those with the transport site facing inward. In addition, binding of Cl− seems to raise the free energy of complex 2 relative to complex 1, thereby reducing the equilibrium binding affinity, but Cl− does not compete directly with WW781. The WW781 binding site, therefore, reveals a part of the AE1 structure that is sensitive to Cl− binding and to transport site orientation, in addition to the disulfonic stilbene binding site. The relationship of the inhibitory potency of WW781 under different conditions to the affinities for the different forms of AE1 provides information on the possible asymmetric distributions of unloaded and Cl−-loaded transport sites that are consistent with the ping-pong model, and supports the conclusion from flux and nuclear magnetic resonance data that both the unloaded and Cl−-loaded sites are very asymmetrically distributed, with far more sites facing the cytoplasm than the outside medium. This asymmetry, together with the ability of WW781 to recruit toward the forms with outward-facing sites, implies that WW781 may be useful for changing the conformation of AE1 in studies of structure–function relationships.

Molecular Modelling of the Interaction of Cyanoacrylate Inhibitors with Photosystem II Part 2. The Effect of Stereochemistry of Inhibitor Binding

1993 ◽  
Vol 48 (9-10) ◽  
pp. 782-787 ◽  
Author(s):  
Simon P. Mackay ◽  
Patrick J. O’Malley
Keyword(s):  
Electron Transfer ◽  
Photosystem Ii ◽  
Binding Site ◽  
Energy Minimization ◽  
Electrostatic Interactions ◽  
D1 Protein ◽  
Spatial Arrangement ◽  
Inhibitor Binding ◽  
Protein Residues ◽  
Quinone Binding

Abstract The 2-cyanoacrylate inhibitors are a potent class of herbicides which block electron transfer in photosystem II. The spatial arrangement of different functional groups are an important factor in determining activity and a number of derivatives have been used as stereospecific probes of the secondary quinone binding site. More than one region of stereoselectivity in the binding site has been identified which influences the interaction with specific groups of the inhibitor. We have studied the interaction of various stereoisomers of the cyanoacrylates with the binding site in the D1 protein (residues Leu 210 to Val 280) by determining the nonbonded intermolecular energies between the modelled structures calculated by van der Waals and electrostatic interactions after energy minimization of the combined structures to reduce inter and intramolecular strain and have found that the results reflect the experimentally determined data

Prediction of Noncompetitive Inhibitor Binding Mode Reveals Promising Site for Allosteric Modulation of Falcipain-2

2019 ◽  
Vol 123 (34) ◽  
pp. 7327-7342 ◽  
Author(s):  
Jorge Enrique Hernández González ◽  
Lilian Hernández Alvarez ◽  
Pedro Geraldo Pascutti ◽  
Vitor B. P. Leite
Keyword(s):  
Binding Mode ◽  
Allosteric Modulation ◽  
Inhibitor Binding ◽  
Noncompetitive Inhibitor

Probing the inhibitor-binding site of aldose reductase with site-directed mutagenesis

1998 ◽  
Vol 256 (2) ◽  
pp. 310-316 ◽  
Author(s):  
Thomas C. Hohman ◽  
Ossama El-Kabbani ◽  
Michael S. Malamas ◽  
Kehdih Lai ◽  
Tatiana Putilina ◽  
...  
Keyword(s):  
Binding Site ◽  
Aldose Reductase ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis ◽  
Inhibitor Binding
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