scholarly journals Glycine Transporter 2: Mechanism and Allosteric Modulation

2021 ◽  
Vol 8 ◽  
Author(s):  
Zachary J. Frangos ◽  
Ryan P. Cantwell Chater ◽  
Robert J. Vandenberg
Keyword(s):  
Protein Interactions ◽  
Drugs Of Abuse ◽  
Allosteric Site ◽  
Allosteric Inhibitors ◽  
Competitive Inhibitors ◽  
Transport Inhibitors ◽  
Modulatory Sites ◽  
Clearance Kinetics ◽  
Major Target ◽  
Glycine Transporter 2

Neurotransmitter sodium symporters (NSS) are a subfamily of SLC6 transporters responsible for regulating neurotransmitter signalling. They are a major target for psychoactive substances including antidepressants and drugs of abuse, prompting substantial research into their modulation and structure-function dynamics. Recently, a series of allosteric transport inhibitors have been identified, which may reduce side effect profiles, compared to orthosteric inhibitors. Allosteric inhibitors are also likely to provide different clearance kinetics compared to competitive inhibitors and potentially better clinical outcomes. Crystal structures and homology models have identified several allosteric modulatory sites on NSS including the vestibule allosteric site (VAS), lipid allosteric site (LAS) and cholesterol binding site (CHOL1). Whilst the architecture of eukaryotic NSS is generally well conserved there are differences in regions that form the VAS, LAS, and CHOL1. Here, we describe ligand-protein interactions that stabilize binding in each allosteric site and explore how differences between transporters could be exploited to generate NSS specific compounds with an emphasis on GlyT2 modulation.

scholarly journals Identification and Biological Evaluation of CK2 Allosteric Fragments through Structure-Based Virtual Screening

Molecules ◽  
2020 ◽  
Vol 25 (1) ◽  
pp. 237 ◽  
Author(s):  
Chunqiong Li ◽  
Xuewen Zhang ◽  
Na Zhang ◽  
Yue Zhou ◽  
Guohui Sun ◽  
...  
Keyword(s):  
Virtual Screening ◽  
Interaction Mechanism ◽  
Pharmacophore Model ◽  
Binding Pocket ◽  
Biological Evaluation ◽  
Atp Binding ◽  
Allosteric Site ◽  
Allosteric Inhibitors ◽  
Competitive Inhibitors ◽  
Reduced Toxicity

Casein kinase II (CK2) is considered as an attractive cancer therapeutic target, and recent efforts have been made to develop its ATP-competitive inhibitors. However, achieving selectivity with respect to related kinases remains challenging due to the highly conserved ATP-binding pocket of kinases. Allosteric inhibitors, by targeting the much more diversified allosteric site relative to the highly conserved ATP-binding pocket, might be a promising strategy with the enhanced selectivity and reduced toxicity than ATP-competitive inhibitors. The previous studies have highlighted the traditional serendipitousity of discovering allosteric inhibitors owing to the complicate allosteric modulation. In this current study, we identified the novel allosteric inhibitors of CK2α by combing structure-based virtual screening and biological evaluation methods. The structure-based pharmacophore model was built based on the crystal structure of CK2α-compound 15 complex. The ChemBridge fragment library was searched by evaluating the fit values of these molecules with the optimized pharmacophore model, as well as the binding affinity of the CK2α-ligand complexes predicted by Alloscore web server. Six hits forming the holistic interaction mechanism with the αD pocket were retained after pharmacophore- and Alloscore-based screening for biological test. Compound 3 was found to be the most potent non-ATP competitive CK2α inhibitor (IC50 = 13.0 μM) with the anti-proliferative activity on A549 cancer cells (IC50 = 23.1 μM). Our results provide new clues for further development of CK2 allosteric inhibitors as anti-cancer hits.

scholarly journals Proposed allosteric inhibitors bind to the ATP site of CK2α

2020 ◽  
Author(s):  
Paul Brear ◽  
Darby Ball ◽  
Katherine Stott ◽  
Sheena D’Arcy ◽  
Marko Hyvönen
Keyword(s):  
Mass Spectrometry ◽  
Crystal Structures ◽  
Specific Inhibition ◽  
Primary Reason ◽  
Allosteric Site ◽  
Allosteric Inhibitors ◽  
Small Molecule Inhibition ◽  
Competitive Inhibitors ◽  
Original Report ◽  
Target Activity

AbstractCK2α is a ubiquitous, well-studied protein kinase that is a target for small molecule inhibition, for treatment of cancers. While many different classes of ATP-competitive inhibitors have been described for CK2α, they tend to suffer from significant off-target activity and new approaches are needed. A series of inhibitors of CK2α has recently been described as allosteric, acting at a previously unidentified binding site. Given the similarity of these inhibitors to known ATP-competitive inhibitors, we have investigated these further. In our thorough structural and biophysical analyses, we have found no evidence that these inhibitors bind to the proposed allosteric site. Rather, we report crystal structures, competitive ITC and NMR, HDX mass spectrometry and chemoinformatic analyses that all point to these compounds binding in the ATP pocket. Our crystal structures however do show that the proposed allosteric site can bind ligands, just not those in the previously described series. Comparison of our results and experimental details with the data presented in the original report suggest several reasons for the disparity in our conclusions, the primary reason being non-specific inhibition by aggregation.Table of Content graphics

Approach in improving potency and selectivity of kinase inhibitors: Allosteric kinase inhibitors

2020 ◽  
Vol 21 ◽  
Author(s):  
Shangfei Wei ◽  
Tianming Zhao ◽  
Jie Wang ◽  
Xin Zhai
Keyword(s):  
Protein Interactions ◽  
Kinase Inhibitors ◽  
Binding Modes ◽  
Allosteric Inhibitors ◽  
Wide Range ◽  
Allosteric Sites ◽  
Protein Functions ◽  
Regulate Protein

: Allostery is an efficient and particular regulatory mechanism to regulate protein functions. Different from conserved orthosteric sites, allosteric sites have distinctive functional mechanism to form the complex regulatory network. In drug discovery, kinase inhibitors targeting the allosteric pockets have received extensive attention for the advantages of high selectivity and low toxicity. The approval of trametinib as the first allosteric inhibitor validated that allosteric inhibitors could be used as effective therapeutic drugs for treatment of diseases. To date, a wide range of allosteric inhibitors have been identified. In this perspective, we outline different binding modes and potential advantages of allosteric inhibitors. In the meantime, the research processes of typical and novel allosteric inhibitors are described briefly in terms of structureactivity relationships, ligand-protein interactions and in vitro and in vivo activity. Additionally, challenges as well as opportunities are presented.

scholarly journals Design of Disruptors of the Hsp90–Cdc37 Interface

Molecules ◽  
2020 ◽  
Vol 25 (2) ◽  
pp. 360 ◽  
Author(s):  
Ilda D’Annessa ◽  
Naama Hurwitz ◽  
Valentina Pirota ◽  
Giovanni Luca Beretta ◽  
Stella Tinelli ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Human Cancer ◽  
Specific Protein ◽  
Cancer Cell Proliferation ◽  
Protein Protein Interactions ◽  
Suitable Candidate ◽  
Structural Stabilization ◽  
Human Cancer Cells ◽  
Theoretical Approaches ◽  
Competitive Inhibitors

The molecular chaperone Hsp90 is a ubiquitous ATPase-directed protein responsible for the activation and structural stabilization of a large clientele of proteins. As such, Hsp90 has emerged as a suitable candidate for the treatment of a diverse set of diseases, such as cancer and neurodegeneration. The inhibition of the chaperone through ATP-competitive inhibitors, however, was shown to lead to undesirable side effects. One strategy to alleviate this problem is the development of molecules that are able to disrupt specific protein–protein interactions, thus modulating the activity of Hsp90 only in the particular cellular pathway that needs to be targeted. Here, we exploit novel computational and theoretical approaches to design a set of peptides that are able to bind Hsp90 and compete for its interaction with the co-chaperone Cdc37, which is found to be responsible for the promotion of cancer cell proliferation. In spite of their capability to disrupt the Hsp90–Cdc37 interaction, no important cytotoxicity was observed in human cancer cells exposed to designed compounds. These findings imply the need for further optimization of the compounds, which may lead to new ways of interfering with the Hsp90 mechanisms that are important for tumour growth.

Anticancer applications of allosteric inhibitors of proteasome.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. e23066-e23066
Author(s):  
Pawel A. Osmulski ◽  
Jodie Cropper ◽  
Matt Giletto ◽  
Corey Jones ◽  
Caleb Killer ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Cell Lines ◽  
Cancer Cell ◽  
Cancer Cell Lines ◽  
26S Proteasome ◽  
Substrate Uptake ◽  
Allosteric Inhibitors ◽  
Catalytic Core ◽  
Competitive Inhibitors ◽  
And Shifts

e23066 Background: Proteasome as a hub protease of the ubiquitin proteasome pathway is an established anticancer drug target. Several drugs that inhibit proteasome are currently used to successfully treat aggressive blood cancers. These drugs are based on their competition with protein substrates of proteasome. However, efficacy of these drugs toward solid cancers is inadequate. Besides, the side effects and developing drug resistance are increasingly hampering the therapy. Therefore, there is an unmet challenge to develop new types of proteasome targeting compounds that are efficient against solid cancers and utilize other mechanisms to stop proteasome. Here we present a compound with a novel molecular mechanism, potentially bypassing limitations of the available drugs. Methods: We rationally designed and synthesized a series of small molecule “B” compounds, derivatives of a binding domain of seco-rapamycin that noncompetitively interfere with peptidase activities of proteasome. We tested effects of the compounds in vitro on purified proteasome, in cellulo with selected cancer cell lines and in a xenograft mouse model of prostate cancer. Results: We found that compound B1 binds to the catalytic core of proteasome far from the catalytic sites, destabilizes assembly of the 26S proteasome responsible for digest of polyUb substrates and allosterically inhibits its proteolytic activities. Molecularly, B1 impedes the gating mechanism responsible for substrate uptake as found with AFM. Tryptophan fluorescence indicates that B1 changes proteasome fold and the binding mode of competitive inhibitors. B1 substantially decreases viability of selected cancer cell lines and shifts their mechanical phenotype toward noncancerous status. B1 synergizes with bortezomib decreasing the IC50 5-10 fold. In a xenograft hormone resistant prostate cancer model, B1 treatment leads to shrinkage of the tumor size, decreases enumeration of aggressive, EpCAM+ CTCs and shifts the macrophage profile toward predator M1 type. Conclusions: B1 compounds constitute a new class of noncompetitive allosteric inhibitors of proteasome that could be useful to develop to treat aggressive prostate cancers alone or in synergy with competitive inhibitors.

Transport of Succinate in Escherichia coli. III. Biochemical and Genetic Studies of the Mechanism of Transport in Membrane Vesicles

1974 ◽  
Vol 52 (10) ◽  
pp. 854-866 ◽  
Author(s):  
Theodore C. Y. Lo ◽  
M. Khalil Rayman ◽  
B. D. Sanwal
Keyword(s):  
Escherichia Coli ◽  
Lactate Dehydrogenase ◽  
Membrane Vesicles ◽  
Coli Strain ◽  
Weight Of Evidence ◽  
Lactate Oxidation ◽  
Dicarboxylate Transport ◽  
Competitive Inhibitors ◽  
Transport Inhibitors

The D-lactate oxidation dependent transport of succinate in membrane vesicles of an Escherichia coli strain lacking succinate dehydrogenase and fumarate reductase is inhibited by several categories of compounds. One category consists of compounds that are electron transport inhibitors (Amytal, Dicumarol, and mercurials), the second of compounds that act as competitive inhibitors of D-lactate dehydrogenase (oxamate and β-chlorolactate), the third of reagents that inhibit the Ca2+–Mg2+-activated ATPase (dicyclohexylcarbodiimide and pyrophosphate), and the fourth of compounds that tap off electrons from the respiratory chain (2,6-dichlorophenolindophenol). None of the succinate transport inhibitors, including mercurials like p-chloromercuribenzoate, interfere with the binding of succinate to the presumed membrane carriers.Membrane preparations from mutants of E. coli lacking D-lactate dehydrogenase are unable to transport succinate in the presence of D-lactate. Whole cells of these mutants, however, take up succinate normally. This observation suggests that D-lactate oxidation is not obligatorily linked in vivo to the uptake of succinate although the possibility is not excluded that transport in such mutants may be linked to some other dehydrogenase. Mutants having altered levels of ATPase, or membrane preparations made from such cells also have greatly reduced capacity to transport succinate. This observation coupled with the finding that ATPase inhibitors block dicarboxylate transport suggests involvement of ATPase in an unknown way in the concentrative uptake of succinate.With the exception of oxamate, β-chlorolactate (competitive inhibitors of D-lactate oxidation), and dicyclohexylcarbodiimide, all of the inhibitors of succinate uptake (including p-chloromercuribenzoate) cause an immediate efflux of preloaded succinate from membrane vesicles. Efflux is also caused by proton conducting reagents. The Km for efflux is 1.9 mM. This value is to be compared with the Km for influx, which is only about 0.02 mM.The weight of evidence favors the view that the active transport of succinate in vesicles occurs as a result of an energization of the membranes by the passage of electrons, although alternate oxidation and reduction of the succinate carrier as a mechanism for transport has not been definitely ruled out.

scholarly journals Detection of Allosteric Kinase Inhibitors by Displacement of Active Site Probes

2012 ◽  
Vol 17 (6) ◽  
pp. 813-821 ◽  
Author(s):  
Connie S. Lebakken ◽  
Laurie J. Reichling ◽  
Jason M. Ellefson ◽  
Steven M. Riddle
Keyword(s):  
Active Site ◽  
Kinase Inhibitors ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Published Data ◽  
Binding Assays ◽  
Allosteric Inhibitors ◽  
Time Resolved ◽  
Inactive Form ◽  
Competitive Inhibitors

Non–adenosine triphosphate (ATP) competitive, allosteric inhibitors provide a promising avenue to develop highly selective small-molecule kinase inhibitors. Although this class of compounds is growing, detection of such inhibitors can be challenging as standard kinase activity assays preferentially detect compounds that bind to active kinases in an ATP competitive manner. We have previously described a time-resolved fluorescence resonance energy transfer (TR-FRET)–based kinase binding assay using the competitive displacement of ATP competitive active site fluorescent probes (“tracers”). Although this format has gained acceptance, published data with this and related formats are almost entirely without examples of non-ATP competitive compounds. Thus, this study addresses whether this format is useful for non-ATP competitive inhibitors. To this end, 15 commercially available non-ATP competitive inhibitors were tested for their ability to displace ATP competitive probes. Despite the diversity of both compound structures and their respective targets, 14 of the 15 compounds displaced the tracers with IC50 values comparable to literature values. We conclude that such binding assays are well suited for the study of non-ATP competitive inhibitors. In addition, we demonstrate that allosteric inhibitors of BCR-Abl and MEK bind preferentially to the nonphosphorylated (i.e., inactive) form of the kinase, indicating that binding assays may be a preferred format in some cases.

scholarly journals In Silico Identification of Potential Allosteric Inhibitors of the SARS-CoV-2 Helicase

2020 ◽  
Author(s):  
Adekunle Rowaiye ◽  
Olukemi Onuh ◽  
Titilayo Asala ◽  
Amoge Ogu ◽  
Doofan Bur ◽  
...  
Keyword(s):  
Small Molecules ◽  
Inhibitory Activity ◽  
In Silico ◽  
Allosteric Site ◽  
Allosteric Inhibitors ◽  
Protein Targets ◽  
Docking Simulations ◽  
Lead Compounds ◽  
The Galaxy ◽  
African Plants

<p>The COVID-19 pandemic ravages the globe causing unprecedented health and economic challenges. As the world prospects for a cure, scientists are looking critically at strategic protein targets within the SARS-CoV-2 that have therapeutic significance. One of such targets is the Helicase which is an enzyme that affects all aspects of SARS-CoV-2 RNA metabolism. The aim of this study is to identify small molecules from natural products that have strong binding affinity with and inhibitory activity against an allosteric site (Pocket 26) of SARS-CoV-2 Helicase. Pyrx was used for the <i>in silico</i> molecular docking simulations of SARS-CoV-2 Helicase (QHD43415-12.pdb) against a library of small molecules obtained from edible African plants. Triphenylmethane which had a docking score of -7.4 kcal/mol was chosen as a reference molecule. Virtual screening for oral bioavailability was done based on the molecular descriptors of the compounds as provided by Pubchem. SwissADME, pkCSM, and Molinspiration were used for further screening for molar refractivity, saturation, promiscuity, pharmacokinetic properties, and bioactivity respectively. The Galaxy webserver which uses the GROMACS software was used for the molecular dynamic simulation and analyses. The lead compounds are Gibberellin A12, A20 and A51 obtained from Green peas and the Okra plant. <a>Gibberellin A20 and A51 </a>performed better than the standard. Gibberellin A51 is predicted to show the greatest inhibitory activity against SARS-CoV-2 Helicase. It is recommended that the inhibitory activities of the lead compounds be further investigated.</p>

Potential therapeutic applications of AKAP disrupting peptides

2020 ◽  
Vol 134 (24) ◽  
pp. 3259-3282
Author(s):  
Alessandra Murabito ◽  
Sophie Cnudde ◽  
Emilio Hirsch ◽  
Alessandra Ghigo
Keyword(s):  
Protein Interactions ◽  
Molecular Mechanisms ◽  
Cyclic Adenosine Monophosphate ◽  
Adenosine Monophosphate ◽  
Pharmacological Intervention ◽  
Protein Protein Interactions ◽  
Multiprotein Complexes ◽  
Anchoring Proteins ◽  
Pka Pathway ◽  
Major Target

Abstract The 3′–5′-cyclic adenosine monophosphate (cAMP)/PKA pathway represents a major target for pharmacological intervention in multiple disease conditions. Although the last decade saw the concept of highly compartmentalized cAMP/PKA signaling consolidating, current means for the manipulation of this pathway still do not allow to specifically intervene on discrete cAMP/PKA microdomains. Since compartmentalization is crucial for action specificity, identifying new tools that allow local modulation of cAMP/PKA responses is an urgent need. Among key players of cAMP/PKA signaling compartmentalization, a major role is played by A-kinase anchoring proteins (AKAPs) that, by definition, anchor PKA, its substrates and its regulators within multiprotein complexes in well-confined subcellular compartments. Different tools have been conceived to interfere with AKAP-based protein–protein interactions (PPIs), and these primarily include peptides and peptidomimetics that disrupt AKAP-directed multiprotein complexes. While these molecules have been extensively used to understand the molecular mechanisms behind AKAP function in pathophysiological processes, less attention has been devoted to their potential application for therapy. In this review, we will discuss how AKAP-based PPIs can be pharmacologically targeted by synthetic peptides and peptidomimetics.

Quinoline-based Protein–protein Interaction Inhibitors of LEDGF/p75 and HIV Integrase: An In Silico Study

2019 ◽  
Vol 18 (32) ◽  
pp. 2800-2815 ◽  
Author(s):  
Nisha Chhokar ◽  
Sourav Kalra ◽  
Monika Chauhan ◽  
Anjana Munshi ◽  
Raj Kumar
Keyword(s):  
Protein Interactions ◽  
Biological Data ◽  
Strand Transfer ◽  
Hiv Integrase ◽  
Protein Protein Interactions ◽  
Allosteric Site ◽  
Protein Protein Interaction ◽  
In Silico Study ◽  
Cellular Cofactor

The failure of the Integrase Strand Transfer Inhibitors (INSTIs) due to the mutations occurring at the catalytic site of HIV integrase (IN) has led to the design of allosteric integrase inhibitors (ALLINIs). Lens epithelium derived growth factor (LEDGF/p75) is the host cellular cofactor which helps chaining IN to the chromatin. The protein-protein interactions (PPIs) were observed at the allosteric site (LEDGF/p75 binding domain) between LEDGF/p75 of the host cell and IN of virus. In recent years, many small molecules such as CX04328, CHIBA-3053 and CHI-104 have been reported as LEDGF/p75-IN interaction inhibitors (LEDGINs). LEDGINs have emerged as promising therapeutics to halt the PPIs by binding at the interface of both the proteins. In the present work, we correlated the docking scores for the reported LEDGINs containing quinoline scaffold with the in vitro biological data. The hierarchal clustering method was used to divide the compounds into test and training set. The robustness of the generated model was validated by q2 and r2 for the predicted set of compounds. The generated model between the docking score and biological data was assessed to predict the activity of the hits (quinoline scaffold) obtained from virtual screening of LEDGINs providing their structureactivity relationships to aim for the generation of potent agents.

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