scholarly journals Discovery of cryptic allosteric sites using reversed allosteric communication by a combined computational and experimental strategy

2021 ◽  
Vol 12 (1) ◽  
pp. 464-476
Author(s):  
Duan Ni ◽  
Jiacheng Wei ◽  
Xinheng He ◽  
Ashfaq Ur Rehman ◽  
Xinyi Li ◽  
...  
Keyword(s):  
Md Simulations ◽  
Allosteric Site ◽  
Experimental Strategy ◽  
Allosteric Communication ◽  
Allosteric Sites

Using reversed allosteric communication, we performed MD simulations, MSMs, and mutagenesis experiments, to discover allosteric sites. It reproduced the known allosteric site for MDL-801 on Sirt6 and uncovered a novel cryptic allosteric Pocket X.

scholarly journals The structural basis for cancer drug interactions with the catalytic and allosteric sites of SAMHD1

2018 ◽  
Author(s):  
Kirsten M. Knecht ◽  
Olga Buzovetsky ◽  
Constanze Schneider ◽  
Dominique Thomas ◽  
Vishok Srikanth ◽  
...  
Keyword(s):  
Cancer Therapy ◽  
Genome Stability ◽  
Viral Infections ◽  
Structural Basis ◽  
Cancer Drug ◽  
Allosteric Site ◽  
Nucleotide Analogues ◽  
Future Design ◽  
Nucleotide Analogue ◽  
Allosteric Sites

AbstractSAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase (dNTPase) that depletes cellular dNTPs in non-cycling cells to promote genome stability and to inhibit retroviral and herpes viral replication. In addition to being substrates, cellular nucleotides also allosterically regulate SAMHD1 activity. Recently, it was shown that high expression levels of SAMHD1 are also correlated with significantly worse patient responses to nucleotide analogue drugs important for treating a variety of cancers, including Acute Myeloid Leukemia (AML). In this study, we used biochemical, structural, and cellular methods to examine the interactions of various cancer drugs with SAMHD1. We found that both the catalytic and the allosteric sites of SAMHD1 are sensitive to sugar modifications of the nucleotide analogs, with the allosteric site being significantly more restrictive. We crystallized cladribine-TP, clofarabine-TP, fludarabine-TP, vidarabine-TP, cytarabine-TP, and gemcitabine-TP in the catalytic pocket of SAMHD1. We find that all of these drugs are substrates of SAMHD1 and that the efficacy of most of these drugs is affected by SAMHD1 activity. Of the nucleotide analogues tested, only cladribine-TP with a deoxyribose sugar efficiently induced the catalytically active SAMHD1 tetramer. Together, these results establish a detailed framework for understanding the substrate specificity and allosteric activation of SAMHD1 with regards to nucleotide analogues, which can be used to improve current cancer and antiviral therapies.SignificanceNucleoside analogue drugs are widely used to treat a variety of cancers and viral infections. With an essential role in regulating the nucleotide pool in the cell by degrading cellular nucleotides, SAMHD1 has the potential to decrease the cellular concentration of frequently prescribed nucleotide analogues and thereby decrease their clinical efficacy in cancer therapy. To improve future nucleotide analogue treatments, it is important to understand SAMHD1 interactions with these drugs. Our work thoroughly examines the extent to which nucleotide analogues interact with the catalytic and allosteric sites of SAMHD1. This work contributes to the assessment of SAMHD1 as a potential therapeutic target for cancer therapy and the future design of SAMHD1 modulators that might improve the efficacy of existing therapies.

scholarly journals The structural basis for cancer drug interactions with the catalytic and allosteric sites of SAMHD1

2018 ◽  
Vol 115 (43) ◽  
pp. E10022-E10031 ◽  
Author(s):  
Kirsten M. Knecht ◽  
Olga Buzovetsky ◽  
Constanze Schneider ◽  
Dominique Thomas ◽  
Vishok Srikanth ◽  
...  
Keyword(s):  
Genome Stability ◽  
Structural Basis ◽  
Cancer Drug ◽  
Allosteric Site ◽  
Nucleotide Analogs ◽  
Antiviral Therapies ◽  
Allosteric Sites ◽  
Catalytically Active ◽  
Deoxynucleoside Triphosphate ◽  
Patient Responses

SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase (dNTPase) that depletes cellular dNTPs in noncycling cells to promote genome stability and to inhibit retroviral and herpes viral replication. In addition to being substrates, cellular nucleotides also allosterically regulate SAMHD1 activity. Recently, it was shown that high expression levels of SAMHD1 are also correlated with significantly worse patient responses to nucleotide analog drugs important for treating a variety of cancers, including acute myeloid leukemia (AML). In this study, we used biochemical, structural, and cellular methods to examine the interactions of various cancer drugs with SAMHD1. We found that both the catalytic and the allosteric sites of SAMHD1 are sensitive to sugar modifications of the nucleotide analogs, with the allosteric site being significantly more restrictive. We crystallized cladribine-TP, clofarabine-TP, fludarabine-TP, vidarabine-TP, cytarabine-TP, and gemcitabine-TP in the catalytic pocket of SAMHD1. We found that all of these drugs are substrates of SAMHD1 and that the efficacy of most of these drugs is affected by SAMHD1 activity. Of the nucleotide analogs tested, only cladribine-TP with a deoxyribose sugar efficiently induced the catalytically active SAMHD1 tetramer. Together, these results establish a detailed framework for understanding the substrate specificity and allosteric activation of SAMHD1 with regard to nucleotide analogs, which can be used to improve current cancer and antiviral therapies.

scholarly journals Sensing the allosteric force

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Olga Bozovic ◽  
Brankica Jankovic ◽  
Peter Hamm
Keyword(s):  
Ligand Binding ◽  
Binding Affinity ◽  
Chemical Reactions ◽  
Peptide Ligand ◽  
Allosteric Site ◽  
Small Peptide ◽  
Changing Environment ◽  
Allosteric Communication ◽  
Signalling Cascades ◽  
Living Organisms

AbstractAllosteric regulation is an innate control in most metabolic and signalling cascades that enables living organisms to adapt to the changing environment by tuning the affinity and regulating the activity of target proteins. For a microscopic understanding of this process, a protein system has been designed in such a way that allosteric communication between the binding and allosteric site can be observed in both directions. To that end, an azobenzene-derived photoswitch has been linked to the α3-helix of the PDZ3 domain, arguably the smallest allosteric protein with a clearly identifiable binding and allosteric site. Photo-induced trans-to-cis isomerisation of the photoswitch increases the binding affinity of a small peptide ligand to the protein up to 120-fold, depending on temperature. At the same time, ligand binding speeds up the thermal cis-to-trans back-isomerisation rate of the photoswitch. Based on the energetics of the four states of the system (cis vs trans and ligand-bound vs free), the concept of an allosteric force is introduced, which can be used to drive chemical reactions.

scholarly journals Unraveling allosteric landscapes of allosterome with ASD

2019 ◽  
Author(s):  
Xinyi Liu ◽  
Shaoyong Lu ◽  
Kun Song ◽  
Qiancheng Shen ◽  
Duan Ni ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Protein Function ◽  
Target Identification ◽  
Allosteric Regulation ◽  
Biological Research ◽  
Missense Mutations ◽  
Allosteric Site ◽  
Comprehensive Information ◽  
Allosteric Sites ◽  
Human Proteins

Abstract Allosteric regulation is one of the most direct and efficient ways to fine-tune protein function; it is induced by the binding of a ligand at an allosteric site that is topographically distinct from an orthosteric site. The Allosteric Database (ASD, available online at http://mdl.shsmu.edu.cn/ASD) was developed ten years ago to provide comprehensive information related to allosteric regulation. In recent years, allosteric regulation has received great attention in biological research, bioengineering, and drug discovery, leading to the emergence of entire allosteric landscapes as allosteromes. To facilitate research from the perspective of the allosterome, in ASD 2019, novel features were curated as follows: (i) >10 000 potential allosteric sites of human proteins were deposited for allosteric drug discovery; (ii) 7 human allosterome maps, including protease and ion channel maps, were built to reveal allosteric evolution within families; (iii) 1312 somatic missense mutations at allosteric sites were collected from patient samples from 33 cancer types and (iv) 1493 pharmacophores extracted from allosteric sites were provided for modulator screening. Over the past ten years, the ASD has become a central resource for studying allosteric regulation and will play more important roles in both target identification and allosteric drug discovery in the future.

scholarly journals Two helices control the dynamic crosstalk between the catalytic domains of LRRK2

2021 ◽  
Author(s):  
Jui-Hung Weng ◽  
Phillop C. Aoto ◽  
Robin Lorenz ◽  
Jian Wu ◽  
Sven H. Schmidt ◽  
...  
Keyword(s):  
Md Simulations ◽  
Kinase Domain ◽  
Pharmacological Intervention ◽  
Exchange Mass Spectrometry ◽  
Allosteric Sites ◽  
Hydrogen Deuterium ◽  
Wd40 Domain ◽  
Deuterium Exchange Mass Spectrometry ◽  
And Function ◽  
Hdx Ms

The two major molecular switches in biology, kinases and GTPases, are both contained in the Parkinson’s Disease-related Leucine-rich repeat kinase 2 (LRRK2). Using hydrogen-deuterium exchange mass spectrometry (HDX-MS) and Molecular Dynamics (MD) simulations, we generated a comprehensive dynamic allosteric portrait of the C-terminal domains of LRRK2 (LRRK2 RCKW). We identified two helices that shield the kinase domain and regulate LRRK2 conformation and function. One docking helix in COR-B (Dk-Helix) tethers the COR-B domain to the αC helix of the kinase domain and faces its Activation Loop, while the C-terminal helix (Ct-Helix) extends from the WD40 domain and interacts with both kinase lobes. The Ct-Helix and the N-terminus of the Dk-Helix create a “cap” that regulates the N-Lobe of the kinase domain. Our analyses reveal allosteric sites for pharmacological intervention and confirm the kinase domain as the central hub for conformational control.

scholarly journals PASSer: Prediction of Allosteric Sites Server

2020 ◽  
Author(s):  
Hao Tian ◽  
Xi Jiang ◽  
Peng Tao
Keyword(s):  
Drug Discovery ◽  
Prior Information ◽  
Gradient Boosting ◽  
Command Line ◽  
Allosteric Site ◽  
Command Line Interface ◽  
And Topology ◽  
Extreme Gradient Boosting ◽  
Allosteric Sites ◽  
Allosteric Mechanisms

Allostery is considered important in regulating protein's activity. Drug development depends on the understanding of allosteric mechanisms, especially the identification of allosteric sites, which is prerequisite in drug discovery and design. Many computational methods have been developed for allosteric site prediction using pocket features and dynamics information. Here, we provide a novel ensembled model, consisting of eXtreme gradient boosting (XGBoost) and graph convolutional neural network (GCNN) to predict allosteric sites. Our model can learn both physical properties and topology structure without any prior information and exhibited good performance under several indicators. Prediction results have shown that 84.9% of allosteric pockets in the testing proteins appeared in the top 3 positions. The PASSer: Protein Allosteric Sites Server (https://passer.smu.edu), along with a command line interface (CLI, https://github.com/smutaogroup/passerCLI) provide insights for further analysis in drug discovery.

scholarly journals PASSer2.0: Accurate Prediction of Protein Allosteric Sites Through Automated Machine Learning

2021 ◽  
Author(s):  
Sian Xiao ◽  
Hao Tian ◽  
Peng Tao
Keyword(s):  
Machine Learning ◽  
Drug Discovery ◽  
Computational Model ◽  
Protein Dynamics ◽  
Allosteric Site ◽  
Multiple Indicators ◽  
Machine Learning Model ◽  
Fundamental Process ◽  
Allosteric Sites ◽  
Automated Machine Learning

Allostery is a fundamental process in regulating proteins’ activity. The discovery, design and development of allosteric drugs demand for better identification of allosteric sites. Several computational methods have been developed previously to predict allosteric sites using static pocket features and protein dynamics. Here, we present a computational model using automated machine learning for allosteric site prediction. Our model, PASSer2.0, advanced the previous results and performed well across multiple indicators with 89.2% of allosteric pockets appeared among the top 3 positions. The trained machine learning model has been integrated with the Protein Allosteric Sites Server (https://passer.smu.edu) to facilitate allosteric drug discovery.

scholarly journals Analyzing In Silico the Relationship Between the Activation of the Edema Factor and Its Interaction With Calmodulin

2020 ◽  
Vol 7 ◽  
Author(s):  
Irène Pitard ◽  
Damien Monet ◽  
Pierre L. Goossens ◽  
Arnaud Blondel ◽  
Thérèse E. Malliavin
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Md Simulations ◽  
Catalytic Site ◽  
Stacking Interactions ◽  
Long Distance ◽  
Edema Factor ◽  
Allosteric Communication ◽  
Network Of Hydrogen Bonds ◽  
The Relationship

Molecular dynamics (MD) simulations have been recorded on the complex between the edema factor (EF) of Bacilllus anthracis and calmodulin (CaM), starting from a structure with the orthosteric inhibitor adefovir bound in the EF catalytic site. The starting structure has been destabilized by alternately suppressing different co-factors, such as adefovir ligand or ions, revealing several long-distance correlations between the conformation of CaM, the geometry of the CaM/EF interface, the enzymatic site and the overall organization of the complex. An allosteric communication between CaM/EF interface and the EF catalytic site, highlighted by these correlations, was confirmed by several bioinformatics approaches from the literature. A network of hydrogen bonds and stacking interactions extending from the helix V of of CaM, and the residues of the switches A, B and C, and connecting to catalytic site residues, is a plausible candidate for the mediation of allosteric communication. The greatest variability in volume between the different MD conditions was also found for cavities present at the EF/CaM interface and in the EF catalytic site. The similarity between the predictions from literature and the volume variability might introduce the volume variability as new descriptor of allostery.

Molecular Design of a “Two-in-One” Orthosteric-Allosteric Chimeric Mutant Selective EGFR Inhibitor

2020 ◽  
Author(s):  
Florian Wittlinger ◽  
david heppner ◽  
Ciric To ◽  
Marcel Guenther ◽  
Bo Hee Shin ◽  
...  
Keyword(s):  
Molecular Design ◽  
Growth Factor Receptor ◽  
Kinase Domain ◽  
Egfr Inhibitor ◽  
Allosteric Site ◽  
Generation Agent ◽  
Design And Synthesis ◽  
Activating Mutations ◽  
Allosteric Sites ◽  
Successive Generations

Inhibitors developed to target the epidermal growth factor receptor (EGFR) are an effective therapy for patients with non-small cell lung cancer harbouring drug-sensitive activating mutations in the EGFR kinase domain. Drug resistance due to treatment-acquired mutations within the receptor itself has motivated development of successive generations of inhibitors that bind in the ATP-site, and third-generation agent osimertinib is now a first-line treatment for this disease. More recently, allosteric inhibitors have been developed to overcome the C797S mutation that confers resistance to osimertinib. In this study, we present the rational structure-guided design and synthesis of a mutant-selective EGFR inhibitor that spans the ATPand allosteric sites. The lead compound consists of a pyridinyl imidazole scaffold that binds irreversibly in the orthosteric site fused with a benzylisoindolinedione occupying the allosteric site. The compound potently inhibits enzymatic activity in L858R/T790M/C797S mutant EGFR (4.9 nM), with relative sparing of wild-type EGFR (47 nM). Additionally, this compound achieves cetuximab-independent, mutant-selective cellular efficacy on the L858R and L858R/T790M variants

scholarly journals Competition and allostery govern substrate selectivity of cyclooxygenase-2

2015 ◽  
Vol 112 (40) ◽  
pp. 12366-12371 ◽  
Author(s):  
Michelle M. Mitchener ◽  
Daniel J. Hermanson ◽  
Erin M. Shockley ◽  
H. Alex Brown ◽  
Craig W. Lindsley ◽  
...  
Keyword(s):  
Mechanistic Model ◽  
Inverse Correlation ◽  
Catalytic Efficiency ◽  
Cyclooxygenase 2 ◽  
Allosteric Site ◽  
Raw264.7 Macrophages ◽  
Allosteric Sites ◽  
Cox 2 ◽  
High Concentrations

Cyclooxygenase-2 (COX-2) oxygenates arachidonic acid (AA) and its ester analog, 2-arachidonoylglycerol (2-AG), to prostaglandins (PGs) and prostaglandin glyceryl esters (PG-Gs), respectively. Although the efficiency of oxygenation of these substrates by COX-2 in vitro is similar, cellular biosynthesis of PGs far exceeds that of PG-Gs. Evidence that the COX enzymes are functional heterodimers suggests that competitive interaction of AA and 2-AG at the allosteric site of COX-2 might result in differential regulation of the oxygenation of the two substrates when both are present. Modulation of AA levels in RAW264.7 macrophages uncovered an inverse correlation between cellular AA levels and PG-G biosynthesis. In vitro kinetic analysis using purified protein demonstrated that the inhibition of 2-AG oxygenation by high concentrations of AA far exceeded the inhibition of AA oxygenation by high concentrations of 2-AG. An unbiased systems-based mechanistic model of the kinetic data revealed that binding of AA or 2-AG at the allosteric site of COX-2 results in a decreased catalytic efficiency of the enzyme toward 2-AG, whereas 2-AG binding at the allosteric site increases COX-2’s efficiency toward AA. The results suggest that substrates interact with COX-2 via multiple potential complexes involving binding to both the catalytic and allosteric sites. Competition between AA and 2-AG for these sites, combined with differential allosteric modulation, gives rise to a complex interplay between the substrates, leading to preferential oxygenation of AA.

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