Combined Rational Design and a High Throughput Screening Platform for Identifying Chemical Inhibitors of a Ras-activating Enzyme

Evelyn, Chris R.; Biesiada, Jacek; Duan, Xin; Tang, Hong; Shang, Xun; Papoian, Ruben; Seibel, William; Nelson, Sandra L.; Meller, Jarosław; Zheng, Yi

doi:10.1074/jbc.m114.634493

Cited by 28 publications

(23 citation statements)

References 51 publications

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“…Evelyn and colleagues reported direct inhibitors of Sos1 in two different screens. [44] In the first, crystal structures of the Ras-Sos complex were used in av irtual screen to enable rational design of compounds that inhibit formation of the complex. [44a] From 18 500 small molecules,3 6w ere chosen for experimental validation.…”

Section: Rasgef Inhibitors (Methods B)mentioning

confidence: 99%

“…Studies in cells indicated 43 reduced tumor growth, metastasis,and angiogenesis,with no apparent toxicity,i ndicating potential as ac ancer therapeutic. [82] Further modifications of the scaffold to bind deeper into the pocket yielded MBQ-167 (44), which inhibited Rac1 activity in cells with an IC 50 value of 103 nm. [83] However,i t also blocked Cdc42 activity with an IC 50 value of 78 nm, meaning selectivity had been lost.…”

Section: Direct Inhibition Of the Rho Gtpases (Methods A)mentioning

confidence: 99%

“…In the second screen, they identified two compounds, UC‐773587 and UC‐857993 ( 15 and 16 , Figure ), which bound selectively to the catalytic site of Sos1 over HRas and ITSN (a RhoGEF) and inhibited nucleotide exchange with IC 50 values of 4.5 and 32 μ m , respectively . Alanine scanning mutagenesis indicated that 15 mapped to the Ras switch II interaction region of the Sos1 catalytic site and 16 to the Ras switch I interaction region.…”

Section: Ras Gtpasesmentioning

confidence: 99%

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Targeting the Small GTPase Superfamily through Their Regulatory Proteins

2020

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The Ras superfamily of small GTPases are guanine‐nucleotide‐dependent switches essential for numerous cellular processes. Mutations or dysregulation of these proteins are associated with many diseases, but unsuccessful attempts to target the small GTPases directly have resulted in them being classed as “undruggable”. The GTP‐dependent signaling of these proteins is controlled by their regulators; guanine nucleotide exchange factors (GEFs), GTPase activating proteins (GAPs), and in the Rho and Rab subfamilies, guanine nucleotide dissociation inhibitors (GDIs). This review covers the recent small molecule and biologics strategies to target the small GTPases through their regulators. It seeks to critically re‐evaluate recent chemical biology practice, such as the presence of PAINs motifs and the cell‐based readout using compounds that are weakly potent or of unknown specificity. It highlights the vast scope of potential approaches for targeting the small GTPases in the future through their regulatory proteins.

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Section: Rasgef Inhibitors (Methods B)mentioning

confidence: 99%

Section: Direct Inhibition Of the Rho Gtpases (Methods A)mentioning

confidence: 99%

Section: Ras Gtpasesmentioning

confidence: 99%

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Targeting the Small GTPase Superfamily through Their Regulatory Proteins

2020

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“…Im zweiten Screening wurden zwei Strukturen identifiziert, UC‐773587 und UC‐857993 ( 15 und 16 , Abbildung ), die beide selektiv über HRas und ITSN (ein RhoGEF) an das katalytische Zentrum von Sos1 banden und den Nukleotidaustausch mit IC 50 ‐Werten von 4.5 bzw. 32 μ m inhibierten . Alanin‐durchsuchende Mutagenesestudien indizierten, dass 15 an der Ras Switch‐II‐Wechselwirkungsregion des katalytischen Zentrums von Sos1 und 16 an der Ras Switch‐I‐Wechselwirkungsregion kartiert wurden.…”

Section: Ras‐gtpasenunclassified

Targeting der kleinen GTPasen über ihre regulatorischen Proteine

2020

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Die kleinen GTPasen der Ras‐Superfamilie sind Guaninnukleotid‐abhängige Schalter, die für eine Vielzahl zellulärer Prozesse essentiell sind. Mutationen oder Dysregulationen dieser Proteine stehen in Verbindung mit zahlreichen Erkrankungen. Erfolglose Versuche, die kleinen GTPasen direkt als Zielstruktur anzugreifen, führten zu ihrer Klassifizierung als pharmakologisch nicht adressierbar (“undruggable”). Der GTP‐abhängige Signalweg dieser Proteine wird durch ihre Regulatoren kontrolliert, sogenannte “guanine nucleotide exchange factors” (GEFs), “GTPase activating proteins” (GAPs) und in der Rho‐ und Rab‐Subfamilie “guanine nucleotide dissociation inhibitors” (GDIs). Dieser Aufsatz beinhaltet die neusten niedermolekularen und biologischen Strategien, um die kleinen GTPasen durch ihre Regulatoren als Zielstruktur anzugreifen. Wir geben eine kritische Re‐Evaluierung der jüngsten chemisch biologischen Vorgehensweisen, wie dem Vorhandensein von PAINs‐Motiven und zellbasierter Auslese mit Verbindungen, die schwach potent sind oder eine unbekannte Spezifität haben, uns diskutieren das breite Feld potentieller Ansätze, um die kleinen GTPasen zukünftig durch ihre regulatorischen Proteine anzugreifen.

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“…Recent studies have demonstrated the effectiveness of in silico prediction of binding affinities between ligands and protein receptors by screening compound libraries [16–18], and peptide mutant structures that were generated by homology modeling [19]. Integration of such HTVS techniques provides a rapid and cost effective way to identify drug leads that can be validated by wet lab biochemical assays.…”

Section: Background and Introductionmentioning

confidence: 99%

Computational exploration of a protein receptor binding space with student proposed peptide ligands

King¹,

Phillips²,

Turner

et al. 2015

Biochem Molecular Bio Educ

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Computational molecular docking is a fast and effective in silico method for the analysis of binding between a protein receptor model and a ligand. The visualization and manipulation of protein to ligand binding in three-dimensional space represents a powerful tool in the biochemistry curriculum to enhance student learning. The DockoMatic tutorial described herein provides a framework by which instructors can guide students through a drug screening exercise. Using receptor models derived from readily available protein crystal structures, docking programs have the ability to predict ligand binding properties, such as preferential binding orientations and binding affinities. The use of computational studies can significantly enhance complimentary wet chemical experimentation by providing insight into the important molecular interactions within the system of interest, as well as guide the design of new candidate ligands based on observed binding motifs and energetics. In this laboratory tutorial, the graphical user interface, DockoMatic, facilitates docking job submissions to the docking engine, AutoDock 4.2. The purpose of this exercise is to successfully dock a 17-amino acid peptide, α-conotoxin TxIA, to the acetylcholine binding protein from Aplysia californica-AChBP to determine the most stable binding configuration. Each student will then propose two specific amino acid substitutions of α-conotoxin TxIA to enhance peptide binding affinity, create the mutant in DockoMatic, and perform docking calculations to compare their results with the class. Students will also compare intermolecular forces, binding energy, and geometric orientation of their prepared analog to their initial α-conotoxin TxIA docking results.

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Combined Rational Design and a High Throughput Screening Platform for Identifying Chemical Inhibitors of a Ras-activating Enzyme

Cited by 28 publications

References 51 publications

Targeting the Small GTPase Superfamily through Their Regulatory Proteins

Targeting the Small GTPase Superfamily through Their Regulatory Proteins

Targeting der kleinen GTPasen über ihre regulatorischen Proteine

Computational exploration of a protein receptor binding space with student proposed peptide ligands

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