Disruption of protein–protein interactions: hot spot detection, structure-based virtual screening and in vitro testing for the anti-cancer drug target – survivin

RSC Advances ◽  
2016 ◽  
Vol 6 (38) ◽  
pp. 31947-31959 ◽  
Author(s):  
Sailu Sarvagalla ◽  
Chun Hei Antonio Cheung ◽  
Ju-Ya Tsai ◽  
Hsing Pang Hsieh ◽  
Mohane Selvaraj Coumar
Keyword(s):  
Protein Interactions ◽  
Drug Target ◽  
Hot Spot ◽  
Cancer Drug ◽  
Protein Protein Interactions ◽  
Protein Protein Interaction ◽  
Spot Detection ◽  
Anti Cancer ◽  
Interaction Interface

Hot spot detection at the protein–protein interaction interface using computational tools helped to identify indinavir as survivin inhibitor.

scholarly journals Evolutionary diversification of protein–protein interactions by interface add-ons

2017 ◽  
Vol 114 (40) ◽  
pp. E8333-E8342 ◽  
Author(s):  
Maximilian G. Plach ◽  
Florian Semmelmann ◽  
Florian Busch ◽  
Markus Busch ◽  
Leonhard Heizinger ◽  
...  
Keyword(s):  
Protein Interaction ◽  
Protein Interactions ◽  
Protein Complexes ◽  
Evolutionary Strategy ◽  
Structural Level ◽  
Protein Protein Interactions ◽  
Protein Protein Interaction ◽  
Evolutionary Diversification

Cells contain a multitude of protein complexes whose subunits interact with high specificity. However, the number of different protein folds and interface geometries found in nature is limited. This raises the question of how protein–protein interaction specificity is achieved on the structural level and how the formation of nonphysiological complexes is avoided. Here, we describe structural elements called interface add-ons that fulfill this function and elucidate their role for the diversification of protein–protein interactions during evolution. We identified interface add-ons in 10% of a representative set of bacterial, heteromeric protein complexes. The importance of interface add-ons for protein–protein interaction specificity is demonstrated by an exemplary experimental characterization of over 30 cognate and hybrid glutamine amidotransferase complexes in combination with comprehensive genetic profiling and protein design. Moreover, growth experiments showed that the lack of interface add-ons can lead to physiologically harmful cross-talk between essential biosynthetic pathways. In sum, our complementary in silico, in vitro, and in vivo analysis argues that interface add-ons are a practical and widespread evolutionary strategy to prevent the formation of nonphysiological complexes by specializing protein–protein interactions.

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.

scholarly journals Mapping of the Hepatitis B Virus Reverse Transcriptase TP and RT Domains by Transcomplementation for Nucleotide Priming and by Protein-Protein Interaction

1999 ◽  
Vol 73 (3) ◽  
pp. 1885-1893 ◽  
Author(s):  
Robert E. Lanford ◽  
Young-Ho Kim ◽  
Helen Lee ◽  
Lena Notvall ◽  
Burton Beames
Keyword(s):  
Amino Acids ◽  
Reverse Transcriptase ◽  
Protein Interaction ◽  
Protein Interactions ◽  
Rnase H ◽  
Genome Replication ◽  
Protein Protein Interactions ◽  
Stem Loop ◽  
Protein Protein Interaction

ABSTRACT Hepadnavirus polymerases initiate reverse transcription in a protein-primed reaction. We previously described a complementation assay for analysis of the roles of the TP and RT domains of HBV reverse transcriptase (pol) in the priming reaction. Independently expressed TP and RT domains form a complex functional for in vitro priming reactions. To map the minimal functional TP and RT domains, we prepared baculoviruses expressing amino- and carboxyl-terminal deletions of both the TP and RT domains and analyzed the proteins for the ability to participate in transcomplementation for the priming reaction. The minimal TP domain spanned amino acids 20 to 175; however, very little activity was observed without a TP domain spanning amino acids 1 to 199. The minimal RT domain spanned amino acids 300 to 775; however, little activity was observed unless the carboxyl end of the RT domain extended to amino acid 800. Thus, most of the RNase H domain was required. In previous studies, we observed a TP inhibitory domain between amino acids 199 and 344. The current analysis narrowed this domain to residues 300 to 334, which is a portion of the minimal RT domain. In addition, the ability of TP and RT deletion mutants to form stable TP-RT complexes was examined in coimmunoprecipitation assays. The minimal TP and RT domains capable of protein-protein interaction were considerably smaller than the domains required for functional interaction in the transcomplementation assays, and unlike priming activity, TP-RT interaction did not require the epsilon RNA stem-loop. These studies help to further define the complex protein-protein interactions required in HBV genome replication.

scholarly journals Circadian Rhythm of Anti-Cancer Drug Target Topoisomerase I As a Proposal Model for Chronotherapy In Vitro

2010 ◽  
Vol 18 (1) ◽  
pp. 19-27
Author(s):  
Teruhide Ishigame ◽  
Yoshihisa Koyama ◽  
Koichiro Ono ◽  
Tomojiro Ono ◽  
Kumiko Watanabe ◽  
...  
Keyword(s):  
Circadian Rhythm ◽  
Drug Target ◽  
Topoisomerase I ◽  
Cancer Drug ◽  
Anti Cancer

scholarly journals Tanshinone IIA Affects the Malignant Growth of Cholangiocarcinoma Cells by Inhibiting the PI3K-Akt-mTOR Pathway

2021 ◽  
Author(s):  
Huayuan Liu ◽  
Caiyun Liu ◽  
Mengya Wang ◽  
Dongxu Sun ◽  
Pengcheng Zhu ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Tanshinone Iia ◽  
Network Pharmacology ◽  
Protein Protein Interactions ◽  
Anticancer Effects ◽  
Anti Cancer ◽  
Cholangiocarcinoma Cell ◽  
And Migration ◽  
Proliferation And Migration

Abstract Purpose: In the present study, we aimed to find the target of Tanshinone IIA (Tan-IIA) in Cholangiocarcinoma by network pharmacology-based prediction and investigate the possible mechanism through experimental verification. Methods: In this study, we combined Tan-IIA-specific and Cholangiocarcinoma-specific targets with protein-protein interactions (PPI) to construct a Tan-IIA targets-Cholangiocarcinoma network, and network pharmacology approach was applied to identify potential targets and mechanisms of Tan-IIA in the treatment of Cholangiocarcinoma. The anti-cancer effects of Tan-IIA were investigated by using subcutaneous tumorigenic model in nude mice and in the human Cholangiocarcinoma cell lines in vitro. Results: Our results showed that Tan-IIA treatment considerably suppressed the proliferation and migration of Cholangiocarcinoma cells while inducing apoptosis of Cholangiocarcinoma cells. Western blot results demonstrated that the expression of PI3K, p-Akt, p-mTOR, and mTOR were inhibited by Tan-IIA. Meanwhile, After treatment with Tan-IIA, the level of Bcl2 was downregulated and cleaved caspase-3 expression increased. Further studies revealed that the anticancer effects of Tan-IIA were severely mitigated by pretreatment with a PI3K agonist.Conclusion: Our research provides a new anticancer strategy and strengthens support for the use of Tan-IIA as an anticancer drug for the treatment of CCA.

scholarly journals BRET-based RAS biosensors that show a novel small molecule is an inhibitor of RAS-effector protein-protein interactions

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Nicolas Bery ◽  
Abimael Cruz-Migoni ◽  
Carole JR Bataille ◽  
Camilo E Quevedo ◽  
Hanna Tulmin ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Protein Protein Interactions ◽  
Protein Protein Interaction ◽  
Human Cancers ◽  
Ras Family ◽  
Ras Inhibitors ◽  
In Cells

The RAS family of proteins is amongst the most highly mutated in human cancers and has so far eluded drug therapy. Currently, much effort is being made to discover mutant RAS inhibitors and in vitro screening for RAS-binding drugs must be followed by cell-based assays. Here, we have developed a robust set of bioluminescence resonance energy transfer (BRET)-based RAS biosensors that enable monitoring of RAS-effector interaction inhibition in living cells. These include KRAS, HRAS and NRAS and a variety of different mutations that mirror those found in human cancers with the major RAS effectors such as CRAF, PI3K and RALGDS. We highlighted the utility of these RAS biosensors by showing a RAS-binding compound is a potent pan-RAS-effector interactions inhibitor in cells. The RAS biosensors represent a useful tool to investigate and characterize the potency of anti-RAS inhibitors in cells and more generally any RAS protein-protein interaction (PPI) in cells.

scholarly journals Photoproximity Profiling of Protein-Protein Interactions in Cells

2019 ◽  
Author(s):  
David C. McCutcheon ◽  
Gihoon Lee ◽  
Anthony Carlos ◽  
Jeffrey E. Montgomery ◽  
Raymond E. Moellering
Keyword(s):  
Protein Interaction ◽  
Protein Interactions ◽  
Live Cells ◽  
High Temporal Resolution ◽  
Protein Protein Interactions ◽  
Redox Stress ◽  
Covalent Interaction ◽  
Protein Protein Interaction ◽  
In Cells

ABSTRACTWe report a novel photoproximity protein interaction (PhotoPPI) profiling method to map protein-protein interactions in vitro and in live cells. This approach utilizes a bioorthogonal, multifunctional chemical probe that can be targeted to a genetically encoded protein of interest (POI) through a modular SNAP-Tag/benzylguanine covalent interaction. A first generation photoproximity probe, PP1, responds to 365 nm light to simultaneously cleave a central nitroveratryl linker and a peripheral diazirine group, resulting in diffusion of a highly reactive carbene nucleophile away from the POI. We demonstrate facile probe loading, and subsequent interaction- and light-dependent proximal labeling of a model protein-protein interaction (PPI) in vitro. Integration of the PhotoPPI workflow with quantitative LC-MS/MS enabled un-biased interaction mapping for the redox regulated sensor protein, KEAP1, for the first time in live cells. We validated known and novel interactions between KEAP1 and the proteins PGAM5 and HK2, among others, under basal cellular conditions. By contrast, comparison of PhotoPPI profiles in cells experiencing metabolic or redox stress confirmed that KEAP1 sheds many basal interactions and becomes associated with known lysosomal trafficking and proteolytic proteins like SQSTM1, CTSD and LGMN. Together, these data establish PhotoPPI as a method capable of tracking the dynamic sub-cellular and protein interaction “social network” of a redox-sensitive protein in cells with high temporal resolution.SYNOPSIS TOC

scholarly journals Drug Target Protein-Protein Interaction Networks: A Systematic Perspective

2017 ◽  
Vol 2017 ◽  
pp. 1-13 ◽  
Author(s):  
Yanghe Feng ◽  
Qi Wang ◽  
Tengjiao Wang
Keyword(s):  
Protein Interactions ◽  
Drug Target ◽  
Drug Targets ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Ppi Network ◽  
Protein Protein Interactions ◽  
Protein Protein Interaction ◽  
Topological Features ◽  
Protein Protein Interaction Networks

The identification and validation of drug targets are crucial in biomedical research and many studies have been conducted on analyzing drug target features for getting a better understanding on principles of their mechanisms. But most of them are based on either strong biological hypotheses or the chemical and physical properties of those targets separately. In this paper, we investigated three main ways to understand the functional biomolecules based on the topological features of drug targets. There are no significant differences between targets and common proteins in the protein-protein interactions network, indicating the drug targets are neither hub proteins which are dominant nor the bridge proteins. According to some special topological structures of the drug targets, there are significant differences between known targets and other proteins. Furthermore, the drug targets mainly belong to three typical communities based on their modularity. These topological features are helpful to understand how the drug targets work in the PPI network. Particularly, it is an alternative way to predict potential targets or extract nontargets to test a new drug target efficiently and economically. By this way, a drug target’s homologue set containing 102 potential target proteins is predicted in the paper.

scholarly journals Tanshinone IIA affects the malignant growth of Cholangiocarcinoma cells by inhibiting the PI3K-Akt-mTOR pathway

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Huayuan Liu ◽  
Caiyun Liu ◽  
Mengya Wang ◽  
Dongxu Sun ◽  
Pengcheng Zhu ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Tanshinone Iia ◽  
Network Pharmacology ◽  
Protein Protein Interactions ◽  
Anticancer Effects ◽  
Anti Cancer ◽  
Cholangiocarcinoma Cell ◽  
And Migration ◽  
Proliferation And Migration

AbstractIn the present study, we aimed to find the target of Tanshinone IIA (Tan-IIA) in Cholangiocarcinoma by network pharmacology-based prediction and investigate the possible mechanism through experimental verification. In this study, we combined Tan-IIA-specific and Cholangiocarcinoma-specific targets with protein–protein interactions (PPI) to construct a Tan-IIA targets-Cholangiocarcinoma network, and network pharmacology approach was applied to identify potential targets and mechanisms of Tan-IIA in the treatment of Cholangiocarcinoma. The anti-cancer effects of Tan-IIA were investigated by using subcutaneous tumorigenic model in nude mice and in the human Cholangiocarcinoma cell lines in vitro. Our results showed that Tan-IIA treatment considerably suppressed the proliferation and migration of Cholangiocarcinoma cells while inducing apoptosis of Cholangiocarcinoma cells. Western blot results demonstrated that the expression of PI3K, p-Akt, p-mTOR, and mTOR were inhibited by Tan-IIA. Meanwhile, After treatment with Tan-IIA, the level of Bcl2 was downregulated and cleaved caspase-3 expression increased. Further studies revealed that the anticancer effects of Tan-IIA were severely mitigated by pretreatment with a PI3K agonist. Our research provides a new anticancer strategy and strengthens support for the use of Tan-IIA as an anticancer drug for the treatment of CCA.

Probing the 14-3-3 Isoform-Specificity Profile of Interactions Stabilized by Fusicoccin A

2020 ◽  
Author(s):  
James Frederich ◽  
Ananya Sengupta ◽  
Josue Liriano ◽  
Ewa A. Bienkiewicz ◽  
Brian G. Miller
Keyword(s):  
Protein Interactions ◽  
Neurological Diseases ◽  
Adapter Proteins ◽  
Protein Protein Interactions ◽  
Specific Expression ◽  
Individual Client ◽  
Isoform Specificity ◽  
Fusicoccin A

Fusicoccin A (FC) is a fungal phytotoxin that stabilizes protein–protein interactions (PPIs) between 14-3-3 adapter proteins and their phosphoprotein interaction partners. In recent years, FC has emerged as an important chemical probe of human 14-3-3 PPIs implicated in cancer and neurological diseases. These previous studies have established the structural requirements for FC-induced stabilization of 14-3-3·client phosphoprotein complexes; however, the effect of different 14-3-3 isoforms on FC activity has not been systematically explored. This is a relevant question for the continued development of FC variants because there are seven distinct isoforms of 14-3-3 in humans. Despite their remarkable sequence and structural similarities, a growing body of experimental evidence supports both tissue-specific expression of 14-3-3 isoforms and isoform-specific functions <i>in vivo</i>. Herein, we report the isoform-specificity profile of FC <i>in vitro</i>using recombinant human 14-3-3 isoforms and a focused library of fluorescein-labeled hexaphosphopeptides mimicking the C-terminal 14-3-3 recognition domains of client phosphoproteins targeted by FC in cell culture. Our results reveal modest isoform preferences for individual client phospholigands and demonstrate that FC differentially stabilizes PPIs involving 14-3-3s. Together, these data provide strong motivation for the development of non-natural FC variants with enhanced selectivity for individual 14-3-3 isoforms.

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