scholarly journals Development of a Split Esterase for Protein-Protein Interaction Dependent Small Molecule Activation

2019 ◽  
Author(s):  
Krysten A. Jones ◽  
Kaitlin Kentala ◽  
Michael Beck ◽  
Weiwei An ◽  
Alexander Lippert ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Small Molecule ◽  
Protein Interaction ◽  
Protein Interactions ◽  
Cell Killing ◽  
Dependent Manner ◽  
Protein Protein Interactions ◽  
Protein Protein Interaction ◽  
Cytotoxic Molecule ◽  
Measured Input

Split reporters based on fluorescent proteins and luciferases have emerged as valuable tools for measuring interactions in biological systems. Relatedly, biosensors that transduce measured input signals into outputs that influence the host system are key components of engineered gene circuits for synthetic biology applications. While small molecule-based imaging agents are widely used in biological studies, and small molecule-based drugs and chemical probes can target a range of biological processes, a general method for generating a target small molecule in a biological system based on a measured input signal is lacking. Here, we develop a proximity-dependent split esterase that selectively unmasks ester-protected small molecules in an interaction-dependent manner. Exploiting the versatility of an ester-protected small molecule output, we demonstrate fluorescent, chemiluminescent, and pharmacological probe generation, each created by masking key alcohol functional groups on a target small molecule. We show the split esterase system can be used in combination with ester-masked fluorescent or luminescent probes to measure a protein-protein interactions and protein-protein interaction inhibitor engagement. We demonstrate the esterase-based reporter system is compatible with other commonly-used split reporter imaging systems for the simultaneous detection of multiple protein-protein interactions. Finally, we develop a system for selective small molecule-dependent cell killing by unmasking a cytotoxic molecule using an inducible split esterase. Presaging utility in future synthetic biology-based therapeutic applications, we also show the system can be used for intercellular cell killing via a bystander effect, where one activated cell unmasks a cytotoxic molecule and kills cells physically adjacent to the activated cells. Collectively, this work illustrates that the split esterase system is a valuable new addition to the split protein toolbox, with particularly exciting potential in synthetic biology applications.

scholarly journals Development of a Split Esterase for Protein-Protein Interaction Dependent Small Molecule Activation

2019 ◽  
Author(s):  
Krysten A. Jones ◽  
Kaitlin Kentala ◽  
Michael Beck ◽  
Weiwei An ◽  
Alexander Lippert ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Small Molecule ◽  
Protein Interaction ◽  
Protein Interactions ◽  
Cell Killing ◽  
Dependent Manner ◽  
Protein Protein Interactions ◽  
Protein Protein Interaction ◽  
Cytotoxic Molecule ◽  
Measured Input

Split reporters based on fluorescent proteins and luciferases have emerged as valuable tools for measuring interactions in biological systems. Relatedly, biosensors that transduce measured input signals into outputs that influence the host system are key components of engineered gene circuits for synthetic biology applications. While small molecule-based imaging agents are widely used in biological studies, and small molecule-based drugs and chemical probes can target a range of biological processes, a general method for generating a target small molecule in a biological system based on a measured input signal is lacking. Here, we develop a proximity-dependent split esterase that selectively unmasks ester-protected small molecules in an interaction-dependent manner. Exploiting the versatility of an ester-protected small molecule output, we demonstrate fluorescent, chemiluminescent, and pharmacological probe generation, each created by masking key alcohol functional groups on a target small molecule. We show the split esterase system can be used in combination with ester-masked fluorescent or luminescent probes to measure a protein-protein interactions and protein-protein interaction inhibitor engagement. We demonstrate the esterase-based reporter system is compatible with other commonly-used split reporter imaging systems for the simultaneous detection of multiple protein-protein interactions. Finally, we develop a system for selective small molecule-dependent cell killing by unmasking a cytotoxic molecule using an inducible split esterase. Presaging utility in future synthetic biology-based therapeutic applications, we also show the system can be used for intercellular cell killing via a bystander effect, where one activated cell unmasks a cytotoxic molecule and kills cells physically adjacent to the activated cells. Collectively, this work illustrates that the split esterase system is a valuable new addition to the split protein toolbox, with particularly exciting potential in synthetic biology applications.

scholarly journals Development of a Split Esterase 1 for Protein-Protein 2 Interaction Dependent Small Molecule Activation

2019 ◽  
Author(s):  
Krysten A. Jones ◽  
Kaitlin Kentala ◽  
Michael Beck ◽  
Weiwei An ◽  
Alexander Lippert ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Small Molecule ◽  
Protein Interactions ◽  
Simultaneous Detection ◽  
Cell Killing ◽  
Dependent Manner ◽  
Protein Protein Interactions ◽  
Biological Studies ◽  
Cytotoxic Molecule ◽  
Measured Input

Split reporters based on fluorescent proteins and luciferases have emerged as valuable tools for measuring interactions in biological systems. Relatedly, biosensors that transduce measured input signals into outputs that influence the host system are key components of engineered gene circuits for synthetic biology applications. While small molecule-based imaging agents are widely used in biological studies, and small molecule-based drugs and chemical probes can target a range of biological processes, a general method for generating a target small molecule in a biological system based on a measured input signal is lacking. Here, we develop a proximity-dependent split esterase that selectively unmasks ester-protected small molecules in an interaction-dependent manner. Exploiting the versatility of an ester-protected small molecule output, we demonstrate fluorescent, chemiluminescent, and pharmacological probe generation, each created by masking key alcohol functional groups on a target small molecule. We show the split esterase system can be used in combination with ester-masked fluorescent or luminescent probes to measure a protein-protein interactions and protein-protein interaction inhibitor engagement. We demonstrate the esterase-based reporter system is compatible with other commonly-used split reporter imaging systems for the simultaneous detection of multiple protein-protein interactions. Finally, we develop a system for selective small molecule-dependent cell killing by unmasking a cytotoxic molecule using an inducible split esterase. Presaging utility in future synthetic biology-based therapeutic applications, we also show the system can be used for intercellular cell killing via a bystander effect, where one activated cell unmasks a cytotoxic molecule and kills cells physically adjacent to the activated cells. Collectively, this work illustrates that the split esterase system is a valuable new addition to the split protein toolbox, with particularly exciting potential in synthetic biology applications.

A systematic molecular dynamics approach to the study of peptide Keap1–Nrf2 protein–protein interaction inhibitors and its application to p62 peptides

2016 ◽  
Vol 12 (4) ◽  
pp. 1378-1387 ◽  
Author(s):  
Meng-Chen Lu ◽  
Zhen-Wei Yuan ◽  
Yong-Lin Jiang ◽  
Zhi-Yun Chen ◽  
Qi-Dong You ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Small Molecule ◽  
Protein Interaction ◽  
Protein Interactions ◽  
Drug Targets ◽  
Protein Protein Interactions ◽  
Protein Protein Interaction ◽  
P Protein ◽  
Nrf2 Protein

Protein–protein interactions (PPIs) as drug targets have been gaining growing interest, though developing drug-like small molecule PPI inhibitors remains challenging.

scholarly journals Small-molecule CaVα1⋅CaVβ antagonist suppresses neuronal voltage-gated calcium-channel trafficking

2018 ◽  
Vol 115 (45) ◽  
pp. E10566-E10575 ◽  
Author(s):  
Xingjuan Chen ◽  
Degang Liu ◽  
Donghui Zhou ◽  
Yubing Si ◽  
David Xu ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Calcium Channel ◽  
Small Molecule ◽  
Protein Interaction ◽  
Protein Interactions ◽  
Protein Protein Interactions ◽  
Channel Trafficking ◽  
Voltage Gated ◽  
Protein Protein Interaction ◽  
Computational Screening

Extracellular calcium flow through neuronal voltage-gated CaV2.2 calcium channels converts action potential-encoded information to the release of pronociceptive neurotransmitters in the dorsal horn of the spinal cord, culminating in excitation of the postsynaptic central nociceptive neurons. The CaV2.2 channel is composed of a pore-forming α1subunit (CaVα1) that is engaged in protein–protein interactions with auxiliary α2/δ and β subunits. The high-affinity CaV2.2α1⋅CaVβ3protein–protein interaction is essential for proper trafficking of CaV2.2 channels to the plasma membrane. Here, structure-based computational screening led to small molecules that disrupt the CaV2.2α1⋅CaVβ3protein–protein interaction. The binding mode of these compounds reveals that three substituents closely mimic the side chains of hot-spot residues located on the α-helix of CaV2.2α1. Site-directed mutagenesis confirmed the critical nature of a salt-bridge interaction between the compounds and CaVβ3Arg-307. In cells, compounds decreased trafficking of CaV2.2 channels to the plasma membrane and modulated the functions of the channel. In a rodent neuropathic pain model, the compounds suppressed pain responses. Small-molecule α-helical mimetics targeting ion channel protein–protein interactions may represent a strategy for developing nonopioid analgesia and for treatment of other neurological disorders associated with calcium-channel trafficking.

An efficient transient assays system using Agrobacterium-mediated transformation of onion (Allium cepa) epidermal cells

2020 ◽  
Vol 80 (03) ◽  
Author(s):  
Yu-Miao Zhang ◽  
Jun Wang ◽  
Tao Wu
Keyword(s):  
Subcellular Localization ◽  
Protein Interaction ◽  
Protein Interactions ◽  
Epidermal Cells ◽  
Cyclin Dependent Kinase ◽  
Protein Subcellular Localization ◽  
Protein Protein Interactions ◽  
Efficient System ◽  
Protein Protein Interaction ◽  
Onion Epidermal Cells

In this study, the Agrobacterium infection medium, infection duration, detergent, and cell density were optimized. The sorghum-based infection medium (SbIM), 10-20 min infection time, addition of 0.01% Silwet L-77, and Agrobacterium optical density at 600 nm (OD600), improved the competence of onion epidermal cells to support Agrobacterium infection at >90% efficiency. Cyclin-dependent kinase D-2 (CDKD-2) and cytochrome c-type biogenesis protein (CYCH), protein-protein interactions were localized. The optimized procedure is a quick and efficient system for examining protein subcellular localization and protein-protein interaction.

Elucidating Protein-protein Interactions Through Computational Approaches and Designing Small Molecule Inhibitors Against them for Various Diseases

2018 ◽  
Vol 18 (20) ◽  
pp. 1719-1736 ◽  
Author(s):  
Sharanya Sarkar ◽  
Khushboo Gulati ◽  
Manikyaprabhu Kairamkonda ◽  
Amit Mishra ◽  
Krishna Mohan Poluri
Keyword(s):  
Small Molecule ◽  
Protein Interactions ◽  
Small Molecule Inhibitors ◽  
Computational Techniques ◽  
Protein Protein Interactions ◽  
Computational Tools ◽  
Computational Approaches ◽  
Protein Protein Interaction ◽  
Wide Range ◽  
Therapeutic Measures

Background: To carry out wide range of cellular functionalities, proteins often associate with one or more proteins in a phenomenon known as Protein-Protein Interaction (PPI). Experimental and computational approaches were applied on PPIs in order to determine the interacting partners, and also to understand how an abnormality in such interactions can become the principle cause of a disease. Objective: This review aims to elucidate the case studies where PPIs involved in various human diseases have been proven or validated with computational techniques, and also to elucidate how small molecule inhibitors of PPIs have been designed computationally to act as effective therapeutic measures against certain diseases. Results: Computational techniques to predict PPIs are emerging rapidly in the modern day. They not only help in predicting new PPIs, but also generate outputs that substantiate the experimentally determined results. Moreover, computation has aided in the designing of novel inhibitor molecules disrupting the PPIs. Some of them are already being tested in the clinical trials. Conclusion: This review delineated the classification of computational tools that are essential to investigate PPIs. Furthermore, the review shed light on how indispensable computational tools have become in the field of medicine to analyze the interaction networks and to design novel inhibitors efficiently against dreadful diseases in a shorter time span.

Furan warheads for covalent trapping of weak protein-protein interactions: cross-linking of thymosin β4 to actin

2021 ◽  
Author(s):  
Laia Miret Casals ◽  
Willem Vannecke ◽  
Kurt Hoogewijs ◽  
Gianluca Arauz ◽  
Marina Gay ◽  
...  
Keyword(s):  
Protein Interaction ◽  
Protein Interactions ◽  
3D Structure ◽  
Cross Linking ◽  
Thymosin Β4 ◽  
Protein Protein Interactions ◽  
Site Specific ◽  
Protein Protein Interaction ◽  
Covalent Trapping

We describe furan as a triggerable ‘warhead’ for site-specific cross-linking using the actin and thymosin β4 (Tβ4)-complex as model of a weak and dynamic protein-protein interaction with known 3D structure...

scholarly journals HMNPPID—human malignant neoplasm protein–protein interaction database

2019 ◽  
Vol 13 (S1) ◽  
Author(s):  
Qingqing Li ◽  
Zhihao Yang ◽  
Zhehuan Zhao ◽  
Ling Luo ◽  
Zhiheng Li ◽  
...  
Keyword(s):  
Protein Interaction ◽  
Protein Interactions ◽  
Molecular Mechanisms ◽  
Malignant Neoplasm ◽  
Biomedical Literature ◽  
Malignant Neoplasms ◽  
Protein Protein Interactions ◽  
Protein Protein Interaction ◽  
Interaction Database ◽  
Protein Interaction Database

Abstract Background Protein–protein interaction (PPI) information extraction from biomedical literature helps unveil the molecular mechanisms of biological processes. Especially, the PPIs associated with human malignant neoplasms can unveil the biology behind these neoplasms. However, such PPI database is not currently available. Results In this work, a database of protein–protein interactions associated with 171 kinds of human malignant neoplasms named HMNPPID is constructed. In addition, a visualization program, named VisualPPI, is provided to facilitate the analysis of the PPI network for a specific neoplasm. Conclusions HMNPPID can hopefully become an important resource for the research on PPIs of human malignant neoplasms since it provides readily available data for healthcare professionals. Thus, they do not need to dig into a large amount of biomedical literatures any more, which may accelerate the researches on the PPIs of malignant neoplasms.

Development of Allosteric Inhibitors of the Interaction of AML1 and CBFβ for the Treatment of Leukemia.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 653-653 ◽  
Author(s):  
Michael G. Douvas ◽  
L. Roudaiya ◽  
J. Grembecka ◽  
N. Speck ◽  
J.H. Bushweller
Keyword(s):  
Small Molecule ◽  
Protein Interaction ◽  
Cellular Proliferation ◽  
Dependent Manner ◽  
Runt Domain ◽  
Cd11b Expression ◽  
Hek 293 ◽  
Protein Protein Interaction ◽  
293 Cells ◽  
Dose Dependent

Abstract The protein-protein interaction between the subunits of the nuclear transcription factor core binding factor, RUNX1 (CBFα) and CBFβ, plays a critical role in hematopoiesis. Chromosomal rearrangements that target CBF genes are among the most common mutations in leukemia, including t(8;21) found in approximately 12% of cases of AML and resulting in the protein AML1-ETO. We describe the development of small molecule inhibitors of the interaction between RUNX1 and CBFβ. We used virtual screening to identify lead compounds. These leads were used to generate a library of compounds to explore the structure-activity relationships and optimize activity, resulting in the identification of low micromolar IC50 inhibitors of this protein-protein interaction. We confirmed by FACS FRET that inhibition also occurs in mammalian cells. HEK-293 cells were transfected with Cerulean-Runt domain and Venus-CBFβ. FRET emission from cells was monitored on a flow cytometer to assess binding of CBFβ and the Runt domain. Results with drug were compared to FRET between Runt and wild-type CBFβ and FRET between Runt and a mutant CBFβ with 2 point mutations abrogating binding to Runt. The small molecule inhibitor KG-3-275 inhibited CBFβ - Runt domain binding in a dose dependent manner (Table 1). Treatment of the t(8;21) leukemia cell lines Kasumi-1 and SKNO-1 results in inhibition of proliferation. SKNO-1 cells are inhibited in a dose-dependent manner by KG-3-275 but not by the weak inhibitor KG-1-253 (Fig 1). KG-3-275 does not inhibit the growth of renal tubular and hepatocellular cell lines (Fig 1). Kasumi-1 and SKNO-1 undergo apoptosis in a dose-dependent manner upon treatment with KG-3-275 (Table 2). Finally, KG-3-275 shows synergy with ATRA in increasing differentiation of Kasumi-1 cells as measured by CD11b expression, consistent with recent published results establishing a link between AML1-ETO and repression of RAR signaling (Fig 2). These data indicate drugs inhibiting CBF interactions hold promise as targeted agents in the treatment of CBF leukemias. Fluorescence Resonance Energy Transfer Geometric Mean in HEK-293 Cells Cerulean-Runt domain + Venus-CBFb 4.07 +/− 0.1 Cerulean-RD + Venus-CBFb61/104 1.85 +/− .09 C-RD + V-CBFb + KG-3-275 200 mcm 3.05 +/− .15 C-RD + V-CBFb + KG-3-275 100 mcm 3.25 +/− 0.1 C-RD + V-CBFb + KG-3-275 50 mcm 3.45 +/− .25 C-RD + V-CBFb + KG-3-275 25 mcm 3.6 +/− 0.2 % Cells Annexin V/PI Negative at 72 Hrs Kasumi-1 0.25% DMSO 91.2 +/− 0.9 KG-3-275 25 mcm 91.2 +/− 1.2 KG-3-275 50 mcm 85.9 +/− 2.4 KG-3-275 100 mcm 66.7 +/− 6.7 SKNO-1 0.25% DMSO 77.6 +/− 3.4 KG-3-275 25 mcm 77.6 +/− 2.3 KG-3-275 50 mcm 63.7 +/− 3.6 KG-3-275 100 mcm 13.7 +/− 6.8 Cellular Proliferation as measured by MTTAssay at 72 Hrs Cellular Proliferation as measured by MTTAssay at 72 Hrs Kasumi-1 Differentiation Measured by CD11b expression at 72 Hrs Kasumi-1 Differentiation Measured by CD11b expression at 72 Hrs

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.

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