scholarly journals Inhibition of Non-ATG Translational Events in Cells via Covalent Small Molecules Targeting RNA

2015 ◽  
Vol 137 (16) ◽  
pp. 5336-5345 ◽  
Author(s):  
Wang-Yong Yang ◽  
Henry D. Wilson ◽  
Sai Pradeep Velagapudi ◽  
Matthew D. Disney
Keyword(s):  
Small Molecules ◽  
In Cells

scholarly journals Screening of a Focused Ubiquitin-Proteasome Pathway Inhibitor Library Identifies Small Molecules as Novel Modulators of Botulinum Neurotoxin Type A Toxicity

2021 ◽  
Vol 12 ◽  
Author(s):  
Edanur Sen ◽  
Krishna P. Kota ◽  
Rekha G. Panchal ◽  
Sina Bavari ◽  
Erkan Kiris
Keyword(s):  
Small Molecules ◽  
Ubiquitin Proteasome Pathway ◽  
Lead Compounds ◽  
Botulinum Neurotoxins ◽  
Ubiquitin Proteasome ◽  
Proteasome Pathway ◽  
The Stability ◽  
Dose Dependent ◽  
In Cells

Botulinum neurotoxins (BoNTs) are known as the most potent bacterial toxins, which can cause potentially deadly disease botulism. BoNT Serotype A (BoNT/A) is the most studied serotype as it is responsible for most human botulism cases, and its formulations are extensively utilized in clinics for therapeutic and cosmetic applications. BoNT/A has the longest-lasting effect in neurons compared to other serotypes, and there has been high interest in understanding how BoNT/A manages to escape protein degradation machinery in neurons for months. Recent work demonstrated that an E3 ligase, HECTD2, leads to efficient ubiquitination of the BoNT/A Light Chain (A/LC); however, the dominant activity of a deubiquitinase (DUB), VCIP135, inhibits the degradation of the enzymatic component. Another DUB, USP9X, was also identified as a potential indirect contributor to A/LC degradation. In this study, we screened a focused ubiquitin-proteasome pathway inhibitor library, including VCIP135 and USP9X inhibitors, and identified ten potential lead compounds affecting BoNT/A mediated SNAP-25 cleavage in neurons in pre-intoxication conditions. We then tested the dose-dependent effects of the compounds and their potential toxic effects in cells. A subset of the lead compounds demonstrated efficacy on the stability and ubiquitination of A/LC in cells. Three of the compounds, WP1130 (degrasyn), PR-619, and Celastrol, further demonstrated efficacy against BoNT/A holotoxin in an in vitro post-intoxication model. Excitingly, PR-619 and WP1130 are known inhibitors of VCIP135 and USP9X, respectively. Modulation of BoNT turnover in cells by small molecules can potentially lead to the development of effective countermeasures against botulism.

scholarly journals Lifespan-increasing drug nordihydroguaiaretic acid inhibits p300 and activates autophagy

2019 ◽  
Author(s):  
Tugsan Tezil ◽  
Manish Chamoli ◽  
Che-Ping Ng ◽  
Roman P. Simon ◽  
Victoria J. Butler ◽  
...  
Keyword(s):  
Small Molecules ◽  
Physiological Function ◽  
Nordihydroguaiaretic Acid ◽  
Mechanistic Insight ◽  
Epigenetic Regulator ◽  
Novel Target ◽  
Cellular Thermal Shift Assay ◽  
Insight Into ◽  
In Cells

AbstractAging is characterized by the progressive loss of physiological function in all organisms. Remarkably, the aging process can be modulated by environmental modifications, including diet and small molecules. The natural compound nordihydroguaiaretic acid (NDGA) robustly increases lifespan in flies and mice, but its mechanism of action remains unclear. Here, we report that NDGA is an inhibitor of the epigenetic regulator p300. We find that NDGA inhibits p300 acetyltransferase activity in vitro and suppresses acetylation of a key p300 target in histones (i.e., H3K27) in cells. We use the cellular thermal shift assay to uniquely demonstrate NDGA binding to p300 in cells. Finally, in agreement with recent findings indicating that p300 is a potent blocker of autophagy, we show that NDGA treatment induces autophagy. These findings identify p300 as a novel target of NDGA and provide mechanistic insight into its role in longevity.

scholarly journals Epistatic mutations in PUMA BH3 drive an alternate binding mode to potently and selectively inhibit anti-apoptotic Bfl-1

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Justin M Jenson ◽  
Jeremy A Ryan ◽  
Robert A Grant ◽  
Anthony Letai ◽  
Amy E Keating
Keyword(s):  
Small Molecules ◽  
Cancer Progression ◽  
Binding Mode ◽  
Mitochondrial Outer Membrane ◽  
Binding Partners ◽  
Peptide Binding Groove ◽  
Cell Permeable Peptide ◽  
Binding Groove ◽  
Resistance To Chemotherapy ◽  
In Cells

Overexpression of anti-apoptotic Bcl-2 family proteins contributes to cancer progression and confers resistance to chemotherapy. Small molecules that target Bcl-2 are used in the clinic to treat leukemia, but tight and selective inhibitors are not available for Bcl-2 paralog Bfl-1. Guided by computational analysis, we designed variants of the native BH3 motif PUMA that are > 150-fold selective for Bfl-1 binding. The designed peptides potently trigger disruption of the mitochondrial outer membrane in cells dependent on Bfl-1, but not in cells dependent on other anti-apoptotic homologs. High-resolution crystal structures show that designed peptide FS2 binds Bfl-1 in a shifted geometry, relative to PUMA and other binding partners, due to a set of epistatic mutations. FS2 modified with an electrophile reacts with a cysteine near the peptide-binding groove to augment specificity. Designed Bfl-1 binders provide reagents for cellular profiling and leads for developing enhanced and cell-permeable peptide or small-molecule inhibitors.

Expedited Mapping of the Ligandable Proteome Using Fully Functionalized Enantiomeric Probe Pairs

2019 ◽  
Author(s):  
Benjamin Cravatt ◽  
Yujia Wang ◽  
melissa dix ◽  
jarrett remsberg ◽  
hsin-yu lee ◽  
...  
Keyword(s):  
Small Molecules ◽  
Protein Interactions ◽  
Binding Potential ◽  
Protein Fragment ◽  
Chemical Proteomics ◽  
Functional Sites ◽  
Structure Activity ◽  
Ligand Discovery ◽  
Absolute Stereochemistry ◽  
In Cells

<div>A fundamental challenge in chemical biology and medicine is to understand and expand the fraction of the human proteome that can be targeted by small molecules. We recently described a strategy that integrates fragment-based ligand discovery with chemical proteomics to furnish global portraits of reversible small molecule-protein interactions in human cells.</div><div>Excavating clear structure-activity relationships from these “ligandability” maps, however, was confounded by the distinct physicochemical properties and corresponding overall protein-binding potential of individual fragments. Here, we describe a compelling solution to this problem by introducing a next-generation set of fully functionalized fragments (FFFs) differing only in absolute stereochemistry. Using these enantiomeric probe pairs, or “enantioprobes”, we identify numerous stereoselective protein-fragment interactions in cells and show that these interactions occur at functional sites on proteins from diverse classes. Our findings thus indicate that incorporating chirality into FFF libraries provides a robust and streamlined method to discover ligandable proteins in cells.</div>

scholarly journals Translation of the intrinsically disordered protein α-synuclein is inhibited by a small molecule targeting its structured mRNA

2020 ◽  
Vol 117 (3) ◽  
pp. 1457-1467 ◽  
Author(s):  
Peiyuan Zhang ◽  
Hye-Jin Park ◽  
Jie Zhang ◽  
Eunsung Junn ◽  
Ryan J. Andrews ◽  
...  
Keyword(s):  
Small Molecules ◽  
Small Molecule ◽  
Intrinsically Disordered Proteins ◽  
Lewy Bodies ◽  
Disordered Proteins ◽  
Lewy Neurites ◽  
Protein Levels ◽  
Intrinsically Disordered ◽  
In Cells

Many proteins are refractory to targeting because they lack small-molecule binding pockets. An alternative to drugging these proteins directly is to target the messenger (m)RNA that encodes them, thereby reducing protein levels. We describe such an approach for the difficult-to-target protein α-synuclein encoded by the SNCA gene. Multiplication of the SNCA gene locus causes dominantly inherited Parkinson’s disease (PD), and α-synuclein protein aggregates in Lewy bodies and Lewy neurites in sporadic PD. Thus, reducing the expression of α-synuclein protein is expected to have therapeutic value. Fortuitously, the SNCA mRNA has a structured iron-responsive element (IRE) in its 5′ untranslated region (5′ UTR) that controls its translation. Using sequence-based design, we discovered small molecules that target the IRE structure and inhibit SNCA translation in cells, the most potent of which is named Synucleozid. Both in vitro and cellular profiling studies showed Synucleozid directly targets the α-synuclein mRNA 5′ UTR at the designed site. Mechanistic studies revealed that Synucleozid reduces α-synuclein protein levels by decreasing the amount of SNCA mRNA loaded into polysomes, mechanistically providing a cytoprotective effect in cells. Proteome- and transcriptome-wide studies showed that the compound’s selectivity makes Synucleozid suitable for further development. Importantly, transcriptome-wide analysis of mRNAs that encode intrinsically disordered proteins revealed that each has structured regions that could be targeted with small molecules. These findings demonstrate the potential for targeting undruggable proteins at the level of their coding mRNAs. This approach, as applied to SNCA, is a promising disease-modifying therapeutic strategy for PD and other α-synucleinopathies.

scholarly journals Synthesis One Pot of Alkyne-2-Chloroquinoline via a Passerini Reaction

Proceedings ◽  
2019 ◽  
Vol 41 (1) ◽  
pp. 76
Author(s):  
Sandra C. Ramírez-López ◽  
Rocío Gámez-Montaño
Keyword(s):  
Carboxylic Acid ◽  
Small Molecules ◽  
Passerini Reaction ◽  
One Pot ◽  
Protein Targets ◽  
Three Component Reaction ◽  
Green Conditions ◽  
In Cells

A series of six new alkyne-2-chloroquinolines were synthesized in moderate yields (40%–65%) via the Passerini three-component reaction (P-3CR) under mild green conditions. The P-3CR takes place when a carboxylic acid, an oxo compound (aldehyde or ketone), and an isocyanide react to give α-acyloxy carboxamides. Recently it has been reported that small molecules containing alkynes promote interactions with different proteins in cells facilitating the detection or identification of protein targets.

Detecting nitrile-containing small molecules by infrared photothermal microscopy

The Analyst ◽  
2021 ◽  
Vol 146 (7) ◽  
pp. 2307-2312
Author(s):  
Fangfang Tai ◽  
Kota Koike ◽  
Hiroyuki Kawagoe ◽  
Jun Ando ◽  
Yasuaki Kumamoto ◽  
...  
Keyword(s):  
Small Molecules ◽  
Nitrile Group ◽  
Carbonyl Cyanide ◽  
Target Molecules ◽  
Photothermal Microscopy ◽  
Photothermal Imaging ◽  
In Cells

We demonstrated IR photothermal imaging of trifluoromethoxy carbonyl cyanide phenylhydrazone (FCCP) in cells. The result indicates that a nitrile group can be used as a vibrational tag to image target molecules.

scholarly journals Subcellular localization of drug distribution by super-resolution ion beam imaging

2019 ◽  
Author(s):  
Xavier Rovira-Clave ◽  
Sizun Jiang ◽  
Yunhao Bai ◽  
Graham Barlow ◽  
Salil Bhate ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Subcellular Localization ◽  
Small Molecules ◽  
Secondary Ion Mass Spectrometry ◽  
Ion Beam ◽  
Drug Distribution ◽  
Super Resolution ◽  
Active Regions ◽  
Nuclear Speckles ◽  
In Cells

AbstractTechnologies that visualize multiple biomolecules at the nanometer scale in cells will enable deeper understanding of biological processes that proceed at the molecular scale. Current fluorescence-based methods for microscopy are constrained by a combination of spatial resolution limitations, limited parameters per experiment, and detector systems for the wide variety of biomolecules found in cells. We present here super-resolution ion beam imaging (srIBI), a secondary ion mass spectrometry approach capable of high-parameter imaging in 3D of targeted biological entities and exogenously added small molecules. Uniquely, the atomic constituents of the biomolecules themselves can often be used in our system as the “tag”. We visualized the subcellular localization of the chemotherapy drug cisplatin simultaneously with localization of five other nuclear structures, with further carbon elemental mapping and secondary electron visualization, down to ∼30 nm lateral resolution. Cisplatin was preferentially enriched in nuclear speckles and excluded from closed-chromatin regions, indicative of a role for cisplatin in active regions of chromatin. These data highlight how multiplexed super-resolution techniques, such as srIBI, will enable studies of biomolecule distributions in biologically relevant subcellular microenvironments.One Sentence SummaryThree-dimensional multiplexed mass spectrometry-based imaging revealed the subcellular localization of proteins and small molecules at super-resolution.

Expedited Mapping of the Ligandable Proteome Using Fully Functionalized Enantiomeric Probe Pairs

2019 ◽  
Author(s):  
Benjamin Cravatt ◽  
Yujia Wang ◽  
melissa dix ◽  
jarrett remsberg ◽  
hsin-yu lee ◽  
...  
Keyword(s):  
Small Molecules ◽  
Protein Interactions ◽  
Binding Potential ◽  
Protein Fragment ◽  
Chemical Proteomics ◽  
Functional Sites ◽  
Structure Activity ◽  
Ligand Discovery ◽  
Absolute Stereochemistry ◽  
In Cells

<div>A fundamental challenge in chemical biology and medicine is to understand and expand the fraction of the human proteome that can be targeted by small molecules. We recently described a strategy that integrates fragment-based ligand discovery with chemical proteomics to furnish global portraits of reversible small molecule-protein interactions in human cells.</div><div>Excavating clear structure-activity relationships from these “ligandability” maps, however, was confounded by the distinct physicochemical properties and corresponding overall protein-binding potential of individual fragments. Here, we describe a compelling solution to this problem by introducing a next-generation set of fully functionalized fragments (FFFs) differing only in absolute stereochemistry. Using these enantiomeric probe pairs, or “enantioprobes”, we identify numerous stereoselective protein-fragment interactions in cells and show that these interactions occur at functional sites on proteins from diverse classes. Our findings thus indicate that incorporating chirality into FFF libraries provides a robust and streamlined method to discover ligandable proteins in cells.</div>

Tenovin-1 as potential Covid-19 treatment agent

2020 ◽  
Author(s):  
Kira Smith
Keyword(s):  
Small Molecules ◽  
Vesicular Stomatitis Virus ◽  
Virus Replication ◽  
Antiviral Defense ◽  
Defense System ◽  
Treatment Agent ◽  
Vesicular Stomatitis ◽  
Novel Coronavirus ◽  
In Cells

P53 reduce coronaviruses replication, 'cause p53 normally activates genes that are involved in the cell's non-specific antiviral defense system. In cells which p53 is too lower, the rate of virus replication is several orders of magnitude higher than that observed in cells in which the p53 is present 1, while SIRT1 inhibitors also down-regulate viruses replication, as showed in my previous publication: "Novel Coronavirus: Hypothesis of Treatment with SIRT1", as well as in other viruses like Mers-CoV, HIV, Epathitis B, VSV (Vesicular Stomatitis Virus).Tenovin-1 or Tenovin-6 are small molecules that inhibit SIRT1/SIRT2 and protect against MDM2-mediated p53 degradation, which involves ubiquitination.

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