2025 Hyper Recent •CC0 1.0 Universal

This work is dedicated to the public domain. No rights reserved.

Access Preprint From Server
April 1st, 2025
Version: 1
The Scripps Research Institute
biochemistry
biorxiv

Targeted Protein Degradation by KLHDC2 Ligands Identified by High Throughput Screening

Zhou, H.Open in Google Scholar•Zhou, T.Open in Google Scholar•Yu, W.Open in Google Scholar•Liu, L.Open in Google Scholar•Ko, Y.Open in Google Scholar•Johnson, K. A.Open in Google Scholar•Wilson, I. A.Open in Google Scholar•Schultz, P. G.Open in Google Scholar•Bollong, M. J.Open in Google Scholar

Proteolysis targeting chimeras (PROTACs) enable the selective and sub-stoichiometric elimination of pathological proteins, yet only two E3 ligases are routinely used for this purpose. Here, we expand the repertoire of PROTAC compatible E3 ligases by identifying a novel small molecule scaffold targeting the ubiquitin E3 ligase KLHDC2 using a fluorescence polarization-based high throughput screen. We highlight the utility of this ligand with the synthesis of PROTACs capable of potently degrading BRD4 in cells. This work affords additional chemical matter for targeting KLHDC2 and suggests a practical approach for identifying novel E3 binders by high throughput screening.

Similar Papers

biorxiv
Wed Apr 02 2025
In vivo activation of the dia BGC allows consolidation of the biosynthetic pathways of diaporthin, dichlorodiaporthin, diaporthinic acid, and diaporthinol
Fungal secondary metabolites exhibit remarkable chemical diversity and biological activity, making them valuable sources of bioactive compounds. A group of polyketides, with a similar core structure, have been isolated previously from different fungi - the phytotoxins diaporthin and orthosporin, the mediocre antimicrobial dichlorodiaporthin, as well as diaporthinol and diaporthinic acid. Previous ...
Burger, I.
•
Leonhartsberger, S.
•
Peikert, K.
•
Fourtis, L.
...•
Zimmermann, C.
biorxiv
Wed Apr 02 2025
Theory on the accurate estimation of Michaelis-Menten enzyme kinetic parameters from steady state and progress curve datasets
Accurate estimation of enzyme kinetic parameters such as KM and vmax from the experimental datasets is critical to characterize any enzyme. The validity of widely used standard quasi steady state approximation over decades relies on a priori information of KM and other kinetic parameters which are generally not available for newly identified enzyme systems. Progress curve analysis of the time cour...
Murugan, R.
biorxiv
Wed Apr 02 2025
Development of a Vibrio natriegens-based plate-clearing assay for rapid screening of PET-hydrolyzing enzymes
Polyethylene terephthalate (PET) is a major contributor to plastic waste. Enzymatic PET degradation offers a sustainable recycling approach, but screening for effective enzymes remains challenging. Herein, we established an experimental plate-clearing assay with Vibrio natriegens, exploiting its protein-secretion ability to rapidly identify catalytic activity without time-consuming downstream proc...
Bolstad, I. M.
•
Trooyen, S. H.
•
Luciano, D.
•
Petersen, E.
•
Courtade, G.
biorxiv
Wed Apr 02 2025
Baseline bioenergetic profile of mitochondria and permeabilized tissue of Aedes aegypti (Diptera: Culicidae) throughout its life cycle
Cellular respiration parameters provide information on the energy metabolism of an organism under physiological or non-conditions and can be determined by isolating mitochondria or even using their permeabilized tissue. The present study aimed to describe the mitochondrial activity of Ae. aegypti throughout its life cycle. For this purpose, we isolated mitochondria and permeabilized tissue (1 and ...
Castillo-Morales, R. M.
•
Urbina-Duitama, D. L.
•
Mendez, S. C.
•
Duque, J. E.
biorxiv
Wed Apr 02 2025
Customizing the Structure of a Minimal TIM Barrel to Craft a De Novo Enzyme
The TIM barrel is the most prevalent fold in natural enzymes, supporting efficient catalysis of diverse chemical reactions. While de novo TIM barrels have been successfully designed, their minimalistic architectures lack structural elements essential for substrate binding and catalysis. Here, we present CANVAS, a computational workflow that introduces a structural lid into a minimal de novo TIM ba...
Beck, J.
•
Smith, B. J.
•
Zarifi, N.
•
Freund, E.
...•
Hoecker, B.
biorxiv
Wed Apr 02 2025
Phosphate-binding pocket on cyclin B governs CDK substrate phosphorylation and mitotic timing
Cell cycle progression is governed by complexes of the cyclin-dependent kinases (CDKs) and their regulatory subunits cyclin and Cks1. CDKs phosphorylate hundreds of substrates, often at multiple sites. Multisite phosphorylation depends on Cks1, which binds initial priming phosphorylation sites to promote secondary phosphorylation at other sites. Here, we describe a similar role for a recently disc...
Ng, H. Y.
•
Whelpley, D. H.
•
Adly, A. N.
•
Maxwell, R. A.
•
Morgan, D. O.
biorxiv
Wed Apr 02 2025
Specific binding modes of SIRT6 C-terminal domain to the nucleosome core particle influence DNA unwrapping and H3K27 accessibility
Sirtuins are a class of NAD-dependent histone deacetylases that regulate important biological pathways in prokaryotes and eukaryotes. This enzyme family comprises seven members, named SIRT1 to SIRT7. Among them, Sirtuin 6 (SIRT6) is a human sirtuin that deacetylates histones and plays a key role in DNA repair, telomere maintenance, carbohydrate and lipid metabolism, and lifespan. SIRT6\'s structur...
Qiu, Y.
•
Papai, G.
•
Ben Shem, A.
•
Bignon, E.
biorxiv
Wed Apr 02 2025
Bayesian analysis and efficient algorithms for single-molecule fluorescence data and step counting
With the growing adoption of single-molecule fluorescence experiments, there is an increasing demand for efficient statistical methodologies and accurate analysis of the acquired measurements. Existing analysis frameworks, such as those that use kinetic models, often rely on strong assumptions on the dynamics of the molecules and fluorophores under study that render them inappropriate for general ...
Mattamira, C.
•
Ward, A.
•
Krishnan, S. T.
•
Lamichhane, R.
...•
Sgouralis, I.
biorxiv
Wed Apr 02 2025
The bacterial chaperone CsgC inhibits functional amyloid CsgA formation by promoting the intrinsically disordered pre-nuclear state
E. coli secretes a functional amyloid called curli during biofilm formation. Curli fibers are composed of polymers of the CsgA protein, which adopts a beta-sheet rich fold upon fibrillization. A chaperone-like protein called CsgC inhibits CsgA amyloid formation. Like other amyloidogenic proteins, CsgA undergoes a 3-stage aggregation process: an initial lag phase where a beta-rich nucleus forms, an...
Balistreri, A.
•
Kolli, D.
•
Jayaweera, S. W.
•
Lundahl, D.
...•
Chapman, M. R.
biorxiv
Wed Apr 02 2025
Discovery and chemical optimisation of a Potent, Bi-cyclic (Bicycle(R)) Antimicrobial Inhibitor of Escherichia coli PBP3
Penicillin binding proteins (PBPs) are well validated antimicrobial targets, but the prevalence of {beta}-lactamase driven resistance and, more rarely, target-based mutations, necessitates new classes of PBP-targeting drugs. Here we describe the discovery and optimisation of novel, bicyclic peptide (Bicycle(R)) inhibitors of E. coli PBP3 (EcPBP3) using a proprietary phage display platform, and the...
Rowland, C. E.
•
Newman, H.
•
Martin, T. T.
•
Dods, R.
...•
Dawson, M. J.