PROTAC degraders as chemical probes for studying target biology and target validation

V Němec, MP Schwalm, S Müller… - Chemical Society Reviews, 2022 - pubs.rsc.org
Small molecule degraders such as PROTACs (PROteolysis TArgeting Chimeras) have
emerged as new promising pharmacological modalities and the first PROTAC drug …

Navigating the ERK1/2 MAPK cascade

A Martin-Vega, MH Cobb - Biomolecules, 2023 - mdpi.com
The RAS-ERK pathway is a fundamental signaling cascade crucial for many biological
processes including proliferation, cell cycle control, growth, and survival; common across all …

De novo design of peptide binders to conformationally diverse targets with contrastive language modeling

S Bhat, K Palepu, L Hong, J Mao, T Ye, R Iyer… - Science …, 2025 - science.org
Designing binders to target undruggable proteins presents a formidable challenge in drug
discovery. In this work, we provide an algorithmic framework to design short, target-binding …

SaLT&PepPr is an interface-predicting language model for designing peptide-guided protein degraders

G Brixi, T Ye, L Hong, T Wang, C Monticello… - Communications …, 2023 - nature.com
Protein-protein interactions (PPIs) are critical for biological processes and predicting the
sites of these interactions is useful for both computational and experimental applications. We …

[PDF][PDF] De Novo Design of Peptide Binders to Conformationally Diverse Targets with Contrastive Language Modeling

S Bhat, K Palepu, L Hong, J Mao, T Ye, R Iyer, L Zhao… - bioRxiv, 2023 - academia.edu
Designing binders to target undruggable proteins presents a formidable challenge in drug
discovery, requiring innovative approaches to overcome the lack of putative binding sites …

Biologics-based degraders—an expanding toolkit for targeted-protein degradation

D VanDyke, JD Taylor, KJ Kaeo, J Hunt… - Current opinion in …, 2022 - Elsevier
Highlights•Targeted-protein degradation supports fundamental discovery and drug
development.•Biologics-based degraders target intracellular, extracellular, and membrane …

Targeted protein degradation using chimeric human E2 ubiquitin-conjugating enzymes

JD Taylor, N Barrett, S Martinez Cuesta… - Communications …, 2024 - nature.com
Proteins can be targeted for degradation by engineering biomolecules that direct them to the
eukaryotic ubiquitination machinery. For instance, the fusion of an E3 ubiquitin ligase to a …

Ubiquitin Engineering for Interrogating the Ubiquitin–Proteasome System and Novel Therapeutic Strategies

JQ Tang, MM Marchand, G Veggiani - Cells, 2023 - mdpi.com
Protein turnover, a highly regulated process governed by the ubiquitin–proteasome system
(UPS), is essential for maintaining cellular homeostasis. Dysregulation of the UPS has been …

Intracellular protein delivery: Approaches, challenges, and clinical applications

A Chan, A Tsourkas - BME frontiers, 2024 - spj.science.org
Protein biologics are powerful therapeutic agents with diverse inhibitory and enzymatic
functions. However, their clinical use has been limited to extracellular applications due to …

DARPins as a novel tool to detect and degrade p73

P Münick, J Zielinski, A Strubel, N Gutfreund… - Cell Death & …, 2024 - nature.com
Abstract The concept of Targeted Protein Degradation (TPD) has been introduced as an
attractive alternative to the development of classical inhibitors. TPD can extend the range of …