Functional E3 ligase hotspots and resistance mechanisms to small-molecule degraders

A Hanzl, R Casement, H Imrichova, SJ Hughes… - Nature chemical …, 2023 - nature.com
Targeted protein degradation is a novel pharmacology established by drugs that recruit
target proteins to E3 ubiquitin ligases. Based on the structure of the degrader and the target …

Modeling the CRL4A ligase complex to predict target protein ubiquitination induced by cereblon-recruiting PROTACs

N Bai, KM Riching, A Makaju, H Wu, TM Acker… - Journal of Biological …, 2022 - ASBMB
PROteolysis TArgeting Chimeras (PROTACs) are hetero-bifunctional small molecules that
can simultaneously recruit target proteins and E3 ligases to form a ternary complex …

Modeling the effect of cooperativity in ternary complex formation and targeted protein degradation mediated by heterobifunctional degraders

D Park, J Izaguirre, R Coffey, H Xu - ACS bio & med Chem Au, 2022 - ACS Publications
Chemically induced proximity between certain endogenous enzymes and a protein of
interest (POI) inside cells may cause post-translational modifications to the POI with …

Rational Prediction of PROTAC-Compatible Protein–Protein Interfaces by Molecular Docking

GP Pereira, B Jiménez-García, R Pellarin… - Journal of Chemical …, 2023 - ACS Publications
Proteolysis targeting chimeras (PROTACs) are heterobifunctional ligands that mediate the
interaction between a protein target and an E3 ligase, resulting in a ternary complex, whose …

On ternary complex stability in protein degradation: In silico molecular glue binding affinity calculations

DR Weiss, A Bortolato, Y Sun, X Cai, C Lai… - Journal of Chemical …, 2023 - ACS Publications
Molecular glues are small molecules that simultaneously bind to two proteins, creating a
chemically induced protein–protein interface. CELMoDs (cereblon E3 ligase modulators) …

Exploring PROTAC cooperativity with coarse-grained alchemical methods

H Mai, MH Zimmer, TF Miller III - The Journal of Physical Chemistry …, 2023 - ACS Publications
Proteolysis targeting chimera (PROTAC) is a novel drug modality that facilitates the
degradation of a target protein by inducing proximity with an E3 ligase. In this work, we …

Charting functional E3 ligase hotspots and resistance mechanisms to small-molecule degraders

A Hanzl, R Casement, H Imrichova, SJ Hughes… - BioRxiv, 2022 - biorxiv.org
Targeted protein degradation is a new pharmacologic paradigm established by drugs that
recruit target proteins to E3 ubiquitin ligases via a ternary ligase-degrader-target complex …

Biochemical principles of targeted protein degradation

RV Agafonov, RW Deibler, WA Elam… - … Homeostasis in Drug …, 2022 - Wiley Online Library
The therapeutic strategy of targeted protein degradation (TPD) has undergone a massive
growth in interest over the last several years. Founded in 2015, C4 Therapeutics was one of …

[图书][B] Predicting the Properties of Ligands Using Molecular Dynamics and Machine Learning

N Donyapour - 2022 - search.proquest.com
The discovery and design of new drugs requires extensive experimental assays that are
usually very expensive and time-consuming. To cut down the cost and time of the drug …

A Different Kind of Restraint Suitable for Molecular Dynamics Simulations

I Kolossváry, W Sherman - biorxiv, 2022 - biorxiv.org
Conformational sampling of complex biomolecules is an emerging frontier in drug discovery.
Indeed, advances in lab-based structural biology and related computational approaches like …