Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry

T Dixon, D MacPherson, B Mostofian… - Nature …, 2022 - nature.com
Targeted protein degradation (TPD) is a promising approach in drug discovery for degrading
proteins implicated in diseases. A key step in this process is the formation of a ternary …

Structural characterization of degrader-induced ternary complexes using hydrogen–deuterium exchange mass spectrometry and computational modeling: implications …

SJ Eron, H Huang, RV Agafonov… - ACS Chemical …, 2021 - ACS Publications
The field of targeted protein degradation (TPD) has grown exponentially over the past
decade with the goal of developing therapies that mark proteins for destruction leveraging …

Biophysical and computational approaches to study ternary complexes: a 'cooperative relationship'to rationalize targeted protein degradation

JA Ward, C Perez‐Lopez, C Mayor‐Ruiz - ChemBioChem, 2023 - Wiley Online Library
Degraders have illustrated that compound‐induced proximity to E3 ubiquitin ligases can
prompt the ubiquitination and degradation of disease‐relevant proteins. Hence, this …

Targeted protein degradation: advances, challenges, and prospects for computational methods

B Mostofian, HJ Martin, A Razavi, S Patel… - Journal of Chemical …, 2023 - ACS Publications
The therapeutic approach of targeted protein degradation (TPD) is gaining momentum due
to its potentially superior effects compared with protein inhibition. Recent advancements in …

Selectivity through Targeted Protein Degradation (TPD) Miniperspective

A Gopalsamy - Journal of Medicinal Chemistry, 2022 - ACS Publications
Targeted protein degradation has become a reliable tool in the medicinal chemist's toolbox,
as seen with rapid progression of PROTACs (proteolysis targeting chimeras) to clinic …

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 …

Affinity and cooperativity modulate ternary complex formation to drive targeted protein degradation

RP Wurz, H Rui, K Dellamaggiore… - Nature …, 2023 - nature.com
Targeted protein degradation via “hijacking” of the ubiquitin-proteasome system using
proteolysis targeting chimeras (PROTACs) has evolved into a novel therapeutic modality …

A kinetic proofreading model for bispecific protein degraders

DW Bartlett, AM Gilbert - Journal of pharmacokinetics and …, 2021 - Springer
Bispecific protein degraders (BPDs) engage the ubiquitin–proteasome system (UPS) to
catalytically degrade intracellular proteins through the formation of ternary complexes with …

Advancing targeted protein degradation via multiomics profiling and artificial intelligence

M Duran-Frigola, M Cigler… - Journal of the American …, 2023 - ACS Publications
Only around 20% of the human proteome is considered to be druggable with small-molecule
antagonists. This leaves some of the most compelling therapeutic targets outside the reach …

Molecular glues: the adhesive connecting targeted protein degradation to the clinic

JM Sasso, R Tenchov, DS Wang, LS Johnson… - Biochemistry, 2022 - ACS Publications
Targeted protein degradation is a rapidly exploding drug discovery strategy that uses small
molecules to recruit disease-causing proteins for rapid destruction mainly via the ubiquitin …