Exploring PROTAC Cooperativity with Coarse-Grained Alchemical Methods

Abstract

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 present a new computational framework to model the cooperativity between PROTAC−E3 binding and PROTAC−target binding principally through protein−protein interactions (PPIs) induced by the PROTAC. Due to the scarcity and low resolution of experimental measurements, the physical and chemical drivers of these non-native PPIs remain to be elucidated. We develop a coarse-grained (CG) approach to model interactions in the target−PROTAC−E3 complexes, which enables converged thermodynamic estimations using alchemical free energy calculation methods despite an unconventional scale of perturbations. With minimal parametrization, we successfully capture fundamental principles of cooperativity, including the optimality of intermediate PROTAC linker lengths that originates from configurational entropy. We qualitatively characterize the dependency of cooperativity on PROTAC linker lengths and protein charges and shapes. Minimal inclusion of sequence-and conformation-specific features in our current force field, however, limits quantitative modeling to reproduce experimental measurements, but further development of the CG model may allow for efficient computational screening to optimize PROTAC cooperativity.

Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods

“…Considering the relatively intricate problem of ternary complex formation, MD simulations hold great promise for rationalizing structure–activity relationships among the different binding partners. To date, simulations of ternary complexes have been applied for tasks such as analyzing interactions between the three binding partners in atomistic detail, probing the binding cooperativity, scoring and ranking given degraders, and assessing the stability of degrader variants, such as covalently binding degraders, macrocyclic degraders, or such aimed at new diseases . In particular, molecular simulations have successfully augmented many biochemical and proteomics assays to inform on the selectivity of distinct degraders ,,, and also structural biophysical techniques to elucidate binding site interactions. ,, Recently, our research team has combined MD simulations with X-ray crystallography, small-angle scattering, HDX, and ubiquitinomics experiments to explore the differential in DC 50 values between three VHL-recruiting SMARCA2 degraders .…”

PROTACs: A novel strategy for cancer drug discovery and development

“…Since then, a series of novel and highly effective VHL E3 ligase ligands have been discovered and reported, typified by compounds VHL‐1–VHL‐8 (Figure 2) with improved lipophilicity 119,120,122 . The studies on the eutectic structure of the VHL ligand with the protein helps to locate the solvent‐exposed region, leading to revelation of four possible linking sites without negatively affecting the interaction between the protein and the corresponding ligand (Figure 2; PDB ID: 4W9H) 123–134 . These sites are (a) terminal amino; (b) sulfhydryl; (c) benzyl; and (d) phenolic hydroxyl group on the benzene ring 113,135–141 .…”

“… 119 , 120 , 122 The studies on the eutectic structure of the VHL ligand with the protein helps to locate the solvent‐exposed region, leading to revelation of four possible linking sites without negatively affecting the interaction between the protein and the corresponding ligand (Figure 2 ; PDB ID: 4W9H). 123 , 124 , 125 , 126 , 127 , 128 , 129 , 130 , 131 , 132 , 133 , 134 These sites are (a) terminal amino; (b) sulfhydryl; (c) benzyl; and (d) phenolic hydroxyl group on the benzene ring. 113 , 135 , 136 , 137 , 138 , 139 , 140 , 141 At present, VHL E3 ligand has been widely and successfully applied in the design and synthesis of PROTAC as one of the most commonly used E3 ligands (Table 1 ).…”

Revolutionizing Drug Targeting Strategies: Integrating Artificial Intelligence and Structure-Based Methods in PROTAC Development

“…Their work provides insights into the binding and dynamics of PROTACs, as well as the impact of flexible linkers on ternary complexes. In a recent study by Mai et al [86], a novel computational framework was introduced to model the cooperativity between PROTAC-E3 binding and PROTAC-target binding using a coarse-grained (CG) approach. Their CG approach effectively captures the essential aspects of cooperativity, including the identification of optimal intermediate linker lengths resulting from configurational entropy.…”