Biology subjects

Izaguirre, J. A.

Publications and source records attributed to Izaguirre, J. A..

4 recordsLinked to original sources

bioRxiv2025

Computational Modeling of Ternary Complex Formation and Targeted Protein Degradation Mediated by Molecular Glues

The rational design of molecular glue degraders is challenging because glue-mediated protein degradation depends on a complex interplay of molecular mechanisms: an effective molecular glue must simultaneously bring together two distinct proteins to form an interface that is both stable and accessible for ubiquitination by E3 ligases. We present GlueMap, a computational platform for discovering and optimizing molecular glues (MGs) through integrative structural and pharmacodynamic modeling. GlueMap combines molecular dynamics (MD) simulations and machine learning (ML) to model targeted protein degradation (TPD) mediated by molecular glues. We validated GlueMap by applying it to two case studies: DDB1-dependent degradation of CDK12 and CRBN-dependent degradation of GSPT1. In the DDB1-CDK12 system, GlueMap revealed strong correlations between ternary-complex stability, quantified through rigorous free-energy calculations, and experimental degradation efficiency. Notable outliers underscored the importance of incorporating conformational dynamics within assembled Cullin-RING ligase complexes. Using a supervised variational autoencoder combined with attention-based regression, GlueMap achieved high predictive accuracy for degradation potency from structural features. For CRBN-GSPT1, GlueMap reproduced known ternary-complex crystal structures and identified previously unrecognized protein-protein interactions (PPIs) that may guide the design of next-generation glues. Hierarchical virtual screening of more than 12 billion compounds successfully recovered known degraders and uncovered nine new potent MGs with DC50 values below 50 nM. Across both systems, GlueMap outperformed Boltz-1 and Boltz-2, state-of-the-art structure-prediction models that failed to reproduce the CDK12-DDB1 crystal structure and captured substantially less PPI diversity. By integrating structural, thermodynamic, and ubiquitination metrics, GlueMap establishes a multi-criteria framework for rational molecular glue design. These results demonstrate that GlueMap provides both mechanistic insight and practical acceleration of molecular glue discovery and optimization across diverse therapeutic targets.

bioinformatics↗

bioRxiv2023

A conserved local structural motif controls the kinetics of PTP1B catalysis

Protein tyrosine phosphatase 1B (PTP1B) is a negative regulator of the insulin and leptin signaling pathways, making it a highly attractive target for the treatment of type II diabetes. For PTP1B to perform its enzymatic function, a loop referred to as the "WPD loop" must transition between open (catalytically incompetent) and closed (catalytically competent) conformations, which have both been resolved by X-ray crystallography. Although prior studies have established this transition as the rate-limiting step for catalysis, the transition mechanism for PTP1B and other PTPs has been unclear. Here we present an atomically detailed model of WPD-loop transitions in PTP1B based on unbiased, long-timescale molecular dynamics simulations and weighted ensemble simulations. We found that a specific WPD-loop region-- the PDFG motif--acted as the key conformational switch, with structural changes to the motif being necessary and sufficient for transitions between long-lived open and closed states of the loop. Simulations starting from the closed state repeatedly visited open states of the loop that quickly closed again unless the infrequent conformational switching of the motif stabilized the open state. The functional role of the PDFG motif is supported by the fact that it (or the similar PDHG motif) is conserved across all PTPs. Bioinformatic analysis shows that the PDFG motif is also conserved, and adopts two distinct conformations, in deiminases, and the related DFG motif is known to function as a conformational switch in many kinases, suggesting that PDFG-like motifs may control transitions between structurally distinct, long-lived conformational states in multiple protein families.

biophysics↗

bioRxiv2022

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

Chemically induced proximity between certain endogenous enzymes and a protein of interest (POI) inside cells may cause post-translational modifications to the POI with biological consequences and potential therapeutic effects. Heterobifunctional (HBF) molecules that bind with one functional part to a target POI and with the other to an E3 ligase induce the formation of a target-HBF-E3 ternary complex, which can lead to ubiquitination and proteasomal degradation of the POI. Targeted protein degra-dation (TPD) by HBFs offers a promising approach to modulating disease-associated proteins, especially those that are intractable using other therapeutic approaches, such as enzymatic inhibition. The three-way interactions among the HBF, the target POI, and the ligase--including the protein-protein interaction (PPI) between the POI and the ligase--contribute to the stability of the ternary complex, manifested as positive or negative binding cooperativity in its formation. How such cooperativity affects HBF-mediated degradation is an open question. In this work, we develop a pharmaco-dynamic model that describes the kinetics of the key reactions in the TPD process, and we use this model to investigate the role of cooperativity in the ternary complex formation and in the target POI degradation. Our model predicts that, under certain conditions, increasing cooperativity may diminish degradation, implying an optimal range of cooperativity values for efficient degradation. We also develop a statistical inference model for determining cooperativity in intracellular ternary complex formation from cellular assay data, and demonstrate it by quantifying the change in cooperativity due to site-directed mutagenesis at the POI-ligase interface of the SMARCA2-ACBI1-VHL ternary complex. Our pharmacodynamic model provides a quantitative framework to dissect the complex HBF-mediated TPD process and may inform the rational design of effective HBF degraders.

biochemistry↗

bioRxiv2021

Atomic-Resolution Prediction of Degrader-mediated Ternary Complex Structures by Combining Molecular Simulations with Hydrogen Deuterium Exchange

Targeted protein degradation (TPD) has emerged as a powerful approach in drug discovery for removing (rather than inhibiting) proteins implicated in diseases. A key step in this approach is the formation of an induced proximity complex, where a degrader molecule recruits an E3 ligase to the protein of interest (POI), facilitating the transfer of ubiquitin to the POI and initiating the proteasomal degradation process. Here, we address three critical aspects of the TPD process: 1) formation of the ternary complex induced by a degrader molecule, 2) conformational heterogeneity of the ternary complex, and 3) assessment of ubiquitination propensity via the full Cullin Ring Ligase (CRL) macromolecular assembly. The novel approach presented here combines experimental biophysical data--in this case hydrogen-deuterium exchange mass spectrometry (HDX-MS, which measures the solvent exposure of protein residues)--with all-atom explicit solvent molecular dynamics (MD) simulations aided by enhanced sampling techniques to predict structural ensembles of ternary complexes at atomic resolution. We present results demonstrating the efficiency, accuracy, and reliability of our approach to predict ternary structure ensembles using the bromodomain of SMARCA2 (SMARCA2BD) with the E3 ligase VHL as the system of interest. The simulations reproduce X-ray crystal structures - including prospective simulations validated on a new structure that we determined in this work (PDB ID: 7S4E) - with root mean square deviations (RMSD) of 1.1 to 1.6 [A]. The simulations also reveal a structural ensemble of low-energy conformations of the ternary complex within a broad energy basin. To further characterize the structural ensemble, we used snapshots from the aforementioned simulations as seeds for Hamiltonian replica exchange molecular dynamics (HREMD) simulations, and then perform 7.1 milliseconds of aggregate simulation time using Folding@home. The resulting free energy surface identifies the crystal structure conformation within a broad low-energy basin and the dynamic ensemble is consistent with solution-phase biophysical experimental data (HDX-MS and small-angle x-ray scattering, SAXS). Finally, we graft structures from the ternary complexes onto the full CRL and perform enhanced sampling simulations, where we find that differences in degradation efficiency can be explained by the proximity distribution of lysine residues on the POI relative to the E2-loaded ubiquitin. Several of the top predicted ubiquitinated lysine residues are validated prospectively through a ubiquitin mapping proteomics experiment.

biophysics↗