Unlocking the Power of Gradient Guidance for Structure-Based Molecule Optimization

ICLR 2025 Conference Submission1147 Authors

Keywords: molecule optimization, structure-based drug design, Bayesian flow network

TL;DR: Enable gradient guidance over molecular data involving continuous coordinates and discrete types

Abstract:

Structure-based molecule optimization (SBMO) aims to optimize molecules with both continuous coordinates and discrete types against protein targets.
A promising direction is to exert gradient guidance on generative models given its remarkable success in images, but it is challenging to guide discrete data and risks inconsistencies between modalities.
To this end, we leverage a continuous and differentiable space derived through Bayesian inference, presenting Molecule Joint Optimization (MolJO), the first gradient-based SBMO framework that facilitates joint guidance signals across different modalities while preserving SE(3)-equivariance.
We introduce a novel backward correction strategy that optimizes within a sliding window of the past histories, allowing for a seamless trade-off between explore-and-exploit during optimization.
Our proposed MolJO achieves state-of-the-art performance on CrossDocked2020 benchmark (Success Rate 51.3% , Vina Dock -9.05 and SA 0.78), more than 4x improvement in Success Rate compared to the gradient-based counterpart, and 2x "Me-Better" Ratio as much as 3D baselines.
Furthermore, we extend MolJO to a wide range of optimization settings, including multi-objective optimization and challenging tasks in drug design such as R-group optimization and scaffold hopping, further underscoring its versatility and potential.

Primary Area: applications to physical sciences (physics, chemistry, biology, etc.)

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Submission Number: 1147