AQBioSim: AI Simulation for Drug Discovery and Development

Hosts: Dario Alessi & Mahmood Ahmed

Venue: MSI Small Lecture Theatre, SLS

This seminar is fully funded by external sources

Abstract:

AQBioSim is SandboxAQ’s enterprise-grade platform for in silico drug discovery, purpose-built to accelerate and de-risk the highest-value phases of the R&D lifecycle. Combining generative AI, physics-based simulation, and biological knowledge graphs, AQBioSim enables a unified, multimodal approach to molecular design, target identification, and translational prediction—delivering precision, speed, and confidence at scale.

At its core, AQBioSim fuses three orthogonal modalities: i) AI for generative design, pattern recognition, and multi-objective optimization; ii) Physics-based simulation for mechanistic validation and quantitative affinity prediction; iii) Biological knowledge graphs for systems-level reasoning and translational grounding. This triad powers a modular, configurable intelligence layer that integrates directly into enterprise R&D workflows—spanning small molecule and antibody discovery, biomarker-enabled translation, and decision support across programs. Underpinning AQBioSim are large-scale proprietary models—including a next-generation absolute FEP engine for binding affinity prediction, physics-refined co-folding, and multimodal PCM/KG models that bridge chemical activity with biological context. These are deployed on a scalable computational backbone, built in partnership with Google and NVIDIA, enabling rapid iteration and large-batch simulations.

In short, AQBioSim transforms fragmented R&D pipelines into connected, computationally driven engines—turning data into decisions, and hypotheses into high-confidence drug candidates.

Bio:

Andrea Bortolato is the Vice President of Drug Discovery at SandboxAQ, bringing over 20 years of experience in computational chemistry and drug discovery. He has worked in biotechnology, pharmaceuticals, and agrochemistry throughout his career, holding more than 50 scientific patents and publications, including three in Nature. Before joining SandboxAQ, Andrea successfully led drug discovery project teams at Bristol-Myers Squibb (BMS), Schrodinger, Heptares (now Nxera Pharma), and Syngenta. He has experience working on both internal projects and collaborations with companies such as Takeda, AstraZeneca, Cubist, Morphic, and Structure Therapeutics. Andrea holds a PhD in computational chemistry, earned in partnership between the University of Padua in Italy and the University of Geneva in Switzerland. He then completed a postdoctoral fellowship at Mount Sinai School of Medicine in New York City.