This work seeks to advance quantitative methods for biomolecular design, especially for predicting biomolecular interactions, via a focused series of community blind prediction challenges. Physical methods for predicting binding free energies, or ?free energy methods?, are poised to dramatically reshape early stage drug discovery, and are already ?nding applications in pharmaceutical lead optimization. However, performance is unreliable, the domain of applicability is limited, and failures in pharmaceutical applications are often hard to understand and ?x. On the other hand, these methods can now typically predict a variety of simple physical properties such as solvation free energies or relative solubilities, though there is still clear room for improvement in accuracy. In recent years, competitions and crowdsourcing have proven an effective model for driving innovations in diverse ?elds. In our ?eld, blind prediction challenges have played a key role in driving innovations in prediction of physical properties and binding, especially in the form of the SAMPL series of challenges. Here, we will continue and extend SAMPL prediction challenges to include new physical properties, more complicated host-guest binding data, and application to biomolecular systems. Carefully selected systems and novel experimental data will provide challenges of gradually increasing complexity spanning between systems which are now tractable to those which are marginally out of reach of today's methods but still slightly simpler than those covered by the Drug Design Data Resource (D3R) series of challenges on existing pharmaceutical data. We will work with D3R to run blind challenges on the data we generate and to ensure it is designed to maximally bene?t the ?eld.
In Aim 1, we will collect new measurements on partitioning, distribution, and protonation of drug-like compounds, in collaboration with partners in the pharmaceutical industry.
In Aim 2, we leverage our expertise in host-guest binding to generate new data on host-guest binding in cucubiturils and deep cavity cavitands. And in Aim 3, we use high-throughput robotic experiments to generate new protein-ligand binding data of biological relevance.
Aim 4 focuses on using this data in the SAMPL series of challenges, applying proven crowdsourcing-based techniques to drive the development of new methods and new understanding of the strengths and weaknesses of existing techniques. We will also run reference calculations with the latest techniques. This work will ensure the continued success of SAMPL challenges which have already driven considerable innovation in the ?eld and been the focus of 100 different publications (each typically cited 5-50 times) since their inception around 2007, and will play a key role in driving the next several generations of improvements in computational techniques for molecular design. The research proposed here will lead to signi?cant improvements in the predictive power of physical models for drug discovery, molecular design and the prediction of physical properties.
Physical methods for designing small molecule therapeutics are poised for a breakthrough, allowing molecular design for targeted treatment of diseases, personalized medicine, and rapid drug development. However, careful stress testing and improvement of these methods is necessary to make them suf?ciently reliable and robust for the enormous range of problems they can potentially solve. Here, we will generate new experimental data on carefully selected and tailored systems, using it to drive a series of blind community challenges which follow a crowdsourcing model for testing and improving these methods, inducing new innovations and preparing the methods to have the dramatic impacts on human health that they promise.
| I??k, Mehtap; Levorse, Dorothy; Rustenburg, Ariën S et al. (2018) pKa measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments. J Comput Aided Mol Des 32:1117-1138 |
