Scaffold-Based Multi-Objective Drug Candidate Optimization

In therapeutic design, balancing various physiochemical properties is crucial for molecule development, similar to how Multiparameter Optimization (MPO) evaluates multiple variables to meet a primary goal. While many molecular features can now be predicted using textitin silico methods, aiding early drug development, the vast data generated from high throughput virtual screening challenges the practicality of traditional MPO approaches. Addressing this, we introduce a scaffold focused graph-based Markov chain Monte Carlo framework (ScaMARS) built to generate molecules with optimal properties. This innovative framework is capable of self-training and handling a wider array of properties, sampling different chemical spaces according to the starting scaffold. The benchmark analysis on several properties shows that ScaMARS has a diversity score of 84.6% and has a much higher success rate of 99.5% compared to conditional models. The integration of new features into MPO significantly enhances its adaptability and effectiveness in therapeutic design, facilitating the discovery of candidates that efficiently optimize multiple properties.