Efficient design of peptide-binding polymers using active learning approaches

Active learning approaches in molecule pKi prediction

During the early stages of drug design, identifying compounds with suitable bioactivities is crucial. Given the vast array of potential drug databases, it's feasible to assay only a limited subset of candidates. The optimal method for selecting the candidates, aiming to minimize the overall number of assays, involves an active learning (AL) approach. In this work, we benchmarked a range of AL strategies with two main objectives: (1) to identify a strategy that ensures high model performance and (2) to select molecules with desired properties using minimal assays. To evaluate the different AL strategies, we employed the simulated AL workflow based on "virtual" experiments. These experiments leveraged ChEMBL datasets, which come with known biological activity values for the molecules. Furthermore, for classification tasks, we proposed the hybrid selection strategy that unified both exploration and exploitation AL strategies into a single acquisition function, defined by parameters n and c. We have also shown that popular minimal margin and maximal variance selection approaches for exploration selection correspond to minimization of the hybrid acquisition function with n=1 and 2 respectively. The balance between the exploration and exploitation strategies can be adjusted using a coefficient (c), making the optimal strategy selection straightforward. The primary strength of the hybrid selection method lies in its adaptability; it offers the flexibility to adjust the criteria for molecule selection based on the specific task by modifying the value of the contribution coefficient. Our analysis revealed that, in regression tasks, AL strategies didn't succeed at ensuring high model performance, however, they were successful in selecting molecules with desired properties using minimal number of tests. In analogous experiments in classification tasks, exploration strategy and the hybrid selection function with a constant c<1 (for n=1) and c≤0.2 (for n=2) were effective in achieving the goal of constructing a high-performance predictive model using minimal data. When searching for molecules with desired properties, exploitation, and the hybrid function with c≥1 (n=1) and c≥0.7 (n=2) demonstrated efficiency identifying molecules in fewer iterations compared to random selection method. Notably, when the hybrid function was set to an intermediate coefficient value (c=0.7), it successfully addressed both tasks simultaneously.

Deep learning for advancing peptide drug development: Tools and methods in structure prediction and design

Peptides can bind challenging disease targets with high affinity and specificity, offering enormous opportunities for addressing unmet medical needs. However, peptides' unique features, including smaller size, increased structural flexibility, and limited data availability, pose additional challenges to the design process compared to proteins. This review explores the dynamic field of peptide therapeutics, leveraging deep learning to enhance structure prediction and design. Our exploration encompasses various facets of peptide research, ranging from dataset curation handling to model development. As deep learning technologies become more refined, we channel our efforts into peptide structure prediction and design, aligning with the fundamental principles of structure-activity relationships in drug development. To guide researchers in harnessing the potential of deep learning to advance peptide drug development, our insights comprehensively explore current challenges and future directions of peptide therapeutics.

Bayesian Optimization in Drug Discovery

Drug discovery deals with the search for initial hits and their optimization toward a targeted clinical profile. Throughout the discovery pipeline, the candidate profile will evolve, but the optimization will mainly stay a trial-and-error approach. Tons of in silico methods have been developed to improve and fasten this pipeline. Bayesian optimization (BO) is a well-known method for the determination of the global optimum of a function. In the last decade, BO has gained popularity in the early drug design phase. This chapter starts with the concept of black box optimization applied to drug design and presents some approaches to tackle it. Then it focuses on BO and explains its principle and all the algorithmic building blocks needed to implement it. This explanation aims to be accessible to people involved in drug discovery projects. A strong emphasis is made on the solutions to deal with the specific constraints of drug discovery. Finally, a large set of practical applications of BO is highlighted.