Implicit-descriptor ligand-based virtual screening by means of collaborative filtering

Artificial Intelligence and Machine Learning for Lead-to-Candidate Decision-Making and Beyond

The use of artificial intelligence (AI) and machine learning (ML) in pharmaceutical research and development has to date focused on research: target identification; docking-, fragment-, and motif-based generation of compound libraries; modeling of synthesis feasibility; rank-ordering likely hits according to structural and chemometric similarity to compounds having known activity and affinity to the target(s); optimizing a smaller library for synthesis and high-throughput screening; and combining evidence from screening to support hit-to-lead decisions. Applying AI/ML methods to lead optimization and lead-to-candidate (L2C) decision-making has shown slower progress, especially regarding predicting absorption, distribution, metabolism, excretion, and toxicology properties. The present review surveys reasons why this is so, reports progress that has occurred in recent years, and summarizes some of the issues that remain. Effective AI/ML tools to derisk L2C and later phases of development are important to accelerate the pharmaceutical development process, ameliorate escalating development costs, and achieve greater success rates.

Development and Evaluation of Health Recommender Systems: Systematic Scoping Review and Evidence Mapping

BACKGROUND

Health recommender systems (HRSs) are information retrieval systems that provide users with relevant items according to the users' needs, which can motivate and engage users to change their behavior.

OBJECTIVE

This study aimed to identify the development and evaluation of HRSs and create an evidence map.

METHODS

A total of 6 databases were searched to identify HRSs reported in studies from inception up to June 30, 2022, followed by forward citation and grey literature searches. Titles, abstracts, and full texts were screened independently by 2 reviewers, with discrepancies resolved by a third reviewer, when necessary. Data extraction was performed by one reviewer and checked by a second reviewer. This review was conducted in accordance with the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews) statement.

RESULTS

A total of 51 studies were included for data extraction. Recommender systems were used across different health domains, such as general health promotion, lifestyle, and generic health service. A total of 23 studies had reported the use of a combination of recommender techniques, classified as hybrid recommender systems, which are the most commonly used recommender techniques in HRSs. In the HRS design stage, only 10 of 51 (19.6%) recommender systems considered personal preferences of end users in the design or development of the system; a total of 29 studies reported the user interface of HRSs, and most HRSs worked on users' mobile interfaces, usually a mobile app. Two categories of HRS evaluations were used, and evaluations of HRSs varied greatly; 62.7% (32/51) of the studies used the offline evaluations using computational methods (no user), and 33.3% (17/51) of the studies included end users in their HRS evaluation.

CONCLUSIONS

Through this scoping review, nonmedical professionals and policy makers can visualize and better understand HRSs for future studies. The health care professionals and the end users should be encouraged to participate in the future design and development of HRSs to optimize their utility and successful implementation. Detailed evaluations of HRSs in a user-centered approach are needed in future studies.

Deep Learning-Based Ligand Design Using Shared Latent Implicit Fingerprints from Collaborative Filtering

In their previous work, Srinivas et al. [ J. Cheminf. 2018, 10, 56] have shown that implicit fingerprints capture ligands and proteins in a shared latent space, typically for the purposes of virtual screening with collaborative filtering models applied on known bioactivity data. In this work, we extend these implicit fingerprints/descriptors using deep learning techniques to translate latent descriptors into discrete representations of molecules (SMILES), without explicitly optimizing for chemical properties. This allows the design of new compounds based upon the latent representation of nearby proteins, thereby encoding druglike properties including binding affinities to known proteins. The implicit descriptor method does not require any fingerprint similarity search, which makes the method free of any bias arising from the empirical nature of the fingerprint models [Srinivas, R.; J. Cheminf. 2018, 10, 56]. We evaluate the properties of the potentially novel drugs generated by our approach using physical properties of druglike molecules and chemical complexity. Additionally, we analyze the reliability of the biological activity of the new compounds generated using this method by employing models of protein-ligand interaction, which assists in assessing the potential binding affinity of the designed compounds. We find that the generated compounds exhibit properties of chemically feasible compounds and are predicted to be excellent binders to known proteins. Furthermore, we also analyze the diversity of compounds created using the Tanimoto distance and conclude that there is a wide diversity in the generated compounds.

Key Topics in Molecular Docking for Drug Design

Molecular docking has been widely employed as a fast and inexpensive technique in the past decades, both in academic and industrial settings. Although this discipline has now had enough time to consolidate, many aspects remain challenging and there is still not a straightforward and accurate route to readily pinpoint true ligands among a set of molecules, nor to identify with precision the correct ligand conformation within the binding pocket of a given target molecule. Nevertheless, new approaches continue to be developed and the volume of published works grows at a rapid pace. In this review, we present an overview of the method and attempt to summarise recent developments regarding four main aspects of molecular docking approaches: (i) the available benchmarking sets, highlighting their advantages and caveats, (ii) the advances in consensus methods, (iii) recent algorithms and applications using fragment-based approaches, and (iv) the use of machine learning algorithms in molecular docking. These recent developments incrementally contribute to an increase in accuracy and are expected, given time, and together with advances in computing power and hardware capability, to eventually accomplish the full potential of this area.

Exploring the Potential of Spherical Harmonics and PCVM for Compounds Activity Prediction

Biologically active chemical compounds may provide remedies for several diseases. Meanwhile, Machine Learning techniques applied to Drug Discovery, which are cheaper and faster than wet-lab experiments, have the capability to more effectively identify molecules with the expected pharmacological activity. Therefore, it is urgent and essential to develop more representative descriptors and reliable classification methods to accurately predict molecular activity. In this paper, we investigate the potential of a novel representation based on Spherical Harmonics fed into Probabilistic Classification Vector Machines classifier, namely SHPCVM, to compound the activity prediction task. We make use of representation learning to acquire the features which describe the molecules as precise as possible. To verify the performance of SHPCVM ten-fold cross-validation tests are performed on twenty-one G protein-coupled receptors (GPCRs). Experimental outcomes (accuracy of 0.86) assessed by the classification accuracy, precision, recall, Matthews’ Correlation Coefficient and Cohen’s kappa reveal that using our Spherical Harmonics-based representation which is relatively short and Probabilistic Classification Vector Machines can achieve very satisfactory performance results for GPCRs.