Advanced In Silico Methods and Digital Platforms for the Prediction of ADMET and Pharmacokinetics Properties

A special issue of Pharmaceutics (ISSN 1999-4923). This special issue belongs to the section "Pharmacokinetics and Pharmacodynamics".

Deadline for manuscript submissions: closed (30 April 2025) | Viewed by 1878

Special Issue Editors


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Division of Medical Genetics, IRCSS Foundation “Casa Sollievo dalla Sofferenza” San Giovanni Rotondo, 71013 Foggia, Italy
Interests: artificial intelligence; machine learning; cheminformatics; molecular docking; molecular dynamics; 3D-pharmacophore modeling; drug repurposing
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Department of Pharmacy, Pharmaceutical Sciences Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy
Interests: peptide–protein interactions; protein–protein interactions; drug repurposing; binding site mapping; machine learning; classification models; molecular docking; predictive toxicology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Nowadays, the lack of efficacy and safety are the two major causes leading to drug failure. In the era of rapid technological progresses, there is a growing demand for innovative approaches to predict absorption, distribution, metabolism, excretion, and toxicity (ADMET) as well as pharmacokinetic (PK) properties of chemicals, having key roles in the evaluation of drug-likeness of compounds. These methods encompass a range of computational techniques, including quantitative structure–activity relationship (QSAR) modeling, physiologically based pharmacokinetic (PBPK) modeling, and molecular dynamics simulations. In this scenario, this Special Issue aims to explore the advancements of computer-aided techniques and technological platforms as emerging powerful tools that are able to accelerate the identification of promising drug candidates by minimizing the risks associated with late-stage failures.

In the light of this, we invite interested researchers to provide practical answers to challenging issues related to drug repurposing, de novo design, structure-based virtual screening, machine learning, artificial intelligence, molecular docking, and dynamics just to name a few, sharing their experiences on the design of novel methods and tools as well as the implementation of technological platforms.

Dr. Nicola Gambacorta
Dr. Daniela Trisciuzzi
Guest Editors

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Keywords

  • ADMET properties prediction
  • physiologically based pharmacokinetic (PBPK) modeling
  • in silico digital platform
  • chemoinformatics
  • computer-aided drug discovery
  • predictive toxicology

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Published Papers (1 paper)

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Research

13 pages, 2643 KiB  
Article
Developing Robust Human Liver Microsomal Stability Prediction Models: Leveraging Inter-Species Correlation with Rat Data
by Pranav Shah, Vishal B. Siramshetty, Ewy Mathé and Xin Xu
Pharmaceutics 2024, 16(10), 1257; https://doi.org/10.3390/pharmaceutics16101257 - 27 Sep 2024
Cited by 1 | Viewed by 1508
Abstract
Objectives: Pharmacokinetic issues were the leading cause of drug attrition, accounting for approximately 40% of all cases before the turn of the century. To this end, several high-throughput in vitro assays like microsomal stability have been developed to evaluate the pharmacokinetic profiles of [...] Read more.
Objectives: Pharmacokinetic issues were the leading cause of drug attrition, accounting for approximately 40% of all cases before the turn of the century. To this end, several high-throughput in vitro assays like microsomal stability have been developed to evaluate the pharmacokinetic profiles of compounds in the early stages of drug discovery. At NCATS, a single-point rat liver microsomal (RLM) stability assay is used as a Tier I assay, while human liver microsomal (HLM) stability is employed as a Tier II assay. We experimentally screened and collected data on over 30,000 compounds for RLM stability and over 7000 compounds for HLM stability. Although HLM stability screening provides valuable insights, the increasing number of hits generated, along with the time- and resource-intensive nature of the assay, highlights the need for alternative strategies. One promising approach is leveraging in silico models trained on these experimental datasets. Methods: We describe the development of an HLM stability prediction model using our in-house HLM stability dataset. Results: Employing both classical machine learning methods and advanced techniques, such as neural networks, we achieved model accuracies exceeding 80%. Moreover, we validated our model using external test sets and found that our models are comparable to some of the best models in literature. Additionally, the strong correlation observed between our RLM and HLM data was further reinforced by the fact that our HLM model performance improved when using RLM stability predictions as an input descriptor. Conclusions: The best model along with a subset of our dataset (PubChem AID: 1963597) has been made publicly accessible on the ADME@NCATS website for the benefit of the greater drug discovery community. To the best of our knowledge, it is the largest open-source model of its kind and the first to leverage cross-species data. Full article
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