ReviewChemical biology & drug design2013
Back to the future: can physical models of passive membrane permeability help reduce drug candidate attrition and move us beyond QSPR?
Review in Chemical biology & drug design, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
28 citing papers in PubMed.
- Elucidating Antibiotic Permeation through theJournal of chemical information and modeling · 2024Article
- Improving the Accuracy of Permeability Data to Gain Predictive Power: Assessing Sources of Variability in Assays Using Cell Monolayers.Membranes · 2024Review
- Leveraging Machine Learning-Guided Molecular Simulations Coupled with Experimental Data to Decipher Membrane Binding Mechanisms of Aminosterols.Journal of chemical theory and computation · 2024Article
- How is Membrane Permeation of Small Ionizable Molecules Affected by Protonation Kinetics?The journal of physical chemistry. B · 2024Article
- Combining SILCS and Artificial Intelligence for High-Throughput Prediction of the Passive Permeability of Drug Molecules.Journal of chemical information and modeling · 2023Article
- Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods.Journal of chemical information and modeling · 2023Review
- Understanding Passive Membrane Permeation of Peptides: Physical Models and Sampling Methods Compared.International journal of molecular sciences · 2023Article
- A Potential In Vitro 3D Cell Model to Study Vascular Diseases by Simulating the Vascular Wall Microenvironment and Its Application.Life (Basel, Switzerland) · 2022Article
- Molecular dynamics simulation study of the positioning and dynamics of α-tocopherol in phospholipid bilayers.European biophysics journal : EBJ · 2021Article
- Predicting the Membrane Permeability of Fentanyl and Its Analogues by Molecular Dynamics Simulations.The journal of physical chemistry. B · 2021Article
- The Whole Is Bigger than the Sum of Its Parts: Drug Transport in the Context of Two Membranes with Active Efflux.Chemical reviews · 2021Article
- Molecular dynamics trajectories for 630 coarse-grained drug-membrane permeations.Scientific data · 2020Article
- Physics-Based Method for Modeling Passive Membrane Permeability and Translocation Pathways of Bioactive Molecules.Journal of chemical information and modeling · 2019Article
- PerMM: A Web Tool and Database for Analysis of Passive Membrane Permeability and Translocation Pathways of Bioactive Molecules.Journal of chemical information and modeling · 2019Article
- The asymmetry of plasma membranes and their cholesterol content influence the uptake of cisplatin.Scientific reports · 2019Article
- Prediction of Membrane Permeation of Drug Molecules by Combining an Implicit Membrane Model with Machine Learning.Journal of chemical information and modeling · 2019Article
- Drug-Membrane Permeability across Chemical Space.ACS central science · 2019Article
- MolMeDB: Molecules on Membranes Database.Database : the journal of biological databases and curation · 2019Article
- Membrane partition of bis-(3-hydroxy-4-pyridinonato) zinc(ii) complexes revealed by molecular dynamics simulations.RSC advances · 2018Article
- Multiscale Methods in Drug Design Bridge Chemical and Biological Complexity in the Search for Cures.Nature reviews. Chemistry · 2018Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
It is widely recognized that adsorption, distribution, metabolism, excretion, and toxicology liabilities kill the majority of drug candidates that progress to clinical trials. The development of computational models to predict small molecule membrane permeability is therefore of considerable scientific and public health interest. Empirical qualitative structure permeability relationship models of permeability have been a mainstay in industrial applications, but lack a deep understanding of the underlying biologic physics. Others and we have shown that implicit solvent models to predict passive permeability for small molecules exhibit mediocre predictive performance when validated across experimental test sets. Given the vast increase in computer power, more efficient parallelization schemes, and extension of current atomistic simulation codes to general use graphical processing units, the development and application of physical models based on all-atom simulations may now be feasible. Preliminary results from rigorous free energy calculations using all-atom simulations indicate that performance relative to implicit solvent models may be improved, but many outstanding questions remain. Here, we review the current state-of-the-art physical models for passive membrane permeability prediction and present a prospective look at promising new directions for all-atom approaches.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.