Atomistic modeling towards predictive cardiotoxicity
Bibliographic record
Abstract
Abstract Current methods for assessing safety pharmacology in the context of cardiac arrhythmia risk are unable to distinguish between drugs that cause cardiac rhythm disturbances and benign drugs. Drugs deemed likely to be unsafe share the common property of blocking the human Ether-à-go-go-Related Gene (hERG) encoded cardiac potassium channel and consequent prolongation of QT interval on the ECG. However, hERG block and QT prolongation alone are not selective indicators for cardiac arrhythmia. Here we present a prototype computational framework to distinguish between safe and unsafe hERG blockers. We used recent cryo-EM hERG structure to build and validate an atomistic structural model of the channel open conducting state. We also developed structural atomistic models of dofetilide, a hERG blocking drug with high pro-arrhythmia risk, in both charged and neutral ionization states. Next, we employed unbiased and enhanced sampling all-atom molecular dynamics (MD) simulations to probe atomic-scale mechanisms of dofetilide interaction with open-state hERG. Multi-microsecond drug “flooding” simulations revealed spontaneous dofetilide binding to the channel pore through the intracellular gate. Umbrella sampling MD was used to compute dofetilide affinity to hERG, in good agreement with experiment, as well as ingress and egress rates, which in a novel linkage between the atomistic and functional scale are utilized in our companion paper (Yang P-C et al. 2019 bioRxiv :635433) to parameterize functional kinetic models of dofetilide - hERG interactions used to predict emergent drug effects on the cardiac rhythm. This study represents the first necessary components of a computational framework for virtual cardiac safety pharmacology screening from the atom to the rhythm.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.004 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.004 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".