Cross clinical-experimental-computational qualification of in silico drug trials on human cardiac purkinje cells for proarrhythmia risk prediction.

The preclinical identification of drug-induced cardiotoxicity and its translation into human risk are still major challenges in pharmaceutical drug discovery. The ICH S7B Guideline and Q&A on Clinical and Nonclinical Evaluation of QT/QTc Interval Prolongation and Proarrhythmic Potential promotes human in silico drug trials as a novel tool for proarrhythmia risk assessment. To facilitate the use of in silico data in regulatory submissions, explanatory control compounds should be tested and documented to demonstrate consistency between predictions and the historic validation data. This study aims to quantify drug-induced electrophysiological effects on in silico cardiac human Purkinje cells, to compare them with existing in vitro rabbit data, and to assess their accuracy for clinical pro-arrhythmic risk predictions. The effects of 14 reference compounds were quantified in simulations with a population of in silico human cardiac Purkinje models. For each drug dose, five electrophysiological biomarkers were quantified at three pacing frequencies, and results compared with available in vitro experiments and clinical proarrhythmia reports. Three key results were obtained: 1) In silico, repolarization abnormalities in human Purkinje simulations predicted drug-induced arrhythmia for all risky compounds, showing higher predicted accuracy than rabbit experiments; 2) Drug-induced electrophysiological changes observed in human-based simulations showed a high degree of consistency with in vitro rabbit recordings at all pacing frequencies, and depolarization velocity and action potential duration were the most consistent biomarkers; 3) discrepancies observed for dofetilide, sotalol and terfenadine are mainly caused by species differences between humans and rabbit. Taken together, this study demonstrates higher accuracy of in silico methods compared to in vitro animal models for pro-arrhythmic risk prediction, as well as a high degree of consistency with in vitro experiments commonly used in safety pharmacology, supporting the potential for industrial and regulatory adoption of in silico trials for proarrhythmia prediction.

Accurate in silico simulation of the rabbit Purkinje fiber electrophysiological assay to facilitate early pharmaceutical cardiosafety assessment: Dream or reality?

As a branch of quantitative systems toxicology, in silico simulations are of growing attractiveness to guide preclinical cardiosafety risk assessments. Traditionally, a cascade of in vitro/in vivo assays has been applied in pharmaceutical research to screen out molecules at risk for cardiac side effects and prevent subsequent risk for patients. Drug cardiosafety assessments typically employ early mechanistic, hazard-oriented in silico/in vitro assays for compound inhibition of cardiac ion channels, followed by induced pluripotent stem cells (iPSCs) or tissue-based models such as the rabbit Purkinje fiber assay, which includes the major mechanisms contributing to action potential (AP) genesis. Additionally, multiscale simulation techniques based on mathematical models have become available, which are performed in silico 'at the heart' of compound triage to substitute Purkinje tests and increase translatability through mechanistic interpretability. To adhere to the 3R principle and reduce animal experiments, we performed a comparative benchmark and investigated a variety of mathematical cardiac AP models, including a newly developed minimalistic model specifically tailored to the AP of rabbit Purkinje cells, for their ability to substitute experiments. The simulated changes in AP duration (dAPD90) at increasing drug concentrations were compared to experimental results from 588 internal Purkinje fiber studies covering 555 different drugs with diverse modes of action. Using our minimalistic model, 80% of the Purkinje experiments could be quantitatively reproduced. This result allows for significant saving of experimental effort in early research and justifies the embedding of electrophysiological simulations into the DMTA (Design, Make, Test, Analyze) cycle in pharmaceutical compound optimization.

Quantification of plasma cell dynamics using mathematical modelling.

Plasma cells (PCs) are the main antibody-producing cells in humans. They are long-lived so that specific antibodies against either pathogens or vaccines are produced for decades. PC longevity is attributed to specific areas within the bone marrow micro-environment, the so-called 'niche', providing the cells with required growth and survival factors. With antigen encounters, e.g. infection or vaccination, new PCs are generated and home to the bone marrow where they compete with resident PCs for the niche. We propose a parametrized mathematical model describing healthy PC dynamics in the bone marrow. The model accounts for competition for the niche between newly produced PCs owing to vaccination and resident PCs. Mathematical analysis and numerical simulations of the model allow explanation of the recovery of PC homoeostasis after a vaccine-induced perturbation, and the fraction of vaccine-specific PCs inside the niche. The model enables quantification of the niche-related dynamics of PCs, i.e. the duration of PC transition into the niche and the impact of different rates for PC transitions into and out of the niche on the observed cell dynamics. Ultimately, it provides a potential basis for further investigations in health and disease.

Raman 2D-band splitting in graphene: theory and experiment.

We present a systematic experimental and theoretical study of the two-phonon (2D) Raman scattering in graphene under uniaxial tension. The external perturbation unveils that the 2D mode excited with 785 nm has a complex line-shape mainly due to the contribution of two distinct double resonance scattering processes (inner and outer) in the Raman signal. The splitting depends on the direction of the applied strain and the polarization of the incident light. The results give new insight into the nature of the 2D band and have significant implications for the use of graphene as reinforcement in composites since the 2D mode is crucial to assess how effectively graphene uptakes an applied stress or strain.

Phonons in bulk CdSe and CdSe nanowires.

We present first-principles calculations for bulk CdSe and CdSe nanowires with diameters of up to 22 A. Their electronic and structural properties are presented and discussed. The vibrational properties of bulk CdSe and the zone-center vibrations of the nanowires are calculated and analyzed. An iterative, symmetry-based relaxation method is used that yields improved results for phonon frequencies. We find that the band gap varies with the surface termination and that strongly size-dependent and nearly constant vibrational modes exist in the nanowires, depending on the displacement directions. A strong shift in frequency for specific modes is found, stemming from surface contributions to the polarization, similar to that reported for thin slabs. A comparison with experimental data from Raman measurements is given.

Direct observation of the radial breathing mode in CdSe nanorods.

We experimentally confirm the existence of the radial breathing mode in CdSe nanorods by Raman spectroscopy, which was deduced from ab initio calculations of the vibrational properties of bare CdSe nanowires and CdSe/ZnS core-shell nanowires. We calculated the modes' frequency for various diameters and measured a set of bare CdSe nanorods and CdSe/ZnS core-shell nanorods to determine the diameter dependence of the modes' frequency. The frequency of this mode is strongly diameter dependent and it can be used to estimate the nanorod diameter from a Raman measurement alone.