A quantitative systems pharmacology workflow toward optimal design and biomarker stratification of atopic dermatitis clinical trials.

BACKGROUND: The development of atopic dermatitis (AD) drugs is challenged by many disease phenotypes and trial design options, which are hard to explore experimentally. OBJECTIVE: We aimed to optimize AD trial design using simulations. METHODS: We constructed a quantitative systems pharmacology model of AD and standard of care (SoC) treatments and generated a phenotypically diverse virtual population whose parameter distribution was derived from known relationships between AD biomarkers and disease severity and calibrated using disease severity evolution under SoC regimens. RESULTS: We applied this workflow to the immunomodulator OM-85, currently being investigated for its potential use in AD, and calibrated the investigational treatment model with the efficacy profile of an existing trial (thereby enriching it with plausible marker levels and dynamics). We assessed the sensitivity of trial outcomes to trial protocol and found that for this particular example the choice of end point is more important than the choice of dosing regimen and patient selection by model-based responder enrichment could increase the expected effect size. A global sensitivity analysis revealed that only a limited subset of baseline biomarkers is needed to predict the drug response of the full virtual population. CONCLUSIONS: This AD quantitative systems pharmacology workflow built around knowledge of marker-severity relationships as well as SoC efficacy can be tailored to specific development cases to optimize several trial protocol parameters and biomarker stratification and therefore has promise to become a powerful model-informed AD drug development and personalized medicine tool.

Advancing cancer drug development with mechanistic mathematical modeling: bridging the gap between theory and practice.

Quantitative predictive modeling of cancer growth, progression, and individual response to therapy is a rapidly growing field. Researchers from mathematical modeling, systems biology, pharmaceutical industry, and regulatory bodies, are collaboratively working on predictive models that could be applied for drug development and, ultimately, the clinical management of cancer patients. A plethora of modeling paradigms and approaches have emerged, making it challenging to compile a comprehensive review across all subdisciplines. It is therefore critical to gauge fundamental design aspects against requirements, and weigh opportunities and limitations of the different model types. In this review, we discuss three fundamental types of cancer models: space-structured models, ecological models, and immune system focused models. For each type, it is our goal to illustrate which mechanisms contribute to variability and heterogeneity in cancer growth and response, so that the appropriate architecture and complexity of a new model becomes clearer. We present the main features addressed by each of the three exemplary modeling types through a subjective collection of literature and illustrative exercises to facilitate inspiration and exchange, with a focus on providing a didactic rather than exhaustive overview. We close by imagining a future multi-scale model design to impact critical decisions in oncology drug development.

Phenyl argentate aggregates [AgnPhn+1]- (n = 2-8): Models for the self-assembly of atom-precise polynuclear organometallics.

Electrospray ionization of phenyl argentates formed by transmetalation reactions between phenyl lithium and silver cyanide provides access to the argentate aggregates, [AgnPhn+1]-, which were individually mass-selected for n = 2-8 in order to generate their gas-phase Ultraviolet Photodissociation (UVPD) "action" spectra over the range 304-399 nm. A strong bathochromic shift in optical spectra was observed with increasing size/n. Theoretical calculations allowed the assignment of the experimental UVPD spectra to specific isomer(s) and provided crucial insights into the transition from the 2D to 3D structure of the metallic component with the increasing size of the complex. The [AgnPhn+1]- aggregates contain neither pronounced metallic cluster properties nor ligated metallic cluster features and are thus not superatom complexes. They therefore represent novel organometallic characteristics built from Ag2Ph subunits.

Ion mobility resolved photo-fragmentation to discriminate protomers.

RATIONALE: Among the sources of structural diversity in biomolecular ions, the co-existence of protomers is particularly difficult to take into account, which in turn complicates structural interpretation of gas-phase data. METHODS: We investigated the sensitivity of gas-phase photo-fragmentation measurements and ion mobility spectrometry (IMS) to the protonation state of a model peptide derivatized with chromophores. Accessible interconversion pathways between the different identified conformers were probed by tandem ion mobility measurement. Furthermore, the excitation coupling between the chromophores has been probed through photo-fragmentation measurements on mobility-selected ions. All results were interpreted based on molecular dynamics simulations. RESULTS: We show that protonation can significantly affect the photo-fragmentation yields. Especially, conformers with very close collision cross sections (CCSs) may display dramatically different photo-fragmentation yields in relation with different protonation patterns. CONCLUSIONS: We show that, even if precise structure assignment based on molecular modeling is in principle difficult for large biomolecular assemblies, the combination of photo-fragmentation and IMS can help to identify the signature of protomer co-existence for a population of biomolecular ions in the gas phase. Such spectroscopic data are particularly suitable to follow conformational changes.

Experimental and theoretical 2p core-level spectra of size-selected gas-phase aluminum and silicon cluster cations: chemical shifts, geometric structure, and coordination-dependent screening.

We present 2p core-level spectra of size-selected aluminum and silicon cluster cations from soft X-ray photoionization efficiency curves and density functional theory. The experimental and theoretical results are in very good quantitative agreement and allow for geometric structure determination. New ground state geometries for Al12+, Si15+, Si16+, and Si19+ are proposed on this basis. The chemical shifts of the 2p electron binding energies reveal a substantial difference for aluminum and silicon clusters: while in aluminum the 2p electron binding energy decreases with increasing coordination number, no such correlation was observed for silicon. The 2p binding energy shifts in clusters of both elements differ strongly from those of the corresponding bulk matter. For aluminum clusters, the core-level shifts between outer shell atoms and the encapsulated atom are of opposite sign and one order of magnitude larger than the corresponding core-level shift between surface and bulk atoms in the solid. For silicon clusters, the core-level shifts are of the same order of magnitude in clusters and in bulk silicon but no obvious correlation of chemical shift and bond length, as present for reconstructed silicon surfaces, are observed.

Dimerization and conformation-related free energy landscapes of dye-tagged amyloid-ß12-28 linked to FRET experiments.

We have investigated the free energy landscape of Aß-peptide dimer models in connection to gas-phase FRET experiments. We use a FRET-related distance coordinate and one conformation-related coordinate per monomer for accelerated structural exploration with well-tempered metadynamics in solvent and in vacuo. The free energy profiles indicate that FRET under equilibrium conditions should be significantly affected by the de-solvation upon the transfer of ions to the gas-phase. In contrast, a change in the protonation state is found to be less impacting once de-solvated. Comparing F19P and WT alloforms, for which we measure different FRET efficiencies in the gas-phase, we predict only the relevant structural differences in the solution populations, not under gas-phase equilibrium conditions. This finding supports the hypothesis that the gas-phase action-FRET measurement after ESI operates under non-equilibrium conditions, with a memory of the solution conditions - even for the dimer of this relatively short peptide. The structural differences in solution are rationalized in terms of conformational propensities around residue 19, which show a transition to a poly-proline type of pattern upon mutation to F19P - a difference that gets lost in the gas-phase.

Correction: Supramolecular influence on cis-trans isomerization probed by ion mobility spectrometry.

Correction for 'Supramolecular influence on cis-trans isomerization probed by ion mobility spectrometry' by Izabella Czerwinska et al., Phys. Chem. Chem. Phys., 2016, 18, 32331-32336.

Sequential Proton Coupled Electron Transfer (PCET): Dynamics Observed over 8 Orders of Magnitude in Time.

Charge transfer mechanisms lay at the heart of chemistry and biochemistry. Proton coupled electron transfers (PCET) are central in biological processes such as photosynthesis and in the respiratory chain, where they mediate long-range charge transfers. These mechanisms are normally difficult to harness experimentally due to the intrinsic complexity of the associated biological systems. Metal-peptide cations experience both electron and proton transfers upon photoexcitation, proving an amenable model system to study PCET. We report on a time-resolved experiment designed to follow this dual charge transfer kinetics in [HG3W+Ag](+) (H = histidine, G = glycine, W = tryptophan) on time scales ranging from femtoseconds to milliseconds. While electron transfer completes in less than 4 ps, it triggers a proton transfer lasting over hundreds of microseconds. Molecular dynamics simulations show that conformational dynamic plays an important role in slowing down this reaction. This combined experimental and computational approach provides a view of PCET as a single phenomenon despite its very wide time-domain span.

Excited States of Xanthene Analogues: Photofragmentation and Calculations by CC2 and Time-Dependent Density Functional Theory.

Action spectroscopy has emerged as an analytical tool to probe excited states in the gas phase. Although comparison of gas-phase absorption properties with quantum-chemical calculations is, in principle, straightforward, popular methods often fail to describe many molecules of interest-such as xanthene analogues. We, therefore, face their nano- and picosecond laser-induced photofragmentation with excited-state computations by using the CC2 method and time-dependent density functional theory (TDDFT). Whereas the extracted absorption maxima agree with CC2 predictions, the TDDFT excitation energies are blueshifted. Lowering the amount of Hartree-Fock exchange in the DFT functional can reduce this shift but at the cost of changing the nature of the excited state. Additional bandwidth observed in the photofragmentation spectra is rationalized in terms of multiphoton processes. Observed fragmentation from higher-lying excited states conforms to intense excited-to-excited state transitions calculated with CC2. The CC2 method is thus suitable for the comparison with photofragmentation in xanthene analogues.

The structure of chromophore-grafted amyloid-ß(12-28) dimers in the gas-phase: FRET-experiment guided modelling.

We present theoretical modelling, ion mobility spectrometry and action-FRET experiments for chromophore-grafted amyloid-ß(12-28) dimers. A first-principles global minimum search based on replica-exchange molecular dynamics (REMD) leads to a compact structure with strong interstrand interactions. We use REMD with a distance restraint that implements an adaptive effective bias upon average FRET-efficiencies and thus guides the sampling by the action-FRET measurement. This procedure leads to a pair of weakly interacting peptides. Ion-mobility confirms that the weakly interacting structure and not the global minimum with strongly interacting peptides is populated in the experiment. The presence of a high energy barrier between the two structural families, as evidenced from the MD data, suggests that a kinetically trapped structure is observed in the experiment.

Supramolecular influence on cis-trans isomerization probed by ion mobility spectrometry.

We used tandem ion mobility spectrometry measurements to investigate how the photo-isomerization of a chromophore (a methylpyridinium derivative) is affected by the complexation with a crown ether. A dramatic blue-shift of the photo-isomerization spectrum was observed upon complexation, which could be well reproduced by ab initio calculations. Our results support that the observed changes in the photo-physical properties of the chromophore originate from the charge-solvation of its pyridinium moiety by the host cage.

The Gas-Phase Photophysics of Eosin Y and its Maleimide Conjugate.

The use of the xanthene family of dyes as fluorescent probes in a wide range of applications has provided impetus for the studying of their photophysical properties. In particular, recent advances in gas-phase techniques such as FRET that utilize such chromophores have placed a greater importance on the characterization of these properties in the gas phase. Additionally, the use of synthetic linker chains to graft the chromophores in a site-specific manner to their target system is ubiquitous. There is, however, often limited information on how the addition of such a linker chain may affect the photophysical properties of the chromophores, which is of fundamental importance for interpretation of experimental data reliant on grafted chromophores. Here, we present data on the optical spectroscopy of different protonation states of Eosin Y, a fluorescein derivative. We compare the photophysics of Eosin Y to its maleimide conjugate, and to the thioether product of the reaction of this conjugate with cysteamine. Comparison of the mass spectra following laser irradiation shows that very different relaxation takes place upon addition of the maleimide moiety but that the photophysics of the bare chromophore are restored upon addition of cysteamine. This radical change in the photophysics is interpreted in terms of charge-transfer states, whose energy relative to the S1 ← S0 transition of the chromophore is dependent on the conjugation of the maleimide moiety. We also show that the shape of the absorption band is unchanged in the gas-phase as compared to the solution-phase, showing a maximum with a shoulder toward the blue, and examination of isotope distributions of the isolated ions show that this shoulder cannot be due to the presence of dimers. Consideration of the fluorescence emission spectrum allows a tentative assignment of the shoulder to be due to a vibrational progression with a high Franck-Condon factor.

Gas-phase conformations of capistruin - comparison of lasso, branched-cyclic and linear topologies.

RATIONALE: Capistruin is a peptide synthesized by Burkholderia thailandensis E264, which displays a lasso topology. This knot-like structure confers interesting properties to peptides (e.g. antibacterial). Therefore, it is important to evaluate the sensitivity of structural characterization methods to such topological constraints. METHODS: Ion mobility mass spectrometry (IMS-MS) experiments, using both drift tube and travelling wave instruments, were performed on lasso capistruin and on peptides with the same sequence, but displaying a branched-cyclic (un-threaded) or linear topology. Molecular dynamics (MD) simulations were then performed to further interpret the IMS results in terms of conformation. RESULTS: The collision cross sections (CCSs) measured via IMS for the different forms of capistruin were found to be similar, despite their different topologies for the doubly charged species, but significant differences arise as the charge state is increased. MD simulations for the doubly charged linear peptide were consistent with the hypothesis that salt bridges are present in the gas phase. Moreover, through CCS measurements for peptides with site-specific mutations, the arginine residue at position 11 was found to play a major role in the stabilization of compact structures for the linear peptide. CONCLUSIONS: Differences in peptide topologies did not yield marked signatures in their respective IMS spectra. Such signatures were only visible for relatively high charge states, that allow Coulomb repulsion to force unfolding. At low charge states, the topologically unconstrained linear form of capistruin was found to adopt charge solvation-constrained structures, possibly including salt bridges, with CCSs comparable to those measured for the topologically constrained lasso form.

Visible and ultraviolet spectroscopy of gas phase rhodamine 575 cations.

The visible and ultraviolet spectroscopy of gas phase rhodamine 575 cations has been studied experimentally by action-spectroscopy in a modified linear ion trap between 220 and 590 nm and by time-dependent density functional theory (TDDFT) calculations. Three bands are observed that can be assigned to the electronic transitions S0 → S1, S0 → S3, and S0 → (S8,S9) according to the theoretical prediction. While the agreement between theory and experiment is excellent for the S3 and S8/S9 transitions, a large shift in the value of the calculated S1 transition energy is observed. A theoretical analysis of thermochromism, potential vibronic effects, and-qualitatively-electron correlation revealed it is mainly the latter that is responsible for the failure of TDDFT to accurately reproduce the S1 transition energy, and that a significant thermochromic shift is also present. Finally, we investigated the nature of the excited states by analyzing the excitations and discussed their different fragmentation behavior. We hypothesize that different contributions of local versus charge transfer excitations are responsible for 1-photon versus 2-photon fragmentation observed experimentally.

Structural exploration and Förster theory modeling for the interpretation of gas-phase FRET measurements: Chromophore-grafted amyloid-ß peptides.

The distance-dependence of excitation energy transfer, e.g., being described by Förster theory (Förster resonance energy transfer (FRET)), allows the use of optical techniques for the direct observation of structural properties. Recently, this technique has been successfully applied in the gas phase. The detailed interpretation of the experimental FRET results, however, relies on the comparison with structural modeling. We therefore present a complete first-principles modeling approach that explores the gas-phase structure of chromophore-grafted peptides and achieves accurate predictions of FRET efficiencies. We apply the approach to amyloid-ß 12-28 fragments, known to be involved in amyloid plaque formation connected to Alzheimer's disease. We sample structures of the peptides that are grafted with 5-carboxyrhodamine 575 (Rh575) and QSY-7 chromophores by means of replica-exchange molecular dynamics simulations upon an Amber-type forcefield parametrization as a function of the charge state. The generated ensembles provide chromophore-distance and -orientation distributions which are used with the spectral parameters of the Rh575/QSY-7 chromophores to model FRET-efficiencies for the systems. The theoretical values agree with the experimental average "action"-FRET efficiencies and motivate to use the herein reported parametrization, sampling, and FRET-modeling technique in future studies on the structural properties and aggregation-behavior of related systems.

Theoretical study of structural and optical properties of noble metal cluster-dipeptide hybrids at defect centers of MgO.

We present the theoretical investigation of structural and optical properties of silver and gold cluster-dipeptide hybrids bound to the F(S) defect of the MgO (100) surface. We use DFT and its TDDFT variant combined with the polarizable embedded cluster model for the description of the extended MgO environment. As model peptide we have chosen CysTrp since the cysteine residue interacts strongly with metal particles through the sulfur atom and tryptophan is the most important chromophoric amino acid. Our results show that in the case of CysTrp bound to the supported Ag(4) cluster an intense optical signal arises at 400 nm. In contrast, in the case of gold no strongly localized absorption is present since the optical response of supported gold-peptide hybrids is dominated by a large number of low intensity d-electron excitations spread over a broad energy range. Such a localized optical signal which is present in supported silver hybrids can be exploited for the optical detection of peptides and thus can serve as basis for the development of biosensing materials.

Silver cluster-biomolecule hybrids: from basics towards sensors.

We focus on the functional role of small silver clusters in model hybrid systems involving peptides in the context of a new generation of nanostructured materials for biosensing. The optical properties of hybrids in the gas phase and at support will be addressed with the aim to bridge fundamental and application aspects. We show that extension and enhancement of absorption of peptides can be achieved by small silver clusters due to the interaction of intense intracluster excitations with the π-π* excitations of chromophoric aminoacids. Moreover, we demonstrate that the binding of a peptide to a supported silver cluster can be detected by the optical fingerprint. This illustrates that supported silver clusters can serve as building blocks for biosensing materials. Moreover, the clusters can be used simultaneously to immobilize biomolecules and to increase the sensitivity of detection, thus replacing the standard use of organic dyes and providing label-free detection. Complementary to that, we show that protected silver clusters containing a cluster core and a shell liganded by thiolates exhibit absorption properties with intense transitions in the visible regime which are also suitable for biosensing applications.

Binding motifs of silver in prion octarepeat model peptides: a joint ion mobility, IR and UV spectroscopies, and theoretical approach.

Transition metal-ion complexation is essential to the function and structural stability of many proteins. We studied silver complexation with the octarepeat motif ProHisGlyGlyGlyTrpGlyGln of the prion protein, which shows competitive sites for metal chelation including amide, indole and imidazole groups. This octapeptide is known as a favourable transition metal binding site in prion protein. We used ion mobility spectrometry (IMS), infrared multiple photon dissociation (IRMPD) spectroscopy and density functional theory calculations (DFT) to identify the binding motifs of a silver cation on HisGlyGlyGlyTrp peptide as well as on peptide subsequences. Ultra-violet photodissociation (UVPD) and collision induced dissociation mass spectrometry together with the time-dependent density functional method was then exploited to study the influence of binding sites on optical properties and on the ground and excited states reactivity of the peptide. We show that the metal cation is bound to the π-system of the indole group and a nitrogen atom of the imidazole group and that charge transfers from the indole group to the silver cation occur in excited electronic states.

Solving the Evidence Interpretability Crisis in Health Technology Assessment: A Role for Mechanistic Models?

Health technology assessment (HTA) aims to be a systematic, transparent, unbiased synthesis of clinical efficacy, safety, and value of medical products (MPs) to help policymakers, payers, clinicians, and industry to make informed decisions. The evidence available for HTA has gaps-impeding timely prediction of the individual long-term effect in real clinical practice. Also, appraisal of an MP needs cross-stakeholder communication and engagement. Both aspects may benefit from extended use of modeling and simulation. Modeling is used in HTA for data-synthesis and health-economic projections. In parallel, regulatory consideration of model informed drug development (MIDD) has brought attention to mechanistic modeling techniques that could in fact be relevant for HTA. The ability to extrapolate and generate personalized predictions renders the mechanistic MIDD approaches suitable to support translation between clinical trial data into real-world evidence. In this perspective, we therefore discuss concrete examples of how mechanistic models could address HTA-related questions. We shed light on different stakeholder's contributions and needs in the appraisal phase and suggest how mechanistic modeling strategies and reporting can contribute to this effort. There are still barriers dissecting the HTA space and the clinical development space with regard to modeling: lack of an adapted model validation framework for decision-making process, inconsistent and unclear support by stakeholders, limited generalizable use cases, and absence of appropriate incentives. To address this challenge, we suggest to intensify the collaboration between competent authorities, drug developers and modelers with the aim to implement mechanistic models central in the evidence generation, synthesis, and appraisal of HTA so that the totality of mechanistic and clinical evidence can be leveraged by all relevant stakeholders.

Modeling the disruption of respiratory disease clinical trials by non-pharmaceutical COVID-19 interventions.

Respiratory disease trials are profoundly affected by non-pharmaceutical interventions (NPIs) against COVID-19 because they perturb existing regular patterns of all seasonal viral epidemics. To address trial design with such uncertainty, we developed an epidemiological model of respiratory tract infection (RTI) coupled to a mechanistic description of viral RTI episodes. We explored the impact of reduced viral transmission (mimicking NPIs) using a virtual population and in silico trials for the bacterial lysate OM-85 as prophylaxis for RTI. Ratio-based efficacy metrics are only impacted under strict lockdown whereas absolute benefit already is with intermediate NPIs (eg. mask-wearing). Consequently, despite NPI, trials may meet their relative efficacy endpoints (provided recruitment hurdles can be overcome) but are difficult to assess with respect to clinical relevance. These results advocate to report a variety of metrics for benefit assessment, to use adaptive trial design and adapted statistical analyses. They also question eligibility criteria misaligned with the actual disease burden.