Mechanistic framework predicts drug-class specific utility of antiretrovirals for HIV prophylaxis.

Currently, there is no effective vaccine to halt HIV transmission. However, pre-exposure prophylaxis (PrEP) with the drug combination Truvada can substantially decrease HIV transmission in individuals at risk. Despite its benefits, Truvada-based PrEP is expensive and needs to be taken once-daily, which often leads to inadequate adherence and incomplete protection. These deficits may be overcome by next-generation PrEP regimen, including currently investigated long-acting formulations, or patent-expired drugs. However, poor translatability of animal- and ex vivo/in vitro experiments, and the necessity to conduct long-term (several years) human trials involving considerable sample sizes (N>1000 individuals) are major obstacles to rationalize drug-candidate selection. We developed a prophylaxis modelling tool that mechanistically considers the mode-of-action of all available drugs. We used the tool to screen antivirals for their prophylactic utility and identify lower bound effective concentrations that can guide dose selection in PrEP trials. While in vitro measurable drug potency usually guides PrEP trial design, we found that it may over-predict PrEP potency for all drug classes except reverse transcriptase inhibitors. While most drugs displayed graded concentration-prophylaxis profiles, protease inhibitors tended to switch between none- and complete protection. While several treatment-approved drugs could be ruled out as PrEP candidates based on lack-of-prophylactic efficacy, darunavir, efavirenz, nevirapine, etravirine and rilpivirine could more potently prevent infection than existing PrEP regimen (Truvada). Notably, some drugs from this candidate set are patent-expired and currently neglected for PrEP repurposing. A next step is to further trim this candidate set by ruling out compounds with ominous safety profiles, to assess different administration schemes in silico and to test the remaining candidates in human trials

Contributions to the Mathematical Systems Medicine of Antimicrobial Therapy and Genotype-Phenotype Inference.

The following summary of my publications describes the main ideas in the corresponding research articles and clarfifies my contribution in multi-author publications. I decided to apply for habilitation according to x2.I.1.(c) of the Habilitationsordnung (this path is usually referred as Kumulative Habilitation"). I selected 13 first- or last author publications for this habilitation that concern contributions to the mathematical systems medicine of antiviral therapy [tMH10, tMS+11, FtK+11, tMMS12, DSt12, DWSt15, Dt16, DSt16, DDKt18, DSD+19, DDKt19], as well as inference of genotype-phenotype associations [SDH+15, SSJ+18]. The selected publications represent my major contributions in this research eld since submitting my doctoral thesis in September 2009

Numerical approaches for the rapid analysis of prophylactic efficacy against HIV with arbitrary drug-dosing schemes

Pre-exposure prophylaxis (PrEP) is an important pillar to prevent HIV transmission. Because of experimental and clinical shortcomings, mathematical models that integrate pharmacological, viral- and host factors are frequently used to quantify clinical efficacy of PrEP. Stochastic simulations of these models provides sample statistics from which the clin- ical efficacy is approximated. However, many stochastic simulations are needed to reduce the associated sampling error. To remedy the shortcomings of stochastic simulation, we developed a numerical method that allows predicting the efficacy of arbitrary prophylactic regimen directly from a viral dynamics model, without sampling. We apply the method to var- ious hypothetical dolutegravir (DTG) prophylaxis scenarios. The approach is verified against state-of-the-art stochastic simulation. While the method is more accurate than stochastic simulation, it is superior in terms of computational performance. For example, a continuous 6-month prophylactic profile is computed within a few seconds on a laptop computer. The method’s computational performance, therefore, substantially expands the horizon of feasi- ble analysis in the context of PrEP, and possibly other applications.Pre-exposure prophylaxis (PrEP) is an important tool to prevent HIV transmission. However, experimental identification of parameters that determine prophylactic efficacy is extremely difficult. Clues about these parameters could prove essential for the design of next-generation PrEP compounds. Integrative mathematical models can fill this void: Based on stochastic simulation, a sample statistic can be generated, from which the prophylactic efficacy is estimated. However, for this sample statistic to be accurate, many simulations need to be performed. Here, we introduce a numerical method to directly compute the prophylactic efficacy from a viral dynamics model, without the need for sampling. Based on several examples with dolutegravir (DTG) -based short- and long-term PrEP, as well as post-exposure prophylaxis we demonstrate the correctness of the new method and its outstanding computational performance. Due to the method’s computational performance, a number of analyses, including formal sensitivity analysis, are becoming feasible with the proposed method.Peer Reviewe

A multiscale systems pharmacology framework to assess the prophylactic utility of antivirals against HIV-1

Pre-exposure prophylaxis (PrEP) has recently been identified as one of the five pillars by UNAIDS to achieve the goal of reducing the new infections to approximately 500,000 by 2020. Truvada is the only medication that is approved for PrEP. Although PrEP with Truvada is beneficial, there are a number of limitations. There are a number of novel compounds and treatment-approved antivirals that might overcome these limitations. The challenge is to screen for potential candidates and to design roll-out strategies. Pre-clinical experiments are very insightful but owning to a number of limitations they do not readily guide the candidate-screening and the designing deployment strategies. Although clinical trials provide these answers, they are ethically problematic and prohibitively costly. This highlights that tools are urgently needed that can determine the prophylactic utility of antivirals in order to prioritize candidates and to design the deployment strategies. To this end, we built a mathematical framework (pipeline) to serve as a tool to predict the prophylactic utility of antivirals. Building such a framework for PrEP is a challenging task, which requires solving modelling and simulation problems owing to the various complex processes occurring at different scales (multiscale). We presented the multiscale systems pharmacology framework that integrates processes occurring at various scales including; 1) microscale interactions of active moiety of NRTIs with viral DNA polymerization; 2) meso- and macroscale processes, such as the drug pharmacokinetics, viral replication dynamics; and 3) population scale processes, such as viral exposure and long-term infection probabilities after repeated virus exposures, similar to a clinical trial. The main algorithmic challenge considered in the work is the task of quantifying the infection probability after a viral challenge within a host under the influence of antiviral pharmacokinetics. Time-invariant reaction propensities are valid for constant target-site antiviral concentrations. We employed the theory of branching processes to derive extinction and infection probabilities for time-invariant reaction propensities. However, for time-varying antiviral concentrations at the target-site, the reaction propensities are time-variant. For time-variant reaction propensities, we introduced the reduced-state chemical master equation as an approximation. Furthermore, we adapted the recently developed rejection-based stochastic simulation algorithm. We tackled the challenge of the classification of stochastic trajectories as infection or extinction events which improves the run-time of the algorithm and at the same time guarantees that the misclassification error is below the user-defined threshold. In this work, we derived drug-class specific concentration-prophylactic efficacy (dose-response) curves. The framework allows for the translation of in vitro and ex vivo parameters into the measure of in vivo potency/efficacy. We analyzed all the treatment-approved antivirals for PrEP using the framework. We quantified the role of TDF and FTC and emphasized their complementary roles in the Truvada combination for PrEP. Furthermore, we suggested cost-effective alternatives, such as lamivudine, efavirenz, nevirapine etc. Using the pharmacokinetic model of DTG, we analyzed various roll-out scheme and found that it is non-inferior to truvada.Die HIV-Epidemie ist nach wie vor ein globales Problem. Während die Suche nach einer Heilung und einem Impfstoff weitergeht, hat sich das Hauptaugenmerk auf antiretrovirale Präventionsstrategien zur Eindämmung der Epidemie gelegt. Eine solche Strategie ist die sogenannte Präexpositionsprophylaxe (PrEP), die kürzlich von UNAIDS als eine der fünf Säulen zur Prävention identifiziert wurde. Dabei ist Truvada das einzige für PrEP zugelassen Medikament. Obwohl der Einsatz von Truvada Erfolge gezeigt hat, bestehen einige Einschränkungen. Eine Reihe neuartiger Wirkstoffe und behandlungserprobter antiviraler Mittel, die noch nicht zur PrEP Behandlung eingesetzt werden, könnten diese Einschränkungen bewältigen. Die große Aufgabe besteht darin, unter diesen Wirkstoffen potenzielle PrEP Kandidaten aus- findig zu machen und Einsatzstrategien zu entwickeln. Präklinische Experimente liefern hierbei nicht genügend Ergebnisse um ein Kandidaten-Screening vorzunehmen und klinische Studien sind ethisch problematisch und sehr kostspielig, da Tausende von Personen über mehrere Jahre hinweg beobachtet und untersucht werden müssen. Als Hilfestellung haben wir ein Systempharmakologie- Framework entwickelt, welches es ermöglicht, den prophylaktischen Nutzen von antiviralen Medikamenten zu bestimmen, Medikamenten-Kandidaten zu priorisieren und Einsatzstrategien zu entwerfen. Um ein solches Framework zu entwickeln müssen verschiedene Modellierungs- und die Simulationensprobleme gelöst werden, da bei der PrEP komplexe Prozesse verschiedene Größenordnungen (Multiskala) involviert sind. Das Framework integriert flexibel Prozesse: (1) molekularen Interaktionen zwischen dem Medikament und den viralen Enzymen auf der mikroskalen Ebene (2) antivirale Pharmakokinetik, Pharmakodynamik (viraler Replikationszyklus) auf den mesoskalen und makroskalen Ebenen und (3) populationsebene Prozesse wie virale Exposition und die Infektionswährscheinlichkeit nach vermehrter viraler Exposition; Prozesse, wie sie auch in klinischen Studien auftreten können. Eine der größten algorithmischen Herausforderungen, die in dieser Arbeit bewältigt wurde, ist die Quantifizierung der Infektionswährscheinlichkeit. Wir haben mit Hilfe der Theorie des Verzweigungsprozesses die Formeln für eine zeitkonstante Wirkstoffkonzentration am Zielort abgeleitet. Für die zeitvariable Wirkstoffkonzentration am Zielort haben wir eine chemische Master-Gleichung mit reduziertem Zustand eingeführt und einen stochastischen Algorithmus (EXTRANDE) adaptiert, die das Problem der Dimensionalität der chemische Master-Gleichung umgehen. Das Framework ermöglicht es präklinisches Wissen in Parameter klinischer Relevanz zu über- setzen. Dabei hilft es unnötige klinische Studien zu vermeiden, die nicht nur Geld und Zeit kosten, sondern auch das Risiko bergen, dass Menschen Schaden nehmen. Mithilfe dieses Frameworks haben wir alle bisherigen für die HIV-behandlung zugelassenen Medikamenten zum Präventionszweck überprüft. Wir haben die komplementäre Rolen von Tenofovir Disoproxil Fumarate and Emtricitabine für PrEP erklärt. Darüber hinaus haben wir einige kostengünstige Alternative (Lamivudine, Nevirapine, Efavirenz u.a.) zu Truvada für weiter Überprüfung vorgeschlagen. Außerdem hat unsere Analyse gezeigt, dass Dolutegravir Truvada nicht unterlegen ist

Exploring the Applications of PBPK Modelling to Optimise HIV-1 Treatment

Human immunodeficiency virus (HIV-1) infection continues to be a significant public health concern, with 36.3 million lives being claimed by the infection thus far. Currently there is no cure for HIV. Antiretroviral (ARV) therapy has considerably increased life expectancy in people living with HIV (PLWH), however, several challenges remain. This thesis investigates the various ways in which physiologically based pharmacokinetic (PBPK) modelling can be developed and applied with the aim of optimising treatment for human immunodeficiency virus (HIV-1) infection. Neonatal patients are considered a vulnerable population as limited clinical studies are conducted in this population. Newborns born to mothers with HIV are at risk of receiving HIV. Lack of pharmacokinetic (PK) data means fewer treatment options are available. Chapters 2 & 3 focus on developing and applying a neonatal PBPK model to investigate the PK of integrase inhibitors, dolutegravir and bictegravir in neonates. Chapter 4 goes on to describe how modelling can be used to predict the PK of novel formulations by simulating long-acting, intramuscular, cabotegravir in neonates. Polypharmacy is routinely observed in PLWH, and drug-drug interactions (DDIs) prove an obstacle in HIV treatment, Chapter 5 involved developing an adult PBPK model to evaluate the magnitude of moderate inducers on novel ARVs. Residual levels of viraemia hinder the ability to develop a cure, Chapter 6 investigated the penetration of ARV drugs in lymphoid tissues using a mechanistic lymphatic PBPK model. Understanding the penetration of drugs in target tissues can help optimise ARV therapy. Collectively, this thesis evaluates the possible ways HIV treatment can be improved and optimised by investigating the potential of treatments in special populations, novel formulations of ARV drugs, management of drug-drug interactions and the penetration of therapy in target tissues

HIV-1 viral load outcomes and the evolution of drug-resistance in low-income settings without virological monitoring

WHO guidelines recommend viral load monitoring for all HIV-1 positive patients on antiretroviral therapy (ART). However, few low-income countries have virological monitoring widely available, and patients may remain on virologically failing regimens. This could compromise future ART through the accumulation of drug resistance mutations and result in worse long-term clinical outcomes. The DART trial was conducted in Uganda and Zimbabwe and compared clinically driven monitoring with or without routine CD4 measurement in ART-naïve adult patients. Annual plasma viral load was retrospectively measured for 1,762 patients. This thesis investigates how no laboratory monitoring impacts virological failure and the development of drug resistance. Time to persistent virological failure was analysed, and analytical weights were calculated to correct for non-random sampling. The long-term durability of first-line ART was remarkable; 21% of patients on an NRTI-NNRTI regimen and 40% on a triple-NRTI regimen experienced persistent virological failure by 240 weeks. Routine CD4 monitoring did not reduce virological failure. Deaths after 48 weeks of ART are widely assumed to be due to virological failure or non-adherence. Analyses revealed that a surprisingly high number of these deaths (40%) occurred without virological criteria for treatment switch being met. Routine CD4 monitoring reduced the rate of death with virological failure but did not impact deaths with virological suppression. Cross-sectional analyses quantified HIV-1 drug resistance at the end of first-line ART. On NRTI-NNRTI regimens, 88% had NRTI resistance, and 66% had NNRTI resistance. Routine CD4 monitoring did not reduce the prevalence or extent of drug resistance. The order and rate of HIV-1 drug resistance mutations were explored using repeated genotypes within patients. On NRTI-NNRTI regimens, NRTI and NNRTI mutations developed at a rate of 0.96 and 0.21 per year respectively. Mutagenic tree models demonstrated that ART regimen influenced the order and rate in which mutations occurred

Physiologically based pharmacokinetic modelling to investigate the impact of aging on drug pharmacokinetics and drug-drug interaction magnitudes in aging people living with HIV

People living with HIV (PLWH) are aging but are often excluded from clinical studies because of pragmatical and ethical concerns. Therefore, the effect of aging on the pharmacokinetics and drug-drug interaction (DDI) magnitudes of antiretroviral drugs remain uncertain. Consequently, clinical guidance regarding dose adjustment for antiretroviral drugs and the clinical management of DDIs with advanced aging are missing. Studies presented in this thesis combined clinically observed data with physiologically based pharmacokinetic (PBPK) modelling to investigate the continuous effect of aging on drug pharmacokinetics and DDI magnitudes. The PBPK model was developed in the mathematical programming language Matlab®. A virtual population considering age-related changes in demographics, physiology, and biology informed the model. Clinically observed data of ten non-HIV drugs being commonly administered as comedications to aging PLWH were used to verify the predictive power of the PBPK model to simulate drug disposition in the elderly. Extrapolating the pharmacokinetics of all investigated ten drugs across adulthood (20 to 99 years) elucidated that the progressively decreasing drug clearance drove age-related pharmacokinetic changes, which itself was caused by the decline of the hepatic and renal blood flow and the glomerular filtration rate. Age-dependent pharmacokinetic alterations were independent of drug characteristics. Additional clinical data of 52 drugs obtained from young and elderly individuals verified this general model-based hypothesis. Concentration-time profiles of ten antiretroviral drugs, belonging to the current first-line treatment, were obtained in two clinical studies including PLWH at least 55 years, who participated in the Swiss HIV Cohort Study. These clinically observed data were generally predicted within the 95% confidence interval of the PBPK model, demonstrating the ability of the used approach to predict real-life plasma concentrations from PLWH, who had a declined kidney function (e.g. the glomerular filtration rate was 65.6 ± 19.2 mL/min/1.73m²) and common comorbidities (e.g. hypertension). Age-related pharmacokinetic changes of antiretroviral drugs across adulthood were found to be similar to non-HIV drugs, indicating a marginal increase in antiretroviral drug exposure with advanced aging. One of the conducted clinical studies in PLWH at least 55 years was designed to investigate DDI magnitudes between amlodipine, atorvastatin, or rosuvastatin and a dolutegravir (no interaction expected) or a boosted darunavir (high interaction potential) containing antiretroviral regimen. The comparison with historical data obtained in young PLWH aged 20 to 50 years yielded no changes in the DDI magnitudes between both investigated age groups. These clinically observed data were used to verify DDI simulations of the developed PBPK framework in the elderly and subsequently DDI magnitudes were predicted across the entire adult lifespan. The model indicated that DDI magnitudes were unchanged across adulthood regardless of the involved drugs, the DDI mechanism, or the sex of the investigated individual. This general model-based hypothesis was verified with independent clinically observed data from 17 DDIs. As DDI magnitudes are not impacted by aging, static methods can be applied to predict DDI magnitudes in elderly patients, who receive two drugs with an uncharacterized DDI magnitude. Predictions are based on the fraction of metabolism by a specific enzyme and the strength of an inhibitor or inducer. In contrast to the PBPK approach, the static method provides a more straightforward supportive tool to rationalize dose adjustments to overcome a given DDI. In conclusion, this thesis demonstrates marginal pharmacokinetic alterations of antiretroviral drugs and no age-related changes of DDI magnitudes. Therefore, a dose adjustment of antiretroviral drugs or a different management of DDIs in clinical practice are a priori not necessary when treating aging male and female PLWH in the absence of severe comorbidities. These general rules being broadly applicable to antiretroviral and non-HIV drugs support the overall care of elderly PLWH beyond HIV and therapies of future effective drugs

Identifying Factors Influencing Drug Distribution and HIV Persistence in the Lymph Node

Despite suppressive antiretroviral (ARV) therapy in plasma, ongoing viral replication or reactivation of latently infected cells within the lymph node may contribute to the persistence of HIV. However, little is known about ARV pharmacology in the lymph nodes. In this dissertation, we used quantitative, translational methods to 1) investigate physiologic and biologic factors affecting ARV penetration in lymph nodes of three species, 2) visualize and quantify the spatial relationship between ARVs and virus, and 3) develop physiologically-based pharmacokinetic (PBPK) models describing ARV concentrations in lymph nodes. Using qPCR and proteomics, we quantified gene and protein expression of drug transporters in mice, nonhuman primates (NHPs), and humans, and found very low transporter expression in lymph nodes from all species. No predictive relationships between gene/protein expression and ARV penetration were identified, likely indicating passive diffusion processes within the lymph node. We found no difference in ARV concentrations or drug transporter expression due to sex or viral infection. Through mass spectrometry imaging of NHP mesenteric lymph nodes, we determined that 31% of the tissue area was not covered by any ARV. However, for the 69% of tissue area exposed to quantifiable drug response, all concentrations exceeded inhibitory thresholds, though the majority of coverage was by one drug alone—usually maraviroc or efavirenz. This heterogeneous tissue coverage also resulted in 21% (cell-associated)-28% (virion) of viral RNA unexposed to any ARV. Variability in drug distribution did not appear to be affected by collagen fibrosis at this stage of infection. Finally, we developed NHP and human PBPK models using drug- and physiology-specific parameters to describe the concentrations of three ARVs in a novel lymph node compartment. Our final NHP and human PBPK models fit observed data well, with predicted plasma AUC and Cmax within 2-fold of observed values. Across-species comparison of lymph node penetration ratios calculated using model-predicted AUCs demonstrated good agreement between NHPs and humans, especially for emtricitabine and efavirenz perfusion-limited models. Taken together, we believe that these translational analyses improve our understanding of ARV pharmacology in the lymph node, and inform the development of future therapies for HIV eradication in this tissue reservoir.Doctor of Philosoph

Doctor of Philosophy

dissertationThree decades have passed since the discovery of HIV and still no viable vaccine technologies exist to prevent the spread of the virus. The concept of interrupting HIV transmission with oral or topical antiretroviral drugs (ARV), also known as pre-exposureprophylaxis (PrEP), has been proven in several clinical efficacy trials. One PrEP strategy has been to formulate the ARV tenofovir (TFV) into topically applied vaginal gels. However, the vaginal gel approach has met with mixed results, likely due to poor user adherence. Globally, high incidence of HIV infection correlates with high incidence of unintended pregnancy, especially in resource-poor regions. Combining HIV PrEP with contraception into a single, easy-to-use product could have a synergistic effect, further motivating women to protect themselves against HIV infection. Thus, a concerted effort is underway to develop long-acting multipurpose prevention technologies (MPT) capable of simultaneously preventing sexual HIV transmission and pregnancy. The nearly half-century-old technology of the intravaginal ring (IVR) has undergone a renaissance in the past decade due to the potential of IVR to leverage both the principles of topical HIV PrEP and of long-acting controlled drug release systems. This dissertation details several new observations and innovations regarding drug delivery from intravaginal rings (IVR). First, an injection-molded, hydrophilic poly(ether urethane) (HPEU) matrix IVR capable of sustained release of milligram-per-day quantities of TFV over 90 days is described. In the final two chapters, a secondiv generation reservoir TFV IVR is combined with a reservoir poly(ether urethane) segment that releases microdoses of the contraceptive progestin levonorgestrel (LNG), in a multisegment IVR design, concluding with assessments of product stability and in vivo pharmacokinetics in order to confirm the suitability of the IVR for clinical investigation. This dissertation represents an engineer's approach to designing and testing IVR, which are most commonly considered a pharmaceutical product rather than a medical device. Accordingly, much attention is given to the development and usage of mathematical models for drug release and mechanical properties from IVR, and in general to a mechanistic understanding of the underlying mechanisms of their operation