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

The utility of efavirenz-based prophylaxis against HIV infection. A systems pharmacological analysis

Pre-exposure prophylaxis (PrEP) is considered one of the five “pillars” by UNAIDS to reduce HIV transmission. Moreover, it is a tool for female self-protection against HIV, making it highly relevant to sub-Saharan regions, where women have the highest infection burden. To date, Truvada is the only medication for PrEP. However, the cost of Truvada limits its uptake in resource-constrained countries. Similarly, several currently investigated, patent-protected compounds may be unaffordable in these regions. We set out to explore the potential of the patent-expired antiviral efavirenz (EFV) as a cost-efficient PrEP alternative. A population pharmacokinetic model utilizing data from the ENCORE1 study was developed. The model was refined for metabolic autoinduction. We then explored EFV cellular uptake mechanisms, finding that it is largely determined by plasma protein binding. Next, we predicted the prophylactic efficacy of various EFV dosing schemes after exposure to HIV using a stochastic simulation framework. We predicted that plasma concentrations of 11, 36, 1287 and 1486ng/mL prevent 90% sexual transmissions with wild type and Y181C, K103N and G190S mutants, respectively. Trough concentrations achieved after 600 mg once daily dosing (median: 2017 ng/mL, 95% CI:445–9830) and after reduced dose (400 mg) efavirenz (median: 1349ng/mL, 95% CI: 297–6553) provided complete protection against wild-type virus and the Y181C mutant, and median trough concentrations provided about 90% protection against the K103N and G190S mutants. As reduced dose EFV has a lower toxicity profile, we predicted the reduction in HIV infection when 400 mg EFV-PrEP was poorly adhered to, when it was taken “on demand” and as post-exposure prophylaxis (PEP). Once daily EFV-PrEP provided 99% protection against wild-type virus, if ≥50% of doses were taken. PrEP “on demand” provided complete protection against wild-type virus and prevented ≥81% infections in the mutants. PEP could prevent >98% infection with susceptible virus when initiated within 24 h after virus exposure and continued for at least 9 days. We predict that 400 mg oral EFV may provide superior protection against wild-type HIV. However, further studies are warranted to evaluate EFV as a cost-efficient alternative to Truvada. Predicted prophylactic concentrations may guide release kinetics of EFV long-acting formulations for clinical trial design

Pharmacokinetics and Pharmacodynamics of the Reverse Transcriptase Inhibitor Tenofovir and Prophylactic Efficacy against HIV-1 Infection

Antiviral pre-exposure prophylaxis (PrEP) through daily drug administration can protect healthy individuals from HIV-1 infection. While PrEP was recently approved by the FDA, the potential long-term consequences of PrEP implementation remain entirely unclear. The aim of this study is to predict the efficacy of different prophylactic strategies with the pro-drug tenofovir- disoproxil-fumarate (TDF) and to assess the sensitivity towards timing- and mode of TDF administration (daily- vs. single dose), adherence and the number of transmitted viruses. We developed a pharmacokinetic model for TDF and its active anabolite tenofovir-diphosphate (TFV-DP) and validated it with data from 4 different trials, including 4 distinct dosing regimes. Pharmacokinetics were coupled to an HIV model and viral decay following TDF mono-therapy was predicted, consistent with available data. Subsequently, a stochastic approach was used to estimate the % infections prevented by (i) daily TDF-based PrEP, (ii) one week TDF started either shortly before, or -after viral exposure and (iii) a single dose oral TDF before viral challenge (sd-PrEP). Analytical solutions were derived to assess the relation between intracellular TFV-DP concentrations and prophylactic efficacy. The predicted efficacy of TDF was limited by a slow accumulation of active compound (TFV-DP) and variable TFV-DP half-life and decreased with increasing numbers of transmitted viruses. Once daily TDF-based PrEP yielded 80% protection, if at least 40% of pills were taken. Sd-PrEP with 300 mg or 600 mg TDF could prevent 50% infections, when given at least before virus exposure. The efficacy dropped to 10%, when given 1 h before 24 h exposure. Efficacy could not be increased with increasing dosage or prolonged administration. Post-exposure prophylaxis poorly prevented infection. The use of drugs that accumulate more rapidly, or local application of tenofovir gel may overcome the need for drug administration long before virus exposure

An example with different dolutegravir prophylaxis schemes

To achieve the 90-90-90 goals set by UNAIDS, the number of new HIV infections needs to decrease to approximately 500,000 by 2020. One of the ‘five pillars’ to achieve this goal is pre-exposure prophylaxis (PrEP). Truvada (emtricitabine-tenofovir) is currently the only medication approved for PrEP. Despite its advantages, Truvada is costly and requires individuals to adhere to the once-daily regimen. To improve PrEP, many next-generation regimen, including long-acting formulations, are currently investigated. However, pre-clinical testing may not guide candidate selection, since it often fails to translate into clinical efficacy. On the other hand, quantifying prophylactic efficacy in the clinic is ethically problematic and requires to conduct long (years) and large (N>1000 individuals) trials, precluding systematic evaluation of candidates and deployment strategies. To prioritize- and help design PrEP regimen, tools are urgently needed that integrate pharmacological-, viral- and host factors determining prophylactic efficacy. Integrating the aforementioned factors, we developed an efficient and exact stochastic simulation approach to predict prophylactic efficacy, as an example for dolutegravir (DTG). Combining the population pharmacokinetics of DTG with the stochastic framework, we predicted that plasma concentrations of 145.18 and 722.23nM prevent 50- and 90% sexual transmissions respectively. We then predicted the reduction in HIV infection when DTG was used in PrEP, PrEP ‘on demand’ and post-exposure prophylaxis (PEP) before/after virus exposure. Once daily PrEP with 50mg oral DTG prevented 99–100% infections, and 85% of infections when 50% of dosing events were missed. PrEP ‘on demand’ prevented 79–84% infections and PEP >80% when initiated within 6 hours after virus exposure and continued for as long as possible. While the simulation framework can easily be adapted to other PrEP candidates, our simulations indicated that oral 50mg DTG is non-inferior to Truvada. Moreover, the predicted 90% preventive concentrations can guide release kinetics of currently developed DTG nano-formulations

Optimal Treatment Strategies in the Context of ‘Treatment for Prevention’ against HIV-1 in Resource-Poor Settings

An estimated 2.7 million new HIV-1 infections occurred in 2010. `Treatment- for-prevention’ may strongly prevent HIV-1 transmission. The basic idea is that immediate treatment initiation rapidly decreases virus burden, which reduces the number of transmittable viruses and thereby the probability of infection. However, HIV inevitably develops drug resistance, which leads to virus rebound and nullifies the effect of `treatment-for-prevention’ for the time it remains unrecognized. While timely conducted treatment changes may avert periods of viral rebound, necessary treatment options and diagnostics may be lacking in resource-constrained settings. Within this work, we provide a mathematical platform for comparing different treatment paradigms that can be applied to many medical phenomena. We use this platform to optimize two distinct approaches for the treatment of HIV-1: (i) a diagnostic-guided treatment strategy, based on infrequent and patient-specific diagnostic schedules and (ii) a pro-active strategy that allows treatment adaptation prior to diagnostic ascertainment. Both strategies are compared to current clinical protocols (standard of care and the HPTN052 protocol) in terms of patient health, economic means and reduction in HIV-1 onward transmission exemplarily for South Africa. All therapeutic strategies are assessed using a coarse-grained stochastic model of within-host HIV dynamics and pseudo-codes for solving the respective optimal control problems are provided. Our mathematical model suggests that both optimal strategies (i)-(ii) perform better than the current clinical protocols and no treatment in terms of economic means, life prolongation and reduction of HIV-transmission. The optimal diagnostic-guided strategy suggests rare diagnostics and performs similar to the optimal pro-active strategy. Our results suggest that ‘treatment-for-prevention’ may be further improved using either of the two analyzed treatment paradigms

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

Hybrid stochastic framework predicts efficacy of prophylaxis against HIV: An example with different dolutegravir prophylaxis schemes

<div><p>To achieve the 90-90-90 goals set by UNAIDS, the number of new HIV infections needs to decrease to approximately 500,000 by 2020. One of the ‘five pillars’ to achieve this goal is pre-exposure prophylaxis (PrEP). Truvada (emtricitabine-tenofovir) is currently the only medication approved for PrEP. Despite its advantages, Truvada is costly and requires individuals to adhere to the once-daily regimen. To improve PrEP, many next-generation regimen, including long-acting formulations, are currently investigated. However, pre-clinical testing may not guide candidate selection, since it often fails to translate into clinical efficacy. On the other hand, quantifying prophylactic efficacy in the clinic is ethically problematic and requires to conduct long (years) and large (N>1000 individuals) trials, precluding systematic evaluation of candidates and deployment strategies. To prioritize- and help design PrEP regimen, tools are urgently needed that integrate pharmacological-, viral- and host factors determining prophylactic efficacy. Integrating the aforementioned factors, we developed an efficient and exact stochastic simulation approach to predict prophylactic efficacy, as an example for dolutegravir (DTG). Combining the population pharmacokinetics of DTG with the stochastic framework, we predicted that plasma concentrations of 145.18 and 722.23nM prevent 50- and 90% sexual transmissions respectively. We then predicted the reduction in HIV infection when DTG was used in PrEP, PrEP ‘on demand’ and post-exposure prophylaxis (PEP) before/after virus exposure. Once daily PrEP with 50mg oral DTG prevented 99–100% infections, and 85% of infections when 50% of dosing events were missed. PrEP ‘on demand’ prevented 79–84% infections and PEP >80% when initiated within 6 hours after virus exposure and continued for as long as possible. While the simulation framework can easily be adapted to other PrEP candidates, our simulations indicated that oral 50mg DTG is non-inferior to Truvada. Moreover, the predicted 90% preventive concentrations can guide release kinetics of currently developed DTG nano-formulations.</p></div

Competitive Mate Choice: How Need for Speed Beats Quests for Quality and Harmony

The choice of a mate is made complicated by the need to search for partners at the same time others are searching. What decision strategies will outcompete others in a population of searchers? We extend previous approaches using computer simulations to study mate search strategies by allowing direct competition between multiple strategies, evaluating success on multiple criteria. In a mixed social environment of searchers of different types, simple strategies can exploit more demanding strategies in unexpected ways. We find that simple strategies that only aim for speed can beat more selective strategies that aim to maximize the quality or harmony of mated pairs

Pharmacokinetic and pharmacodynamic parameters.

<p>median parameter and range. see Table 4 for individual values. value set to 1 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040382#pone.0040382-Gagnieu1" target="_blank">[28]</a>. parameter from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040382#pone.0040382-BarditchCrovo1" target="_blank">[12]</a>. computed using eq. (S2), <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040382#pone.0040382.s008" target="_blank">Text S1</a>.</p