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

In silico, experimental, mechanistic model for extended-release felodipine disposition exhibiting complex absorption and a highly variable food interaction

The objective of this study was to develop and explore new, in silico experimental methods for deciphering complex, highly variable absorption and food interaction pharmacokinetics observed for a modified-release drug product. Toward that aim, we constructed an executable software analog of study participants to whom product was administered orally. The analog is an object- and agent-oriented, discrete event system, which consists of grid spaces and event mechanisms that map abstractly to different physiological features and processes. Analog mechanisms were made sufficiently complicated to achieve prespecified similarity criteria. An equation-based gastrointestinal transit model with nonlinear mixed effects analysis provided a standard for comparison. Subject-specific parameterizations enabled each executed analog's plasma profile to mimic features of the corresponding six individual pairs of subject plasma profiles. All achieved prespecified, quantitative similarity criteria, and outperformed the gastrointestinal transit model estimations. We observed important subject-specific interactions within the simulation and mechanistic differences between the two models. We hypothesize that mechanisms, events, and their causes occurring during simulations had counterparts within the food interaction study: they are working, evolvable, concrete theories of dynamic interactions occurring within individual subjects. The approach presented provides new, experimental strategies for unraveling the mechanistic basis of complex pharmacological interactions and observed variability

Roadmap on semiconductor-cell biointerfaces.

This roadmap outlines the role semiconductor-based materials play in understanding the complex biophysical dynamics at multiple length scales, as well as the design and implementation of next-generation electronic, optoelectronic, and mechanical devices for biointerfaces. The roadmap emphasizes the advantages of semiconductor building blocks in interfacing, monitoring, and manipulating the activity of biological components, and discusses the possibility of using active semiconductor-cell interfaces for discovering new signaling processes in the biological world

Electrochemical biosensors: a nexus for precision medicine

Precision medicine is a field with huge potential for improving a patient's quality of life, wherein therapeutic drug monitoring (TDM) can provide actionable insights. More importantly, incorrect drug dose is a common contributor to medical errors. However, current TDM practice is time-consuming and expensive, and requires specialised technicians. One solution is to use electrochemical biosensors (ECBs), which are inexpensive, portable, and highly sensitive. In this review, we explore the potential for ECBs as a technology for on-demand drug monitoring, including microneedles, continuous monitoring, synthetic biorecognition elements, and multi-material electrodes. We also highlight emerging strategies to achieve continuous drug monitoring, and conclude by appraising recent developments and providing an outlook for the field

Discovery of OJT010 as a Novel Inhibitor of Severe Acute Respiratory Syndrome Coronavirus 2

The current pandemic of coronavirus disease (COVID-19) caused by the highly infectious pathogen, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), represents a global public health challenge. The emergence of deadly SARS-CoV-2 variants with mutations on the viral genes has made it more imperative to discover therapeutics that target the host receptors for COVID-19 treatment. Therefore, our research has targeted the critical host entry receptors: Angiotensin-converting enzyme-2 (ACE2) for SARS-CoV-2 entry into the human cells. SARS-CoV-2 is an enveloped RNA beta coronavirus that infects human cells via interaction with the ACE2 receptor, followed by viral replication and virus dissemination. Spike protein of SARS-CoV-2 has a receptor-binding domain (RBD), which binds to the host ACE2 receptor. ACE2 is an essential component of the Renin-Angiotensin system that converts Angiotensin II (Ang II) to Angiotensin 1-7, a potent vasopressor. Even though ACE2 facilitates viral entry, it provides defense against acute lung injury, indicating that the ACE2/Ang 1-7 pathway must be carefully manipulated to reduce SARS-CoV-2 induced lung injuries. Herein, we discovered that OJT010 targets the interaction between RBD and rhACE2 without inactivating the exopeptidase activity of rhACE2. Our findings reveal that OJT010 binding to rhACE2 may preserve its physiological function and prevention exacerbation of the disease. Furthermore, it will potentially prevent non-target cardiac toxicities observed in other ACE2 modulating drugs. Moreover, we discover that OJT010 inhibits the cellular entry and further replication of the SARS-CoV-2 and B.1.617.2 Delta Variant in three individual assays; Infection Induced Cytopathic Effect (CPE), Nanoluciferase reporter assay (NLRV), and Pseudotyped Lentiviral assay. In addition, we have also assessed the molecular interactions of the compounds with the host and viral receptor using molecular dynamic simulation of the best-fit docking complex to elucidate the binding sites of OJT010. Next, we have determined the pharmacokinetics (PK) parameters of OJT010 in healthy rats. We have further advanced into a hamster of model SARS-CoV-2 infection to evaluate the efficacy of OJT010 against SARS-COV-2 infection in vivo. Based on our findings, OJT010 represents a promising drug class that could be further evaluated as a lead series in developing chemotherapeutics for COVID-19 treatment

Integration of advanced methods and models to study drug absorption and related processes : An UNGAP perspective

Funding Information: AI acknowledges the support of projects icp009 (ALKOOL) of PRACE-ICEI (grant agreement 800858) for awarding access to Piz Daint, at the Swiss National Supercomputing Centre (CSCS), Switzerland and BG05M2OP001–1.001–0004 (UNITe) of the Bulgarian Ministry of Education and Science. For further details on points raised in this article, please contact [email protected]. Funding Information: Acknowledgements. JAGH is supported by the Biocenter Finland, the Helsinki Institute of Life Sciences, and the Faculty of Pharmacy, University of Helsinki. Publisher Copyright: © 2021 The AuthorsThis collection of contributions from the European Network on Understanding Gastrointestinal Absorption-related Processes (UNGAP) community assembly aims to provide information on some of the current and newer methods employed to study the behaviour of medicines. It is the product of interactions in the immediate pre-Covid period when UNGAP members were able to meet and set up workshops and to discuss progress across the disciplines. UNGAP activities are divided into work packages that cover special treatment populations, absorption processes in different regions of the gut, the development of advanced formulations and the integration of food and pharmaceutical scientists in the food-drug interface. This involves both new and established technical approaches in which we have attempted to define best practice and highlight areas where further research is needed. Over the last months we have been able to reflect on some of the key innovative approaches which we were tasked with mapping, including theoretical, in silico, in vitro, in vivo and ex vivo, preclinical and clinical approaches. This is the product of some of us in a snapshot of where UNGAP has travelled and what aspects of innovative technologies are important. It is not a comprehensive review of all methods used in research to study drug dissolution and absorption, but provides an ample panorama of current and advanced methods generally and potentially useful in this area. This collection starts from a consideration of advances in a priori approaches: an understanding of the molecular properties of the compound to predict biological characteristics relevant to absorption. The next four sections discuss a major activity in the UNGAP initiative, the pursuit of more representative conditions to study lumenal dissolution of drug formulations developed independently by academic teams. They are important because they illustrate examples of in vitro simulation systems that have begun to provide a useful understanding of formulation behaviour in the upper GI tract for industry. The Leuven team highlights the importance of the physiology of the digestive tract, as they describe the relevance of gastric and intestinal fluids on the behaviour of drugs along the tract. This provides the introduction to microdosing as an early tool to study drug disposition. Microdosing in oncology is starting to use gamma-emitting tracers, which provides a link through SPECT to the next section on nuclear medicine. The last two papers link the modelling approaches used by the pharmaceutical industry, in silico to Pop-PK linking to Darwich and Aarons, who provide discussion on pharmacometric modelling, completing the loop of molecule to man.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

Strategies for improving peptide stability and delivery

Peptides play an important role in many fields, including immunology, medical diagnostics, and drug discovery, due to their high specificity and positive safety profile. However, for their delivery as active pharmaceutical ingredients, delivery vectors, or diagnostic imaging molecules, they suffer from two serious shortcomings: their poor metabolic stability and short half-life. Major research efforts are being invested to tackle those drawbacks, where structural modifications and novel delivery tactics have been developed to boost their ability to reach their targets as fully functional species. The benefit of selected technologies for enhancing the resistance of peptides against enzymatic degradation pathways and maximizing their therapeutic impact are also reviewed. Special note of cell-penetrating peptides as delivery vectors, as well as stapled modified peptides, which have demonstrated superior stability from their parent peptides, are reported