Beyond the Liver; In Silico Screening for Tissue-Specific Oligonucleotide Delivery Receptors

Abdallah Derbalah (1), Felix Stader (1), Cong Liu (1), Adriana Zyla (1), Armin Sepp (1)

(1) Certara UK Ltd., Certara Predictive Technologies division, Level 2-Acero, 1 Concourse Way, Sheffield, S1 2BJ, UK

Introduction: Oligonucleotide therapeutics represent a promising novel treatment modality that has gained wide traction in the past few years due to its unique mechanism of action and therapeutic potential in many disease areas. These new therapeutics can regulate the gene expression of any target protein regardless of its cellular location by degrading/modifying its encoding mRNA; thus, opening new opportunities to modify the disease process. Despite having similar therapeutic modes of action, oligonucleotide therapeutics can vary in size, structure, and chemical modifications depending on the specific application. There are two types of therapeutic oligonucleotides in use: anti-sense oligonucleotides (ASO), which are single-stranded DNA and small interfering RNA (siRNA), which consists of double-stranded RNA. Delivering oligonucleotides to target tissues remains a formidable challenge due to their large size and hydrophilic properties, impeding efficient membrane penetration. Nevertheless, breakthroughs have emerged with FDA-approved agents effectively targeting the liver through conjugation with a triantennary N-acetylgalactosamine (GN3) molecule, leveraging the hepatic asialoglycoprotein receptor (ASGPR)[1]. Extending this paradigm to other tissues hinges on identifying and evaluating receptors that are as specific as possible to the tissue and/or cell type of interest. As of today, current in vivo experimental evaluation of tissue targeting efficiency can be prohibitively expensive and time intensive. We propose to significantly enhance the process of early target evaluation by introducing an in silico screening approach that combines mechanistic predictive insight into the tissue distribution of dynamics of large molecules with quantitative insight of the respective tissue target expression levels.

Objectives: To develop a mechanistic first principles-based screening tool to evaluate potential target receptors for oligonucleotide delivery to tissues beyond the liver.

Methods: This study utilised a cross-species whole-body physiologically based pharmacokinetic (PBPK) cross-species biologics PBPK modelling platform [2], that has been implemented in QSP Designer (V2.0.0.53; Certara, Sheffield, UK). The two-pore biologics platform incorporates physiological and mechanistic knowledge that govern the pharmacokinetics of large molecules in four different species, namely, mice, rats, monkeys, and humans. The platform model was modified to accommodate the known pharmacokinetic processes that affect oligonucleotides disposition. Fluid-phase endocytosis uptake and redistribution parameters for different tissues were estimated against unconjugated ASO tissue concentrations data following IV administration rats [3]. The model was then validated against another set of ASO tissue concentration data in rats [4-6], as well as mice [7-9]. Subcutaneous (SC) administration was mechanistically modelled through a separate tissue component for the SC administration site which inherited physiological parameters from the adipose tissue. This was then validated against plasma concentration data from a SC administered unconjugated ASO in mice [10]. Receptor mediated endocytosis (RME) uptake was modelled through a target-mediated drug disposition (TMDD) like model. The RME model was parameterised based on literature values for ASGPR abundance and binding affinity to GN3. The model was then validated against IV and SC administered GN3-conjugated ASOs [11] and siRNAs [12].

Results: A total of 136 observations were used to estimate the uptake and redistribution parameter including plasma, liver, kidney, lung, pancreas, spleen, heart, muscle, bone, and gut. Goodness-of-fit plots showed that the model well captured both the plasma and tissue concentrations of the training dataset. The validation datasets were composed of a total of 394 observations. Those were more heterogenous mixture of different compounds, doses, and routes of administration. Nonetheless, the model predicted the central tendencies of both plasma and tissue concentrations reasonably well.

Conclusions: A first of a kind whole-body PBPK model for oligonucleotides has been developed. Trained initially on a single-compound single-species data, this model has demonstrated cross-species and cross-modality extrapolation capabilities. Such groundbreaking versatility positions it as a pivotal instrument in the advancement of novel targeted oligonucleotide therapeutics.

References:

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Reference: PAGE 32 (2024) Abstr 10853 [www.page-meeting.org/?abstract=10853]

Poster: Methodology - New Modelling Approaches

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