A Mechanistic Pharmacodynamic Modeling Framework for the Assessment and Optimization of Proteolysis Targeting Chimeras (PROTACs)

Quantifying antibody binding: techniques and therapeutic implications

The binding kinetics of an antibody for its target antigen represent key determinants of its biological function and success as a novel biotherapeutic. Defining these interactions and kinetics is critical for understanding the pharmacological and pharmacodynamic profiles of antibodies in therapeutic applications, with line of sight to clinical translation. In this review, we discuss the latest developments in approaches to measure and modulate antibody-antigen interactions, including antibody engineering, novel antibody formats, current, and emerging technologies for measuring antibody-antigen binding interactions, and emerging perspectives within the field. We also explore how emerging computational methods are set to become powerful tools for modeling antibody-binding interactions under physiologically relevant conditions. Finally, we consider the therapeutic implications of modulating target engagement in terms of pharmacodynamics and pharmacokinetics.

Exploring the clinical trials, regulatory insights, and challenges of PROTACs in oncology

While various targeted therapies exist for cancer, resistance mechanisms remain a significant challenge. Recent advancements in cancer treatment have led to the emergence of proteolysis-targeting chimeras (PROTACs), a promising technology utilizing hetero-bifunctional molecules to target and degrade proteins implicated in cancer progression through the ubiquitin-proteasome system (UPS). PROTACs offer a novel approach, with recent studies and clinical trials demonstrating promising outcomes in degrading endogenous proteins linked to cancer. This work explores classification, regulatory approvals, and ongoing clinical trials of PROTAC technology in cancer management. It emphasizes the importance of regulatory compliance to expedite approvals from relevant authorities. It also highlights challenges and opportunities associated with their implementation. Despite these preliminary efforts, PROTACs show immense potential in effectively addressing cancer. Their ability to target specific proteins for degradation represents a significant advancement in cancer therapeutics, offering new hope for improved outcomes in patient care.

Targeted degradation of CDK9 potently disrupts the MYC-regulated network

CDK9 coordinates signaling events that regulate transcription and is implicated in oncogenic pathways, making it an actionable target for drug development. While numerous CDK9 inhibitors have been developed, success in the clinic has been limited. Targeted degradation offers a promising alternative. A comprehensive evaluation of degradation versus inhibition is needed to assess when degradation might offer superior therapeutic outcomes. We report a selective and potent CDK9 degrader with rapid kinetics, comparing its downstream effects to those of a conventional inhibitor. We validated that CDK9 inhibition triggers a compensatory feedback mechanism that dampens its anticipated effect on MYC expression and found that this was absent when degraded. Importantly, degradation is more effective at disrupting MYC transcriptional regulation and subsequently destabilizing nucleolar homeostasis, likely by abrogation of both enzymatic and scaffolding functions of CDK9. These findings suggest that CDK9 degradation offers a more robust strategy to overcome limitations associated with its inhibition.

The Peptide PROTAC Modality: A New Strategy for Drug Discovery

In recent years, proteolysis targeting chimera (PROTAC) technology has made significant progress in the field of drug development. Traditional drugs mainly focus on inhibiting or activating specific proteins, while PROTAC technology provides new ideas for treating various diseases by inducing the degradation of target proteins. Especially for peptide PROTACs, due to their unique structural and functional characteristics, they have become a hot research topic. This review provides a detailed description of the key components, mechanisms, and design principles of peptide PROTACs, elaborates on their applications in skin-related diseases, oncology, and other potential therapeutic fields, analyzes their advantages and challenges, and looks forward to their future development prospects. The development of peptide PROTAC technology not only opens up new paths for drug research and development, but also provides new ideas for solving the resistance and safety issues faced by traditional small-molecule drugs. Compared with small-molecule PROTACs, peptide PROTACs have advantages such as multitargeting, biodegradability, low toxicity, and flexibility in structural design. With the deepening of research and the continuous maturity of technology, peptide PROTACs are expected to become one of the important strategies for future drug discovery, providing new hope for the treatment of more intractable diseases. Peptide PROTACs are ushering in a new era of precision medicine.

PK/PD modeling of targeted protein degraders: Charting new waters and navigating the shallows

The development of targeted protein degraders has picked up considerable steam recently, with interest stoked further by the first compounds entering Phase III studies. To keep up with leading biotech start-up firms, big pharma has been keen to venture into this new field, bringing along experienced crews of drug hunters. At their disposal, they find a burgeoning body of literature on pharmacokinetics/pharmacodynamics (PK/PD) models tailor-made for this new therapeutic modality. However, this ocean of opportunities might seem daunting even to veteran scientists. Here, we provide orientation and direction for researchers to find the approach best suited for their respective questions.

Finding a needle in the haystack: ADME and pharmacokinetics/pharmacodynamics characterization and optimization toward orally available bifunctional protein degraders

INTRODUCTION

Degraders are an increasingly important sub-modality of small molecules as illustrated by an ever-expanding number of publications and clinical candidate molecules in human trials. Nevertheless, their preclinical optimization of ADME and PK/PD properties has remained challenging. Significant research efforts are being directed to elucidate underlying principles and to derive rational optimization strategies.

AREAS COVERED

In this review the authors summarize current best practices in terms of in vitro assays and in vivo experiments. Furthermore, the authors collate and comment on the current understanding of optimal physicochemical characteristics and their impact on absorption, distribution, metabolism and excretion properties including the current knowledge of Drug-Drug interactions. Finally, the authors describe the Pharmacokinetic prediction and Pharmacokinetic/Pharmacodynamic -concepts unique to degraders and how to best implement these in research projects.

EXPERT OPINION

Despite many recent advances in the field, continued research will further our understanding of rational design regarding degrader optimization. Machine-learning and computational approaches will become increasingly important once larger, more robust datasets become available. Furthermore, tissue-targeting approaches (particularly regarding the Central Nervous System will be increasingly studied to elucidate efficacious drug regimens that capitalize on the catalytic mode of action. Finally, additional specialized approaches (e.g. covalent degraders, LOVdegs) can enrich the field further and offer interesting alternative approaches.

Future Directions for Quantitative Systems Pharmacology

In this chapter, we envision the future of Quantitative Systems Pharmacology (QSP) which integrates closely with emerging data and technologies including advanced analytics, novel experimental technologies, and diverse and larger datasets. Machine learning (ML) and Artificial Intelligence (AI) will increasingly help QSP modelers to find, prepare, integrate, and exploit larger and diverse datasets, as well as build, parameterize, and simulate models. We picture QSP models being applied during all stages of drug discovery and development: During the discovery stages, QSP models predict the early human experience of in silico compounds created by generative AI. In preclinical development, QSP will integrate with non-animal "new approach methodologies" and reverse-translated datasets to improve understanding of and translation to the human patient. During clinical development, integration with complementary modeling approaches and multimodal patient data will create multidimensional digital twins and virtual populations for clinical trial simulations that guide clinical development and point to opportunities for precision medicine. QSP can evolve into this future by (1) pursuing high-impact applications enabled by novel experimental and quantitative technologies and data types; (2) integrating closely with analytical and computational advancements; and (3) increasing efficiencies through automation, standardization, and model reuse. In this vision, the QSP expert will play a critical role in designing strategies, evaluating data, staging and executing analyses, verifying, interpreting, and communicating findings, and ensuring the ethical, safe, and rational application of novel data types, technologies, and advanced analytics including AI/ML.

Translational modelling to predict human pharmacokinetics and pharmacodynamics of a Bruton's tyrosine kinase-targeted protein degrader BGB-16673

BACKGROUND AND PURPOSE

Bifunctional small molecule degraders, which link the target protein with E3 ubiquitin ligase, could lead to the efficient degradation of the target protein. BGB-16673 is a Bruton's tyrosine kinase (BTK) degrader. A translational PK/PD modelling approach was used to predict the human BTK degradation of BGB-16673 from preclinical in vitro and in vivo data.

EXPERIMENTAL APPROACH

A simplified mechanistic PK/PD model was used to establish the correlation between the in vitro and in vivo BTK degradation by BGB-16673 in a mouse model. Human and mouse species differences were compared using the parameters generated from in vitro human or mouse blood, and human or mouse serum spiked TMD-8 cells. Human PD was then predicted using the simplified mechanistic PK/PD model.

KEY RESULTS

BGB-16673 showed potent BTK degradation in mouse whole blood, human whole blood, and TMD-8 tumour cells in vitro. Furthermore, BGB-16673 showed BTK degradation in a murine TMD-8 xenograft model in vivo. The PK/PD model predicted human PD and the observed BTK degradation in clinical studies both showed robust BTK degradation in blood and tumour at clinical dose range.

CONCLUSION AND IMPLICATIONS

The presented simplified mechanistic model with reduced number of model parameters is practically easier to be applied to research projects compared with the full mechanistic model. It can be used as a tool to better understand the PK/PD behaviour for targeted protein degraders and increase the confidence when moving to the clinical stage.

Methylarginine targeting chimeras for lysosomal degradation of intracellular proteins

A paradigm shift in drug development is the discovery of small molecules that harness the ubiquitin-proteasomal pathway to eliminate pathogenic proteins. Here we provide a modality for targeted protein degradation in lysosomes. We exploit an endogenous lysosomal pathway whereby protein arginine methyltransferases (PRMTs) initiate substrate degradation via arginine methylation. We developed a heterobifunctional small molecule, methylarginine targeting chimera (MrTAC), that recruits PRMT1 to a target protein for induced degradation in lysosomes. MrTAC compounds degraded substrates across cell lines, timescales and doses. MrTAC degradation required target protein methylation for subsequent lysosomal delivery via microautophagy. A library of MrTAC molecules exemplified the generality of MrTAC to degrade known targets and neo-substrates-glycogen synthase kinase 3β, MYC, bromodomain-containing protein 4 and histone deacetylase 6. MrTAC selectively degraded target proteins and drove biological loss-of-function phenotypes in survival, transcription and proliferation. Collectively, MrTAC demonstrates the utility of endogenous lysosomal proteolysis in the generation of a new class of small molecule degraders.

To homeostasis and beyond! Recent advances in the medicinal chemistry of heterobifunctional derivatives

The field of induced proximity therapeutics has expanded dramatically over the past 3 years, and heterobifunctional derivatives continue to form a significant component of the activities in this field. Here, we review recent advances in the field from the perspective of the medicinal chemist, with a particular focus upon informative case studies, alongside a review of emerging topics such as Direct-To-Biology (D2B) methodology and utilities for heterobifunctional compounds beyond E3 ligase mediated degradation. We also include a critical evaluation of the latest thinking around the optimisation of physicochemical and pharmacokinetic attributes of these beyond Role of Five molecules, to deliver appropriate therapeutic exposure in vivo.

Transforming the Discovery of Targeted Protein Degraders: The Translational Power of Predictive PK/PD Modeling

Targeted protein degraders (TPDs), an emerging therapeutic modality, are attracting considerable interest with the promise to address disease-related proteins that are not druggable with conventional small molecule inhibitors. Despite their novel mechanism of action, the PK/PD relationship of degraders is still approached with a mindset deeply rooted in inhibitor drugs. Here, we establish how predictive mechanistic modeling specifically tailored to TPDs can significantly enhance the value of the available information during lead generation and optimization. By integrating the results from in vitro assays with routinely collected PK data, modeling accurately predicts degradation in vivo. These predictions transform the prioritization of compounds for in vivo studies as well as the selection of optimal dose schedules and most informative measurement time points with the least number of animals. Moreover, the comprehensive modeling framework (1) identifies the PK/PD driver of targeted protein degradation and subsequent downstream pharmacodynamic effects, and (2) uncovers the fundamental difference between degrader and inhibitor PK/PD relationships. The practical utility of our predictive modeling is demonstrated with relevant use cases. This framework will allow researchers to transition from current, mostly serendipity-based approaches to more sound model-informed decision making. Going forward, the presented predictive PK/PD modeling framework lays out a rational path to incorporate inter-species differences in the pharmacology and thus promises to help with getting the dose right in clinical trials.

Towards the Targeted Protein Degradation of PRMT1

Targeting the protein arginine methyltransferase 1 (PRMT1) has emerged as a promising therapeutic strategy in cancer treatment. The phase 1 clinical trial for GSK3368715, the first PRMT1 inhibitor to enter the clinic, was terminated early due to a lack of clinical efficacy, extensive treatment-emergent effects, and dose-limiting toxicities. The incidence of the latter two events may be associated with inhibition-driven pharmacology as a high and sustained concentration of inhibitor is required for therapeutic effect. The degradation of PRMT1 using a proteolysis targeting chimera (PROTAC) may be superior to inhibition as proceeds via event-driven pharmacology where a PROTAC acts catalytically at a low dose. PROTACs containing the same pharmacophore as GSK3368715, combined with a motif that recruits the VHL or CRBN E3-ligase, were synthesised. Suitable cell permeability and target engagement were shown for selected candidates by the detection of downstream effects of PRMT1 inhibition and by a NanoBRET assay for E3-ligase binding, however the candidates did not induce PRMT1 degradation. This paper is the first reported investigation of PRMT1 for targeted protein degradation and provides hypotheses and insights to assist the design of PROTACs for PRMT1 and other novel target proteins.

Realizing the promise of Project Optimus: Challenges and emerging opportunities for dose optimization in oncology drug development

Project Optimus is a US Food and Drug Administration Oncology Center of Excellence initiative aimed at reforming the dose selection and optimization paradigm in oncology drug development. This project seeks to bring together pharmaceutical companies, international regulatory agencies, academic institutions, patient advocates, and other stakeholders. Although there is much promise in this initiative, there are several challenges that need to be addressed, including multidimensionality of the dose optimization problem in oncology, the heterogeneity of cancer and patients, importance of evaluating long-term tolerability beyond dose-limiting toxicities, and the lack of reliable biomarkers for long-term efficacy. Through the lens of Totality of Evidence and with the mindset of model-informed drug development, we offer insights into dose optimization by building a quantitative knowledge base integrating diverse sources of data and leveraging quantitative modeling tools to build evidence for drug dosage considering exposure, disease biology, efficacy, toxicity, and patient factors. We believe that rational dose optimization can be achieved in oncology drug development, improving patient outcomes by maximizing therapeutic benefit while minimizing toxicity.

Kinetic Modeling of PROTAC-Induced Protein Degradation

Kinetics of the PROTAC-induced protein degradation were modelled using the equilibrium approximation, accounting for the protein recovery rate with a time lag. The simulated kinetic curves resemble what is experimentally observed, and the physical formulas of the half-maximal degradation concentration (DC50 ) were derived from them. The equations reveal that DC50 is proportional to the dissociation constant of the ternary complex (Kd ) and inversely proportional to the expression level of the E3 ligase and the effective ubiquitylation rate (kub ). The predicted relationships were rigorously confirmed by experimental evidences from a matched molecular pair analysis using a set of published PROTACs.

ATNC: Versatile Nanobody Chimeras for Autophagic Degradation of Intracellular Unligandable and Undruggable Proteins

Targeted protein degradation (TPD) through the autophagy pathway displays broad substrate scope and is gaining increasing interest in biology and medicine. However, current approaches using small-molecule degraders have limitations due to the lack of versatility, modularity, and ease of implementation and are restricted to addressing only ligandable proteins. Herein, we report a nonsmall molecule-based autophagy-targeting nanobody chimera (ATNC), or phagobody, for selective degradation of intracellular targets, which overcomes these limitations. The core of an ATNC features a nanobody for recruiting proteins as well as an autophagic pathway-directing module. ATNC turns out to be a general, modular, and versatile degradation platform. We show that ATNC can be versatilely implemented in different ways including expressed ATNC intrabodies for ease of use, chemically induced proximity (CIP)-operated logic-gated conditional and tunable degradation, and cyclic cell-penetrating peptide-tethered cell-permeable phagobodies that selectively degrade the undruggable therapeutically relevant HE4 protein, resulting in effective suppression of ovarian cancer cell proliferation and migration. Overall, ATNC represents a general, modular, and versatile targeted degradation platform that degrades unligandable proteins and offers therapeutic potential.

Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods

The therapeutic approach of targeted protein degradation (TPD) is gaining momentum due to its potentially superior effects compared with protein inhibition. Recent advancements in the biotech and pharmaceutical sectors have led to the development of compounds that are currently in human trials, with some showing promising clinical results. However, the use of computational tools in TPD is still limited, as it has distinct characteristics compared with traditional computational drug design methods. TPD involves creating a ternary structure (protein-degrader-ligase) responsible for the biological function, such as ubiquitination and subsequent proteasomal degradation, which depends on the spatial orientation of the protein of interest (POI) relative to E2-loaded ubiquitin. Modeling this structure necessitates a unique blend of tools initially developed for small molecules (e.g., docking) and biologics (e.g., protein-protein interaction modeling). Additionally, degrader molecules, particularly heterobifunctional degraders, are generally larger than conventional small molecule drugs, leading to challenges in determining drug-like properties like solubility and permeability. Furthermore, the catalytic nature of TPD makes occupancy-based modeling insufficient. TPD consists of multiple interconnected yet distinct steps, such as POI binding, E3 ligase binding, ternary structure interactions, ubiquitination, and degradation, along with traditional small molecule properties. A comprehensive set of tools is needed to address the dynamic nature of the induced proximity ternary complex and its implications for ubiquitination. In this Perspective, we discuss the current state of computational tools for TPD. We start by describing the series of steps involved in the degradation process and the experimental methods used to characterize them. Then, we delve into a detailed analysis of the computational tools employed in TPD. We also present an integrative approach that has proven successful for degrader design and its impact on project decisions. Finally, we examine the future prospects of computational methods in TPD and the areas with the greatest potential for impact.

Proximity-Based Modalities for Biology and Medicine

Molecular proximity orchestrates biological function, and blocking existing proximities is an established therapeutic strategy. By contrast, strengthening or creating neoproximity with chemistry enables modulation of biological processes with high selectivity and has the potential to substantially expand the target space. A plethora of proximity-based modalities to target proteins via diverse approaches have recently emerged, opening opportunities for biopharmaceutical innovation. This Outlook outlines the diverse mechanisms and molecules based on induced proximity, including protein degraders, blockers, and stabilizers, inducers of protein post-translational modifications, and agents for cell therapy, and discusses opportunities and challenges that the field must address to mature and unlock translation in biology and medicine.

Proteolysis-targeting chimeras in biotherapeutics: Current trends and future applications

The success of inhibitor-based therapeutics is largely constrained by the acquisition of therapeutic resistance, which is partially driven by the undruggable proteome. The emergence of proteolysis targeting chimera (PROTAC) technology, designed for degrading proteins involved in specific biological processes, might provide a novel framework for solving the above constraint. A heterobifunctional PROTAC molecule could structurally connect an E3 ubiquitin ligase ligand with a protein of interest (POI)-binding ligand by chemical linkers. Such technology would result in the degradation of the targeted protein via the ubiquitin-proteasome system (UPS), opening up a novel way of selectively inhibiting undruggable proteins. Herein, we will highlight the advantages of PROTAC technology and summarize the current understanding of the potential mechanisms involved in biotherapeutics, with a particular focus on its application and development where therapeutic benefits over classical small-molecule inhibitors have been achieved. Finally, we discuss how this technology can contribute to developing biotherapeutic drugs, such as antivirals against infectious diseases, for use in clinical practices.

Targeted protein degrader development for cancer: advances, challenges, and opportunities

Anticancer-targeted therapies inhibit various kinases implicated in cancer and have been used in clinical settings for decades. However, many cancer-related targets are proteins without catalytic activity and are difficult to target using traditional occupancy-driven inhibitors. Targeted protein degradation (TPD) is an emerging therapeutic modality that has expanded the druggable proteome for cancer treatment. With the entry of new-generation immunomodulatory drugs (IMiDs), selective estrogen receptor degraders (SERDs), and proteolysis-targeting chimera (PROTAC) drugs into clinical trials, the field of TPD has seen explosive growth in the past 10 years. Several challenges remain that need to be tackled to increase successful clinical translation of TPD drugs. We present an overview of the global landscape of clinical trials of TPD drugs over the past decade and summarize the clinical profiles of new-generation TPD drugs. In addition, we highlight the challenges and opportunities for the development of effective TPD drugs for future successful clinical translation.