1
|
Wang YT, Price E, Feng M, Hulen J, Doktor S, Stresser DM, Maes EM, Ji QC, Jenkins GJ. High-Throughput SFC-MS/MS Method to Measure EPSA and Predict Human Permeability. J Med Chem 2024. [PMID: 38976596 DOI: 10.1021/acs.jmedchem.4c00571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Permeability is a key factor driving the absorption of orally administered drugs. In early discovery, the efficient evaluation of permeability, particularly for compounds violating Lipinski's Rule of 5, remains challenging. Addressing this, we established a high-throughput method to measure the experimental polar surface area (HT-EPSA) as an in vitro surrogate to measure permeability. Compared to earlier methods, HT-EPSA significantly reduces data acquisition time with enhanced sensitivity, selectivity, and data quality. In the effort of translating EPSA to human in vitro and in vivo passive permeability, we demonstrated the application of EPSA for predicting Caco-2 cell and human intestinal permeability, showing improvements over topological polar surface area and the parallel artificial membrane permeability assay for rank-ordering permeability in a proteolysis targeting chimera case study. The HT-EPSA method is expected to be highly beneficial in guiding early stage compound rank-ordering, faster decision-making, and in predicting in vitro and/or in vivo human intestinal permeability.
Collapse
Affiliation(s)
- Yue-Ting Wang
- Quantitative, Translational, and ADME Sciences (QTAS), AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Edward Price
- Quantitative, Translational, and ADME Sciences (QTAS), AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Mei Feng
- Quantitative, Translational, and ADME Sciences (QTAS), AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Jason Hulen
- Quantitative, Translational, and ADME Sciences (QTAS), AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Stella Doktor
- Quantitative, Translational, and ADME Sciences (QTAS), AbbVie Inc., North Chicago, Illinois 60064, United States
| | - David M Stresser
- Quantitative, Translational, and ADME Sciences (QTAS), AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Estelle M Maes
- Quantitative, Translational, and ADME Sciences (QTAS), AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Qin C Ji
- Quantitative, Translational, and ADME Sciences (QTAS), AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Gary J Jenkins
- Quantitative, Translational, and ADME Sciences (QTAS), AbbVie Inc., North Chicago, Illinois 60064, United States
| |
Collapse
|
2
|
Zhang D, Ma B, Dragovich PS, Ma L, Chen S, Chen EC, Ye X, Liu J, Pizzano J, Bortolon E, Chan E, Zhang X, Chen YC, Levy ES, Yauch RL, Khojasteh SC, Hop CECA. Tissue distribution and retention drives efficacy of rapidly clearing VHL-based PROTACs. COMMUNICATIONS MEDICINE 2024; 4:87. [PMID: 38755248 PMCID: PMC11099041 DOI: 10.1038/s43856-024-00505-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 04/19/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Proteolysis-targeting chimeras (PROTACs) are being developed for therapeutic use. However, they have poor pharmacokinetic profiles and their tissue distribution kinetics are not known. METHODS A typical von Hippel-Lindau tumor suppressor (VHL)-PROTAC 14C-A947 (BRM degrader)-was synthesized and its tissue distribution kinetics was studied by quantitative whole-body autoradiography (QWBA) and tissue excision in rats following IV dosing. Bile duct-cannulated (BDC) rats allowed the elucidation of in vivo clearance pathways. Distribution kinetics was evaluated in the tissues and tumors of mice to support PK-PD correlation. In vitro studies enabled the evaluation of cell uptake mechanisms and cell retention properties. RESULTS Here, we show that A947 quickly distributes into rat tissues after IV dosing, where it accumulates and is retained in tissues such as the lung and liver although it undergoes fast clearance from circulation. Similar uptake/retention kinetics enable tumor growth inhibition over 2-3 weeks in a lung cancer model. A947 quickly excretes in the bile of rats. Solute carrier (SLC) transporters are involved in hepatocyte uptake of PROTACs. Sustained BRM protein degradation is seen after extensive washout that supports prolonged cell retention of A947 in NCI-H1944 cells. A947 tissue exposure and pharmacodynamics are inversely correlated in tumors. CONCLUSIONS Plasma sampling for VHL-PROTAC does not represent the tissue concentrations necessary for efficacy. Understanding of tissue uptake and retention could enable less frequent IV administration to be used for therapeutic dosing.
Collapse
Affiliation(s)
- Donglu Zhang
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA.
| | - Bin Ma
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | | | - Li Ma
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Shu Chen
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Eugene C Chen
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Xiaofen Ye
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Joyce Liu
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Jennifer Pizzano
- Arvinas; 5 Science Park, 395 Winchester Ave, New Haven, CT, 06511, USA
| | | | - Emily Chan
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Xing Zhang
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Yi-Chen Chen
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | | | - Robert L Yauch
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | | | | |
Collapse
|
3
|
Kovachka S, Tong Y, Childs-Disney JL, Disney MD. Heterobifunctional small molecules to modulate RNA function. Trends Pharmacol Sci 2024; 45:449-463. [PMID: 38641489 DOI: 10.1016/j.tips.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/21/2024]
Abstract
RNA has diverse cellular functionality, including regulating gene expression, protein translation, and cellular response to stimuli, due to its intricate structures. Over the past decade, small molecules have been discovered that target functional structures within cellular RNAs and modulate their function. Simple binding, however, is often insufficient, resulting in low or even no biological activity. To overcome this challenge, heterobifunctional compounds have been developed that can covalently bind to the RNA target, alter RNA sequence, or induce its cleavage. Herein, we review the recent progress in the field of RNA-targeted heterobifunctional compounds using representative case studies. We identify critical gaps and limitations and propose a strategic pathway for future developments of RNA-targeted molecules with augmented functionalities.
Collapse
Affiliation(s)
- Sandra Kovachka
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Yuquan Tong
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 130 Scripps Way, Jupiter, FL 33458, USA; The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Jessica L Childs-Disney
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Matthew D Disney
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 130 Scripps Way, Jupiter, FL 33458, USA; The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| |
Collapse
|
4
|
Kuemper S, Cairns AG, Birchall K, Yao Z, Large JM. Targeted protein degradation in CNS disorders: a promising route to novel therapeutics? Front Mol Neurosci 2024; 17:1370509. [PMID: 38685916 PMCID: PMC11057381 DOI: 10.3389/fnmol.2024.1370509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 03/27/2024] [Indexed: 05/02/2024] Open
Abstract
Targeted protein degradation (TPD) is a rapidly expanding field, with various PROTACs (proteolysis-targeting chimeras) in clinical trials and molecular glues such as immunomodulatory imide drugs (IMiDs) already well established in the treatment of certain blood cancers. Many current approaches are focused on oncology targets, leaving numerous potential applications underexplored. Targeting proteins for degradation offers a novel therapeutic route for targets whose inhibition remains challenging, such as protein aggregates in neurodegenerative diseases. This mini review focuses on the prospect of utilizing TPD for neurodegenerative disease targets, particularly PROTAC and molecular glue formats and opportunities for novel CNS E3 ligases. Some key challenges of utilizing such modalities including molecular design of degrader molecules, drug delivery and blood brain barrier penetrance will be discussed.
Collapse
Affiliation(s)
- Sandra Kuemper
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, United Kingdom
| | - Andrew G. Cairns
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, United Kingdom
| | | | | | | |
Collapse
|
5
|
Price E, Weinheimer M, Rivkin A, Jenkins G, Nijsen M, Cox PB, DeGoey D. Beyond Rule of Five and PROTACs in Modern Drug Discovery: Polarity Reducers, Chameleonicity, and the Evolving Physicochemical Landscape. J Med Chem 2024; 67:5683-5698. [PMID: 38498697 DOI: 10.1021/acs.jmedchem.3c02332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Developing orally bioavailable drugs demands an understanding of absorption in early drug development. Traditional methods and physicochemical properties optimize absorption for rule of five (Ro5) compounds; beyond rule of five (bRo5) drugs necessitate advanced tools like the experimental measure of exposed polarity (EPSA) and the AbbVie multiparametric score (AB-MPS). Analyzing AB-MPS and EPSA against ∼1000 compounds with human absorption data and ∼10,000 AbbVie tool compounds (∼1000 proteolysis targeting chimeras or PROTACs, ∼7000 Ro5s, and ∼2000 bRo5s) revealed new patterns of physicochemical trends. We introduced a high-throughput "polarity reduction" descriptor: ETR, the EPSA-to-topological polar surface area (TPSA) ratio, highlights unique bRo5 and PROTAC subsets for specialized drug design strategies for effective absorption. Our methods and guidelines refine drug design by providing innovative in vitro approaches, enhancing physicochemical property optimization, and enabling accurate predictions of intestinal absorption in the complex bRo5 domain.
Collapse
Affiliation(s)
- Edward Price
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Manuel Weinheimer
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Alexey Rivkin
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Gary Jenkins
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Marjoleen Nijsen
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Philip B Cox
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - David DeGoey
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| |
Collapse
|
6
|
Apprato G, Poongavanam V, Garcia Jimenez D, Atilaw Y, Erdelyi M, Ermondi G, Caron G, Kihlberg J. Exploring the chemical space of orally bioavailable PROTACs. Drug Discov Today 2024; 29:103917. [PMID: 38360147 DOI: 10.1016/j.drudis.2024.103917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 02/05/2024] [Accepted: 02/09/2024] [Indexed: 02/17/2024]
Abstract
A principal challenge in the discovery of proteolysis targeting chimeras (PROTACs) as oral medications is their bioavailability. To facilitate drug design, it is therefore essential to identify the chemical space where orally bioavailable PROTACs are more likely to be situated. To this aim, we extracted structure-bioavailability insights from published data using traditional 2D descriptors, thereby shedding light on their potential and limitations as drug design tools. Subsequently, we describe cutting-edge experimental, computational and hybrid design strategies based on 3D descriptors, which show promise for enhancing the probability of discovering PROTACs with high oral bioavailability.
Collapse
Affiliation(s)
- Giulia Apprato
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Piazza Nizza 44bis, 10126 Torino, Italy
| | | | - Diego Garcia Jimenez
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Piazza Nizza 44bis, 10126 Torino, Italy
| | - Yoseph Atilaw
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Mate Erdelyi
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Giuseppe Ermondi
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Piazza Nizza 44bis, 10126 Torino, Italy
| | - Giulia Caron
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Piazza Nizza 44bis, 10126 Torino, Italy.
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden.
| |
Collapse
|
7
|
Rossetti P, Apprato G, Caron G, Ermondi G, Rossi Sebastiano M. DegraderTCM: A Computationally Sparing Approach for Predicting Ternary Degradation Complexes. ACS Med Chem Lett 2024; 15:45-53. [PMID: 38229751 PMCID: PMC10788944 DOI: 10.1021/acsmedchemlett.3c00362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 01/18/2024] Open
Abstract
Proteolysis targeting chimeras (PROTACs or degraders) represent a novel therapeutic modality that has raised interest thanks to promising results and currently undergoing clinical testing. PROTACs induce the selective proteasomal degradation of undesired proteins by the formation of ternary complexes (TCs). Having knowledge of the 3D structure of TCs is crucial for the design of PROTAC drugs. Here, we describe DegraderTCM, a new computational method for modeling PROTAC-mediated TCs that requires low computational power and provides sound results in a short time span. We validated DegraderTCM against a selected set of experimentally determined structures and defined a method to predict the PROTAC degradation activity based on the computed TC structure. Finally, we modeled TCs of known degraders holding significance for defining the method's applicability domain. A retrospective analysis of structure-activity relationships unveiled possibilities for utilizing DegraderTCM in the initial stages of designing novel PROTAC drugs.
Collapse
Affiliation(s)
- Paolo Rossetti
- University of Torino, Department of Molecular Biotechnology and Health Sciences,
CASSMedChem, Piazza Nizza
44, 10126 Torino, Italy
| | - Giulia Apprato
- University of Torino, Department of Molecular Biotechnology and Health Sciences,
CASSMedChem, Piazza Nizza
44, 10126 Torino, Italy
| | - Giulia Caron
- University of Torino, Department of Molecular Biotechnology and Health Sciences,
CASSMedChem, Piazza Nizza
44, 10126 Torino, Italy
| | - Giuseppe Ermondi
- University of Torino, Department of Molecular Biotechnology and Health Sciences,
CASSMedChem, Piazza Nizza
44, 10126 Torino, Italy
| | - Matteo Rossi Sebastiano
- University of Torino, Department of Molecular Biotechnology and Health Sciences,
CASSMedChem, Piazza Nizza
44, 10126 Torino, Italy
| |
Collapse
|