Identification and Optimization of Small Molecule Binders for ALK2, USP5, and DCAF1
type: CreativeWork
description: This thesis describes the optimization of small molecule binders targeting three proteins involved in the development of various cancers: Activin receptor-like kinase 2 (ALK2), ubiquitin-specific protease 5 (USP5), and DDB1-cullin4 associated factor 1 (DCAF1). For ALK2, a kinase involved in the development of diffuse intrinsic pontine glioma, we report the design, synthesis, and evaluation of a first-in-class set of 5- to 7-membered ether-linked and 7-membered amine-linked constrained inhibitors of ALK2. We explored novel scaffold modifications using M4K2009 as the lead compound to optimize potency against ALK2 and increase selectivity over important off-targets such as ALK5. Our rigidification strategy led us to generate compounds M4K2308, M4K2281 and M4K2304 which are the most potent inhibitors of ALK2 reported to date (IC50 ≤ 3 nM). Additionally, compounds M4K2304 and M4K2306 exhibited high levels of selectivity for ALK2 over ALK5, surpassing levels exhibited by the reference compound. For USP5, a deubiquitinase overexpressed in most cancers, we conducted structure-activity relationship (SAR) studies to optimize UBTR008295a. Our optimization studies led us to the discovery of compound 22, which exhibited single-digit micromolar affinity for USP5's ZnF-UBD and was >30-fold selective over nine structurally similar ZnF-UBDs. For DCAF1, an E3 ligase involved in protein degradation and a potential drug target for diverse cancers, we report a series of SAR studies to optimize compound ZI391232269. Here we report the discovery of compound 19, a DCAF1 ligand that binds to its WDR domain with a KD of 38 nM and that exhibits cellular target engagement with an EC50 of 10 µM by cellular thermal shift assay. Moreover, we described a second SAR effort to optimize compound 19 with the intent of generating a chemical probe to investigate the biology of DCAF1 in cells. Lastly, we outlined the optimization of an alternative chemical scaffold targeting the WDR domain of DCAF1. This…
abstract: This thesis describes the optimization of small molecule binders targeting three proteins involved in the development of various cancers: Activin receptor-like kinase 2 (ALK2), ubiquitin-specific protease 5 (USP5), and DDB1-cullin4 associated factor 1 (DCAF1). For ALK2, a kinase involved in the development of diffuse intrinsic pontine glioma, we report the design, synthesis, and evaluation of a first-in-class set of 5- to 7-membered ether-linked and 7-membered amine-linked constrained inhibitors of ALK2. We explored novel scaffold modifications using M4K2009 as the lead compound to optimize potency against ALK2 and increase selectivity over important off-targets such as ALK5. Our rigidification strategy led us to generate compounds M4K2308, M4K2281 and M4K2304 which are the most potent inhibitors of ALK2 reported to date (IC50 ≤ 3 nM). Additionally, compounds M4K2304 and M4K2306 exhibited high levels of selectivity for ALK2 over ALK5, surpassing levels exhibited by the reference compound. For USP5, a deubiquitinase overexpressed in most cancers, we conducted structure-activity relationship (SAR) studies to optimize UBTR008295a. Our optimization studies led us to the discovery of compound 22, which exhibited single-digit micromolar affinity for USP5's ZnF-UBD and was >30-fold selective over nine structurally similar ZnF-UBDs. For DCAF1, an E3 ligase involved in protein degradation and a potential drug target for diverse cancers, we report a series of SAR studies to optimize compound ZI391232269. Here we report the discovery of compound 19, a DCAF1 ligand that binds to its WDR domain with a KD of 38 nM and that exhibits cellular target engagement with an EC50 of 10 µM by cellular thermal shift assay. Moreover, we described a second SAR effort to optimize compound 19 with the intent of generating a chemical probe to investigate the biology of DCAF1 in cells. Lastly, we outlined the optimization of an alternative chemical scaffold targeting the WDR domain of DCAF1. This…
author: Gonzalez Alvarez, Hector
keywords: ALK2, Cancer Research, DCAF1, Diffuse Intrinsic Pontine Glioma, Drug Discovery, USP5
date published: 2024-11
date modified: 2026-07-27T21:28:07Z
provider: University of Toronto
publisher: Networked Digital Library of Theses and Dissertations
type: WebPage
source organization: University of Toronto

PropertyValue
property ID: Handle
value: https://hdl.handle.net/1807/149702