Hydroxypyrrolidine Bifunctional Compound for Target Protein Degradation

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Solution Overview

Problem

Current bifunctional compounds for selective target protein degradation have limitations in the range of applicable target proteins and effectiveness of degradation induction, necessitating the development of more effective low-molecular-weight compounds.

Innovation Solution

A compound represented by structural formula (I) with a VHL binding ligand at one end and a target-directed ligand at the other, capable of inducing target protein degradation through the ubiquitin-proteasome system, is developed, allowing for regulation of ubiquitination and degradation of target proteins.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Adaptability or versatility

If existing bifunctional compounds are used for target protein degradation, then some degradation effect is achieved, but the range of applicable target proteins is limited and degradation effectiveness is insufficient

Engineering Contradiction:
Improverange of applicable target proteinsVSAvoideffectiveness of degradation induction
Core Design Contradiction:
Adaptability or versatilityVSReliability

Solution Approach 1:

The patent modifies the chemical structure parameters of the bifunctional compound by changing the core scaffold from proline or cyclopropane to hydroxypyrrolidine, and by optimizing the linker length and composition. These parameter changes enable the compound to bind to a broader range of target proteins while maintaining effective degradation induction, thus expanding the range of applicable target proteins without sacrificing degradation effectiveness.

Inventive Principle:
Principle #35Parameter changes

2Adaptability or versatility

If bifunctional compounds are designed to bind to multiple target proteins, then the range of applicable target proteins expands, but the degradation effectiveness may be diluted

Engineering Contradiction:
Improverange of applicable target proteinsVSAvoideffectiveness of degradation induction
Core Design Contradiction:
Adaptability or versatilityVSManufacturing precision

Solution Approach 1:

The patent employs local quality by designing the hydroxypyrrolidine core with specific functional groups at different positions that can selectively interact with various target proteins. The compound maintains localized high-affinity binding regions while having overall versatility, allowing it to effectively degrade multiple target proteins without diluting its degradation effectiveness. The specific substitution patterns on the hydroxypyrrolidine ring create distinct binding pockets for different targets.

Inventive Principle:
Principle #3Local quality

3Ease of operation

If low-molecular-weight compounds are used for target protein degradation, then the compounds are easier to administer and metabolize, but the effectiveness of degradation induction is insufficient

Engineering Contradiction:
Improveease of administration and metabolismVSAvoideffectiveness of degradation induction
Core Design Contradiction:
Ease of operationVSReliability

Solution Approach 1:

The patent creates a composite bifunctional molecule combining a VHL-binding ligand (e.g., chalcone derivative) with a target protein ligand through a carefully designed linker. This composite structure maintains the low molecular weight advantage for easy administration and metabolism while achieving effective target protein degradation through the synergistic action of both functional moieties. The hydroxypyrrolidine core acts as an efficient scaffold that coordinates both binding functions within a compact molecular framework.

Inventive Principle:
Principle #40Composite materials

Applied Scientific Principles

This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.

Function Achieved in This Case

The compound achieves a wide range of pharmacological activities by effectively inducing the degradation of target proteins, enhancing the range and effectiveness of protein regulation compared to existing compounds.

Implementation Method 1

a bifunctional compound having a portion that binds to Von-Hippel-Lindau, which is a substrate recognition protein of a ubiquitin ligase complex

Methodology Applied
Scientific EffectProtein-protein binding:

Implementation Method 2

a portion that is capable of binding or binds to a target protein (hereinafter sometimes to be referred to as target-directed ligand)

Methodology Applied
Scientific EffectProtein-protein binding:

Implementation Method 3

The ubiquitin-proteasome system is a system that degrades and removes proteins no longer needed in cells, through ubiquitination of target proteins by proteasomes in an ATP-dependent manner

Methodology Applied
Scientific EffectUbiquitination:

Implementation Method 4

degrades and removes proteins no longer needed in cells, through ubiquitination of target proteins by proteasomes in an ATP-dependent manner

Methodology Applied
Scientific EffectATP-dependent degradation:

Implementation Method 5

a target protein that has undergone so-called polyubiquitination, in which a ubiquitin chain is linked via the 48th lysine residue of ubiquitin

Methodology Applied
Scientific EffectPolyubiquitination:

Data Source

PatentUS20230312542A1Hydroxypyrrolidine derivative and medicinal application thereof
Publication Date: 2023.10.05 TANABE PHARMA CORP
  • US20230312542A1 patent drawing
  • US20230312542A1 patent drawing
  • US20230312542A1 patent drawing

AI summary

The present invention provides a target protein degradation-inducing compound that is a bifunctional compound having a portion that binds to VHL, which is a substrate recognition protein of a ubiquitin ligase complex, at one end, and a portion that binds to a target protein at the other end. Specifically, a compound represented by the following structural formula (I):wherein each symbol is as defined in the present specification, or a pharmacologically acceptable salt thereof.