Fine-Tuning Side Chain Substitutions: Impacts on the Lipophilicity-Solubility-Permeability Interplay in Macrocyclic...

Area of Science:

• Medicinal Chemistry
• Chemical Biology
• Drug Discovery

Background:

• Macrocyclic drugs show promise for targeting previously undruggable proteins, particularly in cancer treatment.
• The pancreatic cancer stem cell inhibitor BE-43547A2 (BE) has limited clinical use due to high lipophilicity.

Purpose of the Study:

• To design and synthesize novel macrocyclic drug derivatives with improved physicochemical properties.
• To investigate the structure-activity relationships and target engagement of these derivatives.

Main Methods:

• Concise total synthesis of a versatile late-stage intermediate (compound 17) for modular diversification.
• Modular click chemistry to introduce triazole rings and flexible alkyl spacers.
• Experimental determination of lipophilicity, solubility, and Caco-2 permeability.
• MicroScale Thermophoresis (MST) for direct target engagement studies.
• Molecular dynamics simulations and free-energy calculations to assess transmembrane penalties.

Main Results:

• Synthesized derivatives exhibited reduced lipophilicity and improved solubility.
• Unexpected loss of cellular activity despite improved drug-like properties.
• MST revealed compound-dependent target engagement mechanisms, with some derivatives retaining binding and others losing it.
• Molecular dynamics simulations indicated that tail modifications disrupted drug-membrane and drug-solvent interactions, increasing transmembrane free-energy penalties.

Conclusions:

• Simultaneous optimization of target engagement and cell permeability is crucial for developing effective macrocyclic drugs.
• Compound 17 serves as a valuable scaffold for future lead optimization in macrocyclic therapeutics.
• The study provides a blueprint for balancing drug-like properties with therapeutic potency in macrocyclic drug design.