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How proteins bind macrocycles.

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Synthetic macrocycles (MCs) show promise for targeting difficult proteins. This study provides design guidelines for creating MCs with enhanced protein binding and bioavailability, expanding drug discovery possibilities.

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Area of Science:

  • Medicinal Chemistry
  • Drug Discovery
  • Chemical Biology

Background:

  • Synthetic macrocycles (MCs) are recognized for their potential in drug development, especially for challenging targets like protein-protein interactions.
  • However, limited information exists to guide the design of MCs for optimal target binding and bioavailability.

Purpose of the Study:

  • To analyze macrocycle-protein binding modes and physicochemical properties of approved macrocyclic drugs.
  • To propose evidence-based guidelines for designing synthetic macrocycle libraries with improved target affinity and bioavailability.
  • To explore the potential of natural product-inspired macrocycles for targeting previously undruggable proteins.

Main Methods:

  • Analysis of binding modes in representative macrocycle-protein complexes.
  • Evaluation of physicochemical properties of existing macrocyclic drugs.
  • Integration of binding data with physicochemical properties to formulate design principles.

Main Results:

  • Established specific guidelines for designing synthetic macrocycle libraries.
  • Identified structural and physicochemical features that promote strong target binding and good bioavailability.
  • Demonstrated that large, natural product-derived macrocycles can engage targets intractable to conventional drugs.

Conclusions:

  • The proposed guidelines can aid in the rational design of synthetic macrocycles for drug discovery.
  • Natural product-inspired synthetic macrocycles can significantly broaden the scope of druggable protein targets.
  • This work supports the development of novel therapeutics by expanding the utility of synthetic small molecules.