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Updated: Jun 18, 2025

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Programmable Chemical Evolution with Natural/Non-Natural Building Blocks.

Ping Liu1, Refeya Jannatul2, Juan Chen1

  • 1Department of Nutrition and Health, China Agricultural University, 100091, Beijing, China.

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|July 29, 2024
PubMed
Summary

Programmable chemical evolution (PCEvo) rapidly generates high-affinity binders using diverse non-natural building blocks. This method accelerates drug discovery by exploring vast chemical space for novel molecular recognition agents.

Keywords:
Programmable chemical evolutionancestral moleculemutationnanomolar affinitynatural/non-natural building blocksselection

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Area of Science:

  • Medicinal Chemistry
  • Chemical Biology
  • Drug Discovery

Background:

  • Non-natural building blocks (BBs) offer extensive chemical diversity for molecular recognition and drug discovery.
  • Current laboratory evolution systems face challenges in efficiently generating bioactive molecules with numerous diverse BBs.

Purpose of the Study:

  • Introduce programmable chemical evolution (PCEvo) to overcome limitations in current laboratory evolution systems.
  • Enable rapid generation of high-affinity binders using a large number of diverse non-natural BBs.

Main Methods:

  • Integrate chemoinformatic classification with high-throughput array synthesis and screening.
  • Construct diverse combinatorial libraries to create ancestral molecules for evolution.
  • Employ PCEvo with 108 BBs, exploring over 10^17 chemical space.

Main Results:

  • Identify bicyclic peptidomimetic binders against SAR-CoV-2 RBD and Claudin18.2 targets with nanomolar affinity.
  • Achieve expedited molecular evolution within 2-4 cycles.
  • Claudin18.2 binders selectively stain gastric adenocarcinoma cell lines and patient samples.

Conclusions:

  • PCEvo significantly advances the utilization of non-natural BBs for rapid chemical evolution.
  • This approach is applicable to targets with or without prior structural information or ligand preference.
  • PCEvo accelerates the discovery of novel bioactive molecules for therapeutic applications.