Ancestral Sequence Reconstruction to Enable Biocatalytic Synthesis of Azaphilones

J Am Chem Soc. 2024 Nov 6;146(44):30194-30203. doi: 10.1021/jacs.4c08761. Epub 2024 Oct 23.

Abstract

Biocatalysis can be powerful in organic synthesis but is often limited by enzymes' substrate scope and selectivity. Developing a biocatalytic step involves identifying an initial enzyme for the target reaction followed by optimization through rational design, directed evolution, or both. These steps are time consuming, resource-intensive, and require expertise beyond typical organic chemistry. Thus, an effective strategy for streamlining the process from enzyme identification to implementation is essential to expanding biocatalysis. Here, we present a strategy combining bioinformatics-guided enzyme mining and ancestral sequence reconstruction (ASR) to resurrect enzymes for biocatalytic synthesis. Specifically, we achieve an enantioselective synthesis of azaphilone natural products using two ancestral enzymes: a flavin-dependent monooxygenase (FDMO) for stereodivergent oxidative dearomatization and a substrate-selective acyltransferase (AT) for the acylation of the enzymatically installed hydroxyl group. This cascade, stereocomplementary to established chemoenzymatic routes, expands access to enantiomeric linear tricyclic azaphilones. By leveraging the co-occurrence and coevolution of FDMO and AT in azaphilone biosynthetic pathways, we identified an AT candidate, CazE, and addressed its low solubility and stability through ASR, obtaining a more soluble, stable, promiscuous, and reactive ancestral AT (AncAT). Sequence analysis revealed AncAT as a chimeric composition of its descendants with enhanced reactivity likely due to ancestral promiscuity. Flexible receptor docking and molecular dynamics simulations showed that the most reactive AncAT promotes a reactive geometry between substrates. We anticipate that our bioinformatics-guided, ASR-based approach can be broadly applied in target-oriented synthesis, reducing the time required to develop biocatalytic steps and efficiently access superior biocatalysts.

MeSH terms

  • Acyltransferases / chemistry
  • Acyltransferases / genetics
  • Acyltransferases / metabolism
  • Benzopyrans* / chemical synthesis
  • Benzopyrans* / chemistry
  • Benzopyrans* / metabolism
  • Biocatalysis*
  • Mixed Function Oxygenases* / chemistry
  • Mixed Function Oxygenases* / genetics
  • Mixed Function Oxygenases* / metabolism
  • Pigments, Biological
  • Stereoisomerism
  • Substrate Specificity

Substances

  • azaphilone
  • Benzopyrans
  • Mixed Function Oxygenases
  • Acyltransferases
  • Pigments, Biological