Bacterial Alkaloid Biosynthesis off the Beaten Path: Compartmentalization and Non-Enzymatic Transformations in Non-Canonical Alkaloid Biosynthesis

Introduction

Nature is a remarkable pharmaceutical chemist. More than 50% of approved drugs are natural products (NPs) or have drawn inspiration from them. According to the central dogma of bacterial NP biosynthesis, all transformations responsible for the formation and modification of a NP scaffold are carried out by enzymes encoded in a biosynthetic gene cluster (BGC).

Genome Mining Algorithms

Sophisticated genome mining algorithms have been developed to identify NP BGCs in microbial genome sequences. These algorithms excel in recognizing canonical BGCs. However, non-canonical BGCs associated with NPs that are not biosynthesized following textbook biosynthetic knowledge evade detection by state-of-the-art genome mining algorithms.

Non-Enzymatic Transformations

We have identified alkaloids that undergo non-enzymatic transformations, thus defying the central dogma of NP biosynthesis. Bacteria likely employ specialized micro-compartments to facilitate these spontaneous reactions.

Project Goals

The ComBiNE team will develop machine learning-based genome mining algorithms to systematically identify and characterize alkaloid BGCs that currently elude detection. These non-canonical pathways biosynthesize alkaloids independent of the ribosome and non-ribosomal peptide synthetases.

Focus Areas

We will focus on:

1. Alkaloids that undergo non-enzymatic transformations in bacterial micro-compartments.
2. Establishing a model system to study the level of compartmentalization necessary to facilitate spontaneous reactions.

Expected Outcomes

Insights gained from these studies will be used to engineer NP and primary metabolic pathways for the non-enzymatic fusion of tailor-made NPs or primary metabolites with complementary reactivity.

Applications

Spontaneous reactions in bacterial micro-compartments can be harnessed for:

• The fusion of two NPs with different targets to create bispecific chimeras to combat drug resistance.
• The fusion of bioactive and homing components to mitigate off-target effects.

The proposed research will inspire the development of biomimetic syntheses and expand NP chemical and biosynthetic space.