Structural and biochemical analyses reveal quinic acid inhibits DAHP synthase a key player in shikimate pathway

Kuldeep Jangid; Jai Krishna Mahto; K Amith Kumar; Preeti Dhaka; Anchal Sharma; Amaan Tariq; Ashwani Kumar Sharma; Pravindra Kumar

doi:10.1016/j.abb.2024.110219

Structural and biochemical analyses reveal quinic acid inhibits DAHP synthase a key player in shikimate pathway

Arch Biochem Biophys. 2024 Nov 19:763:110219. doi: 10.1016/j.abb.2024.110219. Online ahead of print.

Authors

Kuldeep Jangid¹, Jai Krishna Mahto¹, K Amith Kumar¹, Preeti Dhaka¹, Anchal Sharma¹, Amaan Tariq¹, Ashwani Kumar Sharma², Pravindra Kumar³

Affiliations

¹ Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India.
² Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India. Electronic address: ashwani.sharma@bt.iitr.ac.in.
³ Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, India. Electronic address: pravindra.kumar@bt.iitr.ac.in.

PMID: 39566672
DOI: 10.1016/j.abb.2024.110219

Abstract

The shikimate pathway, essential for aromatic amino acid biosynthesis, is absent in animals, making its enzymes promising targets for developing antimicrobials. 3-Deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHPS) catalyzes the first committed step, which serves as the primary checkpoint for regulating the flow within the pathway, regulated by its end products (Phe, Tyr and Trp). Previously, we identified chlorogenic acid (CGA), an ester of caffeic and quinic acid, as an inhibitor of DAHPS from Bacillus subtilis, prompting us to investigate quinic acid as a potential inhibitor of Providencia alcalifaciens DAHPS (PaDAHPS). Here, we report the crystal structures of phenylalanine-sensitive DAHPS from Providenciaalcalifaciens in complex with phenylalanine (Phe) and quinic acid (QA) at resolutions of 2.5 Å and 2.68 Å, respectively. Structural analysis reveals that QA binds to the same site as Phe, with biophysical assays showing a similar binding affinity (K_D = 42 μM for QA and K_D = 32 μM for Phe). In vitro inhibition studies demonstrated that QA and Phe inhibit PaDAHPS activity, with ^appK_i values of 382 μM and 132 μM, respectively. Additionally, QA inhibited the growth of several bacterial species, including Pseudomonas aeruginosa, Moraxella catarrhalis, Providencia alcalifaciens, Staphylococcus aureus, Escherichia coli with minimum inhibitory concentrations (MICs) ranging from 2.5 to 5 mg/ml. These findings identify quinic acid as a promising scaffold for developing novel antimicrobial agents targeting the shikimate pathway, providing potential therapeutic strategies for bacterial infections.

Keywords: DAHP synthase; Phenylalanine; Quinic acid; Shikimate pathway; X-ray crystal structure.