Molecular design, synthesis, and antibacterial studies of beta-carboline derivative as potential antibiotic agents

Abstract

Antimicrobial resistance (AMR) poses a critical global health threat, driving increased mortality, morbidity, and healthcare costs. The ability of microbes to mutate and develop resistance against existing antibiotics necessitates the discovery of new antibacterial agents. β-Carboline, a naturally abundant heterocyclic alkaloid, exhibits diverse pharmacological activities, including antibacterial effects. However, limitations in its drug-likeness restrict its potential as a novel antibiotic. This study aimed to design, synthesise, and evaluate β-carboline derivatives in-vitro targeting bacterial DNA gyrase, a key enzyme involved in bacterial replication. Initially, 51 β-carboline derivatives were virtually screened against DNA gyrase (PDB ID: 3G75) using protein’s bound ligand B48 as a reference, followed by ADMET prediction. Most β-carboline derivatives exhibited improved binding energies (-5.8 to -8.3 kcal/mol) with derivative (3.1o) (-6.1 kcal/mol), surpassing B48 (-5.8 kcal/mol) while the β-carboline scaffold (1.1) showed comparable affinity (-5.8 kcal/mol). Derivative (3.1o) interacted with the binding site of the target protein by forming two strong conventional hydrogen bonds with two important residues, Ser55 and Asp81. ADMET analysis showed that all β-carboline derivatives fulfil Lipinski’s Rule of Five with good permeability, although most of the derivatives exhibited low sp3 fraction, indicating poor solubility due high unsaturation. Among them, derivative (3.1o) was further designed using Fragment-Based Drug Design (FBDD) using growing strategy targeting hydrogen atom from each site, R1 and R2 where about 23550 and 67 compounds were generated, respectively. Virtual screening prioritised compound (4.2a) for synthesis as it exhibited improved binding affinity (-8.1 kcal/mol) compared to B48 (-5.8 kcal/mol). The new substituent at the modification site (R2) can accommodate into the binding site of the protein forming few strong conventional hydrogen bonds with critical residues, Ser55 and Asp81. On top of that, it also strictly adhered with Lipinski’s Rule of Five with high GI absorption underscoring its favourable drug-likeness and potential for oral bioavailability However, due to persistent synthetic challenges, an alternative route using Pictet-Spengler condensation with different aromatic aldehydes were proposed and successfully synthesised five tetrahydro-β-carboline derivatives (3.14a–e) with low yields (17.45 – 29.28%). The chemical structures of synthesised compounds were verified using Nuclear Magnetic Resonance (NMR) and Fourier Transform Infrared (FTIR). These derivatives were tested in-vitro for antibacterial activity against Gram-positive (S. aureus, B. subtilis) and Gram-negative bacteria (E. coli, P. aeruginosa). Of these, only compound (3.14a) showed modest activity at 50 µg/mL against Gram-negative strains, where others exhibited a weak inhibition at 100 µg/mL. Molecular docking supported these findings, with compound (3.14a) showing the highest binding affinity (-7.2 kcal/mol), comparable to streptomycin (-7.3 kcal/mol) and novobiocin (-7.5 kcal/mol). This research highlights the need for further optimisation and comprehensive virtual screening of β-carboline derivatives to establish a detailed structure-activity relationship (SAR).