Design, synthesis, characterisation, in vitro and in silico study of s-benzyldithiocarbazate derivatives and their metal complexes as escherichia coli dihydrofolate reductase inhibitors

Abstract

Dihydrofolate reductase (DHFR) is a key enzyme required for bacterial growth because it reduces 7,8-dihydrofolate (DHF) to 5,6,7,8-tetrahydrofolate (THF), an essential compound for DNA synthesis and cell survival. Since DHFR plays a critical role in bacterial survival, it has become an important target for developing drugs to treat infections. With Escherichia coli (E. coli) infections on the rise, there is an urgent need to develop novel antibacterial agents specifically targeting E. coli DHFR to combat this growing threat. In response to this challenge, four new SBDTC derivatives and their sixteen corresponding metal complexes were designed, synthesised, and thoroughly characterised, followed by in vitro and in silico studies. Structural analysis revealed that SB2OME, SB3OME, and SB3NO were formed through substitution at the β-nitrogen of SBDTC, while SB4OME resulted from substitution at the α-nitrogen. Upon complexation, SB2OME, SB3OME, and SB4OME functioned as tridentate ligands via NOS donor atoms, while SB3NO acted as a bidentate ligand through OS donor atoms. ADMET predictions indicated that the SBDTC derivatives adhered to drug-likeness criteria while the metal complexes exhibited some violations. Nonetheless, all compounds were predicted to have low toxicity profiles. Subsequently, antibacterial activity evaluated using minimum inhibitory concentration (MIC) assays, revealed notable efficacy against both gram-positive and gram-negative bacteria. Most metal complexes significantly enhanced the antibacterial activity of their SBDTC derivatives alone. Cu(II), Zn(II), Co(II), and Ni(II) complexes derived from SB4OME reduced the MIC of SB4OME against E. coli (ATCC 25922) by half (MIC = 0.437 mg/mol) outperforming trimethoprim (MIC = 1.750 mg/mol). Molecular docking studies on SB4OME and its metal complexes demonstrated interactions with active site residues of E. coli DHFR (PDB ID: 1RX7), similar to the natural substrate (folic acid) and the commercial antibiotic (trimethoprim), justifying their superior in in-vitro activity. To further validate their efficacy, Molecular dynamicss (MD) simulations were performed on SB4OME and its Cu(II), Co(II), and Ni(II) complexes over a 100 ns timeframe. All systems exhibited stability throughout the simulation, with optimal stability observed from 30 ns onward. Among all these compounds, the DHFR-CUSB4 complex demonstrated the most favourable binding free energy (-36.67 kcal/mol) in MMPBSA calculations, surpassing both folic acid and trimethoprim. Furthermore, several of the investigated compounds, including Cu(SB4OME)₂, demonstrated stable binding at the mutated residues L28R and I94L, highlighting their potential to overcome trimethoprim resistance associated with these clinically relevant DHFR mutations. In conclusion, the exceptional performance of Cu(SB4OME)₂ in both in vitro and in silico studies underscores its potential as a promising antibacterial agent and a targeted inhibitor of E. coli DHFR.