Design, synthesis, and bioevaluation of novel unsaturated cyanoacetamide derivatives: In vitro and in silico exploration

Kabir M Uddin; Mehnaz Hossain Meem; Mokseda Akter; Shofiur Rahman; Mahmoud A Al-Gawati; Nahed Alarifi; Hamad Albrithen; Abdullah Alodhayb; Raymond A Poirier; Md Mosharef H Bhuiyan

doi:10.1016/j.mex.2024.102691

Design, synthesis, and bioevaluation of novel unsaturated cyanoacetamide derivatives: In vitro and in silico exploration

MethodsX. 2024 Apr 9:12:102691. doi: 10.1016/j.mex.2024.102691. eCollection 2024 Jun.

Authors

Affiliations

¹ Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1217, Bangladesh.
² Bioorganic and Medicinal Chemistry Laboratory, Department of Chemistry, University of Chittagong, Chattogram 4331, Bangladesh.
³ Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, Riyadh 11451, Saudi Arabia.
⁴ Research Chair for Tribology, Surface, and Interface Sciences, Department of Physics and Astronomy, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
⁵ Department of Chemistry, Memorial University, St. John's, Newfoundland A1B 3 × 7, Canada.

Abstract

In this study, we synthesized novel α,β-unsaturated 2-cyanoacetamide derivatives (1-5) using microwave-assisted Knoevenagel condensation. Characterization of these compounds was carried out using FTIR and ¹H NMR spectroscopy. We then evaluated their in vitro antibacterial activity against both gram-positive and gram-negative pathogenic bacteria. Additionally, we employed in silico methods, including ADMET prediction and density functional theory (DFT) calculations of molecular orbital properties, to investigate these cyanoacetamide derivatives (1-5). Molecular docking was used to assess the binding interactions of these derivatives (1-5) with seven target proteins (5MM8, 4NZZ, 7FEQ, 5NIJ, ITM2, 6SE1, and 5GVZ) and compared them to the reference standard tyrphostin AG99. Notably, derivative 5 exhibited the most favorable binding affinity, with a binding energy of -7.7 kcal mol^-1 when interacting with the staphylococcus aureus (PDB:5MM8), while also meeting all drug-likeness criteria. Additionally, molecular dynamics simulations were carried out to evaluate the stability of the interaction between the protein and ligand, utilizing parameters such as Root-Mean-Square Deviation (RMSD), Root-Mean-Square Fluctuation (RMSF), Radius of Gyration (Rg), and Principal Component Analysis (PCA). A 50 nanosecond molecular dynamics (MD) simulation was performed to investigate stability further, incorporating RMSD and RMSF analyses on compound 5 within the active binding site of the modeled protein across different temperatures (300, 305, 310, and 320 K). Among these temperatures, compound 5 exhibited an RMSD value ranging from approximately 0.2 to 0.3 nm at 310 K (body temperature) with the 5MM8 target, which differed from the other temperature conditions. The in silico results suggest that compound 5 maintained significant conformational stability throughout the 50 ns simulation period. It is consistent with its low docking energy and in vitro findings concerning α,β-unsaturated cyanoacetamides. Key insights from this study include:•The creation of innovative α,β-unsaturated 2-cyanoacetamide derivatives (1-5) employing cost-effective, licensed, versatile, and efficient software for both in silico and in vitro assessment of antibacterial activity.•Utilization of FTIR and NMR techniques for characterizing compounds 1-5.

Keywords: FTIR and NMR analysis, Density Functional Theory (DFT), in silico simulations, and in vitro experiments for the investigation of α,β-unsaturated cyanoacetamides; MD simulation; Microwave irradiation; Molecular docking; α, β-unsaturated 2-cyanoacetamide;Knoevenagel condensation.