Extraction and comparison of the interactions of tetracycline antibiotics by different types of cyclodextrins using molecular docking studies

Abstract

A hazard to humanity is people's indiscriminate use of pharmacological compounds, such as antibiotics, and their presence in the environment or water supplies, which are not eliminated during the purification process. Either left in open water, they cause sickness in humans and animals. As a result, antibiotic use management is required. This study aims to extract and assess the interactions between α, β, and γ-cyclodextrins (CD) and Tetracycline antibiotics. Studies show these chemicals have not yet been extracted and compared using various CDs. Thus, the molecular docking computational method was used to study the guest-host interaction of the CD with three types of Tetracycline antibiotics, which was helpful before laboratory investigation to achieve the ability to extract antibiotics by CD and to prevent wasting time and money. Although molecular docking provided valuable insights into the host-guest interactions, no molecular dynamics (MD) simulations were conducted in the present study. Future investigations are recommended to perform MD simulations to assess the stability, flexibility (RMSF), and conformational stability (RMSD) of the CD-antibiotic complexes over time. The optimal orientation and manner of molecule binding for antibiotics in the CD cavity's active site were examined using molecular docking studies. To fully capture the stability and flexibility of the docked complexes over time, molecular dynamics (MD) simulations should be employed as a complementary approach to docking studies. MD simulations allow for the observation of real-time structural fluctuations, solvent effects, and entropy contributions, which are not accounted for in standard docking models. Previous research has demonstrated the significance of MD in refining docking predictions and providing a more accurate assessment of host-guest stability in CD-based systems. Future studies should incorporate MD analyses to validate docking results and further enhance our understanding of tetracycline-CD interactions. As a result, the γ-type was the best for Doxycycline with the highest binding energy of - 8.1, and for Minocycline and Tetracycline with a binding energy of - 7.4 compared to α- and β-CD. Furthermore, the poorest host for the formation of the resultant complex was the α-CD cavity.

Keywords: Extraction; Molecular docking; Tetracycline antibiotics; α, β, and γ -cyclodextrin.

Fig. 1

Schematic illustration of molecular docking for a) Minocycline b) Tetracycline c) Doxycycline antibiotics with α, β, and γ-CDs with Mode1.

Fig. 2

Overview of the study on the best result of the complexation of Doxycycline with γ-CD.