In vitro and in silico evaluation of the design of nano-phyto-drug candidate for oral use against Staphylococcus aureus Yasemin Budama-Kilinc 1,2 , Bahar Gok 3 , Cigdem Cetin Aluc 3,4 and Serda Kecel-Gunduz 5 1 Bioengineering Department, Yildiz Technical University, Istanbul, Turkey 2 Health Biotechnology Joint Research and Application Center of Excellence, Istanbul, Turkey 3 Graduate School of Natural and Applied Science, Yildiz Technical University, Istanbul, Turkey 4 Abdi Ibrahim Production Facilities, Abdi Ibrahim Pharmaceuticals, Istanbul, Turkey 5 Physics Department, Istanbul University, Istanbul, Turkey ABSTRACT Onopordum acanthium is a medicinal plant with many important properties, such as antibacterial, anticancer, and anti-hypotensive properties. Although various studies reported the biological activities of O. acanthium, there is no study on its nano- phyto-drug formulation. The aim of this study is to develop a candidate nano-drug based on phytotherapeutic constituents and evaluate its efficiency in vitro and in silico. In this context, poly (lactic-co-glycolic acid) (PLGA) nanoparticles (NPs) of O. acanthium extract (OAE) were synthesized and characterized. It was determined that the average particle size of OAE-PLGA-NPs was 214.9 ± 6.77 nm, and the zeta potential was -8.03 ± 0.85 mV, and PdI value was 0.064 ± 0.013. The encapsulation efficiency of OAE-PLGA-NPs was calculated as 91%, and the loading capacity as 75.83%. The in vitro drug release study showed that OAE was released from the PLGA NPs with 99.39% over the 6 days. Furthermore, the mutagenic and cytotoxic activity of free OAE and OAE-PLGA-NPs were evaluated by the Ames test and MTT test, respectively. Although 0.75 and 0.37 mg/mL free OAE concentrations caused both frameshift mutation and base pair substitution (p < 0.05), the administered OAE–PLGA NP concentrations were not mutagenic. It was determined with the MTT analysis that the doses of 0.75 and 1.5 mg/mL of free OAE had a cytotoxic effect on the L929 fibroblast cell line (p < 0.05), and OAE-PLGA-NPs had no cytotoxic effect. Moreover, the interaction between the OAE and S. aureus was also investigated using the molecular docking analysis method. The molecular docking and molecular dynamics (MD) results were implemented to elucidate the S. aureus MurE inhibition potential of OAE. It was shown that quercetin in the OAE content interacted significantly with the substantial residues in the catalytic pocket of the S. aureus MurE enzyme, and quercetin performed four hydrogen bond interactions corresponding to a low binding energy of -6.77 kcal/mol with catalytic pocket binding residues, which are crucial for the inhibition mechanism of S. aureus MurE. Finally, the bacterial inhibition values of free OAE and OAE–PLGA NPs were determined against S. aureus using a microdilution method. The antibacterial results showed that the inhibition value of the OAE–PLGA NPs was 69%. In conclusion, from the in vitro and in silico results of the nano-sized OAE-PLGA NP formulation How to cite this article Budama-Kilinc Y, Gok B, Cetin Aluc C, Kecel-Gunduz S. 2023. In vitro and in silico evaluation of the design of nano-phyto-drug candidate for oral use against Staphylococcus aureus. PeerJ 11:e15523 DOI 10.7717/peerj.15523 Submitted 16 October 2022 Accepted 17 May 2023 Published 8 June 2023 Corresponding author Yasemin Budama-Kilinc, yaseminbudama@gmail.com Academic editor Sonia Oliveira Additional Information and Declarations can be found on page 19 DOI 10.7717/peerj.15523 Copyright 2023 Budama-Kilinc et al. Distributed under Creative Commons CC-BY 4.0