Molecular docking, molecular dynamics, MM/PBSA approaches and bioactivity studies of nepetanudoside B isolated from endemic Nepeta aristata

Abstract

Nepetanudoside B (NNB) was isolated from aerial parts of endemic Nepeta aristata crude extract (CH₃OH-CHCl₃) using silica gel (n-hexane, methanol, ethyl acetate, and dichlorometane, respectively) and sephadex LH-20 (65% Methanol-35% Chloroform) column chromatographies. Preparative-HPLC was used to purify NNB after activity-guided isolation of methanol sub-fractions with enzyme inhibitory and DNA protective properties. The NNB was determined using ¹H,¹³C, COSY, HSQC, HMBC, and LC-MS/MS. The study compared the effects of NNB with conventional drugs in terms of its ability to inhibit enzymes such as urease, α-amylase, carbonic anhydrase (CA), lipase, α-glucosidase, and tyrosinase, as well as its ability to protect DNA. Enzyme kinetic and molecular docking were also used to evaluate this. NNB exhibited the best inhibitory activity on urease (1.28 ± 0.00 µg/mL), lipase (5.83 ± 0.10 µg/mL), BChE (3.73 ± 0.46 µg/mL), tyrosinase (7.39 ± 0.00 µg/mL), α-glucosidase (10.95 ± 0.00 µg/mL), α-amylase (22.11 ± 1.03 µg/mL) and AChE (25.68 ± 3.32 µg/mL), respectively. NNB has higher MolDock scores with binding energy in α-glucosidase (-233) and BChE (-8.90 kcal/mol). In enzyme kinetics studies, it was determined that urease, AChE, α-glucosidase, lipase, and CA were non-competitive , while BChE and tyrosinase were competitive inhibition mechanisms. Their K_i values were calculated as 0.09, 0.24, 0.09, 0.10, 0.08, 0.05, and 0.07 mM, respectively. Molecular dynamics simulation studies were performed for the interactions of NNB-BChE with MM/PBSA binding free energey RMSD, RMSF, Rg, SASA, and also the number of hydrogen bonds was calculated. The suitability and effectiveness of NNB have been proven in the food and pharmaceutical industries. The NNB molecule may lead to development studies as a BChE inhibitor.

Communicated by Ramaswamy H. Sarma

Keywords:

• Nepetanudoside B
• enzyme inhibition
• molecular docking
• enzyme kinetic
• DNA protection

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

We acknowledge the financial support provided by TUBITAK (The Scientific and Technological Research Council of Turkey) (Project Number: 119Z442).