Molecular docking/dynamics simulations, MEP analysis, bioisosteric replacement and ADME/T prediction for identification of dual targets inhibitors of Parkinson's disease with novel scaffold

Isolation, characterization and evaluation of oxypeucedanin and osthol from local endemic Prangos aricakensis Behçet and Yapar root as antioxidant, enzyme inhibitory, antibacterial and DNA protection: molecular docking and DFT approaches

Prangos species were previously used against many disorders due to their chemical component. Prangos aricakensis Behçet & Yapar is a newly discovered local endemic species in Turkey's eastern region, and there is no research on P. aricakensis in the literature. In this work, oxypeucedanin and osthol molecules have been isolated from the root part of P. aricakensis for the first time. Oxypeucedanin and osthol structures were elucidated by 1D and 2D NMR analysis. For the bioactivities determination, antioxidant (DPPH· and ABTS·+ scavenging), enzyme inhibition (AChE, BChE, tyrosinase, and urease), antibacterial and DNA protection activity studies were applied for both molecules and compared with standard drug molecules, after applying enzyme kinetic assays and in silico approaches to clarify the mechanism of action for both molecules with enzymes, using molecular docking and density functional theory (DFT). Oxypeucedanin (2.19 ± 0.38 µg/mL) and osthol (4.57 ± 1.28 µg/mL) exhibited better activity than standards in DPPH∙ scavenging activity. Osthol (11.76 ± 0.59 µg/mL) showed a better tyrosinase inhibition effect than kojic acid (12.82 ± 0.91 µg/mL), and oxypeucedanin (3.03 ± 0.01 µg/mL) showed better urease inhibition effect than thiourea (5.37 ± 1.86 µg/mL). Our results showed that the osthol molecule was an excellent skin protective agent while the oxypeucedanin molecule could be a remarkable antiulcer agent. Therefore, although this study is the first in its field, it remained in the in vitro and in silico stages and is thought to pave the way for in vivo studies in the future.Communicated by Ramaswamy H. Sarma.

In silico bioprospecting of receptors for Doderlin: an antimicrobial peptide isolated from Lactobacillus acidophilus

The emergence of resistant bacteria strains against traditional antibiotics and treatments increases each year. Doderlin is a cationic and amphiphilic peptide active against gram-positive, negative and yeast stains. The aim of the present work was prospect potentials receptors associated of antimicrobial activity of Doderlin using in silico bioinformatics tools. To search for potential targets of Doderlin, PharmMapper software was used. Molecular docking between Doderlin and the receptor was performed by PatchDock. Additional interaction and ligand site prediction for each receptor was performed by I-TASSER software. Those PDB Id, 1XDJ (score: 11,746), 1JMH (score: 11,046), 1YR3 (score: 10,578), 1NG3 (score: 10,082) showed highest dock score. Doderlin was found to predicted/real sites co-localize with 1XDJ and 1JMH, enzymes accountable for nitrogenic bases synthesis. The resulting receptor bioprospecting is highly correlated and suggests that Doderlin might act by interfering with DNA metabolism/production of bacteria, altering microorganism homeostasis and growth impairment.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-023-00149-1.