Traditional Chinese medicine Luo Tong Formula attenuates retinal injury in experimental diabetic retinopathy via modulation of DNA methylation: In vivo experiment integrated with molecular docking, ADMET assessment, and molecular dynamics simulation

Abstract

Background

Diabetic retinopathy (DR) is a leading cause of blindness in the adult population. Luo-Tong formula (LTF), a traditional Chinese medicine prescription, has been frequently employed in the treatment of DR. However, the ability of LTF to prevent retinal injury and disease progression, as well as potential mechanisms, remain unknown.

Objectives

To investigate the effect of LTF in alleviating DR and uncover the potential hub targets.

Methods

An experimental DR model was established to assess the effect of LTF and elucidate its underlying mechanism. Retinal thickness, morphological changes of retinal microvessels, as well as the numbers of endothelial cells and pericyte ghosts, were examined. Methylation status was evaluated with methylated DNA immunoprecipitation processing. Bioinformatic analysis of array results was used to screen hub genes. Interactions between potential targets and active compounds were assessed by molecular docking. ADMET analysis was used to evaluate drug-likeness characteristics and toxicity. Molecular dynamics (MD) simulation and MMGBSA calculation of binding free energies were conducted for the optimal core active compound-target complexes obtained by molecular docking.

Results

The administration of LTF demonstrated improvements in glycolipid metabolic disorder and a significant reduction in oxidative stress and inflammation in DR rats. Additionally, LTF exhibited protective properties against retinal injury. A quantitative analysis of DNA methylation indicated alterations in the composition and quantity of methylated genes following LTF intervention. Four important functional epigenetic modules and six hub genes (Fgfr1, TOX3, Rps9, Rps15, Rpl7, Mrpl36) were identified. Molecular docking identified ten compounds of LTF and 23 binding complexes with lower binding energy (< 7 kcal/mol), while five compounds were excluded after ADMET analysis. Two complexes (Aloe-emodin-TOX3, Panaxatriol-Fgfr1) with the lowest binding energy were further chosen for MD simulation and both complexes have stable and satisfactory binding systems. Finally, MMGBSA calculation of binding free energies revealed that Panaxatriol-Fgfr1 complex was identified as the drug-target candidate in the pharmacological treatment of DR.

Conclusions

LTF has demonstrated efficacy for DR, and its mechanisms may be associated with the regulation of DNA methylation. Panaxatriol-Fgfr1 complex was identified as the drug-target candidate. Epigenetic modifications following LTF intervention have been implicated in the pathogenesis of DR and offer potential therapeutic opportunities for early diagnosis and treatment in the future.