Research Article

In Silico Evaluation of Feasible Flavonoid-Based MURF-1 Inhibition for Sarcopenia Treatment

Ahn Ji Myung^1,2, Lee Sangmoon^1,2, Park Ho Je^2,3, Sanghyun Ahn²

Abstract

Background/Objectives: Sarcopenia is an age-related syndrome characterized by progressive loss of skeletal muscle mass and strength. Muscle RING Finger-1 (MURF-1), an E3 ubiquitin ligase, plays a pivotal role in muscle protein degradation and is considered a major driver of sarcopenia-associated muscle atrophy. This study aimed to investigate the therapeutic potential of flavonoid-based compounds as inhibitors of MURF-1 activity.

Methods: A variety of flavonoid subclasses—including flavanol, flavanone, flavone, isoflavone, flavonol, and antho-cyanidin—were selected and their 3D structures were generated using ChemDraw, followed by energy mini-mization. Molecular docking simulations were performed using AutoDock to assess binding interactions and affinity with MURF-1. Flavonoid compounds were ranked based on predicted inhibitory potential. A com-prehensive literature review was also conducted through PubMed and Google Scholar to evaluate the relevance of flavonoid–MURF-1 interactions in sarcopenia.

Results: Docking analysis revealed that several flavonoid compounds exhibited strong binding affinity to the active site of MURF-1, suggesting potential inhibitory effects. Among them, flavonols and isoflavones showed particu-larly favorable interaction energies. These results, combined with literature data, highlight the possibility that flavonoids may downregulate MURF-1 expression or activity, contributing to preservation of muscle mass and function

Conclusions: Flavonoid-based compounds show promise as candidate therapeutic agents for suppressing MURF-1–mediated muscle atrophy. These findings provide a foundation for developing novel strategies targeting sarcopenia through nutraceutical or pharmacological interventions.

Keywords

Sarcopenia, MURF-1, Flavonoids, Molecular docking, In silico analysis

Introduction

Sarcopenia is an age-related condition characterized by a progressive decline in muscle mass and function, and is a major contributor to reduced quality of life, falls, and fractures in the elderly population [1]. This condition arises from an imbalance between muscle protein synthesis and degradation. Muscle RING Finger-1 (MURF-1) has been identified as a key factor promoting muscle atrophy [2]. As an E3 ubiquitin ligase, MURF-1 ubiquitinates contractile proteins such as myosin heavy chain (MHC), targeting them for proteasomal degradation [3]. This mechanism accelerates muscle protein breakdown, ultimately leading to muscle wasting.

Current treatments for sarcopenia—such as protein synthesis stimulators, hormone therapy, and exercise interventions—remain limited in their efficacy [4]. Consequently, there is growing interest in developing novel, natural compound-based therapeutic strategies to prevent or treat this condition [5, 6]. Flavonoids, a class of naturally occurring compounds with antioxidant, anti-inflammatory, and antimicrobial properties, have attracted attention for their potential to improve muscle health [7]. Recent studies suggest that certain flavonoids may suppress MURF-1 expression and mitigate muscle atrophy.

In silico approaches have emerged as powerful tools to complement experimental methods and enable efficient screening of drug candidates [8]. Structure-based drug design and molecular docking simulations enable the prediction of novel compounds, significantly reducing the time and cost required for experimental validation. While natural product research often faces challenges due to the structural complexity and lengthy evaluation processes, in silico methods can rapidly predict target binding potential and identify promising candidates for further study. Such approaches offer notable advantages in the investigation of complex, multifactorial diseases such as sarcopenia.

This study evaluates the potential of flavonoid compounds as MURF-1 inhibitors using in silico analysis and establishes a framework for identifying new therapeutic strategies for sarcopenia.

Materials & Methods

Three-dimensional modeling of flavonoid compounds 

A set of flavonoid compounds—including flavanol, flavanone, flavone, isoflavone, flavonol, and anthocyanidin—was selected, and optimized three-dimensional (3D) structures were generated for each. Chemical structures were initially drawn in two dimensions (2D) using ChemDraw software. These structures were then converted into 3D models using Avogadro or Chem3D software, followed by energy minimization to ensure accurate representation of molecular geometry and charge distribution. The resulting optimized 3D structures were saved in Protein Data Bank (PDB) format for subsequent analysis.

Preparation of MURF-1 protein structure

The 3D structure of Muscle RING Finger-1 (MURF-1) was predicted using AlphaFold2. The protein structure was prepared for docking using AutoDockTools, which included the addition of hydrogen atoms and charge assignment. Potential ligand-binding sites were identified, and the predicted active site region was defined as the docking target.

Molecular docking analysis using AutoDock Vina

Molecular docking simulations were performed using AutoDock Vina to predict the binding affinity of each flavonoid compound to MURF-1. The docking procedure consisted of the following steps:

First, grid box setup: The docking grid was positioned around the predicted active site of MURF-1 to encompass the potential binding pocket.

Second, docking execution: AutoDock Vina was used to simulate the possible orientations and conformations of each flavonoid within the defined grid, allowing for translational, rotational, and conformational flexibility.

Third, binding energy calculation: Binding affinities were expressed as docking scores (kcal/mol), with lower values indicating stronger predicted interactions be-tween the ligand and MURF-1.

Last, result visualization and analysis: Docking results were visualized using Au-toDockTools to assess the binding poses and interaction patterns for each compound. Compounds with higher predicted binding affinity were considered potential can-didates for further investigation as MURF-1 inhibitors in sarcopenia therapy.

Results

2D and 3D structure modeling of flavonoid compounds 

A total of eight representative flavonoid compounds were designed in both two-dimensional (2D) and three-dimensional (3D) formats using ChemDraw and Chem3D software (Figure 1). The selected compounds represent major subclasses of flavonoids, including flavone, flavanone, flavanol, isoflavone, flavonol, and anthocyanidin. Figure 1 illustrates the 2D chemical structures, while Figure 2 presents the corresponding energy-minimized 3D structures generated for subsequent molecular docking analysis.

Figure 1. Chemical structures of representative flavonoid compounds drawn using ChemDraw. Structures include: (A) 2-Phenylchromen-4-one (Flavone), (B) 3-Hydroxy-2-phenyl-4H-chromen-4-one (Flavonol), (C) 2,3-Dihydro-2-phenyl-4H-chromen-4-one (Flavanone), (D) 3-Hydroxy-2-(3-hydroxyphenyl)-4H-chromen-4-one (Flavanonol), (E) 2-Phenylchroman-3-ol (Flavanol), (F) 3,4,5-Trihydroxy-1,8-bis[(2R,3R)-3,5,7-trihydroxy-3,4-dihydro-2H-1-benzopyran-2-yl]-6H-benzo[7]annulen-6-one (Theaflavin), (G) 2-phenyl-3,4-dihydro-2H-chromene (Anthocyanidin derivative), (H) 7-Hydroxy-3-(4-hydroxyphenyl)-4H-chromen-4-one (Isoflavone derivative).

Figure 2. Three-dimensional (3D) molecular structures of representative flavonoid compounds were generated for molecular docking analysis. Structures were constructed using ChemDraw and energy-minimized using Chem3D/Avogadro software prior to docking simulations with the MURF-1 protein. Displayed compounds include: flavanol, flavanone, flavone, isoflavone, flavonol, and anthocyanidin derivatives, visualized in ball-and-stick representation to highlight atomic composition (carbon: grey, oxygen: red, hydrogen: white).

In silico prediction of binding affinity between MURF-1 and flavonoids

The predicted binding affinities of each flavonoid compound to the MURF-1 protein are as follows: plibon, −6.796 kcal/mol; flavonol, −6.923 kcal/mol; flavanone, −7.193 kcal/mol; flavadonol, −7.228 kcal/mol; flavanol, −6.943 kcal/mol; theaflavin, −8.039 kcal/mol; anthocyanin, −6.787 kcal/mol; and isoflavone, −7.070 kcal/mol.

Theaflavin exhibited the strongest predicted binding affinity (−8.039 kcal/mol), indicating superior interaction with MURF-1 compared to the other flavonoids. Anthocyanin showed the weakest binding affinity (−6.787 kcal/mol), reflecting lower binding stability. All compounds demonstrated negative binding energy values, which indicates the potential to form stable complexes with MURF-1.

Figure 3. Binding affinity prediction of energy-minimized flavonoid structures with MURF-1 protein using AutoDock Vina. Red circles indicate the binding sites of each flavonoid ligand on the MURF-1 surface. Discussions 

Discussion

This study evaluated the binding potential of various flavonoid compounds to the MURF-1 protein using in silico molecular docking analysis. All tested compounds exhibited negative binding affinity values, indicating potential to form stable complexes with MURF-1. Theaflavin showed the strongest predicted binding affinity (−8.039 kcal/mol), identifying it as a lead candidate for MURF-1 inhibition. Anthocyanin displayed the weakest binding affinity (−6.787 kcal/mol), which may necessitate structural modification or the development of derivatives.

Flavonoids can vary considerably in their interaction with protein binding sites due to structural diversity [9]. The trends observed in this study are consistent with previous reports, highlighting the influence of the number and position of hydroxyl groups, aromatic ring planarity, and glycosidic substitutions on binding affinity[10]. In particular, theaflavin, with its extended aromatic framework and multiple hydroxyl substitutions, may achieve high affinity for MURF-1 by forming strong hydrogen bonds and π–π stacking interactions within the active site.

MURF-1, an E3 ubiquitin ligase, plays a central role in muscle protein degradation and is a key pathological factor in sarcopenia and other muscle-wasting disorders [11]. Previous studies have demonstrated that certain flavonoids modulate the ubiquitin–proteasome system to attenuate muscle atrophy [12]. For example, quercetin has been shown to suppress the expression of MuRF-1 and Atrogin-1 in both high-fat diet-induced obesity models and tail suspension models, thereby alleviating muscle mass loss. Similarly, (−)-epicatechin has been reported to inhibit FoxO1A and MuRF-1, leading to improvements in muscle atrophy. Other flavonoids, such as baicalin and genkwanin, have been reported to suppress MuRF-1–related proteolytic pathways while promoting muscle protein synthesis pathways [13,14].

Meta-analyses have further demonstrated that flavonoid intake improves musculoskeletal health markers in middle-aged and older adults, with increases in muscle mass and improvements in functional performance measures, such as the Timed-Up and Go test, in patients with sarcopenia [15,16,17]. These findings suggest that flavonoids not only suppress muscle atrophy but may also help preserve or enhance muscle function [18,19,20].

This study is limited to in silico analysis. Further evaluation of absorption, distribution, metabolism, and excretion (ADME) profiles, as well as cytotoxicity, is required. High binding affinity does not always correlate with biological activity; therefore, validation using in vitro cell models and in vivo animal studies is necessary to ensure accurate interpretation. Future research should include structure-based optimization based on docking results to enhance the inhibitory potential of flavonoid derivatives against MURF-1.

Conclusion

In conclusion, this study demonstrates a close relationship between flavonoid structural characteristics and binding affinity for MURF-1, highlighting theaflavin as a particularly promising candidate for sarcopenia therapy. Given their multi-target regulatory properties, low toxicity, and high safety profile, flavonoid-based natural compounds offer considerable potential for the development of preventive and therapeutic strategies not only for sarcopenia but also for a range of other muscle disorders.

Acknowledgments

This research was supported by Research Foundation of Seolmyung Keoran Medicine

Conflict of Interest

The authors have no conflicts of interest to declare and agreed to the published version of the manuscript.

Author Contributions

Lee Sagmoon and Park Ho Ge performed molecular docking analysis using AutoDock Vina. Ahn Ji Myung and Sanghyun Ahn participated in the study design and contributed to writing of the manuscript.

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