Cutibacterium acnes (C. acnes), also named Propionibacterium acnes, is a gram-positive, anaerobic bacterium that resides in sebaceous-rich areas of the skin, such as the face, chest and back (Dréno et al., 2018). C. acnes plays a vital role in maintaining the health of the skin against preventing colonization by pathogenic organisms and breaking down skin oils to release free fatty acids (Yang et al., 2020). However, under dysregulated skin conditions such as increased sebum production and follicular occlusion, it can shift toward a pathogenic state and contribute significantly to acne vulgaris. Acne vulgaris is characterized by excess sebum production, hyperkeratinization, and follicular blockage, creating an anaerobic environment conducive to C. acnes proliferation (Svensson et al., 2018).

As C. acnes proliferates, it can release enzymes like lipases, hyaluronidase and neuraminidase which are essential virulence factors to hydrolyze sebum triglycerides into free fatty acids and glycerol, creating a nutrient-rich and immunologically active environment Tomida et al., 2013. The generated fatty acids not only support bacterial growth but also stimulate local inflammation by activating innate immune responses. In this process, skin acidity is maintained and this functions as a natural barrier from harmful pathogens, providing innate skin immunity (Kim et al., 2020). Structural studies reveal that these lipases (_CAlipase) possess a hydrophobic lid covering the catalytic triad, which plays a key role in substrate binding and enzyme regulation (Kim et al., 2020) Furthermore, C. acnes has ability to form biofilm which can act as protective barriers that increase antibiotic resistance and immune evasion, making acne treatment more difficult (Coenye et al., 2007; Feuillolay et al., 2016).

Traditional therapies targeting C. acnes-related conditions typically involves topical and systemic therapies aimed at reducing bacterial load, minimizing inflammation and follicular blockage. Clindamycin and erythromycin were among the earliest topical antibiotics used. However, widespread use has led to increasing antibiotic resistance (Eady et al., 1989; Dessinioti and Katsambas, 2017; Sharma et al., 2003; Kim et al., 2017). Benzoyl peroxide (BPO) works by releasing oxygen into the pores, creating an anaerobic environment. Due to its oxygen-releasing, anti-inflammatory properties and without inducing resistance, BPO has emerged as a preferred alternative for C. acnes (Dréno, B. 2016; Bowe and Kober, 2014; Sagransky et al., 2009). In addition, photodynamic therapy (PDT) and light-based treatments utilize bacterial porphyrin photosensitization to induce C. acnes death are explored as the therapeutic option (Wan and Lin, 2014; Barroso et al., 2021). Nevertheless, there remains a strong demand for novel, non-antibiotic therapeutic strategies with defined molecular mechanisms to treat C. acne.

Andrographolide is a biologically active diterpene lactone extracted from Andrographis paniculate. It is widely known for its anti-inflammatory, antioxidant, antibacterial, antiviral and anticancer effects (Okhuarobo, et al., 2014; Zhang et al., 2020; Mishra et al., 2007; Shen et al., 2002; Gupta et al., 2017). In recent years, AGP has attracted widespread attention from the scientific community due to its therapeutic potential in modern medicine. AGP has been shown to prevent biofilm formation, which may be effective against a variety of bacteria and pathogens, making AGP have significant antibacterial properties (Zhang et al., 2021). Furthermore, AGP inhibits the NF-κB signaling pathway, a key inflammation regulator, making it a potential candidate for treating acne and other inflammatory diseases (Berk et al., 2022; Hu et al., 2025; Banerjee et al., 2017).

In this present work, AGP and the fusidic acid (FA) (in Figure 1) were chosen as title compounds to evaluate the interaction with lipase of C. acnes (_CAlipase). Analysis of both allyl sucrose ether and ordinary organic solvents can be achieved through the use of quantum chemical computations approaches, we present a brief overview of conceptual DFT analysis (Geerlings and Proft, 2008; Fayet et al., 2009; Chakraborty et al., 2013). The Gaussian 16 program and Gauss view 6.0 software were used in order to construct the most optimal geometrical structure of the chemical that was provided (Gaussian 16, 2016). The DFT approach was used to analyze the compound’s electrical characteristics via the Conceptual Density Functional Theory (Raghavachari, 2000; Kryachko and Ludeña, 2014). The electrostatic potential (ESP) and the electric surface area distribution studies from Multiwfn 3.8, a wavefunction analyzer (Lu and Chen, 2012a). To further explore noncovalent interactions, the Independent Gradient Model based on Hirshfeld partitioning (IGMH) was utilized (Lu and Chen, 2022), revealing specific van der Waals and hydrogen-bonding interactions between AGP and CAlipase. The analysis suggests that AGP has a strong binding affinity toward the active site of the enzyme, potentially obstructing substrate access and attenuating lipase activity. Dimethyl sulfoxide (DMSO) was used as a solvent due to its laboratory and industrial applications as solvents for many gases, synthetic fibres and natural products (Nasidi et al., 2024). Our findings highlight the potential of AGP as a non-antibiotic lipase inhibitor targeting C. acnes, providing new mechanistic insights into its antibacterial and anti-inflammatory action. This approach represents a novel application of traditional herbal medicine in dermatology, emphasizing structure-based drug design through quantum chemical descriptors and interaction modeling. By identifying molecular interactions at the electronic level, this work offers a new perspective for targeting virulence factors such as lipases in C. acnes, paving the way for future development of selective and resistance-free acne therapeutics.

The molecular structure computations were conducted using the Gaussian 16 program. The theoretical approach employed the M062X/def2TZVP method for geometry optimization of AGP and FA, with the IGMH portion utilizing the 6-311++g (d,p) basis set and the B3LYP functional (Świderski, et al., 2013). SMD (Solvent Model Density) (Dalessandro and Pliego Jr, 2018) was applied as the solvent model. Graphs were generated using Gaussian View 6 and Origin 8 software. The energy gap of the title compounds was determined by analyzing Frontier Molecular Orbitals (FMO). Wavefunction analysis was performed using the Multiwfn 3.8 program, which provided the wavefunction files and evaluated the electrostatic potential and electric distribution. Isosurface maps were created using VMD 1.9.3 (Humphrey et al., 1996) in conjunction with the output files from Multiwfn. Quantitative studies of the electrostatic potential on the van der Waals (vdW) surface were carried out in Multiwfn with a grid spacing of 0.15 bohr. The IGMH method was particularly useful for gaining insights into intermolecular interactions between specific amino acids and the title compounds.

Molecular docking was employed to predict the combined mode of AGP and FA with the protein 6KHW. As previously reported (Li, et al., 2021), the structure of 6KHW was retrieved from the Protein Data Bank (https://www.rcsb.org/). Subsequently, AGP and FA were downloaded from the PubChem database (https://pubchem.ncbi.nlm.nih.gov/) in sdf format. All molecular docking between title molecules and core targets were performed using Autodock Vina software (Version 1.5.7) (Trott and Olson, 2010; Morris et al., 2009). The docking results of given substrates at the active site of 6KHM were further examined by the LIGPLOT program (Laskowski and Swindells, 2011), which can generate schematic diagrams of protein-ligand interactions.

Molecular dynamics (MD) simulations were performed to monitor the motions of macromolecules over time (Hildebrand et al., 2019). The protein-ligand complex was simulated using the CHARMM36 force field, implemented with GROMACS 2018.2 software. To generate the topology of the compounds and assign force-field parameters, the CGenFF server was utilized. The protein was placed in a cubic box of dimensions (0.8 × 0.8 × 0.8 Å), filled with TIP3P water molecules, and neutralized with Na⁺ and Cl⁻ ions. The system underwent energy minimization via steepest descent minimization. Subsequently, thermalization was achieved by maintaining the system temperature under the NVT (Number of particles, Volume, and Temperature) ensemble, followed by pressure equilibration under the NPT (Number of particles, Pressure, and Temperature) ensemble. Finally, position restraints were released, and a production MD simulation was run for 100 ns to collect dynamic data (Hou et al., 2023).

C. acnes is a bacterium with dual roles as both a commensal organism and an opportunistic pathogen. While it plays a protective role on the skin, under certain conditions, it contributes to the pathogenesis of acne and other infections. Treatment strategies for C. acnes related conditions vary depending on the severity and type of infection, but typically involve a combination of antimicrobial, anti-inflammatory and sebum-reducing therapies.

According to the past researches, lipases of C. acnes hydrolyze sebum triglycerides into free fatty acids and glycerol, which can provide a nutrient source for bacterial growth. And the crystal structure of lipase has shown it features a hydrophobic lid that covers its active site, which opens to interact with lipid substrates.

AGP, a labdane diterpenoid lactone extracted from Andrographis paniculata, has attracted growing interest due to its broad-spectrum pharmacological activities, including anti-inflammatory, antibacterial. Despite this, its specific interaction with _CAlipase has not been thoroughly investigated.

In this work, we utilized computational methods based on molecular structure obtained the chemistry parameters and molecular dynamics results. We compared AGP and FA, which works well against C. acnes s in a clinical setting, and reported that AGP has a certain effective interaction with _CAlipase than FA. Through our computational analyses, we observed that AGP exhibits a notably stronger and more specific interaction with _CAlipase compared to FA, suggesting a potentially more effective inhibitory mechanism.

These findings position AGP as a promising candidate for further development as a therapeutic agent targeting C. acnes. Importantly, our results open the door to more detailed mechanistic studies. Future work we could investigate the precise mechanism by whether it inhibits the growth of C. acnes directly or influences biofilm formation of C. acnes at the genetic level. This study also sets the stage for structure activity relationship analyses and the design of AGP derivatives with enhanced binding affinity and specificity for _CA lipase. The insights gained from this work contribute to a growing body of research exploring small-molecule inhibitors against bacterial lipases and support the use of in silico approaches as powerful tools in drug discovery and development. It should be emphasized that while our computational results are promising, additional research and comprehensive clinical studies are still required to completely evaluate their safety, effectiveness, and potential applications in management.