Journal of Biomedical Engineering and Biosciences (JBEB)

ISSN: 2564-4998

1. Introduction

Molecular docking is a powerful tool that helps optimize resources in drug discovery and the elucidation of drug–target interactions, as well as in studying the effects of certain molecules, such as nanoparticles, on these interactions. This method can reduce the number of required experiments and provide a rational approach prior to conducting in vitro or in vivo assays [1]. Moreover, in the veterinary field, in silico assays are less commonly used compared to human medicine possibly due to a lack of awareness or the lower number of computational chemists working in this area. However, in the present work, this tool is employed to evaluate the effect of a liposome fragment on the interaction between a triazole compound and a Chlamydophila abortus target. This pathogen is an obligate intracellular bacterium, for which the only effective treatment is the prophylactic use of the bacteriostatic antibiotic tetracycline. However, this drug has limited efficacy and carries the risk of promoting bacterial resistance [2].

Liposomes are well-known nanoscale drug delivery systems composed of a lipid bilayer that mimics the structure of cellular membranes. They are easy to prepare and exhibit high biocompatibility. Drug candidates encapsulated in liposomes have demonstrated reduced toxicity and prolonged therapeutic effects [3].

Lecithin derived from soybeans has shown promising potential in drug delivery, enabling efficient encapsulation, controlled release, and successful transport of therapeutic agents to intracellular targets. Recent applications of soy lecithin-derived liposomes have focused on cancer treatment, brain targeting, and vaccinology [4].

In cancer therapy, liposomes have been successfully employed to deliver the anticancer drug paclitaxel, enabling sustained release for up to 96 hours. They have also demonstrated excellent biocompatibility as nanocarriers while reducing the drug’s inherent toxicity [5]. Another example of liposome efficacy is observed in dermal drug delivery, where liposome application enhanced wound healing in rats through free radical scavenging and other medicinal properties [6].

A review of soy lecithin-derived liposomal delivery systems explores in greater detail the medicinal potential of lecithin, highlighting its antimicrobial, antiprotozoal, and antimalarial activities, among others. Ligand-targeted liposomes have also been extensively studied, with several authors reporting high specificity in targeting diseased cells [7–9].

1,2,3-Triazoles are five-membered heterocyclic rings composed of two carbon atoms and three nitrogen atoms [10] and have long served as a source of inspiration in drug development. Due to their unique structural properties, synthetic versatility, and broad pharmacological potential, triazoles have emerged as a critical scaffold in medicinal chemistry. They exhibit enormous potential as pharmacophores, bio-isosteres, or structural platforms for the development of drugs targeting a variety of diseases [11].

1,2,3-Triazole derivatives display diverse pharmacological activities, including anti-tubercular [12], anti-fungal [13], anti-tumor [14], and anti-bacterial effects [15, 16], making them ideal candidates for the development of new drugs against Chlamydophila abortus.

Additionally, triazoles have demonstrated anticarcinogenic potential, and hybrid tetrazole–1,2,3-triazole derivatives have been investigated as protein inhibitors in the treatment of SARS-CoV-2 [17].

The wide range of applications of triazoles in drug discovery highlights their adaptability and ongoing potential for innovative uses in medicinal chemistry and in silico assays.

3. Computational Methods

Based on the state-of-the-art in computational chemistry, the current work was conducted using molecular docking to evaluate the effect of a liposome fragment on triazole-target interactions, considering as the target a protein (deubiquitinase of Chlamydia: ChlaDUB) present in Chlamydophila abortus, which was downloaded from the protein data bank with the PDB code: 6GZU [18]. The evaluated triazole, tetracycline, and liposome fragment were modeled with Avogadro software [19], and the ligand-target interactions were analyzed with the Molegro Virtual Docker (MVD) package [20].

Docking assays were performed using MolDock Scoring Function. With a population size of 50, and a grid resolution of 0.3.

To validate the method, co-cristalized ligand was docked, obtaining a RMSD value of 1.952 Å.

Our main parameters to measure the validity of the experiment are:

• Ligand Efficiency (LE): This measures the binding free energy per non-hydrogen atom in a ligand. It is widely used in drug discovery to compare compounds of different sizes [21]. Its formula is:
  

  (1)
  
  

  Where ΔG is the free Gibbs energy or the Energy docking value, split in de number of heavy atoms (non-hydrogen) of the ligand (N).

  The highest value as a number corresponds to the best result (more negative values means the better ligand).

• Energy: In molecular docking, the total estimated energy from a scoring function represents the stability of the ligand-protein interaction [22]. As for its values, the more negative the number, the better.
• Van der Waals energy (VdW): This are dispersion (London) forces that model attraction and repulsion between non-bonded atoms. When atoms are too close, strong repulsion arises, which defines the Van der Waals radius. These interactions are essential for the geometric complementarity between ligand and protein [23]. Its values, like energy, should be preferably on the negative numbers.

4. Results and discussion

To evaluate the effect of the liposome on triazole-target interactions, four types of interactions were proposed:

1. When the triazole (1A) and control drug tetracyclines (TC) interact alone with the bacterium target.
2. When the liposome fragment interacts alone with the target.
3. When 1A interacts first with the target, and then the liposome (Lip) fragment interacts with the triazole-target complex, as well with TC.
4. When first the liposome fragment interacts with the target, and then 1A interacts with the liposome-target complex, as well with TC.

In Table 1, the results have been filtered by the lowest ligand efficiency (LE) value, as this parameter is considered the most relevant for identifying the best candidate. Ligand efficiency allows for comparison of the average binding energy per heavy atom (i.e., non-hydrogen atoms) in the molecule. It quantifies how effectively a molecule uses its structural features to interact with its target.

The energy values reflect the stability of the molecular complex and its ability to react or interact under various conditions. Specifically, the Van der Waals (VdW) energy describes the attractive or repulsive forces between atoms that are not covalently bonded. This energy represents the contribution of non-bonded interactions to the overall binding affinity.

Table 1. Comparison of Energy and Ligand Efficiency (LE) Among Different Types of Interactionsm in kcal/mol

Type	Energy	LE	VdW
1 – (1A)	-195.57	-5.93	-35.99
1 – (TC)	-139.02	-4.34	92.32
2 – (Lip)	-112.70	-2.13	421.86
3 – (1A-Lip)	-129.74	-2.45	-16.82
3 – (TC-Lip)	-144.71	-2.73	31.75
4 – (Lip-1A)	-116.30	-3.52	-14.17
4 – (Lip-TC)	-51.25	-1.60	11.73

LE = Ligand Efficiency, VdW = Van der Waals Energy

The most favorable interactions occur when 1A (see Figure 1A) freely interacts with the selected target, with a LE of -5.93 kcal/mol, compared to the free interaction of the liposome fragment (-2.13 kcal/mol, see Figure 1B). The difference in LE is 3.8 kcal/mol. However, when the liposome binds first and 1A is subsequently docked into the protein–liposome complex, the LE is higher (-3.52 kcal/mol) than that of the free liposome, with a difference of 1.39 kcal/mol. This suggests a possible controlled release of 1A in the presence of the liposome. In this scenario, binding occurs within a lipidic environment; however, the protein exhibits both hydrophilic and hydrophobic regions, which facilitate liposome docking and enhance the interaction (see Figure 2). The liposome interacts with both the triazole compound and the protein, contributing to increased stability of the docking complex.

All possible interactions were evaluated, with particular emphasis on those involving lecithin/liposomes and triazoles, assessed both as cofactors and as ligands (see Figures 3 and 4).

No hydrogen bond interactions were observed with the 1A triazole ligand; however, electrostatic and steric interactions were identified (see Figure 5). It is important to note that these electrostatic and steric interactions contribute only to repulsive forces between the target and the ligand.

The present results indicate reduced interaction when the liposome enters the system first, as compared to free drug entry into the target. However, this behavior may suggest that the use of liposomes promotes a slower, more controlled drug release, consistent with a sustained delivery mechanism.

5. Conclusion

Given the key characteristics of encapsulated liposomes, combining this delivery system with molecular docking represents one of the most promising strategies currently available against Chlamydophila abortus. The intracellular nature of this bacterium necessitates a sustained release of the drug, as well as enhanced cellular uptake to effectively reach its site of infection. Ligand efficiency analysis supports the potential of liposomes to facilitate controlled drug delivery.

Furthermore, 1,2,3-triazoles exhibit broad-spectrum antibacterial activity, and in silico modeling enables the rational design of these compounds for optimized interaction with the ChlaDUB protein. With continued research and computational modeling, novel drug candidates may emerge within the field of medicinal chemistry as viable therapeutic options.

While in silico approaches such as molecular docking provide a rapid and cost-effective strategy for identifying potential drug candidates, it is important to consider that these methods represent an initial approximation. They offer valuable insights into possible ligand–target interactions, serving as a guiding tool for prioritizing compounds for further study. However, given the inherent simplifications involved—such as the use of static models and approximated scoring functions—experimental validation remains a key step in confirming the biological relevance of the predicted interactions.

To this end, the next phase of the project will involve in vitro assays using the formulated liposome fragments to evaluate their antimicrobial activity against C. abortus. These experiments will allow us to validate the in silico findings and determine whether the predicted interactions translate into measurable biological efficacy. By integrating computational and experimental approaches, we aim to enhance the robustness of our results and assess the potential of the liposomal formulation as a viable therapeutic strategy.

7. Acknowledgments

The first author was funded by the Mexican government through a scholarship program from SECIHTI (Secretaría de Ciencia, Humanidades, Tecnología e Innovación). We acknowledge to Laboratorio Nacional de Caracterización de Propiedades Fisicoquímicas y Estructura Molecular (UG-UAA-CONACYT, Project: 123732) for the computing time provided.

The first author would like to thank Dr. M. Alvarado Alvarez for her contributions and ideas for this paper.

References