Molecular Docking and MD simulations
Molecular docking and MD simulations are important techniques in the computational drug design process, collectively offering a comprehensive understanding of drug-target interactions. Molecular docking, by predicting the binding modes and affinities of potential drug candidates with target proteins, facilitates the identification of promising lead compounds. In contrast, MD simulations are used for exploring the dynamic behavior of these interactions, offering insights into the stability and conformational changes of drug-protein complexes over time. These combined approaches not only aid in optimizing drug candidates for enhanced binding but also accelerate the drug discovery process by reducing the number of costly experimental iterations. Consequently, molecular docking and MD continue to be indispensable tools in modern pharmaceutical research, contributing significantly to the development of innovative therapeutic agents [
22,
44,
45,
46,
47].
It should be highlighted that arylpiperidine and arylpiperazine compounds are heterocyclic structures that possess diverse chemical functionalities, rendering them amenable to molecular modifications for targeted inhibition of TYR. According to Ferro et al. [
19], the incorporation of aryl rings into these heterocyclic frameworks contributes to their binding affinity with the active site of the enzyme. Through systematic structural modifications, these researchers have been able to fine-tune the inhibitory potency and selectivity of these derivatives, enabling the development of lead compounds with enhanced bioactivity and reduced off-target effects. Besides, arylpiperidine and arylpiperazine derivatives exhibit diverse pharmacological activities beyond tyrosinase inhibition, making them attractive candidates for multifunctional therapeutic agents [
48,
49,
50,
51]. Very recently, while our study was in progress, an experimental and computational investigation involving compounds containing the 3-chloro-4-fluorophenyl group underscored the significance of this moiety in the inhibition of
Agaricus bisporus TYR [
52].
It is worth emphasizing that our molecular docking outcomes, employing the MVD package in conjunction with the MOLDOCK method [
28], have demonstrated their efficacy in the context of TYR systems [
23,
24,
25,
26,
27]. The MOLDOCK scoring function for each TYR inhibitor based on arylpiperidine and arylpiperazine moieties has been extracted and subsequently compared with experimental binding data (
Table 3). In the case of the first group of compounds (without benzamide ring), L02–L12, a notable and positive correlation (
r² = 0.73) has been observed between the MOLDOCK scoring and experimental values. However, for arylpiperazine compounds (with benzamide ring), L13–L24, the correlation is notably weaker and negative (
r² = –0.39). These findings align with the expectations in the realm of molecular docking calculations. In many instances, docking algorithms can predict the appropriate binding modes but may not consistently rank various ligands based on their binding affinities [
53].
To carry out MD simulations after molecular docking is of paramount importance in drug discovery and structural biology. While molecular docking provides crucial insights into potential binding modes and initial binding affinities, MD simulations take this a step further by offering a dynamic view of the interactions between ligands and target proteins over time. This enables the exploration of structural changes, conformational dynamics, and the stability of the ligand-protein complex, which are often critical factors in understanding the true binding mechanism and predicting binding affinities accurately [
54,
55].
As detailed in the Computational Methods section, we conducted a total of five random replicas, each lasting 2 ns, utilizing the Q6 program [
39]. This approach was adopted to generate ensembles that would enhance the understanding of the binding dynamics of arylpiperidine and arylpiperazine-based compounds with TYR. Our MD results reveal the robust stability of all simulated compounds within the catalytic site of TYR. Moreover, the structural characteristics of the TYR portion closely resemble those observed in prior computational investigations [
26,
27].
As can be observed in
Table 4, it becomes evident that for the arylpiperidine group, the RMSD values span from 0.41±0.10 Å (L05) to 1.19±0.24 Å (L04), while for the arylpiperazine group, the RMSD values range from 0.39±0.10 Å (L20) to 0.97±0.30 Å (L24). These findings strongly indicate the effective stabilization of all simulated compounds within the TYR catalytic site in their respective complexes. Intriguingly, all inhibitors maintained the interaction between the fluorobenzyl group's fluorine atom and Cu
2+ ion (B) present in the TYR catalytic site, a feature akin to what is observed with natural substrates (L-Tyr and L-DOPA) as well as the KA inhibitor [
56].
Furthermore, this interaction aligns with the findings of Ferro et al. [
19], whose research indicated that the electron density within the TYR active site corroborated the placement of the 4'-fluorobenzyl moiety between the two copper ions. Additionally, the aromatic ring was stabilized through stacking interactions with the residue His208 (
Figure 2). The most potent arylpiperidine-based compound, L12, engages in a hydrogen interaction with Arg209 from TYR (
Figure 2B), an interaction not observed in the case of L04 (
Figure 2A). Additionally, as previously assessed [
26,
27], the CuDum model [
33], employed for describing Cu
2+ ions, appropriately captured all the critical structural characteristics.
Then, by considering the premises of the arylpiperidine group, it can be inferred that compounds interacting with the Arg209 residue possess enhanced inhibitory potential against the TYR enzyme. This interaction is evident in both the most potent inhibitor and the second least potent among the arylpiperazine compounds (
Figure 3). The computational evidence presented here corroborates the observations made by Ferro et al. [
19] regarding the mobility of Arg209, which facilitates the stabilization of bulky compounds within the active site of TYR.