In Silico Molecular Docking Analysis of α-Pinene: An Antioxidant and Anticancer Drug Obtained from Myrtus communis

Abstract

Background: Testis-specific protein on Y chromosome (TSPY) is the output of a tandem gene cluster. TSPY expression has been observed in gonadoblastoma and numerous distinct kinds of germ cell tumors, such as carcinoma in situ/intratubular germ cell neoplasia, seminoma, and extragonadal intracranial germ cell tumors (GCT). Myrtus communis extract rich in α-pinene showed high antioxidant and anticancer activity against a TSPY. Methods: The molecular weight and theoretical isoelectric of the TSPY proteins were calculated, using the ExPASSY ProtParam tools. Some software like mega 6, BioEdit, NEB cutter (New England Biolabs), and CAP3 were used to analyze clustering and find restriction enzymes on the TSPY sequence. To evaluate the nucleotide diversity of all sequences, the number of diverse situations and Tajima’s and Watterson’s estimators of theta were assessed. Nucleotide polymorphism can be measured by several parameters, such as haplotypes diversity, nucleotide diversity, theta using Dnasp software. To find interaction networks of protein-protein search tool for the retrieval of interacting genes/proteins (STRING) tools and to predict 3D structure, SWISS-MODEL was used; however, for docking protein-peptide based on interaction, Swiss Dock, Galaxy web, and CABS-dock software were employed. Results: We report a high (0.91) dN/dS index, positive Tajima's D, Fu, and Li’s tests, and a non-significant D test suggesting the occurrence of old modifications or a decrease of newborn mutations in the TSPY gene family. Interestingly, several hub proteins produced a strong chain or an operative module within their protein groups, such as nucleosome assembly protein (1NAP1L), RBMXL2, TBL1Y, and AMELY, which are all associated with the same cellular appliance elements and/or genetic uses. The docking of the TSPY target with α-pinene using docking revealed that the computationally-prognosticated lowest energy networks of TSPY are established by intermolecular hydrogen bonds and stacking interactions. Conclusions: The results of this study demonstrated that α-pinene interacts with the TSPY protein target and could be developed as a promising candidate for the new anticancer agent.