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-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 andWatterson’ 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 -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 -pinene interacts with the TSPY protein target and could be developed as a promising candidate for the new anticancer agent.

This paper describes a comparative study concerning the molecule 1-methyl-2-[(E)-2-(4-methylphenyl) ethenyl]-4-nitro-1H-imidazole (EMENI). The study involved experimental analysis using high-resolution X-ray diffraction and DFT calculations using the B3LYP functional, along with the 6–311G(d, p) basis set. An accurate depiction of the molecular electron charge density distribution in the compound was achieved using Hansen and Coppens' multipolar model. The study also involved a topological analysis of the total electron density and the location of critical points of the bond, which helps in evaluating the molecular reactivity. Additionally, Hirshfeld surface (HS) and reduced density gradient (RDG) analyses were conducted to explore the specific intermolecular interactions responsible for the stiffness of the molecular arrangement in the compound's packaging. The analyses revealed that H. . . H interactions significantly influenced the intermolecular contacts, comprising 34. 3% of the total interactions as indicated by the 2D fingerprint plots. Furthermore, the study included an exploration of charge transfer and establishment of the electronic characteristics of EMENI through Frontier molecular orbitals (FMO) analysis and HOMO-LUMO energies. Finally, the current study involved an in-silico investigation using molecular docking to evaluate the biological activity of the compound studied. This investigation showed that the title compound exhibits exceptional antiprotozoal activity against Trichomonas.

Background and Objective: In this work, the binding interactions between ssDNA and ssRNA aptamers and safranal, a bioactive substance produced from saffron, were examined using molecular docking and dynamics simulations. The main objective was to find appropriate aptamers that could bind safranal effectively, with an emphasis on dynamic stability and binding affinity. Materials and Methods: ssRNA and ssDNA aptamers with PDB IDs of 6V9B and 8D2B and 6J2W, 7QB3, and 2L5K, respectively, were subjected to molecular docking using AutoDock Tools 1.5.7. Following molecular docking, two candidate aptamers were subjected to 200 ns of molecular dynamics simulation using GROMACS 2020.1, which was employed to evaluate the stability of aptamer-ligand complexes. Findings: According to molecular docking results, the ΔG values for aptamers 6J2W, 7QB3, and 2L5K were determined to be -4.85, -4.39, and -4.53 kcal/mol, respectively, while the values for aptamers 6V9B and 8D2B were -5.27 and -5.31 kcal/mol. Among the ssRNA aptamers, 8D2B performed the best. The lowest ΔG value of the ssDNA aptamer 6J2W also led to its selection. The ssDNA aptamer exhibited higher stability in the molecular dynamics simulation, while the ssRNA aptamer showed notable fluctuations in RMSD after 40 ns and reached instability in interaction with safranal. The ssRNA-safranal interaction exhibited higher fluctuations , according to the RMSF results, than the reference ssRNA. Conclusion: The ssDNA aptamer (6J2W) is proposed as a potential option to develop aptamer-based sensors; nevertheless, further experimental validation is required to confirm its effectiveness. The quality and purity of saffron can be monitored with the use of this study.

This paper examined interaction of Graphene with Amoxicillin antibiotic through density functional theory (DFT) and by using molecular docking method. For this, the structures of Amoxicillin and, Graphene were initially optimized with Gaussian program. Then, by using the molecular docking strategy and its grading system, we computed the arrangement of 10 structures with additional negative binding energy and a fixed state compared with other samples. Finally, for the most fixed arrangement with Graphene, molecular orbitals evaluations were conducted, and binding energy along with thermodynamic evaluated, the results indicated that the adsorption of Amoxicillin antibiotic on Graphene was an exothermic. Finally, the QTAIM calculations were performed to evaluate the type of interaction and bonds created between amoxicillin and graphene.

Introduction: Aldehyde dehydrogenase 1A1 (ALDH1A1) is an enzyme involved in cellular detoxification and plays an important role in maintaining cancer stem cells and chemoresistance. This study explores the potential of four theophylline derivatives (compounds A, B, C, and D) as ALDH1A1 inhibitors using molecular docking, ADME analysis, toxicity predictions, and molecular dynamics simulations. Materials and Methods: Four compounds were chosen based on their strong experimental and predicted biological activities. Docking with human ALDH1A1 was performed using AutoDock Vina (v1.1.2), while ADMET properties were assessed with ADMETlab 3.0 and ProTox 3.0. Molecular dynamics simulations were carried out with GROMACS 2024.2 to evaluate the dynamic behavior and binding stability of the complexes. Results: Molecule A showed the highest binding affinity (–11.3 kcal/mol) and established substantial interactions with important residues such as TRP178, TYR297, and PHE171. ADMET analysis indicated that compounds A and C have high intestinal permeability, and all compounds displayed low toxicity risks, supporting their promise as therapeutic candidates. Molecular dynamics simulations confirmed that ALDH1A1’s overall structure remains stable during the simulation and revealed strong hydrogen bonding in complex A, as supported by favorable RMSD, SASA, and RMSF values. Conclusions: The integrated approach combining molecular docking, ADMET analysis, and molecular dynamics simulations confirms that Molecule A is the most promising ALDH1A1 inhibitor, exhibiting stable binding, favourable pharmacokinetic properties, and robust interactions with several residues. These results provide a strong foundation for further experimental validation and optimization in the development of targeted cancer therapies.

Luciferase enzymes are involved in the bioluminescence reaction (light emission by living organisms), The bioluminescence process is a widespread phenomenon in the Nature, These enzymes are identified in some domains of life, but the luciferases from lampyrid genus are considered of for biological applications, The molecular cloning of a new type of firefly luciferase from Luciola lateralis was reported, previously, Here, we study its substrate binding site and rare codon with molecular docking and bioinformatics studies, By molecular modelling, some rare codons were identified that may have a critical role in structure and function of this luciferase, AutoDock Vina was used in the molecular docking that recognizes some residues that yield closely related with luciferin and AMP binding site, These types of studies help in the discovery of the light production reaction, Evaluation of these hidden information’ s can improve the knowledge of luciferases folding and protein expression challenges and help in design of new drugs,

The field of drug design has undergone remarkable advancements with the advent of in silico methods, which utilize computational approaches that accelerate the discovery and development of novel therapeutics. This review provides an overview of two essential techniques in this domain: molecular docking and molecular dynamics simulation. Molecular docking plays a central role in drug design by predicting the binding interactions between a small molecule (ligand) and its target protein (receptor). By leveraging algorithms and scoring functions, molecular docking enables researchers to evaluate the binding affinity and selectivity of potential drug candidates. Through the exploration of various conformations and orientations, molecular docking facilitates the identification of lead compounds for further optimization. In tandem with molecular docking, molecular dynamics simulation has emerged as a powerful tool for studying the dynamic behavior of biomolecular systems over time. By employing physical principles alongside computational algorithms, molecular dynamics simulations provide insights into the conformational changes, flexibility, and stability of protein-ligand complexes. These simulations not only elucidate binding mechanisms but also reveal critical structural features that influence drug-target interactions. This mini-review highlights the applications of molecular docking and molecular dynamics simulation in drug design, emphasizing their utility in lead identification, optimization, and virtual screening. Collectively, the integration of in silico methods—particularly molecular docking and molecular dynamics simulation—has transformed the field of drug design, enabling researchers to significantly accelerate the identification of novel drug candidates while optimizing their therapeutic properties. As computational technologies continue to evolve, these techniques hold immense promise for facilitating the discovery and development of safer, more effective drugs.

Introduction: African trypanosomiasis is a neglected tropical disease caused by protozoa Trypanosoma brucei and transmitted via the bite of tsetse fly. The target protein of T. brucei is L-threonine-3-dehydrogenase, which has been selected for this study due to its metabolic importance for the parasite’ s survival. Docking of target protein was carried out with phytochemicals that passed in silico drug-likeness filters and have in vitro anti-trypanosomal activity along with the standard drugs eflornithine and pentamidine available against the disease. Materials and Methods: A 3D structure of L-threonine-3-dehyrogenase was downloaded from Protein Data Bank (PDB) with Id: 5K4Y and Pictorial database of 3D structures in the Protein Data Bank (PDBsum) was used to retrieve the active sites of the protein. The reviewed ligands were screened using SwissADME, Lipinski’ s rule of 5, and Molinspiration servers along with standard drugs and docked using AutoDock Vina and AutoDock 4. 2. 6. The 2D and 3D interacting residues were observed using Discovery Studio. Results: Ligand Camptothecin which inhibited T. brucei during in vitro cytotoxic assays gave better binding affinity scores than the standard drugs (eflornithine and pentamidine) selected for this study. Camptothecin showed interaction with those active site residues where ligand NAD (nicotinamide-adenine-dinucleotide) binds to the target protein, which is a significant restricting pocket for the hindrance of the parasite. Conclusions: Camptothecin derived from Camptotheca acuminata trees has the potential to be used as a better alternative than the standard drugs because of its less toxicity, better binding affinity, and specificity towards the inhibition of target protein.

Background and Objectives Despite many studies on the new Coronavirus disease 2019 (COVID-19), there is still a rate of disease mortality, which has made researchers to focus more on finding successful antiviral drugs. In this regard, small molecule inhibitors have been suggested for their higher safety, lower toxicity, and cost-effectiveness. In this study, we applied virtual screening and docking analysis to identify the prospective inhibitors of 3CL protease and ACE-2 receptors Subjects and Methods In this study, 1, 600 natural compounds were assessed by virtual screening. The ligands with a high affinity to bind to active site residues of target proteins were identified using the glide docking method and then were included in the induced-fit docking analysis in Schrö, dinger-Maestro software. Results The found compounds such as Theaflavin and Delphinidin had a high affinity to bind to the receptors. They had higher binding energy and a potent inhibitory effect compared to common drugs such as chloroquine. Conclusion The introduced natural compounds can be used to suppress COVID-19. The results may help develop new drugs or formulations to combat COVID-19,however, clinical trials are needed to examine the potential of these small molecules alone or in combination with other medical procedures.