Molecular docking analysis of PSA-specific aptamers: An in Silico Approach
-
Khodakaram Jahanbin,1 Seyed Amirhosein Mahdavi ,2,* Hamidreza Daneshparvar,3 Kamrooz Amini,4 Fateme Yarinasab,5
1. M.Sc, Legal Medicine Research Center, Legal Medicine Organization,Yasouj, Iran
2. MD, Forensic Medicine Specialist, Assistant Professor, Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
3. Associate professor of legal medicine, legal medicine Reserche Center, Legal medicine Organization, Tehran, Iran.
4. MD, Legal Medicine Research Center, Legal Medicine Organization,Yasouj, Iran.
5. MSc, Legal Medicine Research Center, Legal Medicine Organization,Yasouj, Iran.
- Introduction: One of the most important pieces of information in the forensic is the diagnosis of semen in sexual assaults. Prostate-specific antigen (PSA) is one of the most specific components for semen, so finds a reliable method for identification of semen based on PSA in forensic investigations is a necessity. Although the use of antibody known as a reliable component for biosensors, but antibody production requires complex laboratory equipment and methods, so the process of antibody production and purification is time-consuming and expensive. Aptamers (a group of single-stranded nucleic acids of DNA or RNA) compared to monoclonal antibodies because of their affinity and specificity. The purpose of this computational study is to evaluate the docking process of PSA and its specific Aptamers by a range of bioinformatics tools.
- Methods: In this study, we retrieved the sequence of specific aptamers from a previous study and predicted the secondary structure of each aptamer by RNAfold server. Next, the third structure of each aptamer was designed by 3dRNA server, and the energy of each aptamer minimized by GROMACS tool based on Amber Force-Field. Next, the refinement of each aptamer structure was performed by QRNAS software. Finally, the docking analysis was accomplished by PatchDock and FiberDock tools.
- Results: The purpose of this study was docking analysis of each aptamer and PSA, for this purpose, the predicted structures of each aptamer reached the most stable form, and a simulation run by the GROMACS tool according to the Amber force-field. Next, to refinement the predicted structure of each aptamer, the QRNAS proprietary tool was used. the refined structures of each aptamer used to perform rigid and flexible docking. According to the results of the rigid docking, VI and XIII aptamers get the highest score by rigid docking on the PatchDock server in comparison to the other aptamers. Finally, to identify the most correct transform obtained by rigid docking for each aptamer, we performed Flexible docking. According to the results of this computational study, VI and XIII aptamers seem to be more suitable than other aptamers for PSA detection.
- Conclusion: The results of this study showed that the wide range of accessible bioinformatics tools can be used before wet laboratory analysis in order to design a laboratory and scientific study more wisely and preserve cost and money before running the laboratory analysis. According to the results of this study, we determined the most suitable aptamers for PSA detection and provided valuable information to go-ahead and run laboratory analysis.
- Keywords: molecular docking simulation, aptamer, bioinformatics, computational biology.
