Computational analysis of polydatin, ergotamine, and dydro-ergotamine with apoptotic protease-activating factor 1 (Apaf 1) by docking-based virtual screening with the PyRx tool

Ivan Vito Ferrari¹ , Alex De Gregorio² , Maria Pia Fuggetta³ , Giampietro Ravagnan⁴

Section:Research Paper, Product Type: Journal-Paper
Vol.10 , Issue.5 , pp.19-22, Oct-2023

Online published on Oct 31, 2023

Copyright © Ivan Vito Ferrari, Alex De Gregorio, Maria Pia Fuggetta, Giampietro Ravagnan . This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
 

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Abstract :
In this short communication, we performed Autodock Vina and Autodock-4, using both hundreds of natural compounds and hundreds of drugs with protein apoptotic protease activating factor 1. The goal of this method was to understand, which of the selected drugs and screened natural substances binds better to this protein and which chemical bonds are involved. The technique used for this aim was the Virtual Screening Tool performed by the Pyrx program. From docking results Calculations performed by Autodock Vina, Polydatin, Ergotamine, and Dydro-Ergotamine showed excellent binding energy scores ( -10.1, -10.5, and -12.1 kcal/mol, respectively). All these results lead us to conclude that they could have a Key role in the apoptosis process, even if further studies such as computational and biological tests are necessary.

Key-Words / Index Term :
APAF-1,autodocking approach, Autodock Vina and Autodock-4

References :
[1]. Riedl, S. J., Li, W., Chao, Y., Schwarzenbacher, R., & Shi, Y. . Structure of the apoptotic protease-activating factor 1 bound to ADP. Nature, Vol.434, Issue.7035, pp.926-933, 2005.
[2]. Miura, M. Apoptotic and nonapoptotic caspase functions in animal development. Cold Spring Harbor Perspectives in Biology, Vol.4, Issue.10, pp.a008664, 2012.
[3]. Fan, T. J., Han, L. H., Cong, R. S., & Liang, J. Caspase family proteases and apoptosis. Acta biochimica et biophysica Sinica, Vol.37, Issue.11, pp.719-727, 2005.
[4]. S.K. Sharma, “Performance Analysis of Reactive and Proactive Routing Protocols for Mobile Ad-hoc N/W,” World Academics Journal of Engineering Sciences, Vol.1, Issue.5, pp.1-4, 2013.
[5]. Creagh, E. M., Conroy, H., & Martin, S. J. Caspase?activation pathways in apoptosis and immunity. Immunological reviews, Vol.1, Issue.1, pp.10-21, 2003.
[6]. Kanduc, D., Mittelman, A., Serpico, R. O. S. A. R. I. O., Sinigaglia, E., Sinha, A. A., Natale, C., & Farber, E. M. A. N. U. E. L. Cell death: apoptosis versus necrosis. International journal of oncology, Vol.2, Issue.1, pp.165-170, 2002.
[7]. Trott, O., & Olson, A. J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of computational chemistry, Vol.3, Issue.2, pp.455-461, 2010.
Kanduc, D., Mittelman, A., Serpico, R. O. S. A. R. I. O., Sinigaglia, E., Sinha, A. A., Natale, C., & Farber, E. M. A. N. U. E. L. Cell death: apoptosis versus necrosis. International journal of oncology, Vol.21, Issue.1, pp.165-170, 2002.
[8]. Shakeri, R., Kheirollahi, A., & Davoodi, J. Apaf-1: Regulation and function in cell death. Biochimie, Vol.135, pp.111-125, 2017.
[9]. Gortat, A., Sancho, M., Mondragón, L., Messeguer, À., Pérez-Payá, E., & Orzáez, M. Apaf1 inhibition promotes cell recovery from apoptosis. Protein & cell, Vol.6, Issue.11, pp.833-843, 2015.
[10]. Dallakyan, S., & Olson, A. J. Small-molecule library screening by docking with PyRx. Chemical biology: methods and protocols, pp.243-250, 2015.
[11]. Rizvi, S. M. D., Shakil, S., & Haneef, M. A simple click by click protocol to perform docking: AutoDock 4.2 made easy for non-bioinformaticians. EXCLI journal, Vol.12, pp.831, 2013.