Role of Autodock vina in PyRx Molecular Docking

 

Rutuja P. Pawar*, Sachin H. Rohane

Department of Pharmacy, Yashoda Technical Campus, Satara, 415003.

 

ABSTRACT:

Molecular docking has been widely employed as a fast and inexpensive technique in past decades, both in academic and industrial setting. In current situation molecular docking software is very useful. It’s a need of society. That’s why this review is focused on docking. In that Autodock Vena by pyrx version is very useful software for literature. New approaches continue to be developed and value of published work grows at a rapid pace. In resend developments there will be increase in accuracy, time limite, advances in computing power to eventually accomplish the full potential of the area. This review precents the overview of the method and attempt to summerise recent developments regarding four main aspects of molecular docking approaches: bench marking set, Advances in consensus method, recent applications using, use of machine learning, algorithms in docking. This autodock vena software gives more information related to molecular docking by litareture survey.

 

 

 

INTRODUCTION:

Doking is on the front line of computational biology and drug discovery the explosion of structural and chemical information in recent years has rendered this use the computation approaches to discover developed and analyzed and similar biologically active molecules the computer aided drug discovery leads to virtual screen, energy calculations, ADME models and drug interactions this helps in scientists in minimizing the synthetic and biological testing.

 

Autodock vina in PyRx software is most prefferable software in the molecular docking. This software is important. The molecular docking approach can be used to model the interaction between small molecule and protein at the automic level allow as to characterize the behavior of small molecules in the binding site of target proteins as well as elucidate fundamental biochemical process. In drug discovery, protein –ligand or protein –protein. Docking plays an important role in predicting the orientation of the ligand. The ligand is searched in a six dimentional rotational or translational space to fit in the binding site.^1-3

 

REVIEW OF ARTICLES:

Vina design philosophyis not to require the user to understand its implementation. Autodock is suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug conditions bind to recepter of known 3D structure. Autodock vina does not require choosing atom types and pre-calculating grid maps for them. Docking using autodock version 4.0 of PyRx software. PyRx is an open source software to perform virtual screening it is a combination of sevral software.

 

PyRx includes a docking wizard. Specific aspects for using PyRx as well as consideration for data preparation docking and data analysis also describes. Drug discovery is attractive research area that enables application of cutting edges biomedical research to improve health of man people by active components of natural origin have been under enormous investigation as potential studies that were performed by using PyRx docking tool through autodock vina software M. Venkateshan and Etal used autodock vina PyRx software to check inhibition activity of Azaphenantherena derivatives on or over SARS COV-2. This software to provid the guidance about inhibition activity of Azaphenantherena.⁴

 

Maryam Fatima et al used PyRx software to check bioactivity and docking of Synthesized ligand. the compound can serve as promising lead for the development of new antifungal agents this software is used to check antifungal acivity this compound can serves as promising leads for the development of new antifungal agent.⁵

 

Usman Abdulfatai et al used to autodock vina verion 4.0 of PyRx software to check activity relationship study of anti-convelsant activity of aminobenzothiazole of their quantitative structure. This software is useful to provide guidance about activity of anti-convalsant.⁶

 

Usman Abdulfatai et al used autodock vina of PyRx virtual screening software to, molecular docking and quantitative structure activity relationship studies were carried out and 37 anticonvalsant compounds to develop a robust model for the prediction of anticonvalsant activities against gama aminobutyric acid aminotransferase this softare is useful to analyses of a few aminotransferase inhibitor activity.⁷

 

Ritika Srivastava et al used PyRx software to check a alkylated benzimidazol: designed, Synthesis, Docking, DFT analysis ADMET property activity against HIV and YFV. Series of Alkylated Benzimidazol derivatives was synthesized and screened for their anti-HIV, anti-UFV and broad-spectrum antivirus properties. The software useful to show excellent inhibitory property against the yellow fever virus with.⁸

 

 Muhammad Baba Muh’d et al used PyRx software to study of anti ulcer activity of quinozolinone derivatives of quantitative structure activity relationship by using this software is useful to provide anti ulcer activity. this anti ulcer agents exhibiting good action against the receptor (H/K Atpase).⁹

 

Titilayo Omolara Johnson et al used autodock vina PyRx software to a ulcerative colitis is an implamation of the colon that can progress colorectal cancer if left untreated no medication completely cures ulcerative colitis and natural products are source of alternative approaches the anti imflamatory potential of phyllanthus nivosus leaf as a natural remady and as a source of new drugs against ulcerative colitis is validated.¹⁰

 

Mohammad Abdul Mumit et al used PyRx to study on vibrational and electronicspectra analysis of benzyl-3-N-(2,4,5-trimethoxyphenylmethylene) hydrazine. The absorption, distribution, metabolism, excreation and toxicity investigation predicted that tne compound has good drug like character.¹¹

 

Mohamed Elbadawi et al used PyRx to virtual drugs screening revealing an oxofluorenyl benzamyd and bromonaphthalene sulfonamide hydrobenzoic acid compounds induced apoptosis in a dose dependant manner as analyzed by flow cytomery this two compounds binds to HDAC6 an inhibites its function and exerts cytotoxic activity by apoptosis induction this software used to HDAC6 inhibit.¹²

 

 Shola Elijah Adenji et al used PyRx software to investigating and evaluating some active compounds as potent anti-tubercular agent against MTB CYP121 recepter this. This whole docking result against MTB CYP121 receptor provide a valuable approach for structure based design.¹³

 

 Rina Herowati et al used to PyRx software to studies of chemical constituents of tinos spara cortifolia on glycogen phosphorylase. These software used to give the activity of glycogen phosphorylase in the liver and widely used in the treatment of diabetis mellitus.¹⁴

 

Abhay Jaiprakash Gandhi et al used to PyRx software to study the drug for management of SARS-COV2 with ayurvedic perspective along with silico study. The molecular docking and grid were generated this PyRx software of autodock.¹⁵

 

Nanda Kumar Yellapu et al used to PyRx software to study the modeling, molecular docking, probing catalytic binding mode of acetyl-CoA malate synthase G in brucella melitensis. The core domain pocket of MSC catalytic residue. these ligand leads could be the best prospective inhibitors to treat brucellosis. These software is useful for activity.¹⁶

 

 Sabitu Babatunde Olasupo et al used PyRx software is the antidepressant properties in inhibition of serotonin transporter has been considered to be a good target for the treatment of mood disorders. the phenyl piperidine derivatives as inhibitors of serotonin transporter cheminformatics and molecular docking. this software is used to check the antidepressant activity.¹⁷

 

Aliyu Wappah Mahmud et al used Autodock vina PyRx software to the quantitative structure activity relationships provides a model that link biological activities of compound to their chemical structures and molecular docking study reveal the interathction between drug and it target enzyme. In this software to check the activity of antiplasmodium hybrid compound.¹⁸

 

Adedirin Oluwaseye et al used autodock vina in PyRx software to check on anticonvulsant activity of isoxazole and thiazole derivatives active in animal model. This software useful to provide the information about active in subcutaneous pentylenetetrazole in animal model.¹⁹

 

Aliya Nur Hasanah et al used Autodock vina in PyRx software is useful to extraction of atenolol from spiked blood serum using a molecularly imprinted polymer sorbent obtained by precipitation polymerization is the Atenolol is cardio- selective B-blocker that is used in the Treatment of hypertension over extended periods. in this software is to check activity of extraction of atenolol fom spiked blood serum in polymerization.²⁰

 

CONCLUSION:

This is an open source software. Autodock vina in PyRx is virtual screening software for computational drug discovery that can be used to libraries of computer against potential drug targets. Using this Autodock vina in PyRx software fordocking the several ligands against one macromolecule. This molecular docking software predicted the activity.

 

This softeare is useful for the literature. In this software is essential for research of molecular docking. It is inexpensive, time consuming process, it gives accurate result.

 

REFERENCE:

1.     Rohane S.H, Makwana A.G, 2017. Review on Hydrazone, the fascinating field of investigation in medical chemistry. Asian J Res. Chem 10 410-430.

2.     Rohane S.H, Makwana A G., 2019. In silico study for the prediction of multiple pharmacological activities of hydrazone derivatives.

3.     Rohane.S.H, Makwana A.G., 2020. Synthesis and in vitro antimycobacterial potential of eugenol. Arab.J chem 13, 4495-4504

4.     M. venkateshan, J. Suresh, M. Muthu, R. Ranjith Kumar, chemical data collection 28(2020).

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6.     Usman Abdulfatai, Adamu Uzairu, Sani Uba, Beni-suef University Journal of Basic and Applied Sciences 7 (2018) 204-214.

7.     Usman Abdulftai, Adamu Uzairu, Sani Uba, Journal of Advanced Research (2017) 8, 33-43

8.     Ritika Shrivastava, Sunil K. Gupta, Farha Naaz, Parth Sarthi Sen Gupta, Madhu Yadav, Vishal Kumar Singh, Anuradha Singh, Malay Kumar Rana, Satish Kumar Gupta, Dominique Schols, Ramendra K. Singh, Computational Biology and Chemistry 89 (2020)

9.     Muhammad baba muh’d, Adamu Uzairu, G.A. Shallangwa, Sani Uba, Journal of King University – Science 32 (2020) 657-666.

10.  Titilayo Omolara Johnson, Kenneth Daniel Odoh, Charles Obiora Nwonuma, Augustina Oduje Akinsanmi, Abayomi Emmanuel Adegboyega, Heliyon 6 (2020) e03893.

11.  Mohammad Abdul Mumit, Tarun Kumar Pal, Md Ashraful Alam, Md-Al-Azadul Islam, Subrata Paul, Md Chanmiya Sheikh, Journal of Molecular Structure 1220 (2020) 128715

12.  Mona Dawood, Mohamed Elbadawi, Madeleine Bockers, Gerhard Bringmann, Thomas Efferth, Biomedicine and Pharmacotherapy 129 (2020) 110454.

13.  Shola Elijah Adenji, Sani Uba, Adamu Uzairu, Future Journal of Pharmaceutical Science 4 (2018) 248-295.

14.  Rina Herowati, Gunawan Pamudji Widodo, Procedia Chemistry 13 (2014) 63-68.

15.  Abhay Jayprakash Gandhi, Jalpa Deepak Rupareliya, V J Shukla, Shilpa B. Donga, Rabinarayan Acharya.Journal of Ayurveda and Integrative Medicine.

16.  Pradeepkiran Jangampalli Adi, Nanda Kumar Yellapu, Bhaskar Matcha, Biochemistry and Biophysics Report 8(2016)192-199.

17.  Sabitu Babatunde Olasipo, Adamu Uzairu, Gideon Adamu Shallangwa, Sani Uba, Scientific African 9 (2020) e00517.

18.  Aliyu Wappah Mahmud Gideon Adamu Shallangwa, Adamu Uzairu, heliyon 6 (2020) e03449.

19.  Adedirin Oluwaseye, Adamu Uzairu, Gideon A. Shallangwa, Stephen E. Abechi, Journal of King Saud University–Science 32 (2020) 116-124.

20.  Aliya Nur Hasanah, Driyanti Rahayu, Rimadani Pratiwi, Tina Rostinawati, Sandra Megantara, Febrina Amelia Saputri, Khanifa Hidayati Puspanegara, Heliyon 5 (2019) e01533.

 

 

Received on 08.11.2020                    Modified on 26.11.2020

Accepted on 16.12.2020                   ©AJRC All right reserved