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In Silico Studies of Bioactive Compounds Selected from Four African Plants with Inhibitory Activity Against <i>Plasmodium falciparum</i> Dihydrofolate Reductase-Thymidylate Synthase (pfDHFR-TS)

Article

Last updated: 22 Jan 2023

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-

Tags

Section B: Pharmaceutical Analytical & Organic Chemistry, Medicinal & Biochemistry

Abstract

Objective: This present study aims to assess in silico inhibitory potentials of bioactive compounds present in Vernonia amygdalina (Bitter leaf), Cymbopogon citratus (Lemongrass), Azadirachta indica (Neem leaf), and Carica papaya (Pawpaw leaf) against Plasmodium falciparum Dihydrofolate reductase-thymidylate synthase (pfDHFR-TS) via binding at their active sites. Methods: In silico methods were used in this study. Twenty (20) bioactive compounds were selected from Vernonia amygdalina, Cymbopogon citratus, Azadirachta indica, and Carica papaya. Artemether and Lumefantrine were used as the control drugs. The PubChem identification number (PID), the 3D structure in structure data format (SDF), and the canonical SMILES of the bioactive compounds and the control drugs were obtained using the PubChem online server. The crystal structure of pfDHFR-TS was retrieved from the protein data bank. Drug-likeness of the selected bioactive compounds was assessed using the SwissADME online server. The successful compounds were docked into the protein's active site using AutoDock Vina docking software. The docked complexes were analyzed using proteins plus and protein-ligand interaction profiler web server. The bioactivity of the ligands was determined using the Molinspiration online server. ADMETlab online tool was used to determine the ligands' absorption, distribution, metabolism, excretion, and toxicity (ADMET) characteristics.Results: The drug-likeness screening indicated that eleven (11) out of the twenty bioactive compounds violated two or more of the five rules (Lipinski's, Ghose's, Veber's, Egan's, and Muegge's rules). The control drug Artemether didn't violate any rule, while Lumefantrine violated four out of the five rules. The molecular docking revealed that Nimbolide, Vernomygdin, Luteolin, and Emetine from Azadirachta indica (Neem leaf), Vernonia amygdalina (Bitter leaf), and Carica papaya (Pawpaw leaf) have binding energies of -10.1 kcal/mol, -9.2 kcal/mol, -8.6 kcal/mol, and -9.2 kcal/mol respectively, which are better than the binding energies of Artemether and Lumefantrine (-8.2 kcal/mol, and -7.6 kcal/mol). Thus, these bioactive compounds' binding energies indicate the binding affinity with pfDHFR-TS protein, suggesting that the bioactive compounds may possess a biological activity against malarial. The best four ligands, Nimbolide, Vernomygdin, Luteolin, and Emetine, also showed excellent ADMET properties. Conclusion: Conclusively, the in silico analysis proposes that Nimbolide, Vernomygdin, Luteolin, and Emetine from Azadirachta indica (Neem leaf), Vernonia amygdalina (Bitter leaf), and Carica papaya (Pawpaw leaf) prove to be probable antimalarial drugs, and show better docking with the target protein compared to Artemether and Lumefantrine. To validate this study, an in-vitro and in vivo study is recommended to further this study for validation of the hit compounds, as in silico methods only predict the activity of these bioactive compounds.

DOI

10.21608/aprh.2022.139794.1175

Keywords

bioactive compounds, ADMET, Plasmodium falciparum, In Silico

Authors

First Name

Ishola

Last Name

Akinwumi

MiddleName

-

Affiliation

Department of Chemistry, School of Physical Sciences, Federal University of Technology, Akure, Ondo State, Nigeria, P.M.B.704

Email

akinwumiishola5000@gmail.com

City

Akure

Orcid

-

First Name

Ayodele

Last Name

Faleti

MiddleName

-

Affiliation

Department of Chemistry, School of Physical Sciences, Federal University of Technology, Akure, Ondo State, Nigeria, P.M.B.704

Email

ayodele.ayodele@gmail.com

City

Akure

Orcid

0000-0001-8430-7664

First Name

Adefolarin

Last Name

Owojuyigbe

MiddleName

-

Affiliation

Department of Chemistry, School of Physical Sciences, Federal University of Technology, Akure, Ondo State, Nigeria, P.M.B.704

Email

phebeanowo@gmail.com

City

Akure

Orcid

-

First Name

Faridat

Last Name

Raji

MiddleName

-

Affiliation

Department of Biology, School of Life Sciences, Federal University of Technology, Akure, Ondo State, Nigeria, P.M.B.704

Email

theunique2709@gmail.com

City

Akure

Orcid

-

First Name

Michael

Last Name

Alaka

MiddleName

-

Affiliation

Department of Integrated Science, Lagos State University of Education Otto/Ijanikan, Lagos State, Nigeria, P.M.B.007

Email

segunalaka29@gmail.com

City

Lagos

Orcid

-

Volume

6

Article Issue

3

Related Issue

35929

Issue Date

2022-07-01

Receive Date

2022-05-20

Publish Date

2022-07-01

Page Start

107

Page End

122

Print ISSN

2357-0547

Online ISSN

2357-0539

Link

https://aprh.journals.ekb.eg/article_251805.html

Detail API

https://aprh.journals.ekb.eg/service?article_code=251805

Order

2

Type

Research Article

Type Code

318

Publication Type

Journal

Publication Title

Journal of Advanced Pharmacy Research

Publication Link

https://aprh.journals.ekb.eg/

MainTitle

-

Details

Type

Article

Created At

22 Jan 2023