Antiplasmodial activity of coumarins isolated from
 Polygala boliviensis
 :
 in vitro
 and
 in silico
 studies

Silva, Danielle Figuerêdo da; Souza, Jéssica Lima de; Costa, Diego Mota da; Costa, David Bacelar; Moreira, Paulo Otávio Lourenço; Fonseca, Amanda Luisa da; Varotti, Fernando de Pilla; Cruz, Jorddy Neves; Santos, Cleydson Breno Rodrigues dos; Alves, Clayton Queiroz; Leite, Franco Henrique Andrade; Brandão, Hugo Neves

doi:10.1080/07391102.2023.2173295

Cited by 15 publications

(6 citation statements)

References 75 publications

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“…The molecular docking uses a validation protocol established by the study group, in which the poses (conformation + orientation) of the ligands (I40, GNT, and JHIII) are analyzed within the active sites of the enzyme (PDB IDs 1QON, 4EY6, and 5V13, respectively, in the order mentioned). In this context, the parameter analyzed was the RMSD (mean deviation from the square root), less than or equal to 2.0 Å, considered more appropriate [57][58][59][60]. The values obtained between the reference ligands and the experimental ligands in this study were I40 (1.33 Å), GNT (1.21 Å), and JH31 (1.48 Å), as shown in Figure 4, which determine the best position of the initial structure at around the X-ray crystallographic complex, experimentally analyzing the most stable position so that there is no structural change between the proteins and the ligand reference when complexed with the macromolecule under study.…”

Section: Molecular Dockingmentioning

confidence: 99%

Essential Oil of Ocimum basilicum against Aedes aegypti and Culex quinquefasciatus: Larvicidal Activity of a Nanoemulsion and In Silico Study

de Sousa dos Santos,

Cruz,

da Costa

et al. 2024

Separations

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Diseases transmitted by vectors such as Aedes aegypti and Culex quinquefasciatus (Diptera: Culicidae) have been responsible for endemics and epidemics in several countries, causing irreparable damage to human health. For this reason, vector control is one of the main strategies to prevent the contamination and dissemination of these etiological agents. In this study, the essential oil (EO) of Ocimum basilicum was obtained by hydrodistillation, and the compounds were identified by GC/MS. A nanoemulsion was obtained through a low-energy input method and evaluated by photon correlation spectroscopy. Bioassays were performed against 4th instar larvae of A. aegypti and C. quinquefasciatus. Furthermore, additional in silico studies of biological activity prediction and molecular docking for the acetylcholinesterase enzyme and juvenile hormone protein targets were performed with the 53 identified compounds of the EO. The major compounds identified in greater quantity were linalool (32.66%) and anethole (32.48%). The obtained nanoemulsion had an average size diameter between 244.6 and 280.4 nm and a polydispersity index below 0.250 during the entire storage period. The nanoemulsion was tested at concentrations of 10, 20, 30, 40, and 50 mg/L and the following activity values were observed: LC50 = 42.15 mg/L and 40.94 mg/L and LC90 = 50.35 mg/L and 48.87 mg/L for A. aegypti (24 h and 48 h); LC50 = 39.64 mg/L and 38.08 mg/L and LC90 = 52.58 mg/L and 54.26 mg/L for C. quinquefasciatus (24 h and 48 h). The in silico results showed better activity values for linalool, anethole, carvone, α-selinene, eugenol, and limonene. The α-selinene compound showed the best binding affinity with the insect acetylcholinesterase enzyme (−9.1 Kcal) in molecular docking, showing the importance of antagonist compounds in elucidating the mechanism of action for the investigated targets. Thus, the studied nanoemulsion was considered active against the tested species, becoming a potential alternative as an ecological bioinsecticide due to bioactivity and simplicity of formulation.

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Section: Molecular Dockingmentioning

confidence: 99%

Essential Oil of Ocimum basilicum against Aedes aegypti and Culex quinquefasciatus: Larvicidal Activity of a Nanoemulsion and In Silico Study

de Sousa dos Santos,

Cruz,

da Costa

et al. 2024

Separations

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“…The same set of softwares are used to understand the stability of the complexes formed. The modules, namely, protein preparation, Grid generation, Site map prediction, Ligprep, and glide docking (Da Silva et al 2023 andFahui Li et al 2022) are used to study molecular mechanical interactions of the complex between curcumin derivative and Akt1. Quantum Mechanical procedural software consists of the modules that monitors simulation's real time dynamism, interactions and its quality (Bitencourt-Ferreira et al 2019;Kuki and Nielsen, 2010).…”

Section: Software and Modulesmentioning

confidence: 99%

Analysis of an Insilico Interaction by a Curcumin Derivative Specifically Only With the Akt1 Molecule but not Akt2

Vaithyanathan¹

2023

Preprint

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Akt1 is an important macromolecule expressed excessively in many cancers. Inhibition of Akt1 by natural compounds is always advantageous for there are fewer side effects. It is well known that curcumin modifies the behavior of AKT1/AKT2/AKT3 but a natural ligand or its derivative that interacts specifically with AKT1 is one, that will be of tremendous interest in the world of cancers. For the first time, a derivative of curcumin that interacts only with AKT1 but not AKT2 is proposed by way of bioinformatics-based verification studies. Through simulation-based analysis, this research studies the interactions of curcumin derivative with AKT1 protein and compare the same with the fda approved AKT1 inhibitor, capiversatib. The curcumin derivative’s energy was localized along with optimization using the PDB file 4EKL obtained from RCSB. The stability of the curcumin derivative’s non-bonded interactions with the AKT1 protein was studied using Desmond MD method. The affinity of the curcumin derivative’s interaction was -10.327 kcal/mol and for the fda approved molecule, Capivasertib, it was -8.339 kcal/mol. The MMGBSA value of -60.53 kcal/mol for the curcumin derivative-AKT1 complex was much better than the value of -26.65 kcal/mole for the Capivasertib-AKT1 complex. The curcumin derivative molecule did not interact with Akt2 molecule as indicated by the failure of good docking poses by the docking software. The curcumin derivative molecule was helped by hydrogen bond formations with Glu228, Ala230, Lys179, Glu278, Thr312, Tyr315 whereas for Capivasertib, the hydrogen bonds were formed at Glu234, Glu278, Glu228 and Ala230 in addition to various hydrophobic interactions for both the complexes. Molecular dynamics simulation studies confirmed the stability of the curcumin derivative molecule-Akt1 complex for the entire duration of 100 nanoseconds. Hence, the curcumin derivative molecule may target specifically the Akt1 molecule for its behavioural modification.

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“…To learn about the atomic level interactions and stability of the complex formed between the ligands and proteins, Schrodinger (Zainab R et al 2021), and Desmond simulation software (Ayaz, P et al 2023) were used. The molecular mechanics based interaction studies of Tetrahydro Curcumin derivative with PCSK9 protein was carried out using the modules such as protein preparation, Grid generation, Site map prediction, Ligprep, and glide docking (Da Silva et al 2023 andFahui Li et al 2022). The QM-based procedures helped understand the stability of the complex using the modules such as dynamic simulation, simulation quality, and simulation interaction (Bitencourt-Ferreira et al 2019;Kuki and Nielsen, 2010).…”

Section: Software and Modulesmentioning

confidence: 99%

MOLECULAR AND QUANTUM MECHANICAL STUDIES OF INTERACTION BETWEEN TETRAHYDROCURCUMIN DERIVATIVE AND PCSK9 Protein TO PROVIDE A BASIS FOR AN ORAL PILL TO REMOVE BAD CHOLESTEROL

Vaithyanathan¹

2023

Preprint

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The interaction between Proprotein convertase subtilisin/kexin type 9 (PCSK9) and low-density lipoprotein receptors responsible for causing atherosclerosis. According to estimates, it causes 60% of fatalities worldwide and is the covert precursor to clinical myocardial infarction (MI), stroke, and CVD. Designing tiny compounds that inhibit PCSK9 from interacting with LDL receptors is the need of the hour. Through bioinformatics-based studies, this study seeks to assess the interactions between a derivative of tetrahydrocurcumin and PCSK9 Protein and compare them to interactions with the literature based studies of standard Atorvastatin. Additionally, comparison research was carried out to examine how the new compound interacts in the active and allosteric regions of PCSK9. The above-mentioned compound, a derivative of Tetrahydrocurcumin, was adjusted and optimized to the level of local minimum energy using the RCSB's downloaded PDB file 7S5H. By Desmond MD simulation studies, the stability of the non-bonded interactions of the complexes was examined. An affinity of -9.493 kcal/mol for the active site and -8.148 kcal/mol for the allosteric site was observed by docking studies in comparison with the standard molecule, atorvastatin. Also, the MMGBSA value of -50.7142 kcal/mol indicates the Tetrahydrocurcumin derivative binds well compare to the standard, atorvastatin. The Tetrahydro curcumin derivative molecule was able to orient into the active region with the help of Asp238, Thr377, and Ser381 amino acids. In comparison to atorvastatin, the binding affinity was raised by seven H-bonds with six amino acids and one π interaction of Arg295 amino acids of the allosteric site. The Tetrahydro curcumin molecule's nonbonded interaction was found to be stable for 100 ns by MD simulation tests. This demonstrates that the Tetrahydrocurcumin derivative molecule will prove to be an effective substrate to modify PCSK9 protein behavior.

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Antiplasmodial activity of coumarins isolated from Polygala boliviensis : in vitro and in silico studies

Cited by 15 publications

References 75 publications

Essential Oil of Ocimum basilicum against Aedes aegypti and Culex quinquefasciatus: Larvicidal Activity of a Nanoemulsion and In Silico Study

Essential Oil of Ocimum basilicum against Aedes aegypti and Culex quinquefasciatus: Larvicidal Activity of a Nanoemulsion and In Silico Study

Analysis of an Insilico Interaction by a Curcumin Derivative Specifically Only With the Akt1 Molecule but not Akt2

MOLECULAR AND QUANTUM MECHANICAL STUDIES OF INTERACTION BETWEEN TETRAHYDROCURCUMIN DERIVATIVE AND PCSK9 Protein TO PROVIDE A BASIS FOR AN ORAL PILL TO REMOVE BAD CHOLESTEROL

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