Computational Study of Bioactive Components of Sweet Basil (Ocimum basilicum Linn.), Luyang dilaw (Curcuma longa Linn.) and Lagundi (Vitex negundo) as Inhibitor against Human Immunodeficiency Virus (Hiv-1)

Buan, Ivy Joyce Arenas; Mendoza, Danilet Vi M.

doi:10.13005/ojc/360424

Cited by 3 publications

(2 citation statements)

References 11 publications

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“…The binding affinity (or free energy of binding) is the sum of the final intermolecular energy and torsion-free energy. The negative value of binding affinity depicts that the reaction between bioactive components bonded to the active site occurs spontaneously due to this change in total intermolecular and torsional energies [28]. Therefore, a better inhibitor of the Tat C protein among the selected ligands is the phenolic compound(s) with a high negative value of binding affinity as this corresponds to better bonding of phytochemical components with the receptor; better inhibition of the viral transcription, which then a better inhibition of the virus.…”

Section: Interactions and Mechanisms Of The Ligand-protein Complexes ...mentioning

confidence: 99%

Interactions and mechanisms of phenolic compounds with human immunodeficiency virus-1 Tat protein

S. Delos Santos,

A. Santos,

M. Mendoza

2024

IJPHS

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Human immunodeficiency virus remains a serious health threat, with an increase of 24% newly cases globally. Targeting Tat protein is an emerging therapeutic strategy for inhibiting the feedback loop that drives the exponential increase in viral transcription and particle production of the virus. The study aimed to determine the inhibitory potential of phenolic compounds from Ricinus communis L. and Jatropha curcas L., against the Tat C protein using in silico techniques. Phenolic compounds identified from both plants were screened by absorption-distribution-metabolism-excretion (ADME) analysis using drug-likeness prediction. Molecular docking analysis of the compounds with drug-like properties against the receptor and ligand-protein complexes’ analysis and visualization were performed. The results revealed three phenolic compounds with the highest negative binding affinity to the receptor’s active site: ellagic and neochlorogenic acids with - 7.2 kcal/mol and isohemiphloin with -7.3 kcal/mol. The interacting amino acids of the complexes were majorly His13, Lys19, Lys28, Thr64, His65, Gln66, Pro70, Gln72, and Pro73 via non-covalent interactions: hydrogen bonds, hydrophobic, and electrostatic interactions. The identified phenolic compounds provide a core structure that can be candidate for plant-based antiviral drugs development to potentially aiding in the virus’s therapeutic challenge.

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Section: Interactions and Mechanisms Of The Ligand-protein Complexes ...mentioning

confidence: 99%

Interactions and mechanisms of phenolic compounds with human immunodeficiency virus-1 Tat protein

S. Delos Santos,

A. Santos,

M. Mendoza

2024

IJPHS

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“…A computational study demonstrated that this plant has the potential for antiviral drug development through its mechanism of inhibiting the active site of human immunodeficiency virus (HIV) gp120 and gp41. α-guaiene is the compound with the highest negative value for binding affinity, which was −9.62 Kcal/mol at the active site gp120, and sitosterol displayed a binding affinity for −10.99 Kcal/mol at the active site gp41 [ 79 ]. Furthermore, an in vitro study of the crude ethanolic extract of O. basilicum L. leaves demonstrated antiviral activity against Zika virus (ZIKV) with 97% virus infectivity at the highest concentration (1:16 dilution) [ 80 ].…”

Section: Antimicrobial Activities and Biomedical Usesmentioning

confidence: 99%

Sweet Basil (Ocimum basilicum L.)―A Review of Its Botany, Phytochemistry, Pharmacological Activities, and Biotechnological Development

Azizah,

Irawan,

Kusmoro

et al. 2023

Plants

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An urgent demand for natural compound alternatives to conventional medications has arisen due to global health challenges, such as drug resistance and the adverse effects associated with synthetic drugs. Plant extracts are considered an alternative due to their favorable safety profiles and potential for reducing side effects. Sweet basil (Ocimum basilicum L.) is a valuable plant resource and a potential candidate for the development of pharmaceutical medications. A single pure compound or a combination of compounds exhibits exceptional medicinal properties, including antiviral activity against both DNA and RNA viruses, antibacterial effects against both Gram-positive and Gram-negative bacteria, antifungal properties, antioxidant activity, antidiabetic potential, neuroprotective qualities, and anticancer properties. The plant contains various phytochemical constituents, which mostly consist of linalool, eucalyptol, estragole, and eugenol. For centuries, community and traditional healers across the globe have employed O. basilicum L. to treat a wide range of ailments, including flu, fever, colds, as well as issues pertaining to digestion, reproduction, and respiration. In addition, the current research presented underscores the significant potential of O. basilicum-related nanotechnology applications in addressing diverse challenges and advancing numerous fields. This promising avenue of exploration holds great potential for future scientific and technological advancements, promising improved utilization of medicinal products derived from O. basilicum L.

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In Silico Study of Ayapana Triplinervis Bioactive Compounds Against Quorum-Sensing System of Pseudomonas Aeruginosa

2021

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Quorum sensing (QS) is the way bacterial cells communicate can trigger or regulate pathogenicity in Pseudomonas aeruginosa. Targeting the quorum sensing system with the help of docking algorithms can reduce the cost and time to screen for potential anti-quorum sensing drugs. Ayapana triplinervis, an ethnobotanical from the Philippines is a potential source of bioactive compounds to inhibit quorum sensing. This study shows potential compounds present in Ayapana triplinervis that could disrupt the quorum sensing system in Pseudomonas aeruginosa with the use of molecular docking simulations. Selection and identification of bioactive compounds found in Ayapana triplinervis was based from previous metabolite screening reports. This study utilizes virtual screening in order to identify which among the compounds to be the potent quorum sensing inhibitor. The molecular structures of the thirty-one identified bioactive compounds were obtained from PubChem (nih.gov) in SDF file. These molecular structures of the compounds from Ayapana triplinervis served as the ligands and docked to the active site of the PqsR, PqsD, and LasR of the Pseudomonas aeruginosa using Autodock Vina algorithms. The bioactive compounds were virtually screened using Autodock Vina to determine the binding affinity of each compounds to the active site of PqsR, PqsD, and LasR. Compounds with a low binding affinity has a potential to be developed as anti-quorum agent to Pseudomonas aeruginosa. Results showed that out of the 31 compounds, caryophyllene, trans-nerolidol, 2-(Isobutyryloxy)-Thymol methyl ether, β-elemene, and cyperadiene have successfully inhibited the PqsR, PqsD, and LasR based from the computed binding affinity. 2- (Isobutyryloxy)-Thymol methyl ether formed hydrogen bond in the active site of all the proteins related governing the quorum sensing process of Pseudomonas aeruginosa, making the compound a candidate drug to disrupt the signaling pathway of the system.

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Computational Study of Bioactive Components of Sweet Basil (Ocimum basilicum Linn.), Luyang dilaw (Curcuma longa Linn.) and Lagundi (Vitex negundo) as Inhibitor against Human Immunodeficiency Virus (Hiv-1)

Cited by 3 publications

References 11 publications

Interactions and mechanisms of phenolic compounds with human immunodeficiency virus-1 Tat protein

Interactions and mechanisms of phenolic compounds with human immunodeficiency virus-1 Tat protein

Sweet Basil (Ocimum basilicum L.)―A Review of Its Botany, Phytochemistry, Pharmacological Activities, and Biotechnological Development

In Silico Study of Ayapana Triplinervis Bioactive Compounds Against Quorum-Sensing System of Pseudomonas Aeruginosa

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