Screening Rafflesia and Sapria Metabolites Using a Bioinformatics Approach to Assess Their Potential as Drugs

Wicaksono, Adhityo; Raihandhany, Reza; Zen, Tresa Variyani; Silva, Jaime Teixeira da; Agatha, Aggy; Cristy, Ghea Putri; Ramadhan, Arfan Tri Kusuma; Parikesit, Arli Aditya

doi:10.56899/151.05.20

Cited by 6 publications

(2 citation statements)

References 43 publications

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“…A Pa value above 0.3 indicated that the compound had potential as an in silico antimalarial agent. 13…”

Section: Antimalarial Activity Predictionmentioning

confidence: 99%

In Silico Investigation of Tropical Natural Product for Wild-Type and Quadrupole Mutant PfDHFR Inhibitors as Antimalarial Candidates

2024

TJNPR

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Plasmodium falciparum dihydrofolate reductase (PfDHFR) is an essential enzyme in the development of parasitic DNA and its inhibition often leads to the impediment of parasite growth. Several studies have also shown that a genetic mutation in this enzyme can cause reduced receptor responsiveness and efficacy of antimalarial drugs. Therefore, this study aimed to examine 100 compounds derived from Indonesian medicinal plants as potential antimalarial candidates using a structure-based virtual screening approach. The PASS online was used to screen 100 compounds, and those with Pa values higher than 0.3 were docked with the wild-type (PDB code:1j3i) and quadrupole mutant PfDHFR (PDB code:1j3k). The stability of the chemical complex was then examined using molecular dynamics simulations, followed by an assessment of the pharmacokinetic profile and drug-likeness parameters. The top 5 compounds were then identified with binding energies ranging from -9.7 to -10.0 kcal/mol for the wild-type PfDHFR-TS and from -9.2 to -10.0 kcal/mol for the quadrupole mutant PfDHFR. The results showed that compound C90 exhibited the most stable and impressive score in its pharmacokinetic and drug-likeness assessment.

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“…A Pa value above 0.3 indicated that the compound had potential as an in silico antimalarial agent. 13…”

Section: Antimalarial Activity Predictionmentioning

confidence: 99%

In Silico Investigation of Tropical Natural Product for Wild-Type and Quadrupole Mutant PfDHFR Inhibitors as Antimalarial Candidates

2024

TJNPR

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“…The ligands and standard were retrieved in SMILES (simplified molecular input line entry system) format for QSAR and ADME-Tox analysis, and .sdf format for molecular docking and molecular dynamics simulation (Aurora et al 2022). Their energy was minimized prior to docking and converted to .pdbqt format using OpenBabel wizard in PyRx (Wicaksono et al 2022).…”

Section: Structure Retrieval and Preparationmentioning

confidence: 99%

<i>In silico</i> Screening of Potential Antidiabetic Phenolic Compounds from Banana (<i>Musa</i> spp.) Peel Against PTP1B Protein

Pratama,

Astina,

Parikesit

2023

J.Tropical Biodiversity Biotechnology

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Type 2 diabetes mellitus (T2DM) is a global problem with increasing prevalence. The current treatments have made an immense progress with some side effects, such as drug resistance, acute kidney toxicity, and increased risk of heart attack. Banana (Musa spp.) peel comprises 40% of banana fruit contains high phenolic compounds whilst some studies have suggested a correlation between phenolic compounds and antidiabetic activity. One of the novel protein targets that has been identified as a potential anti-diabetic treatment is PTP1B (PDB ID:2NT7). Therefore, this study aimed to screen the potential PTP1B inhibitor for antidiabetic treatment from phenolic compounds in banana peel. QSAR, molecular docking, ADME-Tox, and molecular dynamics analysis were deployed to examine forty-three phenolic compounds in banana peel. Eighteen ligands were screened by QSAR analysis and eight of them had a lower binding energy than the standard (ertiprotafib) in molecular docking, with urolithin A and chrysin were the lowest. Both passed Lipinski’s rule of five, had a good intestinal absorption, and no blood-brain barrier penetration, however, their mutagenicity, carcinogenicity, and irritation to the skin and eyes were still in questions. Molecular dynamics analysis found both of them were in a stable conformation with PTP1B. This study suggested a potential of urolithin A and chrysin as PTP1B inhibitor for antidiabetic treatment. Additionally, further experimentation is required to validate this finding.

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Most of the world's largest flowers (genus Rafflesia) are now on the brink of extinction

Malabrigo,

Tobias,

Witono

et al. 2023

Plants People Planet

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Societal Impact StatementRafflesia is the genus that contains the world's largest flowers. Despite their global appeal, most of the 42 known species are now at risk of extinction. Urgent action is needed to protect these remarkable flowers. A combined approach to conservation is recommended, including a greater level of habitat protection and support for local community action groups. Rafflesia is a suitable new icon for conservation in the Asian tropics.SummaryThe genus Rafflesia, which includes the world's largest flowers, has aroused curiosity among scientists for centuries and features prominently in local culture across Southeast Asia. The plant has long been used in ethnobotanical medicine and, more recently, as a source of revenue from ecotourism. But despite its acclaim, Rafflesia remains poorly understood in many respects. Taxonomy is disputed, new species are described each year, and the plant has proven recalcitrant to cultivation. This has hindered conservation, and most of the 42 known species are now severely threatened, yet only one is listed by the International Union for Conservation of Nature (IUCN). We estimate that 60% of Rafflesia species face a severe risk of extinction (equivalent to Critically Endangered [CR]). Moreover, we predict that at least 67% of known habitats fall outside protected areas, exacerbating their vulnerability. Alarmingly, recent observations suggest taxa are still being eradicated before they are even known to science. We present recent scientific discoveries and probable extinctions and highlight case studies of conservation success, with a focus on the role of local people. We propose a multi‐pronged conservation approach combining strengthened taxonomy, ex situ propagation, ecotourism, and an extension of protected areas. We suggest action devolved to local communities and awareness campaigns linked to social media networks will be crucial outside of protected jurisdictions. Finally, we propose to establish Rafflesia as a new icon for plant conservation in the Asian tropics. A combined approach might just save some of the world's most remarkable flowers, most of which are now on the brink of being lost.

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Screening Rafflesia and Sapria Metabolites Using a Bioinformatics Approach to Assess Their Potential as Drugs

Cited by 6 publications

References 43 publications

In Silico Investigation of Tropical Natural Product for Wild-Type and Quadrupole Mutant PfDHFR Inhibitors as Antimalarial Candidates

In Silico Investigation of Tropical Natural Product for Wild-Type and Quadrupole Mutant PfDHFR Inhibitors as Antimalarial Candidates

<i>In silico</i> Screening of Potential Antidiabetic Phenolic Compounds from Banana (<i>Musa</i> spp.) Peel Against PTP1B Protein

Most of the world's largest flowers (genus Rafflesia) are now on the brink of extinction

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