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Gholam GM, Mahendra FR, Irsal RAP, Dwicesaria MA, Ariefin M, Kristiadi M, Rizki AFM, Azmi WA, Artika IM, Siregar JE. Computational exploration of compounds in Xylocarpus granatum as a potential inhibitor of Plasmodium berghei using docking, molecular dynamics, and DFT studies. Biochem Biophys Res Commun 2024; 733:150684. [PMID: 39293331 DOI: 10.1016/j.bbrc.2024.150684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 09/02/2024] [Accepted: 09/09/2024] [Indexed: 09/20/2024]
Abstract
Malaria remains a global health concern, with the emergence of resistance to the antimalarial drug atovaquone through cytochrome b (cyt b) being well-documented. This study was prompted by the presence of this mutation in cyt b to enable new drug candidates capable of overcoming drug resistance. Our objective was to identify potential drug candidates from compounds of Xylocarpus granatum by computationally assessing their interactions with Plasmodium berghei cyt b. Using computational methods, we modeled cyt b (GenBank: AF146076.1), identified the binding cavity, and analyzed the Ramachandran plot against cyt b. Additionally, we conducted drug-likeness and absorption, distribution, metabolism, excretion, and toxicity (ADMET) studies, along with density functional theory (DFT) analysis of the compounds. Molecular docking and molecular dynamics simulation (MDS) were used to evaluate the binding energy and stability of the cyt b-ligand complex. Notably, our investigation highlighted kaempferol as a promising compound due to its high binding energy of 7.67 kcal/mol among all X. granatum compounds, coupled with favorable pharmacological properties (ADMET) and antiprotozoal properties at Pa 0.345 > Pi 0.009 (PASS value). DFT analysis showed that kaempferol has an energy gap of 4.514 eV. MDS indicated that all tested ligands caused changes in bonding and affected the structural conformation of cyt b, as observed before MDS (0 ns) and after MDS (100 ns). The most notable differences were observed in the types of hydrogen bonds between 0 and 100 ns. Nevertheles, MDS results from a 100 ns simulation revealed consistent behavior for kaempferol across various parameters including root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent-accessible surface area (SASA), molecular mechanics-Poisson Boltzmann surface area (MM-PBSA), and hydrogen bonds. The cyt b-kaempferol complex demonstrated favorable energy stability, as supported by the internal energy distribution values observed in principal component analysis (PCA), which closely resembled those of the atovaquone control. Additionally, trajectory stability analysis indicated structural stability, with a cumulative eigenvalue of 24.7 %. Dynamic cross-correlation matrix (DCCM) analysis revealed a positive correlation among catalytic cytochrome residues within the amino acid residues range 119-268. The results of our research indicate that the structure of kaempferol holds promise as a potential candidate against Plasmodium.
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Affiliation(s)
- Gusnia Meilin Gholam
- Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Dramaga Campus, Bogor 16680, Indonesia; Bioinformatics Research Center, Indonesian Institute of Bioinformatics (INBIO Indonesia), Malang, East Java, 65145, Indonesia.
| | - Fachrur Rizal Mahendra
- Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Dramaga Campus, Bogor 16680, Indonesia; Bioinformatics Research Center, Indonesian Institute of Bioinformatics (INBIO Indonesia), Malang, East Java, 65145, Indonesia.
| | - Riyan Alifbi Putera Irsal
- Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Dramaga Campus, Bogor 16680, Indonesia.
| | - Maheswari Alfira Dwicesaria
- Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Dramaga Campus, Bogor 16680, Indonesia; Bioinformatics Research Center, Indonesian Institute of Bioinformatics (INBIO Indonesia), Malang, East Java, 65145, Indonesia.
| | - Mokhamat Ariefin
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Palangka Raya, Indonesia.
| | - Mikael Kristiadi
- Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Dramaga Campus, Bogor 16680, Indonesia.
| | - Andita Fitri Mutiara Rizki
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Jalan Raya Bogor Km. 46, Cibinong, Bogor 16911, Indonesia.
| | - Wihda Aisarul Azmi
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Jalan Raya Bogor Km. 46, Cibinong, Bogor 16911, Indonesia.
| | - I Made Artika
- Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Dramaga Campus, Bogor 16680, Indonesia.
| | - Josephine Elizabeth Siregar
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Jalan Raya Bogor Km. 46, Cibinong, Bogor 16911, Indonesia.
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Lubis LD, Prananda AT, Juwita NA, Nasution MA, Syahputra RA, Sumaiyah S, Lubis RR, Lubis MF, Astyka R, Atiqah JF. Unveiling antioxidant capacity of standardized chitosan-tripolyphosphate microcapsules containing polyphenol-rich extract of Portulaca oleraceae. Heliyon 2024; 10:e29541. [PMID: 38644872 PMCID: PMC11031833 DOI: 10.1016/j.heliyon.2024.e29541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/09/2024] [Accepted: 04/09/2024] [Indexed: 04/23/2024] Open
Abstract
The medicinal plant Portulaca oleraceae has a long history of usage in traditional medicine. Plant extracts have several interesting pharmacological effects but have some drawbacks that can be addressed via capsulation with chitosan. This work set out to do just that tally up the antioxidant effects of a polyphenol-rich P. olerace extract and see how capsulation affected them. The reflux extraction and response surface methodology (RSM) were carried out to optimize the phenolic and flavonoid content of P. oleraceae extract. Additionally, high-resolution mass spectrometry was employed to determine the secondary metabolite present in the extract. The microcapsules of extract-loaded chitosan were prepared using the ionic gelation method and characterized in terms of size, encapsulation efficiency (EE), and morphology of microcapsules. Fourier transform infrared (FTIR) was used to observe the successful production of microcapsules with a principal component analysis (PCA) approach. The antioxidant activity of microcapsules was established using the radical scavenging method. According to RSM, the highest amounts of TPC and TFC were obtained at 72.894 % ethanol, 2.031 h, and 57.384 °C. The compounds were employed from the optimized extract of P. oleraceae including phenolics and flavonoids. The microcapsules were secured with a %EE of 43.56 ± 2.31 %. The characteristics of microcapsules were approved for the obtained product's successful synthesis according to the PCA. The microcapsules have antioxidant activity in a concentration-dependent manner (p < 0.0001). The findings of this study underscored the benefits of employing chitosan as a nanocarrier for extract, offering a promising approach to enhance plant-derived therapies.
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Affiliation(s)
- Lokot Donna Lubis
- Department of Histology, Faculty of Medicine, Universitas Sumatera Utara, Medan, 20155, Indonesia
| | - Arya Tjipta Prananda
- Department of Surgery, Faculty of Medicine, Universitas Sumatera Utara, Medan, 20155, Indonesia
| | - Nur Aira Juwita
- Department of Pharmaceutical Biology, Faculty of Pharmacy, Universitas Sumatera Utara, Medan, 20155, Indonesia
| | - Muhammad Amin Nasution
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Muslim Nusantara Al Washliyah, Medan, Indonesia
| | - Rony Abdi Syahputra
- Department of Pharmacology, Faculty of Pharmacy, Universitas Sumatera Utara, Medan, 20155, Indonesia
| | - Sumaiyah Sumaiyah
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Universitas Sumatera Utara, Medan, 20155, Indonesia
- Nanomedicine Center of Innovation, Universitas Sumatera Utara, Medan, 20155, Indonesia
| | - Rodiah Rahmawaty Lubis
- Department of Opthalmology, Faculty of Medicine, Universitas Sumatera Utara, Medan, 20155, Indonesia
| | - Muhammad Fauzan Lubis
- Department of Pharmaceutical Biology, Faculty of Pharmacy, Universitas Sumatera Utara, Medan, 20155, Indonesia
| | - Ririn Astyka
- Department of Pharmaceutical Biology, Faculty of Pharmacy, Universitas Sumatera Utara, Medan, 20155, Indonesia
| | - Jihan Firyal Atiqah
- Bachelor Program, Faculty of Pharmacy, Universitas Sumatera Utara, Medan, 20155, Indonesia
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Santoso P, Simatupang AS, Fajria A, Rahayu R, Jannatan R. Andaliman ( Zanthoxylum acanthopodium DC.) fruit ethanolic extract exerts attenuative effect on hyperglycemia, sensory and motoric function's disorders in alloxan-induced diabetic mice. J Adv Vet Anim Res 2023; 10:608-619. [PMID: 38370902 PMCID: PMC10868678 DOI: 10.5455/javar.2023.j716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/06/2023] [Accepted: 08/20/2023] [Indexed: 02/20/2024] Open
Abstract
Objective Andaliman (Zanthoxylum acanthopodium) is a potent medicinal plant in Asia. This present study aimed to reveal the effectivity of Andaliman fruit extract in alleviating hyperglycemia, sensory and motoric balance disorders, histopathology of the cerebellum, and tissue oxidative stress in diabetic mice induced by alloxan. Materials and Methods Diabetes induction was performed by intraperitoneally injecting alloxan monohydrate [200 mg/kg body weight (BW)]. Subsequently, the mice were treated daily with an ethanolic extract of Andaliman fruit (0, 150, 300, 450 mg/kg BW per oral) for 28 days, followed by measurements of blood glucose, paw sensitivity, motoric balance, histopathology of the cerebellum, and malondialdehyde (MDA) levels. Moreover, the phytochemical constituents of the extract were elucidated by liquid chromatography. Results Higher doses of Andaliman fruit extract could significantly attenuate the elevation of random and fasting blood glucose (p < 0.05) and improve paw sensitivity responses (p < 0.05) and motoric balances (p < 0.05) in diabetic mice. Moreover, Andaliman fruit extract could significantly attenuate the degeneration of cerebellar Purkinje cells (p < 0.05) and suppress MDA levels in the blood (p < 0.05) while blunting the MDA in the brain tissue (p < 0.05). Phytochemical screening revealed 39 compounds in the Andaliman extract belonging to the groups of alkaloids (26 compounds), flavonoids (12 compounds), and terpenoids (1 compound). Conclusion The ethanolic extract of Andaliman fruit is capable of ameliorating diabetic neuropathy, motor balance disorders, and Purkinje cell degeneration while also reducing oxidative stress in the peripheral system. Hence, Andaliman extract is a promising candidate for formulation as an herbal remedy against the detrimental outcomes of diabetes mellitus.
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Affiliation(s)
- Putra Santoso
- Biology Department, Faculty of Mathematics and Natural Sciences, Andalas University, Padang, Indonesia
| | - Arin Saparima Simatupang
- Biology Department, Faculty of Mathematics and Natural Sciences, Andalas University, Padang, Indonesia
| | - Annisha Fajria
- Biology Department, Faculty of Mathematics and Natural Sciences, Andalas University, Padang, Indonesia
| | - Resti Rahayu
- Biology Department, Faculty of Mathematics and Natural Sciences, Andalas University, Padang, Indonesia
| | - Robby Jannatan
- Biology Department, Faculty of Mathematics and Natural Sciences, Andalas University, Padang, Indonesia
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