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Sharma S, Choubey R, Gupta M, Singh S. Heterocyclic-Based Analogues against Sarcine-Ricin Loop RNA from Escherichia coli: In Silico Molecular Docking Study and Machine Learning Classifiers. Med Chem 2024; 20:452-465. [PMID: 38333980 DOI: 10.2174/0115734064266329231228050535] [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: 06/27/2023] [Revised: 10/26/2023] [Accepted: 11/07/2023] [Indexed: 02/10/2024]
Abstract
BACKGROUND Heterocyclic-based drugs have strong bioactivities, are active pharmacophores, and are used to design several antibacterial drugs. Due to the diverse biodynamic properties of well-known heterocyclic cores, such as quinoline, indole, and its derivatives, they have a special place in the chemistry of nitrogen-containing heterocyclic molecules. OBJECTIVES The objective of this study is to analyze the interaction of several heterocyclic molecules using molecular docking and machine learning approaches to find out the possible antibacterial drugs. METHODS The molecular docking analysis of heterocyclic-based analogues against the sarcin-Ricin Loop RNA from E. coli with a C2667-2'-OCF3 modification (PDB ID: 6ZYB) is discussed. RESULTS Many heterocyclic-based derivatives show several residual interaction, affinity, and hydrogen bonding with sarcin-Ricin Loop RNA from E. coli with a C2667-2'-OCF3 alteration which are identified by the investigation of in silico molecular docking analysis of such heterocyclic derivatives. CONCLUSION The dataset from the molecular docking study was used for additional optimum analysis, and the molecular descriptors were classified using a variety of machine learning classifiers, including the GB Classifier, CB Classifier, RF Classifier, SV Classifier, KNN Classifier, and Voting Classifier. The research presented here showed that heterocyclic derivatives may operate as potent antibacterial agents when combined with other compounds to produce highly efficient antibacterial agents.
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Affiliation(s)
- Shivangi Sharma
- Department of Applied Chemistry, Amity School of Engineering & Technology, Amity University Madhya Pradesh, Maharajpura Dang, Gwalior-474 005, India
| | - Rahul Choubey
- Department of Computer Science and Engineering, Amity School of Engineering & Technology, Amity University Madhya Pradesh, Maharajpura Dang, Gwalior-474 005, India
| | - Manish Gupta
- Department of Computer Science and Engineering, Amity School of Engineering & Technology, Amity University Madhya Pradesh, Maharajpura Dang, Gwalior-474 005, India
| | - Shivendra Singh
- Department of Applied Chemistry, Amity School of Engineering & Technology, Amity University Madhya Pradesh, Maharajpura Dang, Gwalior-474 005, India
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Lizazman MA, Jong VYM, Chua P, Lim WK, Karunakaran T. Phytochemicals from Calophyllum canum Hook f. ex T. Anderson and their neuroprotective effects. Nat Prod Res 2022; 37:2043-2048. [PMID: 35997666 DOI: 10.1080/14786419.2022.2116021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Previous phytochemical investigations reported that Calophyllum spp have biosynthesized a wide range of bioactive phenolics such as xanthones and coumarins. The phytochemical study conducted on the stem bark of C. canum has led to the isolation of eight trioxygenated xanthones namely: 5-methoxytrapezifolixanthone (1), 5-methoxyananixanthone (2), caloxanthone C (3), 1,5-dihydroxy-3-methoxy-4-isoprenylxanthone (4), 6-deoxyisojacareubin (5), euxanthone (6), trapezifolixanthone (7), ananixanthone (8), together with three common triterpenoids, β-sitosterol (9), friedelin (10), and stigmasterol (11). Furthermore, xanthones 1 and 2 were isolated for the first time as naturally occurring xanthones from the plant extract. The structures of these compounds were identified and elucidated using advanced spectroscopic techniques such as 1 D & 2 D NMR, MS, and FTIR. The neuroprotective property of selected compounds was tested through in vitro stroke model. Among all tested compounds, 1 µm of compounds 8, 9, and 10 showed significant neuroprotective activity via reduction of apoptosis by ∼ 50%.
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Affiliation(s)
- Mas Atikah Lizazman
- Faculty of Applied Science Studies, Universiti Teknologi MARA, Kota Samarahan, Sarawak, Malaysia
| | - Vivien Yi Mian Jong
- Faculty of Applied Science Studies, Universiti Teknologi MARA, Kota Samarahan, Sarawak, Malaysia
| | - PinFen Chua
- Department of Paraclinical Sciences, Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
| | - William K Lim
- Department of Paraclinical Sciences, Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
| | - Thiruventhan Karunakaran
- Centre for Drug Research, Universiti Sains Malaysia, Pulau Pinang, Malaysia.,School of Chemical Sciences, Universiti Sains Malaysia, Pulau Pinang, Malaysia
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Hambal M, Frengki F, Sari WE, Vanda H. In silico prediction of flavan-3-ol as a bioactive compound of Calophyllum macrophyllum as a potential drug against angiostrongylus eosinophilic meningitis. Vet World 2022; 15:1305-1313. [PMID: 35765470 PMCID: PMC9210856 DOI: 10.14202/vetworld.2022.1305-1313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 04/13/2022] [Indexed: 11/30/2022] Open
Abstract
Background and Aim: Angiostrongylus eosinophilic meningitis is caused by larvae of the rat lungworm Angiostrongylus cantonensis. It manifests as meningitis, radiculitis, cranial nerve abnormalities, and encephalitis, which can be fatal. A flavan-3-ol compound isolated from the bark of Calophyllum macrophyllum Scheff. has several medicinal properties, including antioxidant, anti-inflammatory, antidiabetic, and antibacterial activities. This compound is stronger than other types of flavan-3-ols such as catechin. This study aimed to identify the hydroxylation pattern of this flavan-3-ol compound and evaluated its potential as an anti-meningitis drug, using an in silico approach through pharmacophore and molecular docking methods. Materials and Methods: Pharmacokinetic and toxicological data were analyzed and supported by the server http://www.swissadme.ch/index.php and https://tox-new.charite.de/protox_II/index.php. The hydroxylation pattern of the flavan-3-ol compound was identified using shear reagents (MeOH, NaOH, NaOAc, HCl, and AlCl3). The CviR receptor (pdb id.3QP5) was used in the in silico approach, and seven ligands were downloaded from PubChem in “SMILES” format. Results: The spectroscopic analysis conducted using the shear reagents confirmed that the flavan-3-ol compound has a “p-diOH” pattern on the cinnamoyl ring. Pharmacophore analysis revealed this compound “hit” with pharmacophore features, and molecular docking analysis showed that this compound has a strong affinity with both receptors. Conclusion: The flavan-3-ol compound is a potential drug candidate for meningitis caused by pathogenic bacteria and the worm A. cantonensis. This result was supported by the pharmacokinetic profile, which had a very low toxicity level to the host. However, further investigation is required to confirm the data in vitro and in vivo.
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Affiliation(s)
- Muhammad Hambal
- Department of Parasitology, Faculty of Veterinary Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia
| | - Frengki Frengki
- Department of Pharmacology, Faculty of Veterinary Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia
| | - Wahyu Eka Sari
- Department of Biochemistry, Faculty of Veterinary Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia
| | - Henni Vanda
- Department of Pharmacology, Faculty of Veterinary Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia
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Murthy S, Hazli UHAM, Kong KW, Mai CW, Leong CO, Rahman NA, Lo KM, Chee CF. Identification of Novel Sesamol Dimers with Unusual Methylenedioxy Ring-Opening Skeleton and Evaluation of Their Antioxidant and Cytotoxic Activities. Curr Org Synth 2019; 16:1166-1173. [PMID: 31984923 DOI: 10.2174/1570179416666191003095253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 08/01/2019] [Accepted: 08/28/2019] [Indexed: 02/08/2023]
Abstract
BACKGROUND Sesamol is a widely used antioxidant for the food and pharmaceutical industries. The oxidation products of this compound may be accumulated in foods or ingested. Little is known about its effect on human health. OBJECTIVE It is of great interest to identify the oxidation products of sesamol that may be beneficial to humans. This study was undertaken to identify the oxidation products of sesamol and investigate their antioxidant and cytotoxic activities. MATERIALS AND METHODS Using the ferricyanide oxidation approach, four oxidation products of sesamol (2, 3, 20 & 21) have been identified. Structural elucidation of these compounds was established on the basis of their detailed NMR spectroscopic analysis, mass spectrometry and x-ray crystallography. Additionally, a formation mechanism of compound 20 was proposed based on high-resolution mass spectrometry-fragmentation method. The antioxidant activities of these compounds were determined by the DPPH, FRAP, and ABTS assays. The in vitro antiproliferative activity of these compounds was evaluated against a panel of human cancer cell lines as well as non-cancerous cells. RESULTS Two oxidation products of sesamol were found to contain an unusual methylenedioxy ring-opening skeleton, as evidenced by spectroscopic and x-ray crystallographic data. Among all compounds, 20 displayed impressive antiproliferative activities against a panel of human cancer cell lines yet remained non-toxic to noncancerous cells. The antioxidant activities of compound 20 are significantly weaker than sesamol as determined by the DPPH, FRAP, and ABTS assays. CONCLUSION The oxidation products of sesamol could be a valuable source of bioactive molecules. Compound 20 may be used as a potential lead molecule for cancer studies.
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Affiliation(s)
- Sudtha Murthy
- Nanotechnology and Catalysis Research Centre, University of Malaya, Kuala Lumpur, Malaysia
| | - Ummi H A M Hazli
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kin W Kong
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Chun-Wai Mai
- Department of Pharmaceutical Chemistry, School of Pharmacy, International Medical University, Kuala Lumpur, Malaysia
| | - Chee-Onn Leong
- Centre for Cancer and Stem Cell Research, Institute for Research, Development and Innovation, International Medical University, Kuala Lumpur, Malaysia
| | - Noorsaadah A Rahman
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Kong M Lo
- 8Research Centre for Crystalline Materials, School of Science and Technology, Sunway University, Selangor, Malaysia
| | - Chin F Chee
- Nanotechnology and Catalysis Research Centre, University of Malaya, Kuala Lumpur, Malaysia
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Mai CW, Kang YB, Nadarajah VD, Hamzah AS, Pichika MR. Drug-like dietary vanilloids induce anticancer activity through proliferation inhibition and regulation of bcl-related apoptotic proteins. Phytother Res 2018; 32:1108-1118. [PMID: 29464796 DOI: 10.1002/ptr.6051] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 01/09/2018] [Accepted: 01/11/2018] [Indexed: 02/05/2023]
Abstract
In this study, a series of 20 structurally similar vanilloids (Vn) were tested for their antiproliferative effects against 12 human cancer cells: human breast (MCF-7 and MDA-MB-231), cervical (HeLa), ovarian (Caov-3), lung (A549), liver (HepG2), colorectal (HT-29 and HCT116), nasopharyngeal (CNE-1 and HK-1), and leukemic (K562 and CEM-SS) cancer cells. Among all the tested vanilloids, Vn16 (6-shogaol) exhibited the most potent cytotoxic effects against human colorectal cancer cells (HT-29). The apoptotic induction effects exhibited by Vn16 on HT-29 cells were confirmed using dual staining fluorescence microscopy and enzyme-linked immunosorbent assay. The effects of Vn16 on regulation of 43 apoptotic-related markers were determined in HT-29. The results suggested that 8 apoptotic markers (caspase 8, BAD, BAX, second mitochondrial-derived activator, caspase 3, survivin, bcl-2, and cIAP-2) were either upregulated or downregulated. These results further support the chemopreventive properties of foods that contain vanilloids.
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Affiliation(s)
- Chun-Wai Mai
- Department of Pharmaceutical Chemistry, School of Pharmacy, International Medical University, Kuala Lumpur, Malaysia
| | - Yew-Beng Kang
- Department of Pharmaceutical Chemistry, School of Pharmacy, International Medical University, Kuala Lumpur, Malaysia
| | - Vishna Devi Nadarajah
- Department of Human Biology, School of Medicine, International Medical University, Kuala Lumpur, Malaysia
| | - Ahmad Sazali Hamzah
- Institute of Science, Universiti Teknologi MARA, Shah Alam, Selangor, Malaysia
| | - Mallikarjuna Rao Pichika
- Department of Pharmaceutical Chemistry, School of Pharmacy, International Medical University, Kuala Lumpur, Malaysia
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Chong YS, Mai CW, Leong CO, Wong LC. Lutein improves cell viability and reduces Alu RNA accumulation in hydrogen peroxide challenged retinal pigment epithelial cells. Cutan Ocul Toxicol 2018; 37:52-60. [PMID: 28554225 DOI: 10.1080/15569527.2017.1335748] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
PURPOSE Dysfunction of the microRNA (miRNA)-processing enzyme DICER1 and Alu RNA accumulation are linked to the pathogenesis of age-related macular degeneration (AMD). This study determined the optimal dose of lutein (LUT) and zeaxanthin (ZEA) to protect human retinal pigment epithelium (RPE) cells against hydrogen peroxide (H2O2). The effect of the optimal dose of LUT and ZEA as DICER1 and Alu RNA modulators in cultured human RPE cells challenged with H2O2 was investigated. MATERIALS AND METHODS ARPE-19 cells were pre-treated with LUT, ZEA, or both for 24 h before 200 μM H2O2 challenge. Cell viability was measured by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. DICER1 and Alu RNA were quantified by western blotting and real-time polymerase chain reaction, respectively. RESULTS H2O2 increased cell Alu RNA expression and decreased cell viability of ARPE-19, but had no significant impact on the DICER1 protein level. LUT, alone and in combination with ZEA pre-treatment, prior to H2O2 challenge significantly improved cell viability of ARPE-19 and reduced the level of Alu RNA compared to the negative control. CONCLUSIONS These results support the use of LUT alone, and in combination with ZEA, in AMD prevention and treatment. This study is also the first to report LUT modulating effects on Alu RNA.
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Affiliation(s)
- You Sheng Chong
- a School of Medicine , International Medical University , Kuala Lumpur , Malaysia
| | - Chun Wai Mai
- b Department of Pharmaceutical Chemistry, School of Pharmacy , International Medical University , Kuala Lumpur , Malaysia
| | - Chee Onn Leong
- c Department of Life Sciences, School of Pharmacy , International Medical University , Kuala Lumpur , Malaysia
| | - Lai Chun Wong
- b Department of Pharmaceutical Chemistry, School of Pharmacy , International Medical University , Kuala Lumpur , Malaysia
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Laopian F, Kaennakam S, Rassamee K, Siripong P, Tip-pyang S. Calaxanthones A-C, three new xanthones from the roots of Calophyllum calaba and the cytotoxicity. Nat Prod Res 2018; 33:1584-1590. [DOI: 10.1080/14786419.2018.1425849] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Fuengfa Laopian
- Faculty of Science, Department of Chemistry, Center of Excellence in Natural Products Chemistry, Chulalongkorn University, Bangkok, Thailand
| | - Sutin Kaennakam
- Faculty of Science, Department of Chemistry, Center of Excellence in Natural Products Chemistry, Chulalongkorn University, Bangkok, Thailand
| | - Kitiya Rassamee
- Natural Products Research Section, Research Division, National Cancer Institute, Bangkok, Thailand
| | - Pongpun Siripong
- Natural Products Research Section, Research Division, National Cancer Institute, Bangkok, Thailand
| | - Santi Tip-pyang
- Faculty of Science, Department of Chemistry, Center of Excellence in Natural Products Chemistry, Chulalongkorn University, Bangkok, Thailand
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