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Quintal Bojórquez NDC, Morales Mendoza LF, Hidalgo-Figueroa S, Hernández Álvarez AJ, Segura Campos MR. In silico analysis of the interaction of de novo peptides derived from Salvia hispanica with anticancer targetsEvaluation of the anticancer potential of de novo peptides derived from Salvia hispanica through molecular docking. J Biomol Struct Dyn 2024; 42:6119-6135. [PMID: 37453078 DOI: 10.1080/07391102.2023.2232045] [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: 11/21/2022] [Accepted: 06/25/2023] [Indexed: 07/18/2023]
Abstract
Cancer is one of the leading causes of death worldwide. Conventional cancer therapies are not selective to cancer cells resulting in serious side effects on patients. Thus, the need for complementary treatments that improve the patient's response to cancer therapy is highly important. To predict and evaluate the physicochemical characteristics and potential anticancer activity of the peptides identified from S. hispanica protein fraction <1 kDa through the use of in silico tools. Peptides derived from Salvia hispanica's protein fraction <1 kDa were identified and analyzed for the prediction of their physicochemical properties. The characterized peptide sequences were then submitted to a multi-criteria decision analysis to identify the peptides that possess the characteristics to potentially exert anticancer activity. Through molecular docking analysis, the potential anticancer activity of the Potentially Anticancer Peptide (PAP)-1, PAP-2, PAP-3, PAP-4, and PAP-5 was estimated by their binding interactions with cancer and apoptosis-related molecules. All five evaluated PAPs exhibited strong binding interactions (< -100 kcal/mol). However, PAP-3 showed the lowest binding free energies with several of the targets. Thus, PAP-3 shows potential to be used as a nutraceutical or ingredient for functional foods that adjuvate in cancer treatment. Conclusions: Through the molecular docking studies, the binding of the PAPs to target molecules of interest for cancer treatment was successfully simulated, from which PAP-3 exhibited the lowest binding free energies. Further in vitro and in vivo studies are required to validate the predictions obtained by the in silico analysis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Sergio Hidalgo-Figueroa
- CONAHCYT, Instituto Potosino de Investigación Científica y Tecnológica, San Luis Potosí, Mexico
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Bak-Sypien I, Pawlak T, Paluch P, Wroblewska A, Dolot R, Pawlowicz A, Szczesio M, Wielgus E, Kaźmierski S, Górecki M, Pawlowska R, Chworos A, Potrzebowski MJ. Influence of heterochirality on the structure, dynamics, biological properties of cyclic(PFPF) tetrapeptides obtained by solvent-free ball mill mechanosynthesis. Sci Rep 2024; 14:12825. [PMID: 38834643 DOI: 10.1038/s41598-024-63552-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024] Open
Abstract
Cyclic tetrapeptides c(Pro-Phe-Pro-Phe) obtained by the mechanosynthetic method using a ball mill were isolated in a pure stereochemical form as a homochiral system (all L-amino acids, sample A) and as a heterochiral system with D configuration at one of the stereogenic centers of Phe (sample B). The structure and stereochemistry of both samples were determined by X-ray diffraction studies of single crystals. In DMSO and acetonitrile, sample A exists as an equimolar mixture of two conformers, while only one is monitored for sample B. The conformational space and energetic preferences for possible conformers were calculated using DFT methods. The distinctly different conformational flexibility of the two samples was experimentally proven by Variable Temperature (VT) and 2D EXSY NMR measurements. Both samples were docked to histone deacetylase HDAC8. Cytotoxic studies proved that none of the tested cyclic peptide is toxic.
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Affiliation(s)
- Irena Bak-Sypien
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Tomasz Pawlak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Piotr Paluch
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Aneta Wroblewska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Rafał Dolot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Aleksandra Pawlowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 St., 61-704, Poznan, Poland
| | - Małgorzata Szczesio
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116 St., 90-924, Lodz, Poland
| | - Ewelina Wielgus
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Sławomir Kaźmierski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Marcin Górecki
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52 St., 01-224, Warsaw, Poland
| | - Roza Pawlowska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Arkadiusz Chworos
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Marek J Potrzebowski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland.
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Buthelezi MN, Tshililo VG, Kappo AP, Simelane MBC. Phytochemical evaluation of Ziziphus mucronata and Xysmalobium undulutum towards the discovery and development of anti-malarial drugs. Malar J 2024; 23:141. [PMID: 38734650 PMCID: PMC11088772 DOI: 10.1186/s12936-024-04976-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/04/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND The development of resistance by Plasmodium falciparum is a burdening hazard that continues to undermine the strides made to alleviate malaria. As such, there is an increasing need to find new alternative strategies. This study evaluated and validated 2 medicinal plants used in traditional medicine to treat malaria. METHODS Inspired by their ethnobotanical reputation of being effective against malaria, Ziziphus mucronata and Xysmalobium undulutum were collected and sequentially extracted using hexane (HEX), ethyl acetate (ETA), Dichloromethane (DCM) and methanol (MTL). The resulting crude extracts were screened for their anti-malarial and cytotoxic potential using the parasite lactate dehydrogenase (pLDH) and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, respectively. This was followed by isolating the active compounds from the DCM extract of Z. mucronata using silica gel chromatography and structural elucidation using spectroscopic techniques (NMR: 1H, 12C, and DEPT). The active compounds were then targeted against P. falciparum heat shock protein 70-1 (PfHsp70-1) using Autodock Vina, followed by in vitro validation assays using ultraviolet-visible (UV-VIS) spectroscopy and the malate dehydrogenase (MDH) chaperone activity assay. RESULTS The extracts except those of methanol displayed anti-malarial potential with varying IC50 values, Z. mucronata HEX (11.69 ± 3.84 µg/mL), ETA (7.25 ± 1.41 µg/mL), DCM (5.49 ± 0.03 µg/mL), and X. undulutum HEX (4.9 ± 0.037 µg/mL), ETA (17.46 ± 0.024 µg/mL) and DCM (19.27 ± 0.492 µg/mL). The extracts exhibited minimal cytotoxicity except for the ETA and DCM of Z. mucronata with CC50 values of 10.96 and 10.01 µg/mL, respectively. Isolation and structural characterization of the active compounds from the DCM extracts revealed that betulinic acid (19.95 ± 1.53 µg/mL) and lupeol (7.56 ± 2.03 µg/mL) were responsible for the anti-malarial activity and had no considerable cytotoxicity (CC50 > µg/mL). Molecular docking suggested strong binding between PfHsp70-1, betulinic acid (- 6.8 kcal/mol), and lupeol (- 6.9 kcal/mol). Meanwhile, the in vitro validation assays revealed the disruption of the protein structural elements and chaperone function. CONCLUSION This study proves that X undulutum and Z. mucronata have anti-malarial potential and that betulinic acid and lupeol are responsible for the activity seen on Z. mucronata. They also make a case for guided purification of new phytochemicals in the other extracts and support the notion of considering medicinal plants to discover new anti-malarials.
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Affiliation(s)
- Muzi N Buthelezi
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Auckland Park Kingsway Campus, Johannesburg, South Africa
| | - Vhahangwele G Tshililo
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Auckland Park Kingsway Campus, Johannesburg, South Africa
| | - Abidemi P Kappo
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Auckland Park Kingsway Campus, Johannesburg, South Africa
| | - Mthokozisi B C Simelane
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Auckland Park Kingsway Campus, Johannesburg, South Africa.
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Shi Y, Li W, Hu X, Zhang X, Huang X, Li Z, Zhai X, Shen T, Shi J, He Y, Zou X. A novel sustainable biomass-based fluorescent probe for sensitive detection of salicylic acid in rice. Food Chem 2024; 434:137260. [PMID: 37713760 DOI: 10.1016/j.foodchem.2023.137260] [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: 07/03/2023] [Revised: 08/10/2023] [Accepted: 08/22/2023] [Indexed: 09/17/2023]
Abstract
Herein, a ratiometric fluorescent probe was developed for sensitive detection of salicylic acid (SA) in rice using silk-derived carbon quantum dots @ Curcumin @ iron-based metal organic framework (SCQDs@Cur@Fe-MOFs). Fe-MOFs with porous structure not only provided holes for SCQDs to evade self-aggregation of SCQDs, but Fe2+ ions from MOFs was ingeniously employed to capture active sites of Cur, solving the problem of lacking sufficient specificity of Cur to SA while converting weak response signal to amplified "turn on" mode. Upon exposed to SA, the probe interacted with SA to form Cur-Fe2+-SA ternary complex, which inhibited the internal filtration effect between Cur and SCQDs, and triggered a cascade of response signaling. With this strategy, the proposed probe achieved sensitive determination of salicylic acid in rice with detection limit as low as 0.14 μmol/L. This study provides unique insight into constructing economical and eco-friendly fluorescent sensor for SA detection with superior performance.
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Affiliation(s)
- Yongqiang Shi
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Wenting Li
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Xuetao Hu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Xinai Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Xiaowei Huang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Zhihua Li
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Xiaodong Zhai
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Tingting Shen
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Jiyong Shi
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China; Joint Laboratory of China-UK on Food Nondestructive Sensing, Jiangsu University, Zhenjiang 212013, China; International Joint Research Laboratory of Intelligent Agriculture and Agri-products Processing, Jiangsu University, Zhenjiang 212013, China.
| | - Yong He
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Xiaobo Zou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China; Joint Laboratory of China-UK on Food Nondestructive Sensing, Jiangsu University, Zhenjiang 212013, China; International Joint Research Laboratory of Intelligent Agriculture and Agri-products Processing, Jiangsu University, Zhenjiang 212013, China.
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Patra M, Das D, Dey S, Koschella A, Heinze T. Structural and chemical insights into the prebiotic property of hemicellulosic polysaccharide from Santalum album L. Carbohydr Polym 2023; 321:121291. [PMID: 37739501 DOI: 10.1016/j.carbpol.2023.121291] [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: 06/14/2023] [Revised: 08/02/2023] [Accepted: 08/10/2023] [Indexed: 09/24/2023]
Abstract
Hemicellulose was extracted by alkali treatment of de-pectinated cell wall material of Santalum album L. (sandalwood) suspension culture cells. The physicochemical properties and prebiotic activities of a purified major fraction of Hemicellulose-B, termed as HB-I, were investigated. GC analysis of hydrolyzed and derivatized HB-I showed the presence of arabinose (~64 %), galactose (~16 %) and glucose (~16 %) as major monosaccharide units along with minor amount of rhamnose. Methylation and NMR studies on the purified polysaccharide revealed the presence of 6-β-d-Glcp, β-d-Galp, 3,5-α-l-Araf, α-l-Araf, 5-α-l-Araf, 2,3-α-l-Araf and, α-l-Rhap residues, from which a proposed structure of repeating units was established. The growth of probiotic Lactobacillus spp. strains L. acidophilus, L. casei, L. plantarum and L. rhamnosus was promoted while that of Escherichia coli was suppressed significantly in presence of HB-I. Our results highlight valorization of sandalwood biomass and explore the role of mixed α, β-linked heteroglycan as a potential prebiotic molecule thus indicating the possibility of development of low-cost bioprocesses for production of functional food ingredients.
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Affiliation(s)
- Moumita Patra
- Plant Biotechnology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Debsankar Das
- Department of Chemistry, Prabhat Kumar College, Contai, Purba Medinipur 721404, West Bengal, India.
| | - Satyahari Dey
- Plant Biotechnology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Andreas Koschella
- Friedrich Schiller University Jena, Institute for Organic Chemistry and Macromolecular Chemistry, Center of Excellence for Polysaccharide Research, Humboldtstraße 10, D-07743 Jena, Germany.
| | - Thomas Heinze
- Friedrich Schiller University Jena, Institute for Organic Chemistry and Macromolecular Chemistry, Center of Excellence for Polysaccharide Research, Humboldtstraße 10, D-07743 Jena, Germany.
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Shi Y, Zhang X, Yang Y, Cai T, Peng C, Wu L, Zhou L, Han J, Ma M, Zhu W, Xu Z. D3CARP: a comprehensive platform with multiple-conformation based docking, ligand similarity search and deep learning approaches for target prediction and virtual screening. Comput Biol Med 2023; 164:107283. [PMID: 37536095 DOI: 10.1016/j.compbiomed.2023.107283] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/15/2023] [Accepted: 07/28/2023] [Indexed: 08/05/2023]
Abstract
Resource- and time-consuming biological experiments are unavoidable in traditional drug discovery, which have directly driven the evolution of various computational algorithms and tools for drug-target interaction (DTI) prediction. For improving the prediction reliability, a comprehensive platform is highly expected as some previously reported webservers are small in scale, single-method, or even out of service. In this study, we integrated the multiple-conformation based docking, 2D/3D ligand similarity search and deep learning approaches to construct a comprehensive webserver, namely D3CARP, for target prediction and virtual screening. Specifically, 9352 conformations with positive control of 1970 targets were used for molecular docking, and approximately 2 million target-ligand pairs were used for 2D/3D ligand similarity search and deep learning. Besides, the positive compounds were added as references, and related diseases of therapeutic targets were annotated for further disease-based DTI study. The accuracies of the molecular docking and deep learning approaches were 0.44 and 0.89, respectively. And the average accuracy of five ligand similarity searches was 0.94. The strengths of D3CARP encompass the support for multiple computational methods, ensemble docking, utilization of positive controls as references, cross-validation of predicted outcomes, diverse disease types, and broad applicability in drug discovery. The D3CARP is freely accessible at https://www.d3pharma.com/D3CARP/index.php.
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Affiliation(s)
- Yulong Shi
- State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinben Zhang
- State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yanqing Yang
- State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tingting Cai
- State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Cheng Peng
- State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Leyun Wu
- State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liping Zhou
- State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaxin Han
- State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Minfei Ma
- State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiliang Zhu
- State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhijian Xu
- State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China.
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Jabir NR, Khan MS, Alafaleq NO, Naz H, Ahmed BA. Anticancer potential of yohimbine in drug-resistant oral cancer KB-ChR-8-5 cells. Mol Biol Rep 2022; 49:9565-9573. [PMID: 35970968 DOI: 10.1007/s11033-022-07847-7] [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: 06/07/2022] [Accepted: 08/05/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND The demand for environmentally friendly and cost-effective plant-based products for the development of cancer therapeutics has been increasing. Yohimbine (α2-adrenergic receptor antagonist) is a stimulant and aphrodisiac used to improve erectile dysfunction. In this study, we aimed to evaluate the anticancer potential of yohimbine in drug-resistant oral cancer KB-ChR-8-5 cells using different biomolecular techniques. METHODS We estimated the anticancer efficacy of yohimbine using different assays, such as MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) cell cytotoxicity, cell morphology, cell apoptosis, reactive oxygen species (ROS) formation, and modulation in the mitochondrial membrane potential (MMP). RESULTS Yohimbine showed a dose-dependent increase in cytotoxicity with a 50% inhibitory concentration (IC50) of 44 µM against KB-ChR-8-5 cancer cell lines. Yohimbine treatment at 40 µM and 50 µM resulted in a considerable change in cell morphology, including shrinkage, detachment, membrane blebbing, and deformed shape. Moreover, at the dose of IC50 and above, a significant induction was observed in the generation of ROS and depolarization of MMP. The possible mechanisms of action of yohimbine underlying the dose-dependent increase in cytotoxicity may be due to the induction of apoptosis, ROS generation, and modulation of MMP. CONCLUSION Overall, yohimbine showed a significant anticancer potential against drug-resistant oral cancer KB-ChR-8-5 cells. Our study suggests that besides being an aphrodisiac, yohimbine can be used as a drug repurposing agent. However, more research is required in different in vitro and in vivo models to confirm the feasibility of yohimbine in clinics.
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Affiliation(s)
- Nasimudeen R Jabir
- Department of Biochemistry, Centre for Research and Development, PRIST University, Vallam, Thanjavur, Tamil Nadu, 613403, India
| | - Mohd Shahnawaz Khan
- Department of Biochemistry, College of Sciences, King Saud University, Riyadh, 11451, Saudi Arabia.
| | - Nouf Omar Alafaleq
- Department of Biochemistry, College of Sciences, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Huma Naz
- Department of Medicine, University of Missouri, Columbia, MO, 65201, USA
| | - Bakrudeen Ali Ahmed
- Department of Biochemistry, Centre for Research and Development, PRIST University, Vallam, Thanjavur, Tamil Nadu, 613403, India.
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Cabral MB, Dela Cruz CJ, Sato Y, Oyong G, Rempillo O, Galvez MC, Vallar E. In Silico Approach in the Evaluation of Pro-Inflammatory Potential of Polycyclic Aromatic Hydrocarbons and Volatile Organic Compounds through Binding Affinity to the Human Toll-Like Receptor 4. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19148360. [PMID: 35886213 PMCID: PMC9318662 DOI: 10.3390/ijerph19148360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 06/30/2022] [Accepted: 07/06/2022] [Indexed: 12/04/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) and volatile organic compounds (VOCs) are widespread across the globe, existing in the environment in complex mixtures potentially capable of initiating respiratory illnesses. Here, we use an in silico approach to evaluate the potential pro-inflammatory effects of various carcinogenic PAHs and VOCs through their binding affinity towards the human toll-like receptor 4 (TLR4). For receptors and ligands, RCSB Protein Data Bank and PubChem were used in obtaining their 3D structures, respectively. Autodock Vina was utilized to obtain the best docking poses and binding affinities of each PAH and VOC. Out of the 14 PAHs included in this study, indeno(1,2,3-cd)pyrene, benzo(ghi)perylene, and benzo[a]pyrene had the highest binding affinity values of −10, −9, and −8.9 kcal/mol, respectively. For the VOCs, out of the 10 compounds studied, benzene, 1,4-dichlorobenzene, and styrene had the highest binding affinity values of −3.6, −3.9, and −4.6 kcal/mol, respectively. Compounds with higher affinity than LPS (−4.1 kcal/com) could potentially induce inflammation, while compounds with lower affinity would be less likely to induce an inflammatory response. Meanwhile, molecular dynamics simulation and RMSF statistical analysis proved that the protein, TLR4, stably preserve its conformation despite ligand interactions. Overall, the structure of the TLR4 was considered inflexible.
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Affiliation(s)
- Marie Beatriz Cabral
- Environment and RemoTe Sensing Research (EARTH) Laboratory, Department of Physics, College of Science, De La Salle University Manila, 2401 Taft Avenue, Manila 0922, Philippines; (M.B.C.); (C.J.D.C.); (Y.S.); (O.R.); (M.C.G.)
| | - Celine Joy Dela Cruz
- Environment and RemoTe Sensing Research (EARTH) Laboratory, Department of Physics, College of Science, De La Salle University Manila, 2401 Taft Avenue, Manila 0922, Philippines; (M.B.C.); (C.J.D.C.); (Y.S.); (O.R.); (M.C.G.)
| | - Yumika Sato
- Environment and RemoTe Sensing Research (EARTH) Laboratory, Department of Physics, College of Science, De La Salle University Manila, 2401 Taft Avenue, Manila 0922, Philippines; (M.B.C.); (C.J.D.C.); (Y.S.); (O.R.); (M.C.G.)
| | - Glenn Oyong
- Molecular Science Unit Laboratory, Center for Natural Sciences and Ecological Research, De La Salle University, 2401 Taft Avenue, Manila 0922, Philippines;
| | - Ofelia Rempillo
- Environment and RemoTe Sensing Research (EARTH) Laboratory, Department of Physics, College of Science, De La Salle University Manila, 2401 Taft Avenue, Manila 0922, Philippines; (M.B.C.); (C.J.D.C.); (Y.S.); (O.R.); (M.C.G.)
| | - Maria Cecilia Galvez
- Environment and RemoTe Sensing Research (EARTH) Laboratory, Department of Physics, College of Science, De La Salle University Manila, 2401 Taft Avenue, Manila 0922, Philippines; (M.B.C.); (C.J.D.C.); (Y.S.); (O.R.); (M.C.G.)
| | - Edgar Vallar
- Environment and RemoTe Sensing Research (EARTH) Laboratory, Department of Physics, College of Science, De La Salle University Manila, 2401 Taft Avenue, Manila 0922, Philippines; (M.B.C.); (C.J.D.C.); (Y.S.); (O.R.); (M.C.G.)
- Correspondence:
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9
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Zhang T, Li SM, Li YN, Cao JL, Xue H, Wang C, Jin CH. Atractylodin Induces Apoptosis and Inhibits the Migration of A549 Lung Cancer Cells by Regulating ROS-Mediated Signaling Pathways. Molecules 2022; 27:molecules27092946. [PMID: 35566297 PMCID: PMC9103034 DOI: 10.3390/molecules27092946] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 04/21/2022] [Accepted: 05/03/2022] [Indexed: 12/18/2022] Open
Abstract
Atractylodin (ATR) has anticancer effects on some tumor cells by inducing apoptosis, but its mechanism in lung cancer remains unclear. This study investigates the inhibitory effect of ATR on A549 lung cancer cells. Cell viability was detected by the Cell Counting Kit-8 assay, and results showed that ATR could significantly inhibit the proliferation of A549 cells. Apoptosis was detected by Annexin V-FITC/PI staining, and apoptosis rate and mitochondrial membrane potential were detected by flow cytometry. Results showed that the effect of ATR on the apoptosis of A549 cells was negatively correlated with the change in mitochondrial membrane potential. Western blot analysis showed that ATR regulated apoptosis induced by mitogen-activated protein kinase, signal transducer and activator of transcription 3, and nuclear factor kappa B signaling pathways. Analyses of reactive oxygen species (ROS), cell cycle, and cell migration showed that ATR induced intracellular ROS accumulation as an initiation signal to induce cell cycle arrest regulated by the AKT signaling pathway and cell migration inhibition regulated by the Wnt signaling pathway. Results showed that ATR can inhibit cell proliferation, induce cell apoptosis, induce cell cycle arrest, and inhibit the migration of A549 cells (p < 0.05 was considered statistically significant, * p < 0.05, ** p < 0.01 and *** p < 0.001).
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Affiliation(s)
- Tong Zhang
- College of Life Science & Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (T.Z.); (Y.-N.L.); (J.-L.C.); (H.X.)
| | - Shu-Mei Li
- Hemodialysis Center, Daqing Oilfield General Hospital, Daqing 163001, China;
| | - Yan-Nan Li
- College of Life Science & Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (T.Z.); (Y.-N.L.); (J.-L.C.); (H.X.)
| | - Jing-Long Cao
- College of Life Science & Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (T.Z.); (Y.-N.L.); (J.-L.C.); (H.X.)
| | - Hui Xue
- College of Life Science & Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (T.Z.); (Y.-N.L.); (J.-L.C.); (H.X.)
| | - Chang Wang
- College of Science, Heilongjiang Bayi Agricultural University, Daqing 163319, China
- Correspondence: (C.W.); (C.-H.J.)
| | - Cheng-Hao Jin
- College of Life Science & Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, China; (T.Z.); (Y.-N.L.); (J.-L.C.); (H.X.)
- National Coarse Cereals Engineering Research Center, Daqing 163319, China
- College of Food Science & Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, China
- Correspondence: (C.W.); (C.-H.J.)
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10
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Liao HJ, Tzen JTC. The Potential Role of Cyclopeptides from Pseudostellaria heterophylla, Linum usitatissimum and Drymaria diandra, and Peptides Derived from Heterophyllin B as Dipeptidyl Peptidase IV Inhibitors for the Treatment of Type 2 Diabetes: An In Silico Study. Metabolites 2022; 12:metabo12050387. [PMID: 35629891 PMCID: PMC9146144 DOI: 10.3390/metabo12050387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/17/2022] [Accepted: 04/19/2022] [Indexed: 02/04/2023] Open
Abstract
Dipeptidyl peptidase 4 (DPP4) inhibitors can treat type 2 diabetes by slowing GLP-1 degradation to increase insulin secretion. Studies have reported that Pseudostellaria heterophylla, Linum usita-tissimum (flaxseed), and Drymaria diandra, plants rich in Caryophyllaceae-type cyclopeptides and commonly used as herbal or dietary supplements, are effective in controlling blood sugar. The active site of DPP4 is in a cavity large enough to accommodate their cyclopeptides. Molecular modeling by AutoDock Vina reveals that certain cyclopeptides in these plants have the potential for DPP4 inhibition. In particular, “Heterophyllin B” from P. heterophylla, “Cyclolinopeptide C” from flaxseed, and “Diandrine C” from D. diandra, with binding affinities of −10.4, −10.0, and −10.7 kcal/mol, are promising. Docking suggests that DPP4 inhibition may be one of the reasons why these three plants are beneficial for lowering blood sugar. Because many protein hydrolysates have shown the effect of DPP4 inhibition, a series of peptides derived from Heterophyllin B precursor “IFGGLPPP” were included in the study. It was observed that IFWPPP (−10.5 kcal/mol), IFGGWPPP (−11.4 kcal/mol), and IFGWPPP (−12.0 kcal/mol) showed good binding affinity and interaction for DPP4. Various IFGGLPPP derivatives have the potential to serve as scaffolds for the design of novel DPP4 inhibitors.
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11
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Anjomshoa M, Sahihi M, Fatemi SJ, Shayegan S, Farsinejad A, Amirheidari B. In vitro biological and in silico molecular docking and ADME studies of a substituted triazine-coordinated cadmium(II) ion: efficient cytotoxicity, apoptosis, genotoxicity, and nuclease-like activity plus binding affinity towards apoptosis-related proteins. Biometals 2022; 35:549-572. [PMID: 35366135 DOI: 10.1007/s10534-022-00387-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 03/07/2022] [Indexed: 12/24/2022]
Abstract
A cadmium(II) complex containing dppt ligand with the formula [CdCl2(dppt)2], where dppt is 5,6-diphenyl-3-(2-pyridyl)-1,2,4-triazine was synthesized, elucidated and submitted to in vitro cytotoxicity studies against human breast (MCF-7), glioblastoma (U-87), and lung (A549) cancer cell lines as well as mouse embryo normal cell line (NIH/3T3), in comparison with cisplatin employing MTT assay over 24 and 48 h. The complex exhibited the highest cytotoxic effect against MCF-7 cells among the other three cell lines with IC50 values of 8.7 ± 0.5 (24 h) and 1.2 ± 0.7 µM (48 h). Significantly, flow cytometric assessment of the complex-treated MCF-7 and U-87 cells demonstrated a dose-dependent induced apoptotic cell death. The cellular morphological changes were in concord with cytotoxicity and flow cytometric results. The results of comet assay showed that the complex is able to induce DNA damage in MCF-7 cells. These observations are of importance, as sustained damage to cellular DNA could lead to apoptotic cell death. The results of DNA-binding studies indicated that the complex fits into the DNA minor groove and interacts with DNA via a partial intercalation. Moreover, the complex was able to efficiently cleave pUC19 DNA through a hydrolytic mechanism. The binding affinity between the complex and apoptosis-relevant protein targets including APAF1, Bax, Bcl-2, Cas3, Cas7, and Cas9 was evaluated through molecular docking studies. In silico virtual studies revealed the complex's strong affinity towards apoptosis-related proteins; therefore the complex can act as a potential apoptosis inducer. Physicochemical, pharmacokinetics, lipophilicity, drug-likeness, and medicinal chemistry properties of the complex were also predicted through in silico absorption, distribution, metabolism and excretion studies.
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Affiliation(s)
- Marzieh Anjomshoa
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran.
| | - Mehdi Sahihi
- Roberval Laboratory, Université de Technologie de Compiègne, Alliance Sorbonne Université, Compiègne, France
| | | | - Shika Shayegan
- Department of Pharmacy, Eastern Mediterranean University, TRNC via Mersin 10, Famagusta, Turkey
| | - Alireza Farsinejad
- Cell Therapy and Regenerative Medicine Comprehensive Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Bagher Amirheidari
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran. .,Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran.
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12
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Purnama A, Rizki DR, Qanita I, Iqhrammullah M, Ahmad K, Mardina V, Puspita K, Hasballah K. Molecular docking investigation of calotropone as a potential natural therapeutic agent against pancreatic cancer. J Adv Pharm Technol Res 2022; 13:44-49. [PMID: 35223440 PMCID: PMC8820343 DOI: 10.4103/japtr.japtr_143_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/01/2021] [Accepted: 12/17/2021] [Indexed: 11/12/2022] Open
Abstract
A natural bioactive compound named calotropone has been reported as a drug candidate for several cancers, including pancreatic cancers. Herein, we used molecular docking approach to test the possible mechanisms of action of calotropone in inhibiting the growth of pancreatic cell cancer with gemcitabine as the positive control. By employing AutoDock Vina, we studied the molecular interaction between calotropone and pancreatic cancer-associated proteins, namely Glucosaminyl (N-Acetyl) Transferase 3, Glutamic-Oxaloacetic Transaminase 1, Tyrosine-protein kinase Met (c-Met), peroxisome proliferator-activated receptor γ, Budding Uninhibited by Benzimidazole 1, A Disintegrin and Metalloproteinase 10, Sex-determining region Y and Nuclear Factor kappa Beta (Nf-Kβ). Higher affinity energies of calotropone toward the aforementioned proteins (ranging from ‒7.3 to ‒9.3 kcal/mol) indicate that calotropone may work in the same manner as anticancer drug gemcitabine. Highest docking score was found at the interaction of calotropone and Nf-Kβ (‒9.3 kcal/mol).
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Affiliation(s)
- Agnia Purnama
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Syiah Kuala, Banda Aceh, Indonesia
| | | | - Intan Qanita
- School of Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia
| | - Muhammad Iqhrammullah
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Syiah Kuala, Banda Aceh, Indonesia.,Graduate School of Mathematics and Applied Sciences, Universitas Syiah Kuala, Banda Aceh, Indonesia
| | - Khairunnas Ahmad
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Syiah Kuala, Banda Aceh, Indonesia
| | - Vivi Mardina
- Department of Biology, Faculty of Engineering, Universitas Samudra. Jl. Prof. Dr. Syarief Thayeb, Meurandeh, Langsa Lama, Langsa, Aceh, Indonesia
| | - Kana Puspita
- Department of Chemistry Education, Faculty of Education and Teacher Training, Universitas Syiah Kuala, Banda Aceh, Indonesia
| | - Kartini Hasballah
- Department of Pharmacology, Faculty of Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia
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13
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Ozturk H, Yorulmaz N, Durgun M, Basoglu H. In silicoinvestigation of Alliin as potential activator for AMPA receptor. Biomed Phys Eng Express 2021; 8. [PMID: 34724652 DOI: 10.1088/2057-1976/ac351c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 11/01/2021] [Indexed: 11/12/2022]
Abstract
Natural products from plants, such as flavonoids, arouse immense interest in medicine because of the therapeutic and many other bioactive properties. The molecular docking is a very useful method to screen the molecules based on their free binding energies and give important structural suggestions about how molecules might activate or inhibit the target receptor by comparing reference molecules. Alliin and Allicin differ from many other flavonoids because of containing no benzene rings and having nitrogen and sulfur atoms in their structure. In this study Alliin and Allicin affinity on AMPA, NMDA and GABA-A receptors were evaluated in the central nervous system by using the molecular docking method. Both Alliin and Allicin indicated no inhibitory effects. However Alliin showed significant selectivity to human AMPA receptor (3RN8) as an excitatory. The binding energy of glutamate to 3RN8 was -6.61 kcal mol-1, while the binding energy of Allin was -8.08 kcal mol-1. Furthermore Alliin's affinity to the other AMPA and NMDA receptors is quite satisfactory compared to the reference molecule glutamate. In conclusion based on the molecular docking study, Alliin can be useful for synaptic plasticity studies whereas might be enhance seizure activity because of the increased permeability to cations. It also can be beneficial to improve learning and memory and can be used as a supportive product to the hypofunction of NMDA associated problems.
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Affiliation(s)
- Hilal Ozturk
- Karadeniz Technical University, Faculty of Medicine, Department of Biophysics, Trabzon-Turkey.,Istanbul University-Cerrahpasa , Faculty of Medicine, Department of Biophysics, Istanbul-Turkey
| | - Nuri Yorulmaz
- Harran University, Faculty of Science, Department of Physics, Sanliurfa-Turkey
| | - Mustafa Durgun
- Harran University, Faculty of Science, Department of Chemistry, Sanliurfa-Turkey
| | - Harun Basoglu
- Karadeniz Technical University, Faculty of Medicine, Department of Biophysics, Trabzon-Turkey
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14
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Purnama A, Mardina V, Puspita K, Qanita I, Rizki DR, Hasballah K, Iqbal M, Sarong M. Molecular docking of two cytotoxic compounds from Calotropis gigantea leaves against therapeutic molecular target of pancreatic cancer. NARRA J 2021; 1:e37. [PMID: 38449465 PMCID: PMC10914070 DOI: 10.52225/narraj.v1i2.37] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/03/2021] [Indexed: 03/08/2024]
Abstract
The utilization of natural compounds as therapeutic agents to treat pancreatic cancer has recently focused on natural drug research. Calotropis gigantea has long been believed to be a medicinal plant that helps in treating various diseases. The bioactive compounds 9-metoxipinoresinol and isoliquiritigenin isolated from C. gigantea leaves are proven to act as therapeutic agents by inhibiting the cancer cell growth of Panc-1 cells. This study aimed to screen the potential molecular inhibition mechanisms of 9-metoxipinoresinol and isoliquiritigenin against pancreatic cancer development in-silico. We analyzed the activity of the aforementioned two compounds as inhibitors of several proteins that play a role in the growth of pancreatic cancer cells, such as GCNT3, GOT1, c-Met, PPARγ, BUB1, and NF-κβ, through molecular docking investigation. Our data suggested that 9-metoxipinoresinol and isoliquiritigenin were able to have well interaction with the target proteins, in which the predicted affinity energy ranged between -6.8 and 8.7 kcal/mol. The docking scores of 9-metoxipinoresinol and isoliquiritigenin were higher than the standard drug used (gemcitabine). Based on the binding affinity energy, GCNT3 and BUB1 are potentially to be used as target molecules for cancer therapy using 9-metoxipinoresinol and isoliquiritigenin, respectively.
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Affiliation(s)
- Agnia Purnama
- Department of Chemistry, Universitas Syiah Kuala, Banda Aceh, Aceh, Indonesia
| | - Vivi Mardina
- Department of Biology, Faculty of Engineering, Universitas Samudra, Langsa, Aceh, Indonesia
| | - Kana Puspita
- Department of Chemistry Education, Faculty of Education and Teacher Training, Universitas Syiah Kuala, Banda Aceh, Aceh, Indonesia
| | - Intan Qanita
- School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh, Indonesia
| | - Diva R. Rizki
- School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh, Indonesia
| | - Kartini Hasballah
- Department of Pharmacology, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh, Indonesia
| | - Mudassar Iqbal
- Department of Agricultural Chemistry and Biochemistry, Agricultural University, Peshawar, Pakistan
| | - Murniana Sarong
- Department of Chemistry, Universitas Syiah Kuala, Banda Aceh, Aceh, Indonesia
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15
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Chai TT, Ee KY, Kumar DT, Manan FA, Wong FC. Plant Bioactive Peptides: Current Status and Prospects Towards Use on Human Health. Protein Pept Lett 2021; 28:623-642. [PMID: 33319654 DOI: 10.2174/0929866527999201211195936] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/02/2020] [Accepted: 11/06/2020] [Indexed: 12/28/2022]
Abstract
Large numbers of bioactive peptides with potential applications in protecting against human diseases have been identified from plant sources. In this review, we summarized recent progress in the research of plant-derived bioactive peptides, encompassing their production, biological effects, and mechanisms. This review focuses on antioxidant, antimicrobial, antidiabetic, and anticancer peptides, giving special attention to evidence derived from cellular and animal models. Studies investigating peptides with known sequences and well-characterized peptidic fractions or protein hydrolysates will be discussed. The use of molecular docking tools to elucidate inter-molecular interactions between bioactive peptides and target proteins is highlighted. In conclusion, the accumulating evidence from in silico, in vitro and in vivo studies to date supports the envisioned applications of plant peptides as natural antioxidants as well as health-promoting agents. Notwithstanding, much work is still required before the envisioned applications of plant peptides can be realized. To this end, future researches for addressing current gaps were proposed.
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Affiliation(s)
- Tsun-Thai Chai
- Department of Chemical Science, Faculty of Science, Universiti Tunku Abdul Rahman, Kampar 31900, Malaysia
| | - Kah-Yaw Ee
- Center for Biodiversity Research, Universiti Tunku Abdul Rahman, Kampar 31900, Malaysia
| | - D Thirumal Kumar
- Department of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai 602 105, India
| | - Fazilah Abd Manan
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia
| | - Fai-Chu Wong
- Department of Chemical Science, Faculty of Science, Universiti Tunku Abdul Rahman, Kampar 31900, Malaysia
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16
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Asiedu SO, Kwofie SK, Broni E, Wilson MD. Computational Identification of Potential Anti-Inflammatory Natural Compounds Targeting the p38 Mitogen-Activated Protein Kinase (MAPK): Implications for COVID-19-Induced Cytokine Storm. Biomolecules 2021; 11:653. [PMID: 33946644 PMCID: PMC8146027 DOI: 10.3390/biom11050653] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 02/06/2023] Open
Abstract
Severely ill coronavirus disease 2019 (COVID-19) patients show elevated concentrations of pro-inflammatory cytokines, a situation commonly known as a cytokine storm. The p38 MAPK receptor is considered a plausible therapeutic target because of its involvement in the platelet activation processes leading to inflammation. This study aimed to identify potential natural product-derived inhibitory molecules against the p38α MAPK receptor to mitigate the eliciting of pro-inflammatory cytokines using computational techniques. The 3D X-ray structure of the receptor with PDB ID 3ZS5 was energy minimized using GROMACS and used for molecular docking via AutoDock Vina. The molecular docking was validated with an acceptable area under the curve (AUC) of 0.704, which was computed from the receiver operating characteristic (ROC) curve. A compendium of 38,271 natural products originating from Africa and China together with eleven known p38 MAPK inhibitors were screened against the receptor. Four potential lead compounds ZINC1691180, ZINC5519433, ZINC4520996 and ZINC5733756 were identified. The compounds formed strong intermolecular bonds with critical residues Val38, Ala51, Lys53, Thr106, Leu108, Met109 and Phe169. Additionally, they exhibited appreciably low binding energies which were corroborated via molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations. The compounds were also predicted to have plausible pharmacological profiles with insignificant toxicity. The molecules were also predicted to be anti-inflammatory, kinase inhibitors, antiviral, platelet aggregation inhibitors, and immunosuppressive, with probable activity (Pa) greater than probable inactivity (Pi). ZINC5733756 is structurally similar to estradiol with a Tanimoto coefficient value of 0.73, which exhibits anti-inflammatory activity by targeting the activation of Nrf2. Similarly, ZINC1691180 has been reported to elicit anti-inflammatory activity in vitro. The compounds may serve as scaffolds for the design of potential biotherapeutic molecules against the cytokine storm associated with COVID-19.
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Affiliation(s)
- Seth O. Asiedu
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra P.O. Box LG 581, Ghana; (S.O.A); (M.D.W)
| | - Samuel K. Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 77, Ghana;
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra P.O. Box LG 54, Ghana
| | - Emmanuel Broni
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 77, Ghana;
| | - Michael D. Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra P.O. Box LG 581, Ghana; (S.O.A); (M.D.W)
- Department of Medicine, Loyola University Medical Center, Maywood, IL 60153, USA
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17
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Wong FC, Ong JH, Kumar DT, Chai TT. In Silico Identification of Multi-target Anti-SARS-CoV-2 Peptides from Quinoa Seed Proteins. Int J Pept Res Ther 2021; 27:1837-1847. [PMID: 33867899 PMCID: PMC8034280 DOI: 10.1007/s10989-021-10214-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2021] [Indexed: 12/23/2022]
Abstract
Peptides are promising antagonists against severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2). To expedite drug discovery, a computational approach is widely employed for the initial screening of anti-SARS-CoV-2 candidates. This study aimed to investigate the potential of peptides from quinoa seed proteins as multi-target antagonists against SARS-CoV-2 spike glycoprotein receptor-binding domain, main protease, and papain-like protease. Five quinoa proteins were hydrolyzed in silico by papain and subtilisin. Among the 1465 peptides generated, seven could interact stably with the key binding residues and catalytic residues of the viral targets, mainly via hydrogen bonds and hydrophobic interactions. The seven peptides were comparable or superior to previously reported anti-SARS-CoV-2 peptides based on docking scores. Key residues in the seven peptides contributing to binding to viral targets were determined by computational alanine scanning. The seven peptides were predicted in silico to be non-toxic and non-allergenic. The peptides ranged between 546.66 and 3974.87 g/mol in molecular mass, besides exhibiting basic and cationic properties (isoelectric points: 8.26-12.10; net charges: 0.1-4.0). Among the seven peptides, VEDKGMMHQQRMMEKAMNIPRMCGTMQRKCRMS was found to bind the largest number of key residues on the targets. In conclusion, seven putative non-toxic, non-allergenic, multi-target anti-SARS-CoV-2 peptides were identified from quinoa seed proteins. The in vitro and in vivo efficacies of the seven peptides against SARS-CoV-2 deserve attention in future bench-top testing. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10989-021-10214-y.
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Affiliation(s)
- Fai-Chu Wong
- Department of Chemical Science, Faculty of Science, Universiti Tunku Abdul Rahman, 31900 Kampar, Malaysia
- Center for Agriculture and Food Research, Universiti Tunku Abdul Rahman, 31900 Kampar, Malaysia
| | - Joe-Hui Ong
- Department of Chemical Science, Faculty of Science, Universiti Tunku Abdul Rahman, 31900 Kampar, Malaysia
| | - D. Thirumal Kumar
- Department of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, 602 105 Tamil Nadu India
| | - Tsun-Thai Chai
- Department of Chemical Science, Faculty of Science, Universiti Tunku Abdul Rahman, 31900 Kampar, Malaysia
- Center for Agriculture and Food Research, Universiti Tunku Abdul Rahman, 31900 Kampar, Malaysia
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18
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Malami I, Bunza AM, Alhassan AM, Muhammad A, Abubakar IB, Yunusa A, Waziri PM, Etti IC. Dihydroartemisinin as a potential drug candidate for cancer therapy: a structural-based virtual screening for multitarget profiling. J Biomol Struct Dyn 2020; 40:1347-1362. [PMID: 32964804 DOI: 10.1080/07391102.2020.1824811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Cancer is a rapidly growing non-communicable disease worldwide that is responsible for high mortality rates, which account for 9.6 million death in 2018. Dihydroartemisinin (DHA) is an active metabolite of artemisinin, an active principle present in the Chinese medicinal plant Artemisia annua used for malaria treatment. Dihydroartemisinin possesses remarkable and selective anticancer properties however the underlying mechanism of the antitumor effects of DHA from the structural point of view is still not yet elucidated. In the present study, we employed molecular docking simulation techniques using Autodock suits to access the binding properties of dihydroartemisinin to multiple protein targets implicated in cancer pathogenesis. Its potential targets with comprehensive pharmacophore were predicted using a PharmMapper database. The co-crystallised structures of the protein were obtained from a Protein Data Bank and prepared for molecular docking simulation. Out of the 24 selected protein targets, DHA has shown about 29% excellent binding to the targets compared to their co-crystallised ligand. Additionally, 75% of the targets identified for dihydroartemisinin binding are protein kinases, and 25% are non-protein kinases. Hydroxyl functional group of dihydroartemisinin contributed to 58.5% of the total hydrogen interactions, while pyran (12.2%), endoperoxide (9.8%), and oxepane (19.5%) contributed to the remaining hydrogen bonding. The present findings have elucidated the possible antitumor properties of dihydroartemisinin through the structural-based virtual studies, which provides a lead to a safe and effective anticancer agent useful for cancer therapy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ibrahim Malami
- Department of Pharmacognosy and Ethnopharmacy, Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria.,Centre for Advanced Medical Research and Training (CAMRET), Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Aisha Muktar Bunza
- Department of Pharmacognosy and Ethnopharmacy, Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Alhassan Muhammad Alhassan
- Department of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Aliyu Muhammad
- Department of Biochemistry, Faculty of life Sciences, Ahmadu Bello University, Zaria, Nigeria
| | | | - Abdulmajeed Yunusa
- Department of Pharmacology and Therapeutics, College of Health Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Peter M Waziri
- Department of Biochemistry, Kaduna State University, Kaduna, Nigeria
| | - Imaobong C Etti
- Department of Pharmacology and Toxicology, University of Uyo, Uyo, Nigeria
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