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Zhang L, Lin L, Hu Y, Wu D, Zhang Z, Chen C, Wang L, Li J. Debittering of Emblica ( Phyllanthus emblica L.) fruit powder: Preparation and biological activity. Food Chem X 2024; 21:100853. [PMID: 38282828 PMCID: PMC10818184 DOI: 10.1016/j.fochx.2023.100853] [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: 05/16/2023] [Revised: 08/27/2023] [Accepted: 08/29/2023] [Indexed: 01/30/2024] Open
Abstract
Emblica, also known as Phyllanthus emblica L., is a drug homologous food that is rich in polyphenols with various biological activities. However, its bitterness and astringency pose a significant challenge to its utilization in food products. In this study, we aimed to identify the optimal conditions for debittering Emblica. Our findings revealed that the best debittering conditions were: temperature = 50 °C, pH = 4, α-l-rhamnosidase concentration 200 U/g, and time = 5 h. High-performance liquid chromatography (HPLC) and molecular docking analysis revealed that enzymatic hydrolysis partially removed bitterness compounds. The results of antioxidant activity, xanthine oxidase, and α-glucosidase inhibitory activity assays confirmed that the Emblica fruit powder still exhibited good biological activity after enzymatic debitterization. Moreover, gastric fluids treatment might contribute to the above enhancing effect of enzymatic hydrolysates of Emblica. This study provided a theoretical basis for promoting the processing and utilization of Emblica fruit powder, as well as understanding its biological activity.
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Affiliation(s)
- Lingyu Zhang
- College of Marine Food and Biological Engineering, Jimei University, Xiamen 361021, China
- Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Xiamen 361021, China
| | - Liting Lin
- College of Marine Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Yunxuan Hu
- College of Marine Food and Biological Engineering, Jimei University, Xiamen 361021, China
- Dazhou Xinyan (Xiamen) Biotechnology Co., Ltd, Xiamen 361021, Fujian, China
| | - Daren Wu
- College of Marine Food and Biological Engineering, Jimei University, Xiamen 361021, China
- Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Xiamen 361021, China
| | - Zhengxiao Zhang
- College of Marine Food and Biological Engineering, Jimei University, Xiamen 361021, China
- Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Xiamen 361021, China
| | - Chaoxiang Chen
- College of Marine Food and Biological Engineering, Jimei University, Xiamen 361021, China
- Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Xiamen 361021, China
| | - Li Wang
- College of Marine Food and Biological Engineering, Jimei University, Xiamen 361021, China
- Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Xiamen 361021, China
| | - Jian Li
- College of Marine Food and Biological Engineering, Jimei University, Xiamen 361021, China
- Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Xiamen 361021, China
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Ahmad B, Saeed A, Al-Amery A, Celik I, Ahmed I, Yaseen M, Khan IA, Al-Fahad D, Bhat MA. Investigating Potential Cancer Therapeutics: Insight into Histone Deacetylases (HDACs) Inhibitions. Pharmaceuticals (Basel) 2024; 17:444. [PMID: 38675404 PMCID: PMC11054547 DOI: 10.3390/ph17040444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Histone deacetylases (HDACs) are enzymes that remove acetyl groups from ɛ-amino of histone, and their involvement in the development and progression of cancer disorders makes them an interesting therapeutic target. This study seeks to discover new inhibitors that selectively inhibit HDAC enzymes which are linked to deadly disorders like T-cell lymphoma, childhood neuroblastoma, and colon cancer. MOE was used to dock libraries of ZINC database molecules within the catalytic active pocket of target HDACs. The top three hits were submitted to MD simulations ranked on binding affinities and well-occupied interaction mechanisms determined from molecular docking studies. Inside the catalytic active site of HDACs, the two stable inhibitors LIG1 and LIG2 affect the protein flexibility, as evidenced by RMSD, RMSF, Rg, and PCA. MD simulations of HDACs complexes revealed an alteration from extended to bent motional changes within loop regions. The structural deviation following superimposition shows flexibility via a visual inspection of movable loops at different timeframes. According to PCA, the activity of HDACs inhibitors induces structural dynamics that might potentially be utilized to define the nature of protein inhibition. The findings suggest that this study offers solid proof to investigate LIG1 and LIG2 as potential HDAC inhibitors.
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Affiliation(s)
- Basharat Ahmad
- School of Life Science and Technology, Center for Informational Biology, University of Electronics Science and Technology of China, Chengdu 610056, China
| | - Aamir Saeed
- Department of Bioinformatics, Hazara University Mansehra, Mansehra 21120, Pakistan
| | - Ahmed Al-Amery
- Department of Physiology and Medical Physics, College of Medicine, University of Thi-Qar, Nasiriyah 64001, Iraq
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, 38280 Kayseri, Turkey;
| | - Iraj Ahmed
- Atta-Ur-Rehman School of Applied Biosciences (ASAB), National University of Science and Technology (NUST), Islamabad 44000, Pakistan;
| | - Muhammad Yaseen
- Institute of Chemical Sciences, University of Swat, Charbagh 19130, Pakistan;
| | - Imran Ahmad Khan
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan;
| | - Dhurgham Al-Fahad
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Thi-Qar, Nasiriyah 64001, Iraq;
| | - Mashooq Ahmad Bhat
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11421, Saudi Arabia
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Taysi MR, Kirici M, Kirici M, Tuzun B, Poustforoosh A. Antioxidant enzyme activities, molecular docking studies, MM-GBSA, and molecular dynamic of chlorpyrifos in freshwater fish Capoeta umbla. J Biomol Struct Dyn 2024; 42:163-176. [PMID: 36974945 DOI: 10.1080/07391102.2023.2192807] [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: 10/15/2022] [Accepted: 03/10/2023] [Indexed: 03/29/2023]
Abstract
Chlorpyrifos (CPF), which was started to be used in 1965, is a broad spectrum organophosphate insecticide that is used more and more day by day. Commonly used to control pests in farmland and homes, CPF is more toxic to fish than organochlorine compounds. CPF poses a serious threat to the health of humans and aquatic organisms. This paper studies the relationship between CPF exposure and antioxidant enzyme activities in gill, kidney and liver tissues of Capoeta umbla. Different time intervals (12, 24, 48, 72, and 96 h) and CPF doses (55 and 110 µg L-1) were used in the study. Spectrophotometrical measures were taken in all tissues for antioxidant enzyme activities and malondialdehyde (MDA) levels, as indices of the lipid peroxidation (LPO). A positive relationship between CPF and MDA levels was found in the study at a statistically significant level (p < 0.05). The study also found a negative relationship between CPF levels and catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GPx), and glutathione reductase (GR) activity. Independent variables in the study can act as biomarkers of CPF exposure. The study recommends employing proper ecotoxicological risk evaluations in cases of CPF usage as a pesticide. The activities of the studied molecules against various proteins that are crystal structure of human peroxiredoxin 5 (PDB ID: 1HD2) has docking score value is -2.67, crystal structure of Bovine Xanthine Oxidase (PDB ID: 3NRZ) has docking score value is -3.76, and crystal structure of antibacterial FabH (PDB ID: 4Z8D) has docking score value is -3.16, were compared. Molecular dynamic (MD) calculations were made in 100 ns. MM/GBSA methods are calculated binding free energy. Afterwards, ADME/T analysis was performed to examine the some properties of the molecules.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mehmet Reşit Taysi
- Department of Fisheries, Faculty of Agriculture, Bingol University, Bingöl, Turkey
| | - Muammer Kirici
- Department of Veterinary Health, Food Agriculture and Livestock Vocational School, Bingöl University, Bingöl, Turkey
| | - Mahinur Kirici
- Department of Chemistry, Faculty of Arts and Science, Bingöl University, Bingöl, Turkey
| | - Burak Tuzun
- Plant and Animal Production Department, Technical Sciences Vocational School of Sivas, Sivas Cumhuriyet University, Sivas, Turkey
| | - Alireza Poustforoosh
- Chemical Engineering Department, Faculty of Engineering, Shahid Bahonar University of Kerman, Kerman, Iran
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4
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Georgiou N, Kakava MG, Routsi EA, Petsas E, Stavridis N, Freris C, Zoupanou N, Moschovou K, Kiriakidi S, Mavromoustakos T. Quercetin: A Potential Polydynamic Drug. Molecules 2023; 28:8141. [PMID: 38138630 PMCID: PMC10745404 DOI: 10.3390/molecules28248141] [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: 11/27/2023] [Revised: 12/12/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023] Open
Abstract
The study of natural products as potential drug leads has gained tremendous research interest. Quercetin is one of those natural products. It belongs to the family of flavonoids and, more specifically, flavonols. This review summarizes the beneficial pharmaceutical effects of quercetin, such as its anti-cancer, anti-inflammatory, and antimicrobial properties, which are some of the quercetin effects described in this review. Nevertheless, quercetin shows poor bioavailability and low solubility. For this reason, its encapsulation in macromolecules increases its bioavailability and therefore pharmaceutical efficiency. In this review, a brief description of the different forms of encapsulation of quercetin are described, and new ones are proposed. The beneficial effects of applying new pharmaceutical forms of nanotechnology are outlined.
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Affiliation(s)
- Nikitas Georgiou
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (N.G.); (E.A.R.); (E.P.); (N.S.); (N.Z.); (K.M.); (S.K.)
| | - Margarita Georgia Kakava
- Laboratory of Organic Chemistry and Biochemistry, Department of Chemistry, University of Patras, 26504 Patras, Greece;
| | - Efthymios Alexandros Routsi
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (N.G.); (E.A.R.); (E.P.); (N.S.); (N.Z.); (K.M.); (S.K.)
- Center of Excellence for Drug Design and Discovery, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Errikos Petsas
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (N.G.); (E.A.R.); (E.P.); (N.S.); (N.Z.); (K.M.); (S.K.)
| | - Nikolaos Stavridis
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (N.G.); (E.A.R.); (E.P.); (N.S.); (N.Z.); (K.M.); (S.K.)
| | - Christoforos Freris
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece;
| | - Nikoletta Zoupanou
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (N.G.); (E.A.R.); (E.P.); (N.S.); (N.Z.); (K.M.); (S.K.)
| | - Kalliopi Moschovou
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (N.G.); (E.A.R.); (E.P.); (N.S.); (N.Z.); (K.M.); (S.K.)
| | - Sofia Kiriakidi
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (N.G.); (E.A.R.); (E.P.); (N.S.); (N.Z.); (K.M.); (S.K.)
- Departamento de Quimica Orgánica, Facultade de Quimica, Universidade de Vigo, 36310 Vigo, Spain
| | - Thomas Mavromoustakos
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (N.G.); (E.A.R.); (E.P.); (N.S.); (N.Z.); (K.M.); (S.K.)
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Ballav S, Lokhande KB, Yadav RS, Ghosh P, Swamy KV, Basu S. Exploring binding mode assessment of novel kaempferol, resveratrol, and quercetin derivatives with PPAR-α as potent drug candidates against cancer. Mol Divers 2023; 27:2867-2885. [PMID: 36544031 DOI: 10.1007/s11030-022-10587-2] [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: 07/18/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
Peroxisome proliferator-activated receptors (PPAR)-α, a ligand-activated transcription factor stands out to be a valuable protein target against cancer. Given that ligand binding is the crucial process for the activation of PPAR-α, fibrate class of synthetic compounds serves as potent agonist for the receptor. However, their serious side effects limit the long-term application in cancer. This emphasizes the dire need to identify new candidates that would exert desired activation by abrogating the adverse effects caused by synthetic agonists. Natural dietary products serve as an important source of drug discovery. Hence, the present study encompasses the investigation of the role of natural plant phenolic compounds: kaempferol, resveratrol, and quercetin and their 8708 derivatives by the means of computational pipeline comprising molecular docking and molecular dynamic (MD) simulation techniques. Docking calculations shortlisted potential candidates, namely 6-cinnamylchrysin (6-CC), resveratrol potassium-4-sulfate (RPS) and 6-[2-(3,4-Dihydroxyphenyl)-5-hydroxy-4-oxochromen-7-yl]oxyhexyl nitrate (DHOON), and derivatives of kaempferol, resveratrol, and quercetin, respectively. 6-CC, RPS, and DHOON manifested better affinities of - 32.83 kcal/mol (Ala333, Lys358, His440), - 27.22 kcal/mol (Tyr314, Met355), and - 30.18 kcal/mol (Ser280, Tyr314, Ala333), respectively, and were found to act as good stimulants for PPAR-α. Among these three compounds, 6-CC caused relatively least deviations and fluctuations analyzed through MD simulation which judiciously held responsible to attain most favorable interaction with PPAR-α. Followed by the binding free energy (ΔG) calculations using MM-GBSA confirmed the key role of 6-CC toward PPAR-α. The compound 6-CC also achieved high drug-likeness and pharmacokinetic properties. Thus, these findings stipulate new drug leads for PPAR-α receptor which abets a way to develop new anti-cancer drugs.
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Affiliation(s)
- Sangeeta Ballav
- Cancer and Translational Research Laboratory, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, 411033, India
| | - Kiran Bharat Lokhande
- Bioinformatics Research Laboratory, Dr. D. Y. Patil Biotechnology & Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Pune, 411033, Maharashtra, India
- Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, 201314, India
| | - Rohit Singh Yadav
- Cancer and Translational Research Laboratory, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, 411033, India
- Bioinformatics Research Laboratory, Dr. D. Y. Patil Biotechnology & Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Pune, 411033, Maharashtra, India
| | - Payel Ghosh
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, 411007, India
| | - K V Swamy
- Bioinformatics Research Laboratory, Dr. D. Y. Patil Biotechnology & Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Pune, 411033, Maharashtra, India
- Bioinformatics Research Group, MIT School of Bioengineering Science & Research, MIT Art, Design and Technology University, Pune, Maharashtra, 412201, India
| | - Soumya Basu
- Cancer and Translational Research Laboratory, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, 411033, India.
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Abdullahi M, Uzairu A, Shallangwa GA, Mamza PA, Ibrahim MT, Chandra A, Goel VK. Molecular modelling studies of substituted indole derivatives as novel influenza a virus inhibitors. J Biomol Struct Dyn 2023:1-20. [PMID: 37964590 DOI: 10.1080/07391102.2023.2280735] [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: 09/25/2023] [Accepted: 11/01/2023] [Indexed: 11/16/2023]
Abstract
The emergence of drug-resistant strains motivate researchers to find new innovative anti-IAV candidates with a different mode of action. In this work, molecular modelling strategies, such as 2D-QSAR, 3D-QSAR, molecular docking, molecular dynamics, FMOs, and ADMET were applied to some substituted indoles as IAV inhibitors. The best-developed 2D-QSAR models, MLR (Q2 = 0.7634, R2train = 0.8666) and ANN[4-3-1] (Q2 = 0.8699, R2train = 0.8705) revealed good statistical validation for the inhibitory response predictions. The 3D-QSAR models, CoMFA (Q2 = 0.504, R2train = 0.805) and CoMSIA/SEDHA (Q2 = 0.619, R2train = 0.813) are selected as the best 3D models following the global thresholds. In addition, the contour maps generated from the CoMFA and CoMSIA models illustrate the relationship between the molecular fields and the inhibitory effects of the studied molecules. The results of the studies led to the design of five new molecules (24a-e) with enhanced anti-IAV activities and binding potentials using the most active molecule (24) as the template scaffold. The conformational stability of the best-designed molecules with the NA protein showed hydrophobic and H-bonds with the key residues from the molecular dynamics simulations of 100 ns. Furthermore, the global reactivity indices from the DFT calculations portrayed the relevance of 24c in view of its smaller band gap as also justified by our QSAR and molecular simulation studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mustapha Abdullahi
- Department of Chemistry, Faculty of Physical Sciences, Ahmadu Bello University, Zaria, Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, Kaduna State University, Kaduna, Nigeria
| | - Adamu Uzairu
- Department of Chemistry, Faculty of Physical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Gideon Adamu Shallangwa
- Department of Chemistry, Faculty of Physical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Paul Andrew Mamza
- Department of Chemistry, Faculty of Physical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Muhammad Tukur Ibrahim
- Department of Chemistry, Faculty of Physical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Anshuman Chandra
- School of Physical Science, Jawaharlal Nehru University, New Delhi, India
| | - Vijay Kumar Goel
- School of Physical Science, Jawaharlal Nehru University, New Delhi, India
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Deshpande N S, Dwivedi PSR, Revanasiddappa BC. Virtual screening, pharmacokinetics & MD simulation study of active phytoconstituents of Ficus Carica Linn. against PPAR-γ in diabetes mellitus. J Biomol Struct Dyn 2023:1-17. [PMID: 37948295 DOI: 10.1080/07391102.2023.2279286] [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: 07/11/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023]
Abstract
F. carica is a small tree and commonly used as a traditional medicine against several disorders. Diabetes is currently treated with insulin and oral hypoglycemic medicines such as sulphonyl urea derivatives, bigunides, thiazolidinediones and alpha-glucosidase inhibitors. Peroxisome proliferator-activated receptor gamma (PPAR-γ) agonists were found to be very much beneficial in the management of diabetes by inhibiting hepatic gluconeogenesis. The aim of this study is to evaluate the bioactive phytoconstituents from Ficus carica Linn. against the target PPAR-γ agonist by in silico docking approach. We investigated 68 phytoconstituents as potential inhibitors of PPAR-γ agonists and the top 24 phytoconstituents were further selected for molecular docking studies. Drug ability, side effects, and ADMET analysis were determined by using MolSoft, toxtree freeware, and ADMET SAR web server, respectively. The phytoconstituents were docked with the target PPAR-γ (PDB ID: 4Y29, 1.98 Å) receptor. Quercetin-3-o-rutinoside possessed the highest G score -14.22 kcal/mol, followed by Angelicin with a G score of -13.56 kcal/mol. All the other phytoconstituents displayed good pharmacokinetic and toxicological parameters with values within the permissible limits. The ligand-protein interaction was calculated by molecular dynamic (MD) simulation study. Subsequently, the binding free energy of the Quercetin-3-o-rutinosideand Pioglitazone complex was calculated using MMPBSA analysis. The results indicated that some of the phytoconstituents from Ficus carica have potency as an anti-diabetic agents. So, these bioactive phytoconstituents like Quercetin-3-o-glucoside, 5-O-caffeoylquinic acids may act as a good agonist for PPAR-γ.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shridhar Deshpande N
- Department of Pharmaceutical Chemistry, NGSM Institute of Pharmaceutical Sciences (NGSMIPS) Nitte (Deemed to Be University, Mangalore, Karnataka, India
| | - Prarambh S R Dwivedi
- Department of Pharmacology, NGSM Institute of Pharmaceutical Sciences (NGSMIPS) Nitte (Deemed to Be University), Mangalore, Karnataka, India
| | - B C Revanasiddappa
- Department of Pharmaceutical Chemistry, NGSM Institute of Pharmaceutical Sciences (NGSMIPS) Nitte (Deemed to Be University, Mangalore, Karnataka, India
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8
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Wong AR, Yang AWH, Gill H, Lenon GB, Hung A. Mechanisms of Nelumbinis folium targeting PPARγ for weight management: A molecular docking and molecular dynamics simulations study. Comput Biol Med 2023; 166:107495. [PMID: 37742414 DOI: 10.1016/j.compbiomed.2023.107495] [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: 05/07/2023] [Revised: 09/08/2023] [Accepted: 09/15/2023] [Indexed: 09/26/2023]
Abstract
The lotus leaf, Nelumbinis folium (NF), has frequently appeared in obesity clinical trials as an intervention to promote weight loss and improve metabolic profiles. However, the molecular mechanisms by which it interacts with important obesity targets and pathways, such as the peroxisome proliferator-activated receptor gamma (PPARγ) within the PPAR signalling pathway, were not well understood. This study aims to screen for candidate compounds from NF with desirable pharmacokinetic properties and examine their binding feasibility at the PPARγ ligand-binding domain (LBD). Ligand- and structure-based screening of NF compounds were performed, and a consensus approach has been applied to identify druggable candidates. By examining the pharmacokinetic profiles, a large proportion of NF compounds exhibited favourable drug-likeness and oral bioavailability properties. Furthermore, the binding affinity scores and poses provided new insights on the distinctive binding behaviours of NF compounds at the LBD of PPARγ in its inactive form. Several NF compounds could bind strongly to PPARγ at sub-pockets where partial agonists and antagonists were found to bind and may induce conformational changes that influence co-repressor binding, trans-repression, and gene expression inhibition. Subsequent molecular dynamics simulations of a candidate compound (NF129 narcissin) bound to PPARγ revealed conformational stability, residue fluctuation, and binding behaviours comparable to that of the known inhibitor, SR1664. Therefore, it can be proposed that narcissin exhibits characteristics of a PPARγ antagonist. Further experimental validation to support the development of NF129 as a future anti-obesity agent is warranted.
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Affiliation(s)
- Ann Rann Wong
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia
| | - Angela Wei Hong Yang
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia
| | - Harsharn Gill
- School of Science, RMIT University, Melbourne, Victoria, Australia
| | - George Binh Lenon
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia
| | - Andrew Hung
- School of Science, RMIT University, Melbourne, Victoria, Australia.
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Ballav S, Bhosale M, Lokhande KB, Paul MK, Padhye S, Swamy KV, Ranjan A, Basu S. Design, Synthesis, and Biological Evaluation of Novel Quercetin Derivatives as PPAR-γ Partial Agonists by Modulating Epithelial-Mesenchymal Transition in Lung Cancer Metastasis. Adv Biol (Weinh) 2023; 7:e2300036. [PMID: 37017501 DOI: 10.1002/adbi.202300036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/09/2023] [Indexed: 04/06/2023]
Abstract
Epithelial-to-mesenchymal transition (EMT) is responsible for driving metastasis of multiple cancer types including lung cancer. Peroxisome proliferator-activated receptor (PPAR)-γ, a ligand-activated transcription factor, controls expression of variety of genes involved in EMT. Although several synthetic compounds act as potent full agonists for PPAR-γ, their long term application is restricted due to serious adverse effects. Therefore, partial agonists involving reduced and balanced PPAR-γ activity are more effective and valued. A previous study discerned the efficacy of quercetin and its derivatives to attain favorable stabilization with PPAR-γ. Here this work is extended by synthesizing five novel quercetin derivatives (QDs) namely thiosemicarbazone (QUETSC)) and hydrazones (quercetin isonicotinic acid hydrazone (QUEINH), quercetin nicotinic acid hydrazone (QUENH), quercetin 2-furoic hydrazone (QUE2FH), and quercetin salicyl hydrazone (QUESH)) and their effects are analyzed in modulating EMT in lung cancer cell lines via PPAR-γ partial activation. QDs-treated A549 cells diminish cell proliferation strongly at nanomolar concentration compared to NCI-H460 cells. Of the five screened derivatives, QUETSC, QUE2FH, and QUESH exhibit the property of partial activation as compared to the overexpressive level of rosiglitazone. Consistently, these QDs also suppress EMT process by markedly downregulating the levels of mesenchymal markers (Snail, Slug, and zinc finger E-box binding homeobox 1) and concomitant upregulation of epithelial marker (E-cadherin).
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Affiliation(s)
- Sangeeta Ballav
- Cancer and Translational Research Centre, Dr. D.Y. Patil Biotechnology and Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Tathawade, Pune, Maharashtra, 411 033, India
| | - Mrinalini Bhosale
- Department of Chemistry, Interdisciplinary Science and Technology Research Academy, Abeda Inamdar Senior College, University of Pune, Maharashtra, 411001, India
| | - Kiran Bharat Lokhande
- Bioinformatics Research Laboratory, Dr. D.Y. Patil Biotechnology and Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Tathawade, Pune, Maharashtra, 411 033, India
| | - Manash K Paul
- Department of Pulmonary and Critical Care Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Subhash Padhye
- Department of Chemistry, Interdisciplinary Science and Technology Research Academy, Abeda Inamdar Senior College, University of Pune, Maharashtra, 411001, India
| | - K Venkateswara Swamy
- Bioinformatics Research Laboratory, Dr. D.Y. Patil Biotechnology and Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Tathawade, Pune, Maharashtra, 411 033, India
- MIT School of Bioengineering Science and Research, MIT - Art, Design and Technology University, Pune, Maharashtra, 412201, India
| | - Amit Ranjan
- Cancer and Translational Research Centre, Dr. D.Y. Patil Biotechnology and Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Tathawade, Pune, Maharashtra, 411 033, India
| | - Soumya Basu
- Cancer and Translational Research Centre, Dr. D.Y. Patil Biotechnology and Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Tathawade, Pune, Maharashtra, 411 033, India
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Patel S, Hasan H, Umraliya D, Sanapalli BKR, Yele V. Marine drugs as putative inhibitors against non-structural proteins of SARS-CoV-2: an in silico study. J Mol Model 2023; 29:176. [PMID: 37171714 PMCID: PMC10176293 DOI: 10.1007/s00894-023-05574-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 04/26/2023] [Indexed: 05/13/2023]
Abstract
INTRODUCTION Coronavirus disease 2019 (COVID-19) is an unprecedented pandemic, threatening human health worldwide. The need to produce novel small-molecule inhibitors against the ongoing pandemic has resulted in the use of drugs such as chloroquine, azithromycin, dexamethasone, favipiravir, ribavirin, remdesivir and azithromycin. Moreover, the reports of the clinical trials of these drugs proved to produce detrimental effects on patients with side effects like nephrotoxicity, retinopathy, cardiotoxicity and cardiomyopathy. Recognizing the need for effective and non-harmful therapeutic candidates to combat COVID-19, we aimed to develop promising drugs against SARS-COV-2. DISCUSSION In the current investigation, high-throughput virtual screening was performed using the Comprehensive Marine Natural Products Database against five non-structural proteins: Nsp3, Nsp5, Nsp12, Nsp13 and Nsp15. Furthermore, standard precision (SP) docking, extra precision (XP) docking, binding free energy calculation and absorption, distribution, metabolism, excretion and toxicity studies were performed using the Schrӧdinger suite. The top-ranked 5 hits obtained by computational studies exhibited to possess a greater binding affinity with the selected non-structural proteins. Amongst the five hits, CMNPD5804, CMNPD20924 and CMNPD1598 hits were utilized to design a novel molecule (D) that has the capability of interacting with all the key residues in the pocket of the selected non-structural proteins. Furthermore, 200 ns of molecular dynamics simulation studies provided insight into the binding modes of D within the catalytic pocket of selected proteins. CONCLUSION Hence, it is concluded that compound D could be a promising inhibitor against these non-structural proteins. Nevertheless, there is still a need to conduct in vitro and in vivo studies to support our findings.
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Affiliation(s)
- Simran Patel
- Faculty of Pharmacy, Marwadi University, Rajkot, Gujarat, 360003, India
| | - Haydara Hasan
- Faculty of Pharmacy, Marwadi University, Rajkot, Gujarat, 360003, India
| | - Divyesh Umraliya
- Faculty of Pharmacy, Marwadi University, Rajkot, Gujarat, 360003, India
| | - Bharat Kumar Reddy Sanapalli
- Department of Pharmacology, Faculty of Pharmacy, Marwadi University, Rajkot, Gujarat, 360003, India.
- Department of Pharmacology, School of Pharmaceutical Sciences, MB University, Tirupati, Andhra Pradesh, 517102, India.
| | - Vidyasrilekha Yele
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Marwadi University, Rajkot, Gujarat, 360003, India.
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Duan M, Li K, Zhang L, Zhou Y, Bian L, Wang C. Screening, characterization and specific binding mechanism of aptamers against human plasminogen Kringle 5. Bioorg Chem 2023; 137:106579. [PMID: 37149949 DOI: 10.1016/j.bioorg.2023.106579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/30/2023] [Accepted: 04/26/2023] [Indexed: 05/09/2023]
Abstract
Plasminogen Kringle 5 is one of the most potent cytokines identified to inhibit the proliferation and migration of vascular endothelial cells. Herein, six aptamer candidates that specifically bind to Kringle 5 were generated by the systematic evolution of ligands by exponential enrichment (SELEX). After 10 rounds of screening against Kringle 5, a highly enriched ssDNA pool was sequenced and the representative aptamers were subjected to binding assays to evaluate their affinity and specificity. The preferred aptamer KG-4, which demonstrated a low dissociation constant (Kd) of ∼ 432 nM and excellent selectivity for Kringle 5. A conserved "motif" of eight bases located at the stem-loop intersection, common to the aptamer, was further confirmed as the recognition element for binding with Kringle 5. The bulge formed by the motif and depression on the lysine binding site of Kringle 5 were both located at the binding interface, and the "induced fit" between their structures played a central role in the recognition process. Kringle 5 interacts KG-4 primarily through enthalpy-driven van der Waals forces and hydrogen bond. The key nucleotides A34 and C35 at motif on KG-4 and the positively charged amino acids in the loop 1 and loop 4 regions on Kringle 5 play a major role in the interaction. Furthermore, KG-4 dose-dependently reduced the proliferation inhibition of vascular endothelial cells by Kringle 5 and had a blocking effect on the function of Kringle 5 in inhibiting migration and promoting apoptosis of vascular endothelial cells in vitro. This study put a new light on protein-aptamer binding mechanism and may provide insight into the treatment of ischemic diseases by target depletion of Kringle 5.
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Affiliation(s)
- Meijiao Duan
- College of Life Science, Northwest University, Xi'an 710069, Shaanxi, China
| | - Kewei Li
- College of Life Science, Northwest University, Xi'an 710069, Shaanxi, China
| | - Ling Zhang
- College of Life Science, Northwest University, Xi'an 710069, Shaanxi, China
| | - Yaqi Zhou
- College of Life Science, Northwest University, Xi'an 710069, Shaanxi, China
| | - Liujiao Bian
- College of Life Science, Northwest University, Xi'an 710069, Shaanxi, China.
| | - Cuiling Wang
- College of Life Science, Northwest University, Xi'an 710069, Shaanxi, China.
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12
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Zhou HF, Yang C, Li JY, He YY, Huang Y, Qin RJ, Zhou QL, Sun F, Hu DS, Yang J. Quercetin serves as the major component of Xiang-lian Pill to ameliorate ulcerative colitis via tipping the balance of STAT1/PPARγ and dictating the alternative activation of macrophage. JOURNAL OF ETHNOPHARMACOLOGY 2023; 313:116557. [PMID: 37142141 DOI: 10.1016/j.jep.2023.116557] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/06/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The traditional Chinese herbal formula, Xiang-lian Pill (XLP), is commonly prescribed for ulcerative colitis (UC) patients to relieve their clinical symptom. Nonetheless, the underlying cellular and molecular mechanisms of XLP's anti-UC effect remain incompletely understood. AIM OF THE STUDY To evaluate the therapeutic effect and elucidate the possible working mechanisms of XLP in UC treatment. The major active component of XLP was also characterized. MATERIALS AND METHODS Colitis was induced in C57BL/6 mice with 3% dextran sulfate sodium (DSS) dissolved in drinking water for 7 consecutive days. The UC mice were grouped and treated with XLP (3640 mg/kg) or vehicle orally during the procedure of DSS induction. Mouse body weight, disease activity index (DAI) score and colon length were recorded. Histopathological changes and inflammatory cell infiltration were evaluated by pathological staining and flow cytometric analysis (FACS). Network pharmacology, bioinformatic analysis, widely targeted and targeted metabolomics analysis were performed to screen the potential effective ingredients and key targets. Bone marrow derived macrophages (BMDMs), peripheral blood mononuclear cells (PBMCs), RAW264.7 and THP-1 cells were used to dissect the anti-inflammatory effect of XLP. RESULTS Oral administration of XLP ameliorated DSS induced mouse colitis, as evidenced by reduced DAI and colonic inflammatory destruction. FACS results demonstrated that XLP treatment effectively restored immune tolerance in colon, inhibited the generation of monocyte derived macrophages and skewed macrophage polarization into M2 phenotype. Network pharmacology analysis suggested that innate effector modules related to macrophage activation comprise the major targets of XLP, and the counter-regulatory STAT1/PPARγ signaling possibly serves as the critical downstream pathway. Subsequent experiments unveiled an imbalance of STAT1/PPARγ signaling in monocytes derived from UC patients, and validated that XLP suppressed LPS/IFN-γ induced macrophage activation (STAT1 mediated) but facilitated IL-4 induced macrophage M2 polarization (PPARγ dependent). Meanwhile, our data showed that quercetin served as the major component of XLP to recapitulate the regulatory effect on macrophages. CONCLUSION Our findings revealed that quercetin serves as the major component of XLP that regulates macrophage alternative activation via tipping the balance of STAT1/PPARγ, which provides a mechanistic explanation for the therapeutic effect of XLP in UC treatment.
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Affiliation(s)
- Hai-Feng Zhou
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Chao Yang
- Department of Geratology, Hubei Provincial Hospital of Integrated Chinese & Western Medicine, Wuhan, 430015, China.
| | - Jun-Yi Li
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Yu-Yao He
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Yun Huang
- Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, China.
| | - Ren-Jie Qin
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Qiao-Li Zhou
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Fei Sun
- The Center for Biomedical Research, Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, 430030, China.
| | - De-Sheng Hu
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Jia Yang
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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13
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Rational design, molecular docking, dynamic simulation, synthesis, PPAR-γ competitive binding and transcription analysis of novel glitazones. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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14
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Faloye KO, Mahmud S, Fakola EG, Oyetunde YM, Fajobi SJ, Ugwo JP, Olusola AJ, Famuyiwa SO, Olajubutu OG, Oguntade TI, Obaidullah AJ. Revealing the Acetylcholinesterase Inhibitory Potential of Phyllanthus amarus and Its Phytoconstituents: In Vitro and in Silico Approach. Bioinform Biol Insights 2022; 16:11779322221118330. [PMID: 36046175 PMCID: PMC9421041 DOI: 10.1177/11779322221118330] [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: 04/01/2022] [Accepted: 07/18/2022] [Indexed: 11/16/2022] Open
Abstract
The inhibition of acetylcholinesterase plays a vital role in the treatment of Alzheimer disease. This study aimed to explore the acetylcholinesterase inhibition potential of Phyllanthus amarus and its phytoconstituents through an in vitro and in silico approach. The in vitro acetylcholinesterase inhibitory activity of P amarus was carried out, followed by the molecular docking studies of its phytoconstituents. The top-ranked molecules identified through molecular docking were subjected to molecular dynamics simulation (MDS) and density functional theory (DFT) studies. The results obtained revealed the methanolic extract of P amarus as a potent acetylcholinesterase inhibitor, while amarosterol A, hinokinin, β-sitosterol, stigmasterol and ellagic acid were identified as potential acetylcholinesterase inhibitors. The MDS and DFT results are in agreement with those obtained from the docking studies. Our findings suggest further studies on the hit molecules.
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Affiliation(s)
- Kolade O Faloye
- Department of Chemistry, Faculty of Science, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Shafi Mahmud
- Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Emmanuel G Fakola
- Department of Chemistry, Faculty of Science, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Yemisi M Oyetunde
- Department of Pharmacognosy, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Sunday J Fajobi
- Department of Pharmacology, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Jeremiah P Ugwo
- Department of Chemistry, School of Science, Federal College of Education, Okene, Okene, Nigeria
| | - Ayobami J Olusola
- Department of Pharmacology, Faculty of Pharmacy, Federal University Oye-Ekiti, Oye-Ekiti, Nigeria
| | - Samson O Famuyiwa
- Department of Chemistry, Faculty of Science, Obafemi Awolowo University, Ile-Ife, Nigeria
| | | | - Temitope I Oguntade
- Department of Chemical Sciences, Adekunle Ajasin University, Akungba-Akoko, Nigeria
| | - Ahmad J Obaidullah
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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Kaempferol antagonizes adipogenesis by repressing histone H3K4 methylation at PPARγ target genes. Biochem Biophys Res Commun 2022; 617:48-54. [DOI: 10.1016/j.bbrc.2022.05.098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 05/31/2022] [Indexed: 01/13/2023]
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16
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Fadaka AO, Taiwo OA, Dosumu OA, Owolabi OP, Ojo AB, Sibuyi NRS, Ullah S, Klein A, Madiehe AM, Meyer M, Ojo OA. Computational prediction of potential drug-like compounds from Cannabis sativa leaf extracts targeted towards Alzheimer therapy. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Molecular Interaction Studies and Phytochemical Characterization of Mentha pulegium L. Constituents with Multiple Biological Utilities as Antioxidant, Antimicrobial, Anticancer and Anti-Hemolytic Agents. Molecules 2022; 27:molecules27154824. [PMID: 35956775 PMCID: PMC9370026 DOI: 10.3390/molecules27154824] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/20/2022] [Accepted: 07/23/2022] [Indexed: 12/14/2022] Open
Abstract
Multiple biological functions of Mentha pulegium extract were evaluated in the current work. Phytochemical components of the M. pulegium extract were detected by Gas Chromatography-Mass Spectrometry (GC-MS) and High-performance liquid chromatography (HPLC). Moreover, M. pulegium extract was estimated for antioxidant potential by 2,2-Diphenyl-1-picryl-hydrazyl-hydrate (DPPH) free radical scavenging, antimicrobial activity by well diffusion, and anticoagulant activity via prothrombin time (PT) and activated partial thromboplastin time (APTT). GC-MS analysis detected compounds including cholesterol margarate, stigmast-5-en-3-ol, 19-nor-4-androstenediol, androstan-17-one, pulegone-1,2-epoxide, isochiapin B, dotriacontane, hexadecanoic acid and neophytadiene. Chrysoeriol (15.36 µg/mL) was followed by kaempferol (11.14 µg/mL) and 7-OH flavone (10.14 µg/mL), catechin (4.11 µg/mL), hisperdin (3.05 µg/mL), and luteolin (2.36 µg/mL) were detected by HPLC as flavonoids, in addition to ferulic (13.19 µg/mL), cinnamic (12.69 µg/mL), caffeic (11.45 µg/mL), pyrogallol (9.36 µg/mL), p-coumaric (5.06 µg/mL) and salicylic (4.17 µg/mL) as phenolics. Antioxidant activity was detected with IC50 18 µg/mL, hemolysis inhibition was recorded as 79.8% at 1000 μg/mL, and PT and APTT were at 21.5 s and 49.5 s, respectively, at 50 μg/mL of M. pulegium extract. The acute toxicity of M. pulegium extract was recorded against PC3 (IC50 97.99 µg/mL) and MCF7 (IC50 80.21 µg/mL). Antimicrobial activity of M. pulegium extract was documented against Bacillus subtilis, Escherichia coli, Pseudomonasaureus, Candida albicans, Pseudomonas aeruginosa, but not against black fungus Mucor circinelloides. Molecular docking was applied using MOE (Molecular Operating Environment) to explain the biological activity of neophytadiene, luteolin, chrysoeriol and kaempferol. These compounds could be suitable for the development of novel pharmacological agents for treatment of cancer and bacterial infections.
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Zhang K, Wang K, Zhang C, Teng X, Li D, Chen M. Exploring the potential mechanism of emetine against coronavirus disease 2019 combined with lung adenocarcinoma: bioinformatics and molecular simulation analyses. BMC Cancer 2022; 22:687. [PMID: 35733175 PMCID: PMC9214478 DOI: 10.1186/s12885-022-09763-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 06/08/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Patients with lung adenocarcinoma (LUAD) may be more predisposed to coronavirus disease 2019 (COVID-19) and have a poorer prognosis. Currently, there is still a lack of effective anti-LUAD/COVID-19 drugs. Thus, this study aimed to screen for an effective anti-LUAD/COVID-19 drug and explore the potential mechanisms. METHODS Firstly, we performed differentially expressed gene (DEG) analysis on LUAD transcriptome profiling data in The Cancer Genome Atlas (TCGA), where intersections with COVID-19-related genes were screened out. Then, we conducted Cox proportional hazards analyses on these LUAD/COVID-19 DEGs to construct a risk score. Next, LUAD/COVID-19 DEGs were uploaded on Connectivity Map to obtain drugs for anti-LUAD/COVID-19. Finally, we used network pharmacology, molecular docking, and molecular dynamics (MD) simulation to explore the drug's therapeutic targets and potential mechanisms for anti-LUAD/COVID-19. RESULTS We identified 230 LUAD/COVID-19 DEGs and constructed a risk score containing 7 genes (BTK, CCL20, FURIN, LDHA, TRPA1, ZIC5, and SDK1) that could classify LUAD patients into two risk groups. Then, we screened emetine as an effective drug for anti-LUAD/COVID-19. Network pharmacology analyses identified 6 potential targets (IL6, DPP4, MIF, PRF1, SERPING1, and SLC6A4) for emetine in anti-LUAD/COVID-19. Molecular docking and MD simulation analyses showed that emetine exhibited excellent binding capacities to DDP4 and the main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). CONCLUSIONS This study found that emetine may inhibit the entry and replication of SARS-CoV-2 and enhance tumor immunity by bounding to DDP4 and Mpro.
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Affiliation(s)
- Kun Zhang
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, No. 277 Yanta West Road, Xi'an, 710061, Shaanxi Province, China
| | - Ke Wang
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, No. 277 Yanta West Road, Xi'an, 710061, Shaanxi Province, China
| | - Chaoguo Zhang
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, No. 277 Yanta West Road, Xi'an, 710061, Shaanxi Province, China
| | - Xiuli Teng
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, No. 277 Yanta West Road, Xi'an, 710061, Shaanxi Province, China
| | - Dan Li
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, No. 277 Yanta West Road, Xi'an, 710061, Shaanxi Province, China
| | - Mingwei Chen
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, No. 277 Yanta West Road, Xi'an, 710061, Shaanxi Province, China.
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19
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In Silico Studies of Tumor Targeted Peptide-Conjugated Natural Products for Targeting Over-Expressed Receptors in Breast Cancer Cells Using Molecular Docking, Molecular Dynamics and MMGBSA Calculations. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12010515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this work, in silico studies were carried out for the design of diterpene and polyphenol-peptide conjugates to potentially target over-expressed breast tumor cell receptors. Four point mutations were induced into the known tumor-targeting peptide sequence YHWYGYTPQN at positions 1, 2, 8 and 10, resulting in four mutated peptides. Each peptide was separately conjugated with either chlorogenate, carnosate, gallate, or rosmarinate given their known anti-tumor activities, creating dual targeting compounds. Molecular docking studies were conducted with the epidermal growth factor receptor (EGFR), to which the original peptide sequence is known to bind, as well as the estrogen receptor (ERα) and peroxisome proliferator-activated receptor (PPARα) using both Autodock Vina and FireDock. Based on docking results, peptide conjugates and peptides were selected and subjected to molecular dynamics simulations. MMGBSA calculations were used to further probe the binding energies. ADME studies revealed that the compounds were not CYP substrates, though most were Pgp substrates. Additionally, most of the peptides and conjugates showed MDCK permeability. Our results indicated that several of the peptide conjugates enhanced binding interactions with the receptors and resulted in stable receptor-ligand complexes; Furthermore, they may successfully target ERα and PPARα in addition to EGFR and may be further explored for synthesis and biological studies for therapeutic applications.
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20
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Thakur A, Patwa J, Pant S, Sharma A, Flora SJS. Interaction study of monoisoamyl dimercaptosuccinic acid with bovine serum albumin using biophysical and molecular docking approaches. Sci Rep 2021; 11:4068. [PMID: 33603022 PMCID: PMC7892868 DOI: 10.1038/s41598-021-83534-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/04/2021] [Indexed: 12/21/2022] Open
Abstract
Monoisoamyl 2,3-dimercaptosuccinic acid (MiADMSA), a lipophilic chelator has been evaluated for its potential use as an antidote in arsenic poisoning. The pharmacokinetics and pharmacodynamics properties of a drug could be understood via study its mechanism of interaction with bovine serum albumin protein (BSA). Therefore, the interaction between MiADMSA with BSA was investigated using various spectroscopic techniques and computational methods. Linear quenching of BSA intrinsic fluorescence intensity with the increasing concentration of MiADMSA was observed in the fluorescence study. Furthermore, synchronous results revealed that MiADMSA slightly changed the conformation of BSA. The binding constant value of the BSA-MiADMSA complex was found 1.60 × 104 M-1 at 298 K. The value of thermodynamic parameters ΔG, ΔH, and ΔS described that the process is spontaneous, endothermic, and hydrophobic forces are involved in the interaction of MiADMSA with BSA. Competitive site marker experiments showed that MiADMSA binds to site-II of BSA. Conformational changes of BSA with the interaction of MiADMSA were apparent by CD, UV-Visible, FT-IR, and 3D fluorescence spectroscopy. To strengthen the experimental findings we have also performed a theoretical study on the BSA-MiADMSA complex. Two sites were identified with docking score of - 6.642 kcal/mol at site IIa and - 3.80 kcal/mol for site IIb via molecular docking study. Molecular dynamics simulation study inferred the stability of the BSA-MiADMSA complex which was analyzed in a long simulation run. The experimental and computational studies have shown the effective binding of MiADMSA with BSA which is essential for the transportation and elimination of a drug from the body.
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Affiliation(s)
- Ashima Thakur
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Raebareli, Lucknow, UP, 226002, India
| | - Jayant Patwa
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Raebareli, Lucknow, UP, 226002, India
| | - Suyash Pant
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Abha Sharma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Raebareli, Lucknow, UP, 226002, India.
| | - S J S Flora
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Raebareli, Lucknow, UP, 226002, India.
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Umar HI, Siraj B, Ajayi A, Jimoh TO, Chukwuemeka PO. Molecular docking studies of some selected gallic acid derivatives against five non-structural proteins of novel coronavirus. J Genet Eng Biotechnol 2021; 19:16. [PMID: 33492492 PMCID: PMC7829640 DOI: 10.1186/s43141-021-00120-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 01/12/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND The World Health Organization has recently declared a new coronavirus disease (COVID-19) a pandemic and a global health emergency. The pressure to produce drugs and vaccines against the ongoing pandemic has resulted in the use of some drugs such as azithromycin, chloroquine (sulfate and phosphate), hydroxychloroquine, dexamethasone, favipiravir, remdesivir, ribavirin, ivermectin, and lopinavir/ritonavir. However, reports from some of the clinical trials with these drugs have proved detrimental on some COVID-19 infected patients with side effects more of which cardiomyopathy, cardiotoxicity, nephrotoxicity, macular retinopathy, and hepatotoxicity have been recently reported. Realizing the need for potent and harmless therapeutic compounds to combat COVID-19, we attempted in this study to find promising therapeutic compounds against the imminent threat of this virus. In this current study, 16 derivatives of gallic acid were docked against five selected non-structural proteins of SARS-COV-2 known to be a good target for finding small molecule inhibitors against the virus, namely, nsp3, nsp5, nsp12, nsp13, and nsp14. All the protein crystal structures and 3D structures of the small molecules (16 gallic acid derivatives and 3 control drugs) were retrieved from the Protein database (PDB) and PubChem server respectively. The compounds with lower binding energy than the control drugs were selected and subjected to pharmacokinetics screening using AdmetSAR server. RESULTS 4-O-(6-galloylglucoside) gave binding energy values of - 8.4, - 6.8, - 8.9, - 9.1, and - 7.5 kcal/mol against Mpro, nsp3, nsp12, nsp13, and nsp15 respectively. Based on the ADMET profile, 4-O-(6-galloylglucoside) was found to be metabolized by the liver and has a very high plasma protein binding. CONCLUSION The result of this study revealed that 4-O-(6-galloylglucoside) could be a promising inhibitor against these SAR-Cov-2 proteins. However, there is still a need for further molecular dynamic simulation, in vivo and in vitro studies to support these findings.
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Affiliation(s)
- Haruna Isiyaku Umar
- Department of Biochemistry, School of Sciences, Federal University of Technology, Along Owo-Ilesha Express Way, P.M.B. 704, Akure, Ondo State Nigeria
- Ioncure Tech Pvt. Ltd., Delhi, 110085 India
| | - Bushra Siraj
- Ioncure Tech Pvt. Ltd., Delhi, 110085 India
- Dr. Zafar H. Zaidi Center for Proteomics, University of Karachi, Karachi, Pakistan
| | - Adeola Ajayi
- Department of Biochemistry, School of Sciences, Federal University of Technology, Along Owo-Ilesha Express Way, P.M.B. 704, Akure, Ondo State Nigeria
| | - Tajudeen O. Jimoh
- Faculty of Pharmaceutical Sciences, Department of Pharmacognosy and Pharmaceutical Botany, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Habib Medical School, Islamic University in Uganda, P. O. Box 7689, Kampala, Uganda
| | - Prosper Obed Chukwuemeka
- Department of Biotechnology, School of sciences, Federal University of Technology, Akure, Ondo State Nigeria
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