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Prinsa, Saha S, Bulbul MZH, Ozeki Y, Alamri MA, Kawsar SMA. Flavonoids as potential KRAS inhibitors: DFT, molecular docking, molecular dynamics simulation and ADMET analyses. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2024; 26:955-992. [PMID: 38647682 DOI: 10.1080/10286020.2024.2343821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/11/2024] [Indexed: 04/25/2024]
Abstract
KRAS mutations linked with cancer. Flavonoids were docked against KRAS G12C and G12D receptors. Abyssinone III, alpha naphthoflavone, beta naphthoflavone, abyssinone I, abyssinone II and beta naphthoflavone, genistin, daidzin showed good docking scores against KRAS G12C and G12D receptors, respectively. The MD simulation data revealed that Rg, RMSD, RMSF, and SASA values were within acceptable limits. Alpha and beta naphthoflavone showed good binding energies with KRAS G12C and G12D receptors. DFT and MEP analysis highlighted the nucleophilic and electrophilic zones of best-docked flavonoids. A novel avenue for the control of KRAS G12C and G12D mutations is made possible by flavonoids.
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Affiliation(s)
- Prinsa
- Department of Pharmaceutical Chemistry, Siddhartha Institute of Pharmacy, Near IT-Park, Dehradun, Uttarakhand, India
| | - Supriyo Saha
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, Uttarakhand, India
| | - Md Zahidul Haque Bulbul
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
| | - Yasuhiro Ozeki
- Graduate School of Nanobio Sciences, Yokohama City University, Yokohama, Japan
| | - Mubarak A Alamri
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Sarkar M A Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
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Alamri MA, Prinsa, Kawsar SMA, Saha S. Exploring marine-derived bioactive compounds for dual inhibition of Pseudomonas aeruginosa LpxA and LpxD: integrated bioinformatics and cheminformatics approaches. Mol Divers 2024:10.1007/s11030-024-10888-8. [PMID: 38780832 DOI: 10.1007/s11030-024-10888-8] [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: 03/28/2024] [Accepted: 04/27/2024] [Indexed: 05/25/2024]
Abstract
Pseudomonas aeruginosa can cause serious nosocomial infections. Targeting the biosynthesis of Lipid A, a major structural domain of lipopolysaccharide (LPS) in P. aeruginosa has emerged as a valuable strategy for developing novel therapeutic agents. The biosynthesis of Lipid A involves the activation of homolog enzymes including LpxA and LpxD. LpxA enzyme facilitates the transfer of R-3-hydroxydecanoic fatty acid to uridine diphosphate N-acetylglucosamine in the first step. While LPxD is accountable in third step, wherein R-3-hydroxydodecanoate is transferred to the 2' amine of UDP-3-O-(3-hydroxydecanoyl) utilizing an ACP donor. The exploration of LpxA and LpxD has been largely neglected, as no specific small-molecule inhibitors have been identified, thus far, except for peptide inhibitors. Here, we report the identification of potential dual inhibitors of the lipid A biosynthesis pathway that target both the LpxA and LpxD enzymes as novel antibiotic agents. Among the virtually screened 32,000 marine bioactive compounds Oscillatoxin A, NCI60_041046, and LTS0192263 exhibited optimal docking interactions with LpxA and LpxD, respectively. MD simulation and MMPBSA data showcased stable interactions between selected marine products and LpxA/LpxD. FMO analysis showed that Oscillatoxin A and NCI60_041046 are the most chemically active molecules. MEP analysis data highlighted the possible electrophilic and nucleophilic distribution zones present in the structure. In addition, these bioactive molecules showed acceptable ADMET profiles. These data confirmed that Oscillatoxin A, NCI60_041046, and LTS0192263 could serve as seeds for the development of potential therapeutics to combat P. aeruginosa infection.
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Affiliation(s)
- Mubarak A Alamri
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, P.O. Box 173, 11942, Al-Kharj, Saudi Arabia
| | - Prinsa
- Siddhartha Institute of Pharmacy, Near IT-Park, Sahastradhara Road, Dehradun, 248001, Uttarakhand, India
| | - Sarkar M A Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Supriyo Saha
- Department of Pharmaceutical Chemistry, Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, 248001, Uttarakhand, India.
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Guo L, Zhang M, Fei Y, Zhao W. Natural Sweetener, Glycyrrhetinic Acid 3- O-Mono-beta-d-glucuronide, for Postprandial Hyperglycemia Management. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4747-4756. [PMID: 38335161 DOI: 10.1021/acs.jafc.3c07188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
This study examines the inhibitory effects of a range of sweeteners on α-glucosidase. Our findings revealed that only one natural sweetener, namely, glycyrrhetinic acid 3-O-mono-beta-d-glucuronide (GAMG), derived from licorice, exhibited a mixed-type inhibition against α-glucosidase with a IC50 value of 0.73 ± 0.05 mg/mL. The fluorescence intensity of α-glucosidase was quenched by GAMG in the formation of an α-glucosidase-GAMG complex. GAMG has been shown to induce conformational changes in α-glucosidase, likely through hydrogen bonding, van der Waals force, and alkyl-alkyl interactions with amino acid residues, including Arg 281, Leu 283, Trp 376, Asp 404, Asp 443, Trp 481, Asp 518, Phe 525, Ala 555, and Asp 616. Additional animal validation experiments demonstrated that GAMG slowed starch digestion, thereby attenuating the postprandial glycemic response. Taken together, these findings provide evidence that GAMG is a natural sweetener with potent inhibitory activity that selectively targets α-glucosidase. This study supports the use of GAMG as a natural sweetener, which holds a high biological value and may be beneficial for managing postprandial hyperglycemia.
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Affiliation(s)
- Lichun Guo
- School of Food Science and Technology, State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Mengqing Zhang
- School of Food Science and Technology, State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Ying Fei
- Wuxi Langke/Suzhou Langbang Biotechnological Co., Ltd., Wuxi, Jiangsu 214122, PR China
| | - Wei Zhao
- School of Food Science and Technology, State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
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Parasher M, Pandey DK, Manhas RK. Traditionally used anti-diabetic plants in Kathua district of Union Territory of Jammu and Kashmir, India. JOURNAL OF ETHNOPHARMACOLOGY 2024; 319:117087. [PMID: 37683931 DOI: 10.1016/j.jep.2023.117087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/27/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023]
Affiliation(s)
- Madhvi Parasher
- School of Bioengineering & Biosciences, Lovely Professional University, Phagwara, 144411, Punjab, India; Department of Botany, Govt. Degree College, Marh, 181206, Jammu, JKUT, India.
| | - Devendra Kumar Pandey
- School of Bioengineering & Biosciences, Lovely Professional University, Phagwara, 144411, Punjab, India.
| | - R K Manhas
- Department of Botany, Govt. Degree College, Basohli, 184201, JKUT, India.
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Almehmadi M, Alsaiari AA, Allahyani M, Alsharif A, Aljuaid A, Saha S, Asif M. Computational Studies and Antimicrobial Activity of 1-(benzo[d]oxazol-2- yl)-3,5-diphenylformazan Derivatives. Curr Comput Aided Drug Des 2024; 20:835-846. [PMID: 37403393 DOI: 10.2174/1573409919666230703103135] [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: 04/06/2023] [Revised: 05/09/2023] [Accepted: 05/30/2023] [Indexed: 07/06/2023]
Abstract
BACKGROUND Due to the biological importance of the benzoxazole derivatives, some 1- (benzo[d]oxazol-2-yl)-3,5-diphenyl-formazans 4a-f were synthesized and screened for in-silico studies and in-vitro antibacterial activity. METHODS The benzo[d]oxazole-2-thiol (1) was prepared by reacting with 2-aminophenol and carbon disulfide in the presence of alcoholic potassium hydroxide. Then 2-hydrazinylbenzo[d] oxazole (2) was synthesized from the reaction of compound 1 with hydrazine hydrate in the presence of alcohol. Compound 2 was reacted with aromatic aldehydes to give Schiff base, 2-(2- benzylidene-hydrazinyl)benzo[d]oxazole derivatives 3a-f. The title compounds, formazan derivatives 4a-f, were prepared by a reaction of benzene diazonium chloride. All compounds were confirmed by their physical data, FTIR, 1H-NMR, and 13CNMR spectral data. All the prepared title compounds were screened for in-silico studies and in-vitro antibacterial activity on various microbial strains. RESULTS Molecular docking against the 4URO receptor demonstrated that molecule 4c showed a maximum dock score of (-) 8.0 kcal/mol. MD simulation data reflected the stable ligand-receptor interaction. As per MM/PBSA analysis, the maximum free binding energy of (-) 58.831 kJ/mol was exhibited by 4c. DFT calculation data confirmed that most of the molecules were soft molecules with electrophilic nature. CONCLUSION The synthesized molecules were validated using molecular docking, MD simulation, MMPBSA analysis, and DFT calculation. Among all the molecules, 4c showed maximum activity. The activity profile of the synthesized molecules against tested micro-organisms was found to be 4c>4b>4a>4e>4f>4d.
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Affiliation(s)
- Mazen Almehmadi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, 21944, Saudi Arabia
| | - Ahad Amer Alsaiari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, 21944, Saudi Arabia
| | - Mamdouh Allahyani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, 21944, Saudi Arabia
| | - Abdulaziz Alsharif
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, 21944, Saudi Arabia
| | - Abdulelah Aljuaid
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, 21944, Saudi Arabia
| | - Supriyo Saha
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, Uttrakhand, 248007, India
| | - Mohammad Asif
- Era College of Pharmacy, Era University, Lucknow, 226003, Uttar Pradesh, India
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AYDIN E. Ceviz Erkek Çiçeklerinin In Vitro Antioksidan ve Enzim İnhibitör Aktiviteleri. AKADEMIK GIDA 2023; 21:112-118. [DOI: 10.24323/akademik-gida.1350684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Walnut (Juglans regia L.) male flowers are known for their high phenolic content and associated health benefits, including anti-hypoxic, antihaemolytic, anti-inflammatory, antidepressant, and antioxidant activities. This study represents the first investigation of the inhibitory effects of walnut male flower extract on α-amylase and α-glucosidase enzymes, employing HPAE-PAD (High-Performance Anion-Exchange Chromatography with Pulsed Amperometric Detection). The inhibitory potential of the extract was compared to that of acarbose, a chemical drug commonly used for this purpose. Furthermore, the antioxidant activity of the extract was also evaluated. The extract demonstrated significant inhibition of α-amylase and α-glucosidase, with half maximal inhibitory concentration (IC50) values of 1.507 mg/mL and 0.803 mg/mL, respectively. In contrast, acarbose exhibited IC50 values of 1.031 mg/mL and 0.985 mg/mL for α-amylase and α-glucosidase, respectively. Although the walnut male flower showed greater inhibition of α-glucosidase than acarbose, acarbose exhibited stronger inhibition of α-amylase activity than walnut male flowers. The extract exhibited a DPPH (1,1-Diphenyl-2-picrylhydrazyl radical) free radical scavenging activity, with an IC50 value of 19.51 µg/mL. Additionally, the total phenolic content of 277 mg GAE (gallic acid equivalent)/g dry weight (dw) was determined in the extract. These results may highlight the potential of walnut male flowers as a novel enzyme inhibitor for managing type 2 diabetes mellitus. The findings of this study could provide valuable insights for further investigation into the potential applications of walnut male flowers in the food and pharmaceutical industries.
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Affiliation(s)
- Ebru AYDIN
- Department of Food Engineering, Faculty of Engineering, Suleyman Demirel University
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Alamri MA, Alawam AS, Alshahrani MM, Kawsar SMA, Saha S. Establishing the Role of Iridoids as Potential Kirsten Rat Sarcoma Viral Oncogene Homolog G12C Inhibitors Using Molecular Docking; Molecular Docking Simulation; Molecular Mechanics Poisson-Boltzmann Surface Area; Frontier Molecular Orbital Theory; Molecular Electrostatic Potential; and Absorption, Distribution, Metabolism, Excretion, and Toxicity Analysis. Molecules 2023; 28:5050. [PMID: 37446713 DOI: 10.3390/molecules28135050] [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: 06/09/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
The RAS gene family is one of the most frequently mutated oncogenes in human cancers. In KRAS, mutations of G12D and G12C are common. Here, 52 iridoids were selected and docked against 8AFB (KRAS G12C receptor) using Sotorasib as the standard. As per the docking interaction data, 6-O-trans-p-coumaroyl-8-O-acetylshanzhiside methyl ester (dock score: -9.9 kcal/mol), 6'-O-trans-para-coumaroyl geniposidic acid (dock score: -9.6 kcal/mol), 6-O-trans-cinnamoyl-secologanoside (dock score: -9.5 kcal/mol), Loganic acid 6'-O-beta-d-glucoside (dock score: -9.5 kcal/mol), 10-O-succinoylgeniposide (dock score: -9.4), Loganic acid (dock score: -9.4 kcal/mol), and Amphicoside (dock score: -9.2 kcal/mol) showed higher dock scores than standard Sotorasib (dock score: -9.1 kcal/mol). These common amino acid residues between iridoids and complexed ligands confirmed that all the iridoids perfectly docked within the receptor's active site. The 100 ns MD simulation data showed that RMSD, RMSF, radius of gyration, and SASA values were within range, with greater numbers of hydrogen bond donors and acceptors. MM/PBSA analysis showed maximum binding energy values of -7309 kJ/mol for 6-O-trans-p-coumaroyl-8-O-acetylshanzhiside methyl ester. FMO analysis showed that 6-O-trans-p-coumaroyl-8-O-acetylshanzhiside methyl ester was the most likely chemically reactive molecule. MEP analysis data highlighted the possible electrophilic and nucleophilic attack regions of the best-docked iridoids. Of all the best-docked iridoids, Loganic acid passed Lipinski, Pfizer, and GSK filters with a similar toxicity profile to Sotorasib. Thus, if we consider these iridoids to be KRAS G12C inhibitors, they will be a boon to mankind.
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Affiliation(s)
- Mubarak A Alamri
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Abdullah S Alawam
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh 11623, Saudi Arabia
| | - Mohammed Merae Alshahrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, 1988, Najran 61441, Saudi Arabia
| | - Sarkar M A Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh
| | - Supriyo Saha
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Premnagar, Dehradun 248007, Uttarakhand, India
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Health-Promoting Potential of Millet: A Review. SEPARATIONS 2023. [DOI: 10.3390/separations10020080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Being a key source of animal food, millet production has been sharply increasing over the last few years in order to cope with the dietary requirements of the ever-increasing world population. It is a splendid source of essential nutrients such as protein, carbohydrates, fat, minerals, vitamins, and also some other bioactive compounds that eventually help through multiple biological activities, including antioxidant, anti-hyperglycemic, anti-cholesterol, anti-hypertensive, anthropometric effects and regulation of gut microbiota composition. These bioactive compounds, nutrients, and functions of cereal grains can be affected by processing techniques such as decortication, soaking, malting, milling, fermentation, etc. This study discusses the nutritional and functional properties of millet-incorporated foods and their impact on health, based on around 150 articles between 2015 and 2022 from the Web of Science, Google Scholar, Food and Agriculture Organization of the United Nations (FAO), Breeding Bid Survey (BBS), and FoodData Central (USDA) databases. Analyzing literature reviews, it is evident that the incorporation of millet and its constituents into foodstuffs could be useful against undernourishment and several other health diseases. Additionally, this review provides crucial information about the beneficial features of millet, which can serve as a benchmark of guidelines for industry, consumers, researchers, and nutritionists.
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A Review of the Potential Consequences of Pearl Millet (Pennisetum glaucum) for Diabetes Mellitus and Other Biomedical Applications. Nutrients 2022; 14:nu14142932. [PMID: 35889889 PMCID: PMC9322144 DOI: 10.3390/nu14142932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 07/03/2022] [Accepted: 07/08/2022] [Indexed: 11/25/2022] Open
Abstract
Diabetes mellitus has become a troublesome and increasingly widespread condition. Treatment strategies for diabetes prevention in high-risk as well as in affected individuals are largely attributed to improvements in lifestyle and dietary control. Therefore, it is important to understand the nutritional factors to be used in dietary intervention. A decreased risk of diabetes is associated with daily intake of millet-based foods. Pearl millet is a highly nutritious grain, nutritionally comparable and even superior in calories, protein, vitamins, and minerals to other large cereals, although its intake is confined to lower income segments of society. Pearl millet contains phenolic compounds which possess antidiabetic activity. Thus, it can be used to prepare a variety of food products for diabetes mellitus. Moreover, it also has many health benefits, including combating diabetes mellitus, cancer, cardiovascular conditions, decreasing tumour occurrence, lowering blood pressure, heart disease risk, cholesterol, and fat absorption rate. Therefore, the current review addresses the role of pearl millet in managing diabetes.
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