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Senger MR, da Costa Latgé SG, von Ranke NL, de Aquino GAS, Dantas RF, Genta FA, Ferreira SB, Junior FPS. Kinetics and molecular modeling studies on the inhibition mechanism of GH13 α-glycosidases by small molecule ligands. Int J Biol Macromol 2024; 269:132036. [PMID: 38697429 DOI: 10.1016/j.ijbiomac.2024.132036] [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: 02/23/2024] [Revised: 04/17/2024] [Accepted: 04/30/2024] [Indexed: 05/05/2024]
Abstract
Alpha-glucosidase inhibitors play an important role in Diabetes Mellitus (DM) treatment since they prevent postprandial hyperglycemia. The Glycoside Hydrolase family 13 (GH13) is the major family of enzymes acting on substrates containing α-glucoside linkages, such as maltose and amylose/amylopectin chains in starch. Previously, our group identified glycoconjugate 1H-1,2,3-triazoles (GCTs) inhibiting two GH13 α-glycosidases: yeast maltase (MAL12) and porcine pancreatic amylase (PPA). Here, we combined kinetic studies and computational methods on nine GCTs to characterize their inhibitory mechanism. They all behaved as reversible inhibitors, and kinetic models encompassed noncompetitive and various mechanisms of mixed-type inhibition for both enzymes. Most potent inhibitors displayed Ki values of 30 μM for MAL12 (GPESB16) and 37 μM for PPA (GPESB15). Molecular dynamics and docking simulations indicated that on MAL12, GPESB15 and GPESB16 bind in a cavity adjacent to the active site, while on the PPA, GPESB15 was predicted to bind at the entrance of the catalytic site. Notably, despite its putative location within the active site, the binding of GPESB15 does not obstruct the substrate's access to the cleavage site. Our study contributes to paving the way for developing novel therapeutic strategies for managing DM-2 through GH13 α-glycosidases inhibition.
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Affiliation(s)
- Mario Roberto Senger
- Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Samara Graciane da Costa Latgé
- Laboratório de Bioquímica e Fisiologia de Insetos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Natalia Lidmar von Ranke
- Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Gabriel Alves Souto de Aquino
- Laboratório de Síntese Orgânica e Prospecção Biológica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafael Ferreira Dantas
- Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Fernando Ariel Genta
- Laboratório de Bioquímica e Fisiologia de Insetos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Sabrina Baptista Ferreira
- Laboratório de Síntese Orgânica e Prospecção Biológica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Floriano Paes Silva Junior
- Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
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Akoonjee A, Lanrewaju AA, Balogun FO, Makunga NP, Sabiu S. Waste to Medicine: Evidence from Computational Studies on the Modulatory Role of Corn Silk on the Therapeutic Targets Implicated in Type 2 Diabetes Mellitus. BIOLOGY 2023; 12:1509. [PMID: 38132335 PMCID: PMC10740667 DOI: 10.3390/biology12121509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/02/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023]
Abstract
Type 2 diabetes mellitus (T2DM) is characterized by insulin resistance and/or defective insulin production in the human body. Although the antidiabetic action of corn silk (CS) is well-established, the understanding of the mechanism of action (MoA) behind this potential is lacking. Hence, this study aimed to elucidate the MoA in different samples (raw and three extracts: aqueous, hydro-ethanolic, and ethanolic) as a therapeutic agent for the management of T2DM using metabolomic profiling and computational techniques. Ultra-performance liquid chromatography-mass spectrometry (UP-LCMS), in silico techniques, and density functional theory were used for compound identification and to predict the MoA. A total of 110 out of the 128 identified secondary metabolites passed the Lipinski's rule of five. The Kyoto Encyclopaedia of Genes and Genomes pathway enrichment analysis revealed the cAMP pathway as the hub signaling pathway, in which ADORA1, HCAR2, and GABBR1 were identified as the key target genes implicated in the pathway. Since gallicynoic acid (-48.74 kcal/mol), dodecanedioc acid (-34.53 kcal/mol), and tetradecanedioc acid (-36.80 kcal/mol) interacted well with ADORA1, HCAR2, and GABBR1, respectively, and are thermodynamically stable in their formed compatible complexes, according to the post-molecular dynamics simulation results, they are suggested as potential drug candidates for T2DM therapy via the maintenance of normal glucose homeostasis and pancreatic β-cell function.
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Affiliation(s)
- Ayesha Akoonjee
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban 4000, South Africa; (A.A.); (A.A.L.); (F.O.B.)
| | - Adedayo Ayodeji Lanrewaju
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban 4000, South Africa; (A.A.); (A.A.L.); (F.O.B.)
| | - Fatai Oladunni Balogun
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban 4000, South Africa; (A.A.); (A.A.L.); (F.O.B.)
| | - Nokwanda Pearl Makunga
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa;
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban 4000, South Africa; (A.A.); (A.A.L.); (F.O.B.)
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Landeros-Martínez LL, Campos-Almazán MI, Sánchez-Bojorge NA, Flores R, Palomares-Báez JP, Rodríguez-Valdez LM. Theoretical Studies for the Discovery of Potential Sucrase-Isomaltase Inhibitors from Maize Silk Phytochemicals: An Approach to Treatment of Type 2 Diabetes. Molecules 2023; 28:6778. [PMID: 37836621 PMCID: PMC10574772 DOI: 10.3390/molecules28196778] [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: 08/09/2023] [Revised: 09/15/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
A theoretical analysis of the potential inhibition of human sucrase-isomaltase (SI) by flavonoids was carried out with the aim of identifying potential candidates for an alternative treatment of type 2 diabetes. Two compounds from maize silks, maysin and luteolin, were selected to be studied with the structure-based density functional theory (DFT), molecular docking (MDock), and molecular dynamics (MD) approaches. The docking score and MD simulations suggested that the compounds maysin and luteolin presented higher binding affinities in N-terminal sucrase-isomaltase (NtSI) than in C-terminal sucrase-isomaltase (CtSI). The reactivity parameters, such as chemical hardness (η) and chemical potential (µ), of the ligands, as well as of the active site amino acids of the NtSI, were calculated by the meta-GGA M06 functional in combination with the 6-31G(d) basis set. The lower value of chemical hardness calculated for the maysin molecule indicated that this might interact more easily with the active site of NtSI, in comparison with the values of the acarbose and luteolin structures. Additionally, a possible oxidative process was proposed through the quantum chemical calculations of the electronic charge transfer values (∆N) between the active site amino acids of the NtSI and the ligands. In addition, maysin displayed a higher ability to generate more oxidative damage in the NtSI active site. Our results suggest that maysin and luteolin can be used to develop novel α-glucosidase inhibitors via NtSI inhibition.
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Affiliation(s)
| | | | | | | | | | - Luz María Rodríguez-Valdez
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Chihuahua 31125, Mexico; (L.-L.L.-M.); (M.I.C.-A.); (N.-A.S.-B.); (R.F.); (J.P.P.-B.)
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Sánchez-García YI, Gutiérrez-Méndez N, Landeros-Martínez LL, Ramos-Sánchez VH, Orozco-Mena R, Salmerón I, Leal-Ramos MY, Sepúlveda DR. Crystallization of Lactose-Protein Solutions in the Presence of Flavonoids. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:2684-2694. [PMID: 35175029 DOI: 10.1021/acs.jafc.1c05315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Lactose is commonly crystallized in the presence of whey proteins, forming co-crystals of lactose and proteins. This work hypothesized that flavonoids such as rutin or epigallocatechin-3-gallate (EGCG) could be incorporated into the lactose and protein co-crystal structure since flavonoids may interact with both lactose and proteins. The interactions between whey proteins and flavonoids were first studied. Then, lactose-protein solutions were crystallized with and without flavonoids, measuring the kinetic parameters of crystallization and characterizing the resulting crystals. The incorporation of flavonoids in lactose-protein co-crystals depended on the hydrophilic nature of flavonoids. The hydrophilic EGCG was scarcely enclosed in the crystal lattice of lactose and avoided the inclusion of whey proteins in the crystals. In contrast, the less water-soluble rutin interacted with whey proteins and lactose, leading to the formation of co-crystals containing lactose, protein, and a large concentration of rutin (3.468 ± 0.392 mg per 100 mg of crystals).
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Affiliation(s)
- Yanira I Sánchez-García
- The Graduate School, Graduate Program in Chemistry, Chemistry School, Autonomous University of Chihuahua, Chihuahua PC 31125, México
| | - Néstor Gutiérrez-Méndez
- The Graduate School, Graduate Program in Chemistry, Chemistry School, Autonomous University of Chihuahua, Chihuahua PC 31125, México
| | - Linda L Landeros-Martínez
- The Graduate School, Graduate Program in Chemistry, Chemistry School, Autonomous University of Chihuahua, Chihuahua PC 31125, México
| | - Víctor H Ramos-Sánchez
- The Graduate School, Graduate Program in Chemistry, Chemistry School, Autonomous University of Chihuahua, Chihuahua PC 31125, México
| | - Raúl Orozco-Mena
- The Graduate School, Graduate Program in Chemistry, Chemistry School, Autonomous University of Chihuahua, Chihuahua PC 31125, México
| | - Iván Salmerón
- The Graduate School, Graduate Program in Chemistry, Chemistry School, Autonomous University of Chihuahua, Chihuahua PC 31125, México
| | - Martha Y Leal-Ramos
- The Graduate School, Graduate Program in Chemistry, Chemistry School, Autonomous University of Chihuahua, Chihuahua PC 31125, México
| | - David R Sepúlveda
- Research Center for Food and Development, Civil Association (CIAD A.C.), Cuauhtémoc PC 31125, México
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Yuan L, Bao Z, Ma T, Lin S. Hypouricemia effects of corn silk flavonoids in a mouse model of potassium oxonated-induced hyperuricemia. J Food Biochem 2021; 45:e13856. [PMID: 34250618 DOI: 10.1111/jfbc.13856] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/13/2021] [Accepted: 06/21/2021] [Indexed: 12/01/2022]
Abstract
The hypouricemic effect of corn silk flavonoids (CSFs) in vivo that were extracted by ethanol and fractionated by continuous elution with 40% (CSF-A) and 60% (CSF-B) ethanol solutions on polyamide column were investigated in this study. CSFs reduced serum uric acid (UA) level in a mouse model of potassium oxonate-induced hyperuricemia. CSF-B had the best hypouricemic effect, as it decreased the serum UA level by 26.69% and xanthine oxidase (XO) activity in the serum by 11.29%. The mechanism of action of CSF-B was related to the inhibition of XO activity and the promotion of UA excretion. CSF-B was found to contain 12 kinds of major flavonoids, five of which were speculated to influence its activity in the hyperuricemia mice. The five flavonoids were apigenin-6-C-glucoside-7-O-glucoside, kaempferol-3-O-rutinoside, luteolin-7-glucoside, luteolin-3',7-di-O-glucoside, and naringenin, respectively. Structure analysis revealed that C-4', C5 hydroxyl groups, and C2=C3 double bonds in CSF-B gave the latter its hypouricemic effect. PRACTICAL APPLICATIONS: The prevalence of hyperuricemia has increased in recent times. Current hypouricemic drugs have side effects and can easily lead to various complications. Therefore, it is of great practical significance to find safer and more effective hypouricemic drugs. This study demonstrated that corn silk flavonoids may be used as a dietary supplement to manage hyperuricemia.
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Affiliation(s)
- Liyan Yuan
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, PR China
| | - Zhijie Bao
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, PR China
| | - Tiecheng Ma
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, PR China
| | - Songyi Lin
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, PR China
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A new functionality study of vanillin as the inhibitor for α-glucosidase and its inhibition kinetic mechanism. Food Chem 2021; 353:129448. [PMID: 33711702 DOI: 10.1016/j.foodchem.2021.129448] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/20/2021] [Accepted: 02/21/2021] [Indexed: 12/20/2022]
Abstract
Vanillin is a natural phenolic compound mainly used as flavors in food industry. In this work, a new functionality of vanillin as the α-glucosidase inhibitor was studied based on the inhibition kinetic mechanism. The inhibitory effect (IC50) of vanillin against α-glucosidase was 28.34 ± 0.89 mg/mL, which belongs to mixed inhibition mechanism and its process was spontaneous. Vanillin could bind to α-glucosidase by hydrophobic interactions and hydrogen bonds with -8.42 kcal/mol intermolecular energy to form the steric hindrance. The average binding distances was calculated as 2.20 nm according to energy transfer theory. In addition, the protein secondary structure and denaturation temperature (decreasing about 10 °C) were changed significantly after vanillin binding to α-glucosidase, resulting in an inhibitory effect. The findings of this research provide insights for the development of vanillin as potential inhibitor for α-glucosidase in special dietary foods.
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