Computational Study of Asian Propolis Compounds as Potential Anti-Type 2 Diabetes Mellitus Agents by Using Inverse Virtual Screening with the DIA-DB Web Server, Tanimoto Similarity Analysis, and Molecular Dynamic Simulation

Propolis contains a wide range of pharmacological activities because of their various bioactive compounds. The beneficial effect of propolis is interesting for treating type-2 diabetes mellitus (T2DM) owing to dysregulation of multiple metabolic processes. In this study, 275 of 658 Asian propolis co...

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Published inMolecules (Basel, Switzerland) Vol. 27; no. 13; p. 3972
Main Authors Syaifie, Putri Hawa, Harisna, Azza Hanif, Nasution, Mochammad Arfin Fardiansyah, Arda, Adzani Gaisani, Nugroho, Dwi Wahyu, Jauhar, Muhammad Miftah, Mardliyati, Etik, Maulana, Nurwenda Novan, Rochman, Nurul Taufiqu, Noviyanto, Alfian, Banegas-Luna, Antonio J., Pérez-Sánchez, Horacio
Format Journal Article
LanguageEnglish
Published Switzerland MDPI AG 21.06.2022
MDPI
Subjects
Aldehyde Reductase
Asian People
Binding sites
Dehydrogenases
DIA-DB
Diabetes
Diabetes Mellitus, Type 2 - drug therapy
Disease
Drugs
Fatty acids
Flavonoids
Glucagon
Glucose
Herbal medicine
Homeostasis
Humans
in silico
Insulin Resistance
Kinases
Lipids
Medicine
Metabolism
molecular dynamic
Molecular Dynamics Simulation
propolis
Propolis - chemistry
Proteins
Retinol-Binding Proteins, Plasma
type-2 diabetes mellitus
virtual screening
Asia
propolis
DIA-DB
in silico
virtual screening
molecular dynamic
type-2 diabetes mellitus
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Abstract Propolis contains a wide range of pharmacological activities because of their various bioactive compounds. The beneficial effect of propolis is interesting for treating type-2 diabetes mellitus (T2DM) owing to dysregulation of multiple metabolic processes. In this study, 275 of 658 Asian propolis compounds were evaluated as potential anti-T2DM agents using the DIA-DB web server towards 18 known anti-diabetes protein targets. More than 20% of all compounds could bind to more than five diabetes targets with high binding affinity (<−9.0 kcal/mol). Filtering with physicochemical and pharmacokinetic properties, including ADMET parameters, 12 compounds were identified as potential anti-T2DM with favorable ADMET properties. Six of those compounds, (2R)-7,4′-dihydroxy-5-methoxy-8-methylflavone; (RR)-(+)-3′-senecioylkhellactone; 2′,4′,6′-trihydroxy chalcone; alpinetin; pinobanksin-3-O-butyrate; and pinocembrin-5-methyl ether were first reported as anti-T2DM agents. We identified the significant T2DM targets of Asian propolis, namely retinol-binding protein-4 (RBP4) and aldose reductase (AKR1B1) that have important roles in insulin sensitivity and diabetes complication, respectively. Molecular dynamic simulations showed stable interaction of selected propolis compounds in the active site of RBP4 and AKR1B1. These findings suggest that Asian propolis compound may be effective for treatment of T2DM by targeting RBP4 and AKR1B1.
AbstractList Propolis contains a wide range of pharmacological activities because of their various bioactive compounds. The beneficial effect of propolis is interesting for treating type-2 diabetes mellitus (T2DM) owing to dysregulation of multiple metabolic processes. In this study, 275 of 658 Asian propolis compounds were evaluated as potential anti-T2DM agents using the DIA-DB web server towards 18 known anti-diabetes protein targets. More than 20% of all compounds could bind to more than five diabetes targets with high binding affinity (<−9.0 kcal/mol). Filtering with physicochemical and pharmacokinetic properties, including ADMET parameters, 12 compounds were identified as potential anti-T2DM with favorable ADMET properties. Six of those compounds, (2R)-7,4′-dihydroxy-5-methoxy-8-methylflavone; (RR)-(+)-3′-senecioylkhellactone; 2′,4′,6′-trihydroxy chalcone; alpinetin; pinobanksin-3-O-butyrate; and pinocembrin-5-methyl ether were first reported as anti-T2DM agents. We identified the significant T2DM targets of Asian propolis, namely retinol-binding protein-4 (RBP4) and aldose reductase (AKR1B1) that have important roles in insulin sensitivity and diabetes complication, respectively. Molecular dynamic simulations showed stable interaction of selected propolis compounds in the active site of RBP4 and AKR1B1. These findings suggest that Asian propolis compound may be effective for treatment of T2DM by targeting RBP4 and AKR1B1.Propolis contains a wide range of pharmacological activities because of their various bioactive compounds. The beneficial effect of propolis is interesting for treating type-2 diabetes mellitus (T2DM) owing to dysregulation of multiple metabolic processes. In this study, 275 of 658 Asian propolis compounds were evaluated as potential anti-T2DM agents using the DIA-DB web server towards 18 known anti-diabetes protein targets. More than 20% of all compounds could bind to more than five diabetes targets with high binding affinity (<−9.0 kcal/mol). Filtering with physicochemical and pharmacokinetic properties, including ADMET parameters, 12 compounds were identified as potential anti-T2DM with favorable ADMET properties. Six of those compounds, (2R)-7,4′-dihydroxy-5-methoxy-8-methylflavone; (RR)-(+)-3′-senecioylkhellactone; 2′,4′,6′-trihydroxy chalcone; alpinetin; pinobanksin-3-O-butyrate; and pinocembrin-5-methyl ether were first reported as anti-T2DM agents. We identified the significant T2DM targets of Asian propolis, namely retinol-binding protein-4 (RBP4) and aldose reductase (AKR1B1) that have important roles in insulin sensitivity and diabetes complication, respectively. Molecular dynamic simulations showed stable interaction of selected propolis compounds in the active site of RBP4 and AKR1B1. These findings suggest that Asian propolis compound may be effective for treatment of T2DM by targeting RBP4 and AKR1B1.
Propolis contains a wide range of pharmacological activities because of their various bioactive compounds. The beneficial effect of propolis is interesting for treating type-2 diabetes mellitus (T2DM) owing to dysregulation of multiple metabolic processes. In this study, 275 of 658 Asian propolis compounds were evaluated as potential anti-T2DM agents using the DIA-DB web server towards 18 known anti-diabetes protein targets. More than 20% of all compounds could bind to more than five diabetes targets with high binding affinity (<−9.0 kcal/mol). Filtering with physicochemical and pharmacokinetic properties, including ADMET parameters, 12 compounds were identified as potential anti-T2DM with favorable ADMET properties. Six of those compounds, (2R)-7,4′-dihydroxy-5-methoxy-8-methylflavone; (RR)-(+)-3′-senecioylkhellactone; 2′,4′,6′-trihydroxy chalcone; alpinetin; pinobanksin-3-O-butyrate; and pinocembrin-5-methyl ether were first reported as anti-T2DM agents. We identified the significant T2DM targets of Asian propolis, namely retinol-binding protein-4 (RBP4) and aldose reductase (AKR1B1) that have important roles in insulin sensitivity and diabetes complication, respectively. Molecular dynamic simulations showed stable interaction of selected propolis compounds in the active site of RBP4 and AKR1B1. These findings suggest that Asian propolis compound may be effective for treatment of T2DM by targeting RBP4 and AKR1B1.
Propolis contains a wide range of pharmacological activities because of their various bioactive compounds. The beneficial effect of propolis is interesting for treating type-2 diabetes mellitus (T2DM) owing to dysregulation of multiple metabolic processes. In this study, 275 of 658 Asian propolis compounds were evaluated as potential anti-T2DM agents using the DIA-DB web server towards 18 known anti-diabetes protein targets. More than 20% of all compounds could bind to more than five diabetes targets with high binding affinity (<−9.0 kcal/mol). Filtering with physicochemical and pharmacokinetic properties, including ADMET parameters, 12 compounds were identified as potential anti-T2DM with favorable ADMET properties. Six of those compounds, (2 R )-7,4′-dihydroxy-5-methoxy-8-methylflavone; ( RR )-(+)-3′-senecioylkhellactone; 2′,4′,6′-trihydroxy chalcone; alpinetin; pinobanksin-3- O -butyrate; and pinocembrin-5-methyl ether were first reported as anti-T2DM agents. We identified the significant T2DM targets of Asian propolis, namely retinol-binding protein-4 (RBP4) and aldose reductase (AKR1B1) that have important roles in insulin sensitivity and diabetes complication, respectively. Molecular dynamic simulations showed stable interaction of selected propolis compounds in the active site of RBP4 and AKR1B1. These findings suggest that Asian propolis compound may be effective for treatment of T2DM by targeting RBP4 and AKR1B1.
Author Pérez-Sánchez, Horacio
Banegas-Luna, Antonio J.
Syaifie, Putri Hawa
Nugroho, Dwi Wahyu
Noviyanto, Alfian
Harisna, Azza Hanif
Nasution, Mochammad Arfin Fardiansyah
Arda, Adzani Gaisani
Mardliyati, Etik
Rochman, Nurul Taufiqu
Jauhar, Muhammad Miftah
Maulana, Nurwenda Novan
AuthorAffiliation 2 Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia; marfin.f@sci.ui.ac.id
3 Research Center for Vaccine and Drug, National Research and Innovation Agency (BRIN), Bogor 16911, Indonesia
4 Research Center for Advanced Material, National Research and Innovation Agency (BRIN), South Tangerang 15314, Indonesia; nurul@nano.or.id
1 Nano Center Indonesia, South Tangerang 15314, Indonesia; putri@nano.or.id (P.H.S.); harisna@nano.or.id (A.H.H.); gaisani.arda@nano.or.id (A.G.A.); wahyu@nano.or.id (D.W.N.); mmiftahjauhar@nano.or.id (M.M.J.); novan@nano.or.id (N.N.M.); a.noviyanto@nano.or.id (A.N.)
6 Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC), Universidad Católica de Murcia, 30107 Murcia, Spain; ajbanegas@ucam.edu
5 Department of Mechanical Engineering, Faculty of Engineering, Mercu Buana University, Jakarta 11650, Indonesia
AuthorAffiliation_xml – name: 2 Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia; marfin.f@sci.ui.ac.id
– name: 6 Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC), Universidad Católica de Murcia, 30107 Murcia, Spain; ajbanegas@ucam.edu
– name: 3 Research Center for Vaccine and Drug, National Research and Innovation Agency (BRIN), Bogor 16911, Indonesia
– name: 4 Research Center for Advanced Material, National Research and Innovation Agency (BRIN), South Tangerang 15314, Indonesia; nurul@nano.or.id
– name: 1 Nano Center Indonesia, South Tangerang 15314, Indonesia; putri@nano.or.id (P.H.S.); harisna@nano.or.id (A.H.H.); gaisani.arda@nano.or.id (A.G.A.); wahyu@nano.or.id (D.W.N.); mmiftahjauhar@nano.or.id (M.M.J.); novan@nano.or.id (N.N.M.); a.noviyanto@nano.or.id (A.N.)
– name: 5 Department of Mechanical Engineering, Faculty of Engineering, Mercu Buana University, Jakarta 11650, Indonesia
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/35807241$$D View this record in MEDLINE/PubMed
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Issue 13
Keywords propolis
DIA-DB
in silico
virtual screening
molecular dynamic
type-2 diabetes mellitus
Language English
License https://creativecommons.org/licenses/by/4.0
Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
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Snippet Propolis contains a wide range of pharmacological activities because of their various bioactive compounds. The beneficial effect of propolis is interesting for...
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SubjectTerms Aldehyde Reductase
Asian People
Binding sites
Dehydrogenases
DIA-DB
Diabetes
Diabetes Mellitus, Type 2 - drug therapy
Disease
Drugs
Fatty acids
Flavonoids
Glucagon
Glucose
Herbal medicine
Homeostasis
Humans
in silico
Insulin Resistance
Kinases
Lipids
Medicine
Metabolism
molecular dynamic
Molecular Dynamics Simulation
propolis
Propolis - chemistry
Proteins
Retinol-Binding Proteins, Plasma
type-2 diabetes mellitus
virtual screening
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Title Computational Study of Asian Propolis Compounds as Potential Anti-Type 2 Diabetes Mellitus Agents by Using Inverse Virtual Screening with the DIA-DB Web Server, Tanimoto Similarity Analysis, and Molecular Dynamic Simulation
URI https://www.ncbi.nlm.nih.gov/pubmed/35807241
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Volume 27
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