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Kenneth C, Anugrah DSB, Julianus J, Junedi S. Molecular insights into the inhibitory potential of anthocyanidins on glucokinase regulatory protein. PLoS One 2023; 18:e0288810. [PMID: 37467274 DOI: 10.1371/journal.pone.0288810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 07/05/2023] [Indexed: 07/21/2023] Open
Abstract
Computational methods were used to investigate six anthocyanidins exhibiting antidiabetic activity by inhibiting glucokinase regulatory protein (GKRP) activity. Density functional theory was used to optimise the geometry of anthocyanidins and calculate their quantum chemical properties. A blind docking method was employed to conduct a molecular docking study, which revealed that delphinidin (Del), cyanidin (Cya), and pelargonidin (Pel) as potential GKRP inhibitors with the lowest binding free energy of -8.7, -8.6, and -8.6 kcal/mol, corresponding to high binding affinity. The molecular dynamics study further verified the blind docking results by showing high GKRP-F1P complex stability and high binding affinity calculated through the MM/GBSA method, upon the binding of pelargonidin. The lower RMSF values of pivotal GK-interacting residues for GKRP-F1P-Pel compared to GKRP-F1P, as a positive control, indicating pelargonidin ability to maintain the inactive conformation of GKRP through the inhibition of GK binding. The key residues that control the binding of the F1P to GKRP and anthocyanidin to GKRP-F1P were also identified in this study. Altogether, pelargonidin is anthocyanidins-derived natural products that have the most potential to act as inhibitors of GKRP and as antidiabetic nutraceuticals.
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Affiliation(s)
- Christian Kenneth
- Biotechnology Study Program, Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Daru Seto Bagus Anugrah
- Biotechnology Study Program, Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Jeffry Julianus
- Faculty of Pharmacy, Sanata Dharma University, Yogyakarta, Indonesia
| | - Sendy Junedi
- Faculty of Biotechnology, Universitas Atma Jaya Yogyakarta, Yogyakarta, Indonesia
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Virginia DM, Patramurti C, Fenty , Setiawan CH, Julianus J, Hendra P, Susanto NAP. Single Nucleotide Polymorphism in the 3’ Untranslated Region of PRKAA2 on Cardiometabolic Parameters in Type 2 Diabetes Mellitus Patients Who Received Metformin. Ther Clin Risk Manag 2022; 18:349-357. [PMID: 35414746 PMCID: PMC8995000 DOI: 10.2147/tcrm.s349900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/14/2022] [Indexed: 11/29/2022] Open
Abstract
Purpose This study aimed to explore the association of rs857148 A>C as 3ʹUTR variants with blood pressure, HbA1c profile, and lipid profiles as cardiometabolic parameters among patients with T2DM receiving metformin. Patients and Methods This cross-sectional analytic research was conducted with 114 consecutively selected patients with T2DM. Polymerase chain reaction-restriction fragment length polymorphism was conducted to determine rs857148. A total of 108 patients fulfilled inclusion and exclusion criteria. Results Genotype distribution agreed with the Hardy Weinberg Equation for Equilibrium (p>0.05) but wildtype allele was found as the minor allele. Subjects with CC genotype and C allele had enhanced HbA1c levels (OR=7.12; 95% CI=1.05–48.26; p=0.04; OR=1.66; 95% CI=1.06–2.60; p=0.03, respectively). It was confirmed by dominant model whereas subjects with AA tended to have reduced HbA1c compared to AC+CC genotype (OR=0.15; 95% CI=0.02–0.97; p=0.047). AC genotype had significant correlation to total cholesterol (OR=1.05; 95% CI=1.01–1.10; p=0.03) compared to AA genotype. Conclusion We conclude that polymorphism of rs87148, specifically CC genotype and C allele, has a significant association with HbA1c and total cholesterol after considering oral hypoglycemia agent dose, age, gender, and combination therapy, compared to AA genotype. Future studies that involve a larger sample population and more rigorous selection criteria are required. ![]()
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Kurniawan YS, Priyangga KTA, Jumina, Pranowo HD, Sholikhah EN, Zulkarnain AK, Fatimi HA, Julianus J. An Update on the Anticancer Activity of Xanthone Derivatives: A Review. Pharmaceuticals (Basel) 2021; 14:1144. [PMID: 34832926 PMCID: PMC8625896 DOI: 10.3390/ph14111144] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 12/27/2022] Open
Abstract
The annual number of cancer deaths continues increasing every day; thus, it is urgent to search for and find active, selective, and efficient anticancer drugs as soon as possible. Among the available anticancer drugs, almost all of them contain heterocyclic moiety in their chemical structure. Xanthone is a heterocyclic compound with a dibenzo-γ-pyrone framework and well-known to have "privileged structures" for anticancer activities against several cancer cell lines. The wide anticancer activity of xanthones is produced by caspase activation, RNA binding, DNA cross-linking, as well as P-gp, kinase, aromatase, and topoisomerase inhibition. This anticancer activity depends on the type, number, and position of the attached functional groups in the xanthone skeleton. This review discusses the recent advances in the anticancer activity of xanthone derivatives, both from natural products isolation and synthesis methods, as the anticancer agent through in vitro, in vivo, and clinical assays.
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Affiliation(s)
- Yehezkiel Steven Kurniawan
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (Y.S.K.); (K.T.A.P.); (H.D.P.)
| | - Krisfian Tata Aneka Priyangga
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (Y.S.K.); (K.T.A.P.); (H.D.P.)
| | - Jumina
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (Y.S.K.); (K.T.A.P.); (H.D.P.)
| | - Harno Dwi Pranowo
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (Y.S.K.); (K.T.A.P.); (H.D.P.)
| | - Eti Nurwening Sholikhah
- Department of Pharmacology and Therapy, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia;
| | - Abdul Karim Zulkarnain
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (A.K.Z.); (H.A.F.)
| | - Hana Anisa Fatimi
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (A.K.Z.); (H.A.F.)
| | - Jeffry Julianus
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Sanata Dharma, Yogyakarta 55282, Indonesia;
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Hariono M, Nuwarda RF, Yusuf M, Rollando R, Jenie RI, Al-Najjar B, Julianus J, Putra KC, Nugroho ES, Wisnumurti YK, Dewa SP, Jati BW, Tiara R, Ramadani RD, Qodria L, Wahab HA. Arylamide as Potential Selective Inhibitor for Matrix Metalloproteinase 9 (MMP9): Design, Synthesis, Biological Evaluation, and Molecular Modeling. J Chem Inf Model 2019; 60:349-359. [PMID: 31825614 DOI: 10.1021/acs.jcim.9b00630] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Previous studies have reported that compounds bearing an arylamide linked to a heterocyclic planar ring have successfully inhibited the hemopexin-like domain (PEX9) of matrix metalloproteinase 9 (MMP9). PEX9 has been suggested to be more selectively targeted than MMP9's catalytic domain in a degrading extracellular matrix under some pathologic conditions, especially in cancer. In this study, we aim to synthesize and evaluate 10 arylamide compounds as MMP9 inhibitors through an enzymatic assay as well as a cellular assay. The mechanism of inhibition for the most active compounds was investigated via molecular dynamics simulation (MD). Molecular docking was performed using AutoDock4.0 with PEX9 as the protein model to predict the binding of the designed compounds. The synthesis was carried out by reacting aniline derivatives with 3-bromopropanoyl chloride using pyridine as the catalyst at room temperature. The MMP9 assay was conducted using the FRET-based MMP9 kits protocol and gelatin zymography assay. The cytotoxicity assay was done using the MTT method, and the MD simulation was performed using AMBER16. Assay on MMP9 demonstrated activities of three compounds (2, 7, and 9) with more than 50% inhibition. Further inhibition on MMP9 expressed by 4T1 showed that two compounds (7 and 9) inhibited its gelatinolytic activity more than 50%. The cytotoxicity assay against 4T1 cells results in the inhibition of the cell growth with an EC50 of 125 μM and 132 μM for 7 and 9, respectively. The MD simulation explained a stable interaction of 7 and 9 in PEX9 at 100 ns with a free energy of binding of -8.03 kcal/mol and -6.41 kcal/mol, respectively. Arylamides have potential effects as selective MMP9 inhibitors in inhibiting breast cancer cell progression.
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Affiliation(s)
- Maywan Hariono
- Faculty of Pharmacy , Sanata Dharma University , Depok, Sleman 55282 , Yogyakarta , Indonesia
| | - Rina F Nuwarda
- Faculty of Pharmacy , Padjadjaran University , Jatinangor, Sumedang 45363 , West Java , Indonesia
| | - Muhammad Yusuf
- Chemistry Department, Faculty of Mathematics and Natural Sciences , Padjadjaran University , Jatinangor, Sumedang 45363 , West Java , Indonesia
| | - Rollando Rollando
- Pharmacy Program, Faculty of Science and Technology , Ma Chung University , Malang 65151 , Indonesia
| | - Riris I Jenie
- Cancer Chemoprevention Research Center, Faculty of Pharmacy , Gadjah Mada University , Sekip Utara 55281 , Yogyakarta , Indonesia
| | - Belal Al-Najjar
- Faculty of Pharmacy and Medical Sciences , AlAhliyya Amman University , Amman 19328 , Jordan
| | - Jeffry Julianus
- Faculty of Pharmacy , Sanata Dharma University , Depok, Sleman 55282 , Yogyakarta , Indonesia
| | - Kevin C Putra
- Faculty of Pharmacy , Sanata Dharma University , Depok, Sleman 55282 , Yogyakarta , Indonesia
| | - Ervan S Nugroho
- Faculty of Pharmacy , Sanata Dharma University , Depok, Sleman 55282 , Yogyakarta , Indonesia
| | - Yohanes K Wisnumurti
- Faculty of Pharmacy , Sanata Dharma University , Depok, Sleman 55282 , Yogyakarta , Indonesia
| | - Sangga P Dewa
- Faculty of Pharmacy , Sanata Dharma University , Depok, Sleman 55282 , Yogyakarta , Indonesia
| | - Benedictus W Jati
- Faculty of Pharmacy , Sanata Dharma University , Depok, Sleman 55282 , Yogyakarta , Indonesia
| | - Reynaldo Tiara
- Faculty of Pharmacy , Sanata Dharma University , Depok, Sleman 55282 , Yogyakarta , Indonesia
| | - Ratna D Ramadani
- Cancer Chemoprevention Research Center, Faculty of Pharmacy , Gadjah Mada University , Sekip Utara 55281 , Yogyakarta , Indonesia
| | - Lailatul Qodria
- Cancer Chemoprevention Research Center, Faculty of Pharmacy , Gadjah Mada University , Sekip Utara 55281 , Yogyakarta , Indonesia
| | - Habibah A Wahab
- Pharmaceutical Technology Department, School of Pharmaceutical Sciences and USM-RIKEN Centre for Ageing Science (URICAS) , Universiti Sains Malaysia , 11800 Minden , Pulau Pinang , Malaysia
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