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Itakura M, Utomo DH, Kita M. Development of actin dimerization inducers inspired by actin-depolymerizing macrolides. Chem Commun (Camb) 2024; 60:4910-4913. [PMID: 38623638 DOI: 10.1039/d4cc01304b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Several natural cytotoxic C2-symmetric bis-lactones, such as swinholide A and rhizopodin, sequester actin dimer from the actin network and potently inhibit actin dynamics. To develop new protein-protein interaction (PPI) modulators, we synthesized structurally simplified actin-binding side-chain dimers of antitumor macrolide aplyronine A. By fixing the two side-chains closer than those of rhizopodin, the C4 linker analog depolymerized filamentous actin more potently than natural aplyronines. Cross-link experiments revealed that actin dimer was formed by treatment with the C4 linker analog. Molecular dynamics simulations showed that this analog significantly changed the interaction and spatial arrangement of the two actins compared to those in rhizopodin to provide a highly distorted and twisted orientation in the complex. Our study may promote the development of PPI-based anticancer and other drug leads related to cytoskeletal dynamics.
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Affiliation(s)
- Moeka Itakura
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.
| | - Didik Huswo Utomo
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.
- Bioinformatics Research Center, Indonesian Institute of Bioinformatics, Malang, Jawa Timur 65162, Indonesia
| | - Masaki Kita
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.
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Luthfiana D, Utomo DH. Network pharmacology reveals the potential of Dolastatin 16 as a diabetic wound healing agent. In Silico Pharmacol 2023; 11:23. [PMID: 37719716 PMCID: PMC10504231 DOI: 10.1007/s40203-023-00161-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 08/26/2023] [Indexed: 09/19/2023] Open
Abstract
Dolastatin 16, a marine cyclic depsipeptide, was initially isolated from the sea hare Dolabella Auricularia by Pettit et al. Due to the lack of information regarding its bioactivity, target identification becomes an indispensable strategy for revealing the potential targets and mechanisms of action of Dolastatin 16. Network pharmacology was utilized to identify targets associated with the disease, gene ontology, and KEGG pathways. The results highlighted Matrix Metalloproteinase-9 (MMP9) as a potential target of Dolastatin 16 through network pharmacology analysis. This target was found to be primarily involved in the TNF signaling pathway and in foot ulceration-associated diabetic polyneuropathy. Furthermore, the binding mode and dynamic behavior of the complex were investigated through molecular docking and molecular dynamics studies. In the docking study, a native ligand (a hydroxamate inhibitor) and (R)-ND-336 were employed as ligand controls, demonstrating binding energy values of - 6.6 and - 8.9 kcal/mol, respectively. The Dolastatin 16 complex exhibited a strong affinity for MMP9, with a binding energy value of - 9.7 kcal/mol, indicating its high potential as an inhibitor. Molecular dynamics also confirmed the stability of the MMP9-Dolastatin complex throughout the simulation process. Dolastatin 16 has the potential to act as an MMP9 inhibitor, offering promise for accelerating the wound healing process in diabetic foot conditions. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-023-00161-5.
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Affiliation(s)
- Dewi Luthfiana
- Bioinformatics Research Center, Indonesian Institute of Bioinformatics (INBIO), Malang, Indonesia
| | - Didik Huswo Utomo
- Bioinformatics Research Center, Indonesian Institute of Bioinformatics (INBIO), Malang, Indonesia
- Department of Biology, Faculty of Mathematics and Natural Sciences, Brawijaya University, Malang, East Java Indonesia
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Priyandoko D, Widowati W, Kusuma HSW, Afifah E, Wijayanti CR, Rizal R, Sholihah IA, Permatasari GW, Ramadhani A, Utomo DH. Inflammation inhibitory activity of green tea, soybean, and guava extracts during Sars-Cov-2 infection through TNF protein in cytokine storm. Comput Biol Chem 2023; 105:107898. [PMID: 37247574 DOI: 10.1016/j.compbiolchem.2023.107898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 02/05/2023] [Accepted: 05/22/2023] [Indexed: 05/31/2023]
Abstract
Coronavirus disease is caused by the pathogen severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) known as COVID-19. COVID-19 has caused the deaths of 6,541,936 people worldwide as of September 27th, 2022. SARS-CoV-2 severity is determined by a cytokine storm condition, in which the innate immune system creates an unregulated and excessive production of pro-inflammatory such IL-1, IL-6, NF Kappa B, and TNF alpha signaling molecules known as cytokines. The patient died due to respiratory organ failure and an acute complication because of the hyper-inflammation phenomenon. Green tea, soybean, and guava bioactive substances are well-known to act as anti-inflammation, and antioxidants become prospective COVID-19 illness candidates to overcome the cytokine storm. Our research aims to discover the bioactivity, bioavailability, and protein targets of green tea, soybean, and guava bioactive compounds as anti-inflammatory agents via the TNF inhibition pathway. The experiment uses in silico methods and harnesses the accessible datasets. Samples of 3D structure and SMILE identity of bioactive compounds were retrieved from the KNApSAck and Dr Duke databases. The QSAR analysis was done by WAY2DRUG web server, while the ADME prediction was performed using SWISSADME web server, following the Lipinsky rules of drugs. The target protein and protein-protein interaction were analyzed using STRING DB and Cytoscape software. Lastly, molecular docking was performed using Autodock 4.2 and visualization with BioVia Discovery Studio 2019. The identified study showed the potential of green tea, soybean, and guava's bioactive compounds have played an important role as anti-inflammation agents through TNF inhibitor pathway.
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Affiliation(s)
- Didik Priyandoko
- Biology Study Program, Universitas Pendidikan Indonesia, Indonesia.
| | - Wahyu Widowati
- Faculty of Medical, Maranatha Christian University, Indonesia.
| | | | - Ervi Afifah
- Aretha Medika Utama, Biomolecular and Biomedical Research Center, Indonesia
| | | | - Rizal Rizal
- Aretha Medika Utama, Biomolecular and Biomedical Research Center, Indonesia; Biomedical Engineering, Faculty of Engineering, Universitas Indonesia, Indonesia
| | - Ika Adhani Sholihah
- Aretha Medika Utama, Biomolecular and Biomedical Research Center, Indonesia; School of Life Sciences and Technology, Institut Teknologi Bandung, Indonesia
| | | | - Anggia Ramadhani
- Indonesian Research Institute for Bioinformatics and Biomolecular, Malang, Indonesia
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Miftahussurur M, Alfaray RI, Fauzia KA, Dewayani A, Doohan D, Waskito LA, Rezkitha YAA, Utomo DH, Somayana G, Fahrial Syam A, Lubis M, Akada J, Matsumoto T, Yamaoka Y. Low-grade intestinal metaplasia in Indonesia: Insights into the expression of proinflammatory cytokines during Helicobacter pylori infection and unique East-Asian CagA characteristics. Cytokine 2023; 163:156122. [PMID: 36640695 DOI: 10.1016/j.cyto.2022.156122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 12/28/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023]
Abstract
Helicobacter pylori infection is a major cause of intestinal metaplasia. In this study, we aimed to understand the reason underlying the low grade and incidence of intestinal metaplasia in Indonesia, based on the expression of genes encoding proinflammatory cytokines in gastric biopsy specimens. The possible reasons for the lesser virulence of the East-Asian-type CagA in Indonesia than that of the Western-type CagA, which is not common in other countries, were also investigated. The mRNA expression of cytokines was evaluated using real-time PCR. CagA characteristics were analyzed using in silico analysis. The expression of cytokines was typically not robust, among H. pylori-infected subjects in Indonesia, despite them predominantly demonstrating the East-Asian-type CagA. This might partially be explained by the characteristics of the East-Asian-type CagA in Indonesia, which showed a higher instability index and required higher energy to interact with proteins related to the cytokine induction pathway compared with the other types (p < 0.001 and p < 0.05, respectively). Taken together, besides the low prevalence of H. pylori, the low inflammatory response of the host and low CagA virulence, even among populations with high infection rates, may play an essential role in the low grade and low incidence of intestinal metaplasia in Indonesia. We believe that these findings would be relevant for better understanding of intestinal metaplasia, which is closely associated with the development of gastric cancer.
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Affiliation(s)
- Muhammad Miftahussurur
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine-Dr. Soetomo Teaching Hospital, Universitas Airlangga, Jalan Mayjend Prof, Dr. Moestopo, No. 6-8, Surabaya, Surabaya 60131, Indonesia; Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia.
| | - Ricky Indra Alfaray
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia; Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu Oita 879-5593, Japan.
| | - Kartika Afrida Fauzia
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia; Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu Oita 879-5593, Japan; Department of Public Health and Preventive Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia.
| | - Astri Dewayani
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia; Department of Infectious Disease Control, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu, Oita 879-5593, Japan; Department of Anatomy, Histology and Pharmacology, Universitas Airlangga, Surabaya 60131, Indonesia.
| | - Dalla Doohan
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia; Department of Anatomy, Histology and Pharmacology, Universitas Airlangga, Surabaya 60131, Indonesia.
| | - Langgeng Agung Waskito
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia; Department of Physiology and Medical Biochemistry, Faculty of Medicine, Universitas Airlangga, Surabaya, 60132, Indonesia; Department of Internal Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia.
| | - Yudith Annisa Ayu Rezkitha
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia; Department of Internal Medicine, Faculty of Medicine, University of Muhammadiyah, Surabaya, Surabaya 60113, Indonesia.
| | - Didik Huswo Utomo
- Research and Education Center for Bioinformatics, Indonesia Institute of Bioinformatics, Malang 65162, Indonesia.
| | - Gde Somayana
- Gastroentero Hepatology Division, Department of Internal Medicine, Faculty of Medicine-Sanglah Hospital, Udayana University, Denpasar, Bali 80114, Indonesia.
| | - Ari Fahrial Syam
- Division of Gastroenterology, Department of Internal Medicine, Faculty of Medicine-Cipto Mangunkusumo Teaching Hospital, University of Indonesia, Jakarta 10430, Indonesia.
| | - Masrul Lubis
- Division of Gastroenterology, Department of Internal Medicine, Faculty of Medicine-Cipto Mangunkusumo Teaching Hospital, Universitas Sumatera Utara, Medan 20222, Indonesia
| | - Junko Akada
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu Oita 879-5593, Japan.
| | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu Oita 879-5593, Japan.
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu Oita 879-5593, Japan; Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX 77030, USA.
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Utomo DH, Kita M. Binding Mode of Actin–aplyronine A–tubulin Heterotrimeric Complex Revealed by Molecular Dynamics Simulation. BCSJ 2023. [DOI: 10.1246/bcsj.20220299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Didik Huswo Utomo
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601
| | - Masaki Kita
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601
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Utomo DH, Fujieda A, Tanaka K, Takahashi M, Futaki K, Tanabe K, Kigoshi H, Kita M. The C29-C34 parts of antitumor macrolide aplyronine A serve as versatile actin-affinity tags. Chem Commun (Camb) 2021; 57:10540-10543. [PMID: 34553712 DOI: 10.1039/d1cc04259a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Anticancer drug development inspired by natural products based on protein-protein interactions (PPI) is a promising strategy. We developed structurally-simplified C29-C34 side-chain analogs of aplyronine A (ApA), an antitumor marine macrolide. Among them, the analog possessing the C23 acyloxy group, the C29 N,N-dimethyl-L-alanine ester and the C34 N-methyl enamide showed potent actin-depolymerizing activity. Binding kinetics, molecular docking, and affinity-purification experiments revealed that they are versatile actin-affinity tags to accelerate studies on the mode of action related to cytoskeletal dynamics and the development of PPI-based drug leads.
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Affiliation(s)
- Didik Huswo Utomo
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.
| | - Akari Fujieda
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.
| | - Kentaro Tanaka
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.
| | - Momoko Takahashi
- Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba 305-8571, Japan.
| | - Kentaro Futaki
- Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba 305-8571, Japan.
| | - Kenta Tanabe
- Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba 305-8571, Japan.
| | - Hideo Kigoshi
- Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba 305-8571, Japan.
| | - Masaki Kita
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan. .,Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba 305-8571, Japan.
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Permatasari GW, Utomo DH, Purwaningroom DL, Soeatmadji D. The correlation of structural and binding affinity of insulin analog to the onset of action for diabetic therapy. hsji 2021. [DOI: 10.22435/hsji.v12i1.4783] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Background: These days, insulin analog production has been improved and becoming popular. The advantages of insulin analog have been extensively reviewed in terms of effectiveness compared to human insulin. Each of the insulin analog industries has claimed their safety and efficacy based on in vivo and in vitro to overcome type 2 diabetes. Hereby, we report on the identification of highly effective analog-based insulin on structure and binding affinity computationally, to confirm its potential and give a broader point of view to insulin analog users.
Methods: Five types of insulin analogs, Aspart, Glargine, Detemir, Lispro and Degludec, were analyzed. We grouped and clustered the sequence by alignment to identify the closeness and sequence similarity between samples, continued by superimposing analysis and undertaking binding affinity identification utilizing of a docking analysis approach.
Results: Lispro had the least sequence similarity to other types, close to Aspart (96%) and Glargine (90.5%), while Detemir and Degludec showed 100% similarity we decide to only use Degludec for the next analysis. Furthermore, Lispro, Aspart, and Glargine exhibited structural similarity strengthened by the lack of significant difference in the RMSD data. Importantly, Aspart had the highest binding affinity score (-66.1 +/- 7.1 Kcal/mol) in the docking analysis to the insulin receptor (INSR) and similar binding site areas to human insulin.
Conclusion: Our finding revealed that the strength of insulin analogs towards insulin receptors is identic with its rapid mechanism in the human body.
Keywords: computation, docking, insulin analog, sequence similarity, structure
Abstrak
Latar belakang: Saat ini, produksi analog insulin meningkat dan menjadi popular. Keuntungan analog insulin telah ditinjau secara ekstensif dalam hal efektivitas dibandingkan dengan insulin manusia. Masing-masing industri analog insulin mengklaim keamanan dan kemanjurannya berdasarkan in vivo dan in vitro untuk mengatasi diabetes tipe 2. Kami melaporkan identifikasi insulin analog yang efektif berdasarkan struktur dan afinitas pengikatan secara komputasi, untuk mengonfirmasi potensi serta memberikan sudut pandang yang lebih luas kepada pengguna insulin analog.
Metode: Lima jenis analog insulin, Aspart, Glargine, Detemir, Lispro, dan Degludec, dianalisis. Kami membandingkan dan mengelompokkan urutan tersebut dengan penyelarasan untuk mengidentifikasi kedekatan dan kesamaan urutan antar sampel dilanjutkan dengan superimposing analysis dan melakukan identifikasi binding affinity menggunakan pendekatan analisis docking.
Hasil: Lispro memiliki kemiripan sekuen paling rendah dengan jenis lainnya, mendekati Aspart (96%) dan glargine (90,5%), sedangkan Determir dan Degludec menunjukkan kemiripan 100% sehingga kami menggunakan Degludec untuk analisis selanjutnya. Selain itu, Lispro, Aspart, dan Glargine menunjukkan kesamaan struktural yang diperkuat oleh rendahnya nilai signifikansi pada data RMSD. Perlu digarisbawahi bahwa Aspart memiliki skor afinitas pengikatan tertinggi (-66.1 +/- 7.1 kkal / mol) dalam analisis docking ke reseptor insulin (INSR) dan memiliki area pengikatan yang serupa dengan insulin manusia.
Kesimpulan: Penemuan kami mengungkapkan bahwa kekuatan insulin analog sejalan dengan laju mekanismenya di dalam tubuh manusia
Kata kunci: komputasi, docking, insulin analog, kemiripan sekuen, struktur
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Murlistyarini S, Sardjono TW, Hakim L, Widyarti S, Utomo DH, Permatasari GW, Hernowaty TE. miRNA-17-5p Target Prediction and its Role in Senescence Mechanism through p21 Interference. Open Access Maced J Med Sci 2021. [DOI: 10.3889/oamjms.2021.5986] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND: Cellular senescence is known to be correlated with the cessation of cell cycle. The progression of cell cycle is promoted by activities of various proteins, including cyclin-dependent kinase (CDK) and cyclin proteins, which work synergistically. CDK-cyclin complexes are influenced by other proteins, such as retinoblastoma (Rb) and E2F proteins. In cell cycle, both Rb and E2F proteins could be affected by one of the CDK inhibitors, that is, p21. MicroRNA (miRNA) is well known for its role in biological processes, including cell cycle. However, the contribution of miRNA in cell cycle is still poorly understood. Some miRNAs play a role in pro-proliferation and anti-proliferation.
AIM: This study was performed an in silico study analysis to reveal the relationship between miRNA-17-5p and p21 in the process of cellular senescence.
METHODS: The extensive data mining was conducted to determine the miRNA that contributes to the process of anti-aging prevention and the desired target genes through the Human Protein Atlas and cancer database. miRNA target prediction was performed using DIANA-microT-CDS. Gene function of the miRNA-17-5p target was annotated using DAVID GO.
RESULTS: The sequence of hsa-miRNA-17-5p (CAAAGUGCUUACAGUGCAGGUAG) has three attachment sites with binding types of 8 mer, 6 mer, and 8 mer at the transcription sites of 447–474, 485–513, and 1132–1154, respectively. The main profile of hsa-miRNA-17-5p showed that it bound to 3’-untranslated region and the coding region (exon).
CONCLUSIONS: The miRNA-17-5p was involved in cellular senescence by influencing the process of cell proliferation in the cell cycle pathway.
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Gondokesumo ME, Sumitro SB, Handono K, Pardjianto B, Widowati W, Utomo DH. A Computational Study to Predict Wound Healing Agents from the Peel of the Mangosteen (Garcinia mangostana L.) Extract. Int J Bioautomation 2020. [DOI: 10.7546/ijba.2020.24.3.000607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Susanto AH, Widodo, Rohman MS, Utomo DH, Lukitasari M. Analysis in silico of the single nucleotide polymorphism G–152A in the promoter of the angiotensinogen gene of Indonesian patients with essential hypertension. ASIAN BIOMED 2018. [DOI: 10.1515/abm-2018-0027] [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] [Indexed: 11/15/2022]
Abstract
Abstract
Background
Single nucleotide polymorphism (SNP) G–152A (rs11568020) in the promoter of the angiotensinogen gene (AGT) may modulate its transcription. Translation of mRNA to angiotensinogen induces hypertension during hypoxia. The G allele at position –152 is located within the hypoxia-response element (HRE) transcription factor-binding site for the hypoxia-inducible factor 1 (HIF-1) heterodimer. However, the function of the –152 site in HIF-1 binding is not fully elucidated.
Objectives
To determine the frequency of SNP G–152A in Indonesian patients with hypertension and the function of this SNP.
Methods
We determined the frequency of the SNP in 100 patients by direct sequencing, and the influence of SNP G–152A on predicted binding of HIF-1 to the HRE using a docking approach in silico.
Results
The AGT promoter in our patients had genetic variants –152G and –152A (19:1). Predicted binding indicated that HIF-1 directly contacts the major groove of the G allele, but not the A allele. Scoring according to weighted sum High Ambiguity Driven biomolecular DOCKing showed that the score for the A allele–HIF-1 complex (–47.1 ± 6.9 kcal/mol) was higher than that for the G allele–HIF-1 complex (–94.6 ± 14.1 kcal/mol), indicating more favorable binding of HIF-1 to the G allele.
Conclusions
SNP G–152A reduces the favorability of binding of HIF-1 to the HRE. The occurrence of this SNP in the AGT promoter of Indonesian patients with essential hypertension suggests that the G allele is a genetic susceptibility factor in hypertension regulated by HIF-1.
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Affiliation(s)
- Akhiyan Hadi Susanto
- Basic Nursing Department , School of Nursing, Faculty of Medicine , Universitas Brawijaya , Malang 65145 , Indonesia
| | - Widodo
- Biology Department , Faculty of Mathematics and Natural Sciences , Universitas Brawijaya , Malang 65145 , Indonesia
| | - Mohammad Saifur Rohman
- Department of Cardiology and Vascular Medicine , Faculty of Medicine , Universitas Brawijaya – Saiful Anwar General Hospital , Malang 65145 , Indonesia
| | - Didik Huswo Utomo
- Biology Department , Faculty of Mathematics and Natural Sciences , Universitas Brawijaya , Malang 65145 , Indonesia
| | - Mifetika Lukitasari
- Medical Surgical Nursing Department , School of Nursing, Faculty of Medicine , Universitas Brawijaya , Malang 65145 , Indonesia
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Damayanti DS, Utomo DH, Kusuma C. Revealing the potency of Annona muricata leaves extract as FOXO1 inhibitor for diabetes mellitus treatment through computational study. In Silico Pharmacol 2017; 5:3. [PMID: 28653156 DOI: 10.1007/s40203-017-0023-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 06/08/2017] [Indexed: 12/18/2022] Open
Abstract
FOXO1 protein inactivation in the nucleus is one of targets for the treatment of diabetes mellitus. Annona muricata leaves contain flavonoid and phenolic compound alkaloids that were known to be able to increase pancreatic β cell proliferation in animal experiment. This research aimed to predict the active compound ability of the Annona muricata leaves to bind and inhibit FOXO1 protein through in silico study. Analysis of molecular docking was performed by using Autodock Vina PyRx. this research proved that anonaine, rutin, muricatocin a, isolaureline, xylopine, and kaempferol 3-O-rutinoside had an equal or smaller free binding energy compared to the control compound. Rutin and Muricatocin A had the same binding ability toward 66% amino acid residues, compared to control compound with hydrogen bond type, while xylopine, anonaine, isolaureline, kaempferol 3-O-rutinoside had a similar binding ability towards 33% amino acid residues compared to control compound with hydrogen bond type.
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Affiliation(s)
- Dini Sri Damayanti
- Faculty of Medicine, Brawijaya University, Malang, East Java, Indonesia.
| | - Didik Huswo Utomo
- Department of Biology, Faculty of Mathematics and Natural Sciences, Brawijaya University, Malang, East Java, Indonesia
| | - Chandra Kusuma
- Faculty of Medicine, Brawijaya University, Malang, East Java, Indonesia
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Mahrus, Sumitro SB, Utomo DH, Sartimbul A, Toha AH, Widodo N. Genetic relationship of Sardinella lemuru from lombok strait with fish rich in omega-3 fatty acid. Bioinformation 2012; 8:1271-6. [PMID: 23275733 PMCID: PMC3532013 DOI: 10.6026/97320630081271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 12/10/2012] [Indexed: 11/23/2022] Open
Abstract
Lombok Strait has abundance of Sardine, Sardinella lemuru, which contains such high amount of omega-3 fatty acid (omega-3). However, the genetic relationship of S. lemuru with other commercial fish rich in omega-3 has not been widely studied yet. Studies on genetic proximity of S. lemuru with the other marine fish using 12S rRNA gene is very important in order to obtain genetic information of the Sardine to develop an appropriate strategy for future conservation of the fish in Lombok Strait. The aim of this study was to find out the genetic relationship of Sardinella lemuru living in Lombok Strait with the economically valuable fish and its correlation with omega-3 production. Sardinella lemuru were collected from Lombok Strait, the phylogenetic tree was done based on 12S rRNA gene through a neighbor-joining method to identify the relationship of Sardines and fish rich in omega-3 fatty acid. The phylogenetic tree showed that Sardinella lemuru is similar to Sardinella aurita and has a close similarity with Sardinella maderensis. However, the relationship did not correspond to omega-3 production. Based on the results of the study, it is suggested that the production of omega-3 is not specifically based on the proximity of the species, but it is more associated with conserved domain of Δ6-desaturase. Nevertheless, detailed mechanisms still need to be elucidated.
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Affiliation(s)
- Mahrus
- Doctoral Program, Faculty of Agriculture, Brawijaya University, Indonesia
- Biology Department, Faculty of Teacher Training and Education, University of Mataram, Indonesia
| | - Sutiman Bambang Sumitro
- Biology Department, Faculty of Mathematics and Natural Sciences, Brawijaya University, Indonesia
| | - Didik Huswo Utomo
- Biology Department, Faculty of Mathematics and Natural Sciences, Brawijaya University, Indonesia
| | - Aida Sartimbul
- Faculty of Fishery and Marine Sciences, Brawijaya University, Indonesia
| | - Abdul Hamid Toha
- Biology Department, Faculty of Mathematics and Natural Sciences, Brawijaya University, Indonesia
- Faculty of Husbandry, Fisheries and Marine Sciences, State University of Papua, Indonesia
| | - Nashi Widodo
- Biology Department, Faculty of Mathematics and Natural Sciences, Brawijaya University, Indonesia
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