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The interaction among cyanidin (a), cyanidin-3-O-glucoside (b), peonidin (c), and peonidin-3-O-glucoside (d) with Toll-like receptor-4 protein. Numerical legend demonstrated 3D and 2D views. Blue color is TLR4 protein and pink color is anthocyanins.
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Obesity is one of metabolic syndrome and have several complications including type 2 diabetes mellitus and inflammations. To reduce the complications and prevent the obesity, some natural constituents has been tested. This study proved the screening of cyanidin, cyanidin-3-O-glucoside, peonidin and peonidin-3-O-glucoside for inhibiting TLR4 and JNK...
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Context 1
... bound to TLR4 protein in binding site SER207, HIS179, LYS153, GLU178, GLN129, LYS130 and GLU154. The active site of peonidin-3-O-glucoside with TLR4 protein are HIS229, GLU154, GLU178, LYS230 and HIS179 (Figure 1 & Table 1). Interestingly, cyanidin, peonidin and peonidin-3-O-glucoside associated with TLR4 in the same residues. ...
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... shown as Figure 1, cyanidin, peonidin and peonidin-3-O-glucoside tend to bind in the same area, but cyanidin-3-O-glucoside binds on a different side to the other three anthocyanins. Although in different amino acid residue regions, the four black rice anthocyanins bind in the substrate binding region (lipopolysaccharide/LPS) and prevent the LPS activating TLR4 signaling pathway. ...
Context 3
... bound to TLR4 protein in binding site SER207, HIS179, LYS153, GLU178, GLN129, LYS130 and GLU154. The active site of peonidin-3-O-glucoside with TLR4 protein are HIS229, GLU154, GLU178, LYS230 and HIS179 (Figure 1 & Table 1). Interestingly, cyanidin, peonidin and peonidin-3-O-glucoside associated with TLR4 in the same residues. ...
Context 4
... shown as Figure 1, cyanidin, peonidin and peonidin-3-O-glucoside tend to bind in the same area, but cyanidin-3-O-glucoside binds on a different side to the other three anthocyanins. Although in different amino acid residue regions, the four black rice anthocyanins bind in the substrate binding region (lipopolysaccharide/LPS) and prevent the LPS activating TLR4 signaling pathway. ...
Citations
... Penelitian sebelumnya mengungkapkan bahwa konsumsi beras berpigmen terutama pada beras merah dapat menghambat mekanisme AGE-RAGE pada diabetes mellitus, sehingga diabetes mellitus dapat dicegah [7]. Selain itu beras berpigmen seperti beras hitam juga mengandung senyawa bioaktif berupa antosianin yang mampu menghambat sintesis kolesterol dalam penanganan obesitas yang mengarah pada diabetes mellitus tipe -2 [8], [9], [10], [11], [12]. Berbagai rempah juga dilaporkan berpotensi sebagai antidiabetes. ...
Diabetes mellitus merupakan penyakit metabolisme kronik yang disebabkan oleh peningkatan glukosa dalam darah. Mekanisme terjadinya diabetes mellitus sangat kompleks, salah satunya melalui aktivasi fosforilasi jalur MAPK. Penelitian ini bertujuan untuk mengidentifikasi potensi senyawa siphonaxantin sebagai antidiabetes melalui penghambatan protein kinase C (PKC) dalam mekanisme fosforilasi secara in silico. Penelitian menggunakan pendekatan in silico dengan molecular docking. Struktur 3D protein kinase C (PKC) diunduh dari database Protein Data Bank dengan kode akses PDB ID 3TXO. Struktur siphonaxantin diunduh dari PubChem NCBI dengan ID 11204185. Senyawa 2,6 – Naphthyridines digunakan sebagai kontrol pembanding yang diperoleh dari protein data Bank 3TXO. Protein, senyawa pembanding dan siphonaxanting di docking dengan program molegro virtual docker dan dianalisis dengan PyMol 2.3 dan Discovery Studio ver.21.1..1. Senyawa siphonaxanthin berikatan dengan protein kinase C pada beberapa residu dengan 4 ikatan hydrogen dan 11 interaksi hidrofobik. Siphonaxantin juga menunjukkan daerah ikatan yang sama dengan 2, 6 – Naphthyridines, inhibitor control pada residu VAL369 dan PHE366. Berdasarkan energi ikatan, senyawa siphonaxanthin menunjukkan energi ikatan yang lebih rendah dari 2,6 napthyridines, yakni -258,6 kJ/mol. Penelitian ini disimpulkan bahwa siphonaxantin berpotensi sebagai kandidat obat antidiabetes dengan menghambat aktivasi fosforilasi oleh protein kinase C (PKC). Penelitian in vitro dan in vivo diperlukan untuk identifikasi lebih lanjut.
... Te arsenal of VEGF inhibitors reported to date encompasses a diverse array of compounds, each with its unique mechanisms and potential applications in preventing chronic endometriosis. Tese include soluble truncated VEGF receptor, iodamin, endostatin, anginex, sorafenib, statin, lipoxin, parecoxib, pycnogenol, melatonin, resveratrol, metformin, and colchicine [25,26]. Te sheer variety of these inhibitors underscores the intricate nature of the molecular pathways involved in endometriosis and the need for a multifaceted approach in developing therapeutic strategies. ...
Endometriosis (EM) is a gynecological disorder that causes morbidity in women and is characterized by endometrial tissue in the uterus cavity. This study investigated the mechanism of genistein in the VEGF-A and ER-α expression through in vivo and in silico approaches. An in vivo study was conducted by thirty-six mice that were divided into six groups including control, EM, and EM treatment with genistein with the doses of 1.3, 1.95, 2.6, and 3.25 mg/day for 14 days. Peritoneal tissues with lesions were collected and analyzed by immunohistochemistry to measure the VEGF-A and ER-α expression. The data were analyzed using a statistical approach using one-way ANOVA followed by Tukey HSD test with a significant value p < 0.05 . In silico study was conducted for investigating the inhibition mechanism of genistein in VEGF-A and ER-α protein. Genistein significantly reduced the VEGF-A and ER-α expression with the optimum dose of 3.25 mg/day. Molecular docking showed that genistein inhibited VEGF-A in several active site residues of VEGF-A, also blocked the ER-α protein in estradiol binding sites. This study concluded that genistein prevented endometriosis by performing the antiangiogenic activity and showed a similar function to estradiol.
... The formation of the formed bond energy is influenced by the number of hydrogen bonds, hydrophobic interactions, and Van Der Waals forces (Bare, 2021;Elfi et al., 2021). The lower the bond energy formed and the stronger the bond between the compound and protein, the more complex the compound with the interacting protein and the greater the number of bonds in the complex (Bare et al., 2019(Bare et al., , 2020(Bare et al., , 2021Sari et al., 2020aSari et al., , 2020bKrisnamurti et al., 2021). ...
The goal of this study was to genetically link natural materials derived from Tinospora crispa L with Berberine to dihydrofolate reductase-thymidylate synthase (DHFR-TS). Method: The ligand berberine (CID: 2353) was obtained from Pubchem, while the protein DHFR-TS (PDB ID 2bl9) was obtained from Protein Data Bank. The ligands and proteins interacted with HEX 8.0.0.0 and were visualized with Discovery Studio. The researchers discovered a positive interaction between berberine and DHFR-TS, observed at four amino acid residues that bind to the protein TYR125, ILE121, LEU45, and MET54. Van der Waals interactions, hydrogen bonds, Pi-Sulfur, Pi-Alkyl, and Pi-Stalked interactions all contribute to strength and stability. In conclusion, berberine has the potential to act as a DHFR-TS inhibitor and thus prevent malaria.
ABSTRAK: Tujuan penelitian ini adalah memanfaatkan bahan alam yang berasal dari Tinospora crispa L dengan kandungan utama Berberin dengan dihydrofolate reductase-thymidylate synthase (DHFR-TS) secara genetik. Metode, Ligan berberin (CID: 2353 ) diperoleh dari Pubchem sedangkan protein DHFR-TS (PDB ID 2bl9) diperoleh dari Protein Data Bank, ligan dan protein diinteraksikan menggunakan HEX 8.0.0.0 dan divisualisasikan menggunakan discovery studio. Ditemukan interaksi positif antara berberin dan DHFR-TS yang menunjukkan interaksi pada empat residu asam amino yang berikatan dengan protein. Mereka adalah TYR125, ILE121, LEU45 dan MET54. Beberapa interaksi yang dilakukan Van der Waals, ikatan hidrogen, Pi-Sulfur, Pi-Alkyl dan Pi-Stalked juga memberikan dukungan dalam rangka meningkatkan kekuatan dan stabilisasi. Kesimpulannya, berberin memiliki potensi fungsi sebagai penghambat DHFR-TS dan mengarah pada malaria.
... Low energy indicated tight interactions of ligandprotein complex. The binding energy score was affected by type of interactions, number of hydrogen and hydrophobic interactions [21,22,[24][25][26]. ...
Introduction: Endometriosis is a gynaecological disorder in women and causes infertility. Several therapeutic were developed to reduce endometriosis cases, one of them was matrix metalloproteinase (MMP) inhibitor. This study investigated the potential activity of the flavonoids in Phaleria macrocarpa fruit as MMP1 inhibitors for endometriosis. Methods: In silico modelling was used in this study. Six flavonoid structures were retrieved from PubChem NCBI database. A targeted protein, MMP1 was taken out from Protein Data Bank with ID 1CGE and predicted the active sites. Six flavonoids and MMP1 was interacted by molecular docking using Molegro virtual Docker version 5 and analyzed using PyMol 2.2 and Discovery Studio version 21.1.1. Three-dimensional complex structure of flavonoids – MMP1 showed interaction in the same active sites and performed an amino acid residue Glu219 as catalytic site. Results: Six flavonoids of Phaleria macrocarpa were divided into two patterns and generated varied binding energy. Glycitin and Catechin 7-O-beta-D-xyloside showed low score of binding energy and depicted similar structure with four aromatic rings. 8-Prenylnaringenin performed lower binding energy than naringenin, eriodictyol, and 5-O-methylgenistein. Conclusion: In silico analysis suggested that six flavonoids compounds is potent as MMP1 inhibitor and might be interfered endometriosis pathophysiology. In vivo and in vivo investigations are required for further analysis.
... Analisis interaksi molekuler kolumbin-DHFR-TS mengadopsi Metode in silico (Bare, 2021;Elfi et al., 2021). Ikatan antara ligan kolumbin dan protein DHFR-TS menjadi lebih kuat karena adanya kompleks senyawa dengan protein yang berinteraksi, dan semakin banyak jumlah ikatan (Bare et al., 2019(Bare et al., , 2020Krisnamurti et al., 2021;Sari et al., 2020aSari et al., , 2020b ...
The Brotowali plant is used to treat malaria. Tinospora crispa L contains active compounds that are good for health and has been widely used for medicine. Crude extract from Tinospora crispa L can be used as target dihydrofolate reductase-thymidylate synthase (DHFR-TS). This research study was to analyse the potential chemical content of Tinospora crispa L in the form of columbine compounds as a focus of malaria therapy through inhibition of dihydrofolate reductase-thymidylate synthase (DHFR-TS). In silico research method, columbine (CID: 188289) ligand was obtained from Pubchem while DHFR-TS (PDB ID 2bl9) protein was obtained from Protein Data Bank, ligands and proteins were interacted using HEX 8.0.0.0 and visualised using discovery studio. The results obtained are six amino acid residues that bind to the DHFR-TS protein. This binding has an impact on the work function of the DHFR-TS protein. Physicochemical analysis shows that the ligand acts as a donor and acceptor so that the protein is formed and the ligand becomes very strong. This interaction is also supported by amino acid residues that act as supports by forming Van der Waals forces outside of the Van hydrogen bonding forces, pi-Alkyl and Pi also provide support in order to increase the strength and stabilisation of the. Based on the discussion, it can be concluded that the columbine content in Tinospora crispa L has potential as a therapy and treatment for malaria through inhibition of DHFR-TS.Tanaman Brotowali digunakan untuk mengobati penyakit malaria. Tinospora crispa L mengandung senyawa aktif yang baik untuk kesehatan dan telah banyak digunakan untuk pengobatan. Ekstrak kasar dari Tinospora crispa L dapat digunakan sebagai target dihydrofolate reductase-thymidylate synthase (DHFR-TS). Penelitian ini bertujuan untuk menganalisis potensi kandungan kimia Tinospora crispa L berupa senyawa kolumbin sebagai fokus terapi malaria melalui penghambatan dihydrofolate reductase-thymidylate synthase (DHFR-TS). Metode penelitian in silico diperoleh ligan kolumbin (CID: 188289) dari Pubchem sedangkan protein DHFR-TS (PDB ID 2bl9) diperoleh dari Protein Data Bank, ligan dan protein diinteraksikan menggunakan HEX 8.0.0.0 dan divisualisasikan menggunakan discovery studio. Hasil yang diperoleh adalah enam residu asam amino yang berikatan dengan protein DHFR-TS. Pengikatan ini berdampak pada fungsi kerja protein DHFR-TS. Analisis fisikokimia menunjukkan bahwa ligan berperan sebagai donor dan akseptor sehingga protein yang terbentuk dan ligan menjadi sangat kuat. Interaksi ini juga didukung oleh residu asam amino yang bertindak sebagai pendukung dengan membentuk gaya Van der Waals di luar gaya ikatan hidrogen Van, pi-Alkil dan Pi juga memberikan dukungan dalam rangka meningkatkan kekuatan dan stabilisasi. Berdasarkan pembahasan dapat disimpulkan bahwa kandungan kolumbin pada Tinospora crispa L berpotensi sebagai terapi dan pengobatan malaria melalui penghambatan DHFR-TS.
... Dietary fibers also delayed cholesterol absorption, monacolin inhibited the activity of the HMG-CoA receptor. Phytosterol was reported that inhibit cholesterol absorption [14,15,[17][18][19][20]. Anthocyanins from black rice also ameliorated hyperlipidemia based on in vivo and silico studies [21][22][23][24]. Previous research reported that an isoflavone from lactic-acid fermented soy milk lowered lipid gene metabolism expression in rats fed a high cholesterol diet [17]. ...
Introduction: Menopause is defined as the last menstruation cycle in women. Estrogen concentration in menopausal women was decreased and altered the lipid metabolism profiles. Menopausal women reportedly have a high risk of cardiovascular disease, arthritis, diabetes mellitus, and stroke. This study focused on the effect of the black-eyed pea diet on the lipid profiles in menopausal women. Material and Methods: A randomized clinical study was performed to analyzedd the effect of the black-eyed pea diet on lipid profiles. Fifty-four menopausal women were selected as respondents and classified into two groups, black-eyed pea diet and placebo. Black-eyed pea diet treatment was performed by consuming black-eyed powder containing 67.5 mg of isoflavones and were monitored in week – 0 and week – 12 after treatment. Lipid profile of black-eyed pea diet and placebo in 12 weeks monitoring showed no significant value. After 12 weeks of treatment, total cholesterol and triglyceride were higher than before treatment. Results: Interestingly, the black-eyed pea diet increased the HDL and lowered the LDL after 12 weeks of treatment. Conclusion: This study concluded that black-eyed pea improved lipid profile, especially in elevating HDL level and decreasing LDL level in 12 weeks consumption.
Pemanfaatan Capsicum frutescens L sebagai terapi berbagai penyakit salah satunya inflamasi di dalam tubuh, menjadi fokus saat ini dikarenakan mengandung senyawa bersifat farmakologis seperti homodihydrocapsaicin. Senyawa yang diperoleh homodihydrocapsaicin didownload SMILES dari aplikasi PubChem dengan (CID: 3084336) diunduh dari database PubChem, Protein COX-2 (ID 6cox) diunduh dari Protein Data Bank. Proses preparasi protein dan ligan, docking, visualisasi maupun analisis mengadopsi penelitian sebelumnya. Tujuan penelitian menganalisis interaksi molekuler senyawa homodihydrocapsaicin sebagai Inhibitor COX-2. Interaksi senyawa homodihydrocapsaicin dan COX-2 membentuk beberapa ikatan residu asam amino yang membentuk ikatan hidrofobik, ikatan hydrogen, dan gaya van der Waals. Energi ikatan yang terbentuk adalah -284.86 cal/mol, sehingga senyawa homodihydrocapsaicin sebagai terapi inflamasi dengan menghambat mediator inflamasi (COX-2). Capsicum frutescens L. dapat dimanfaatkan sebagai terapi inflamasi didalam tubuh.
cJun NH2 terminal Kinase (JNK) merupakan protein kinase family MAPK yang berperan dalam j alur pensinyalan penyakit metabolisme, salah satunya dalam regulasi faktor resiko obesitas. Penelitian in bertujuan untuk mengeksplorasi potensi asemanan dan glukomanan dalam menghambat JNK sebagai antidiabetes.metode pendekatan molecular docking digunakan untuk mengidentifikasi interaksi antara senyawa asemanan dan glukomanan terhadap protein JNK. Asemanan dan glukomanan berikatan di sisi aktif yang berbeda satu sama lain. Residu sisi aktif asemanan berada di close gate protein JNK, sedangkan glukomanan menunjukkan sisi aktif jalur ikatan inhibitor dari JNK. Asemanan dan glukomanan menghambat aktivitas JNK dengan berikatan di sisi non-katalitik dan diprediksi penghambatan protein JNK oleh kedua senyawa secara alosterik yang dapat merubah konformasi protein JNK. Selain itu, asemanan berikatan dengan kuat terhadap protein JNK dengan jenis ikatan hydrogen, interaksi hidrofobik dan elektrostatik dengan energi ikatan yang lebih rendah dari glukomanan – JNK. Penelitian disimpulkan bahwa senyawa asemanan dan glukomanan berpotensi sebagai antiobesitas dengan peranannya sebagai inhibitor terhadap protein JNK.
