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All Journal The Journal of Pure and Applied Chemistry Research Majalah Obat Tradisional Herb-Medicine Journal Eksakta : Berkala Ilmiah Bidang MIPA Jurnal Jamu Indonesia Majalah Patologi Indonesia Narra J Jurnal Sehat Indonesia (JUSINDO) Indonesian Journal of Medical Chemistry and Bioinformatics Jurnal Tumbuhan Obat Indonesia Indonesian Journal of Jamu
Aryo Tedjo
Departemen Kimia Kedokteran, Fakultas Kedokteran Universitas Indonesia, Indonesia
Agriculture, Biological Sciences & Forestry Astronomy Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Civil Engineering, Building, Construction & Architecture Computer Science & IT Dentistry Energy Engineering Environmental Science Health Professions Immunology & microbiology Materials Science & Nanotechnology Mathematics Mechanical Engineering Medicine & Pharmacology Nursing Public Health Veterinary Other

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Ethanol extract from Ziziphus nummularia stem inhibits MCF-7 breast cancer cell proliferation through TP53 regulating kinase (TP53RK)-mediated p53 activation: In silico and genes expression investigations Elya, Berna; Rosmalena, Rosmalena; Fajrin, Ajeng M.; Tedjo, Aryo; Ramadanti, Nur A.; Azizah, Norma N.; Hashim, Najihah BM.
Narra J Vol. 5 No. 1 (2025): April 2025
Publisher : Narra Sains Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52225/narra.v5i1.1382

Abstract

The p53 signaling pathway plays a critical role in regulating the cell cycle, apoptosis, and senescence, making it a key target in cancer research. The aim of this study was to investigate the effects of an ethanol extract from the stem of Ziziphus nummularia on the proliferation and expression of genes involved in the p53 pathway in MCF-7 breast cancer cells. To achieve this, real-time quantitative PCR (RT-qPCR) was used to evaluate the mRNA expression of downstream genes linked to cell cycle and senescence, including CycE or CCNE1, RBL1, and E2F1. Molecular docking simulations using Molegro Virtual Docker (MVD) were also performed to assess the potential inhibitory activity of metabolite compounds from Z. nummularia stem against p53-regulating kinase (TP53RK). The results showed that the IC50 value of Z. nummularia stem ethanol extract against MCF-7 cells was 38.27±0.72 µg/mL. The results also revealed a reduction in the expression of downstream genes linked to cell senescence and the cell cycle: CycE or CCNE1 (p=0.011), RBL1 (p=0.008), and E2F1 (p=0.005), which was observed through RT-qPCR analysis of mRNA expression. This fact indicated that the inhibitory effects on proliferation by the ethanol extract of Z. nummularia stem might occur via pathways associated with cell senescence and cell cycle arrest.  Molecular docking results of metabolite compounds from Z. nummularia stem suggested that squalene (Rerank score -112.70 kJ/mol), and nummularine B (Rerank score -110.68 kJ/mol) had potential as TP53RK inhibitors. These Rerank scores were smaller compared to the Rerank score of adenyl-imidodiphosphate (AMP-PNP), which was the native ligand of TP53RK, as confirmed by molecular dynamics analysis. These in silico results were confirmed by the decrease in p21 (CDKN1A) mRNA expression. In conclusion, the anti-proliferative effects of the ethanol extract from Z. nummularia stem on breast cancer cells occurred by affecting cell cycle-related genes and inhibiting apoptosis protection mediated by overexpression of p21 (CDKN1A) through p53 activity.
Prediksi Mekanisme Kerja Whey Protein Sebagai Suplemen Anti-Diabetes dan Anti-Obesitas Berdasarkan Analisis Diffrentially Genes Expressed (DEG) Inflamasi Nurbaya, Siti; Tedjo, Aryo
Jurnal Sehat Indonesia (JUSINDO) Vol. 6 No. 02 (2024): Jurnal Sehat Indonesia (JUSINDO)
Publisher : CV. Publikasi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.59141/jsi.v6i02.182

Abstract

Obesitas sering dikaitkan dengan inflamasi, yang memicu pelepasan mediator inflamasi dan menurunkan produksi adiponektin. Beberapa teori menyebutkan bahwa peradangan kronis akibat obesitas merupakan mekanisme dominan diabetes tipe 2 (T2D). Penelitian ini melakukan analisis Differentially Genes Expressed (DEG) terkait inflamasi menggunakan basis data Gene Expression Omnibus (GEO) untuk melihat perubahan transkripsi (ekspresi gen) pada hati manusia yang berkontribusi pada akumulasi lipid hati dan resistensi insulin terkait T2D. DEG yang dihasilkan kemudian digunakan untuk melihat apakah whey protein (WP) dapat mempengaruhi DEG tersebut. Konsumsi WP dipercaya dapat menurunkan kelebihan berat badan dan kadar gula darah. Hasil analisis DEG menunjukkan terdapat 22 gen terkait inflamasi  pada liver yang berbeda ekspresinya antara Lean dengan kelompok pasien obesitas tanpa T2D (Obese_noT2D) dan dengan kelompok pasien obesitas dengan T2D yang tidak terkontrol (Obese_T2D-poorly controlled). Berdasarkan  penelitian ini, tidak satu-pun gen-gen tersebut yang dipengaruhi oleh asupan WP. Namun demikian beberapa gen yang diduga berperan dalam inflamasi, obesitas, dan T2D seperti FOXJ1, NLRP1, LGALS2, LIME1, NOTCH3, ARBB2, SIM2, dan TAT berpotensi dipengaruhi oleh asupan WP.
Penentuan Aktivitas Gabungan Ekstrak Etanol Pulosari (Alyxia reinwardtii) dan Secang (Sappan Lignum) Sebagai Inhibitor Tirosinase Yang Potensial Untuk Bahan Kosmetik Melalui Pendekatan In Silico dan In Vitro Fadilah, Fadilah; Tedjo, Aryo; Heryanto, Rudi
Jurnal Jamu Indonesia Vol. 1 No. 1 (2016): Jurnal Jamu Indonesia
Publisher : Tropical Biopharmaca Research Center, IPB University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29244/jji.v1i1.4

Abstract

Tirosinase atau fenol oksidase adalah enzim utama yang terlibat dalam biosintesis melanin. Untuk menghindari produksi melanin secara berlebihan pada lapisan epidermal, maka dicari senyawa yang mampu menghambat tirosinase sehingga dapat digunakan sebagai bahan pemutih kulit. Inhibitor enzim tirosinase dapat diperoleh dari senyawa bahan alam diantaranya, polifenol, kumarin, stilben sebagai pengganti senyawa sintetik. Tirosinase telah diketahui struktur molekular sehingga dapat diketahui mekanisme kerjanya melaui uji in-silico dan pembuktian secara in-vitro. Penelitian ini digunakan untuk mendeteksi keefektifan gabungan dari ekstrak etanol pulosari (Alyxia reinwardtii) dan secang (Sappan lignum) sebagai inhibitor tirosinase. Dari hasil in-silico pengujian aktivitas inhibisi tirosinase menggunakan software MOE 2008 menunjukkan bahwa dalam ekstrak etanol dari secang yaitu senyawa brazilin dan rhamnitin berturut-turut memiliki nilai ∆G -15.6582 kkal/mol, -13.3378 kkal/mol dengan inhibisi 10.021 μM, 8.331 μM dan Hdon-acc 6, 8. Sedangkan dalam ektrak etanol dari pulosari dengan senyawa scopoletin dan zhebeiresinol berturut-turut memiliki nilai ∆G -12.1661 kkal/mol; -13.8982 kkal/mol dengan inhibisi 7.279 μM; 9.104 μM dan Hdon-acc 5 dan 6. Sedangkan senyawa parameter L-DOPA dan pembanding asam kojat berturut-turut memiliki nilai ∆G -9.8247 kkal/mol; -8.8047 kkal/mol dengan inhibisi 5.592 μM; 4.976 μM dan Hdon-acc 3; 3. Dari pembuktian secara in-vitro menunjukkan bahwa uji aktivitas inhibisi tirosinase berturut-turut dari secang (Sl), pulosari (Ar), gabungan Sl dan Ar dengan pembanding asam kojat memiliki nilai IC50 berturut-turut 797.090 ppm, 1962.934 ppm, 571.352 ppm dan 93.557 ppm. Sehingga dari hasil in-silico dan in-vitro disimpulkan bahwa penggabungan antara pulosari dan secang memiliki tingkat IC50 lebih baik dibandingkan pemberian masing-masing ekstrak.
In Silico Study of Acetogenin Compounds from Soursop (Annona muricata) Leaves as Sodium-Glucose Cotransporter-2 (SGLT2) Inhibitors: Studi In Silico Senyawa Acetogenin dari Daun Sirsak (Annona muricata) Sebagai Inhibitor Sodium-Glucose Cotransporter-2 (SGLT2) Tedjo, Aryo
Jurnal Tumbuhan Obat Indonesia Vol. 17 No. 1 (2024): July 2024
Publisher : Universitas Tidar

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.31002/jtoi.v17i1.1156

Abstract

Acetogenin derived from soursop (Annona muricata) leaves are known to have antidiabetic and anticancer activities. Nevertheless, there has been no study related to the compounds found in A. muricata leaves, such as acetogenin, as SGLT2 inhibitors. This research aims to investigate the activity of acetogenin compounds as SGLT2 inhibitors while maintaining low selectivity against SGLT1 using molecular docking methods using Molegro Virtual Docker (MVD). Based on the Rerank score, five acetogenin compounds, namely muricin H, annonacin A, annopentocin B, murihexocin C, and corossolone, are predicted to be SGLT2 inhibitors with better selectivity compared to empagliflozin. Among these five compounds, muricin H and corossolone exhibit the most similarity in interaction with amino acid residues in the SGLT2 A-chain compared to empagliflozin. In silico ADMET analysis results indicate that both compounds have absorption, distribution, and metabolism capabilities, similar to empagliflozin. However, it should be noted that both compounds are more toxic, with muricin H predicted to have hepatotoxic properties.
In Silico Evaluation of Natural Compounds as Dual Inhibitors of Exotoxin A and LasB (Elastase) Virulence Proteins in Pseudomonas aeruginosa Fariska, Andrias Bayu; Linda Erlina; Ade Arsianti; Aryo Tedjo
EKSAKTA: Berkala Ilmiah Bidang MIPA Vol. 26 No. 04 (2025): Eksakta : Berkala Ilmiah Bidang MIPA (E-ISSN : 2549-7464) In Progress
Publisher : Faculty of Mathematics and Natural Sciences (FMIPA), Universitas Negeri Padang, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/eksakta/vol26-iss04/631

Abstract

Pseudomonas aeruginosa is an opportunistic pathogen whose virulence is largely mediated by Exotoxin A and LasB (elastase), making them promising anti-virulence drug targets. This study aimed to evaluate the inhibitory potential of natural compounds against these two key proteins using an in silico approach. Pharmacophore-based virtual screening of HerbalDB compounds was performed by LigandScout software, followed by molecular docking using AutoDockTools-1.5.7 against Exotoxin A (PDB ID: 1AER) and LasB (PDB ID: 1U4G). Native ligands and co-crystallized inhibitors were used as docking controls to validate binding accuracy. Among the screened compounds, Epicatechin-(4β-6)-epicatechin-(4β-8)-catechin exhibited the strongest binding affinity to Exotoxin A (ΔG = −10.72 kcal·mol⁻¹), while Carpaine showed the highest affinity for LasB (ΔG = −8.91 kcal·mol⁻¹). The predicted interactions involved hydrogen bonds and hydrophobic interactions with active-site residues, comparable to the native inhibitors. Furthermore, ADMET analysis indicated favorable pharmacokinetic and drug-likeness properties. These findings suggest that selected natural compounds possess potential dual inhibitory activity against Exotoxin A and LasB, warranting further experimental validation as anti-virulence candidates for controlling P. aeruginosa infections.
Potential of Dietary Flavonoids in The Prevention and Therapy of COVID-19 : Focusing in Mast Cell - Calcium Ion Channel Axis Tedjo, Aryo
Indonesian Journal of Medical Chemistry and Bioinformatics Vol. 1, No. 2
Publisher : UI Scholars Hub

Show Abstract | Download Original | Original Source | Check in Google Scholar

Abstract

Syndrome Acute Respiratory Syndrome Corona Virus-2 (SARS COV2) is the virus that causes the COVID19 disease and has caused more than 4 million deaths worldwide. This virus infects the host cell through the interaction between the virus’s glycoprotein S molecule with the ACE2 which is the virus receptor, binding, undergoes membrane fusion and enters the cell and replicates in it. Currently, several strategies used in developing anti-viral compounds are targeting compounds that play a role in the process of entering the virus into host cells such as ACE2, S glycoprotein, and TMPRSS2, while some target main proteases such as RNA dependent Polymerase and N proteins. On the other hand, one of the causes for the worsening of COVID-19 cases is hyperinflammation. This condition can also be caused by an increase in calcium consumption activity which is responsible for the process of viral endocytosis, mast cell recruitment, and also the recruitment of surrounding cells to form syncytia. Under these conditions, virions that are trapped and accumulated in the syncytia can initiate the release of virions and pro-inflammatory molecules, leading to hyperinflammation and second week crash. This review will explain the importance of the role of calcium ions and mast cells in mediating inflammation as well as the prospect of inhibiting hyperinflammation in COVID19 using flavonoid compounds contained in daily food ingredients.
Biomarker Metabolite Discovery for Pancreatic Cancer using Machine Learning Kezia, Immanuelle; Erlina, Linda; tedjo, aryo; Fadilah, Fadilah
Indonesian Journal of Medical Chemistry and Bioinformatics Vol. 1, No. 2
Publisher : UI Scholars Hub

Show Abstract | Download Original | Original Source | Check in Google Scholar

Abstract

Pancreatic cancer is one of the deadliest cancers in the world. This cancer is caused by multiple factors and mostly detected at late stadium. Biomarker is a marker that can identify some diseases very specific. For pancreatic cancer, biomarker has been recognized using blood sample known as liquid biopsy, breath, pancreatic secret, and tumor marker CA19-9. Those biomarkers are invasive, so we want to identify the disease using a very convenient method. Metabolite is product from cell metabolism. Metabolites can become a biomarker especially from difficult diseases. In this paper, we want to find biomarker from metabolite using machine learning and enrichment. Metabolites data was obtained from Metabolomic workbench, while the detection and identification is done using in silico. From 106 samples, control and cancer, we found 61 metabolites and analyze them. We got 8 metabolites that play important role in pancreatic cancer and found out 2 of them are the most impactful. From that we found that ethanol is one of the best candidate of biomarker that we provide for pancreatic detection cancer. However, the simulation need to be improved to find another biomarker that provide a better marker for prognosis. Keyword : metabolite, pancreatic, cancer, machine learning
In silico Prediction of Sodium-Glucose Co-Transporter-2 (SGLT2) Inhibition Activity by Allium Fistulosum Compound Based on SkelSpheres Molecular Descriptor Heryanto, Rudy; tedjo, aryo; Noor, Dimas
Indonesian Journal of Medical Chemistry and Bioinformatics Vol. 2, No. 1
Publisher : UI Scholars Hub

Show Abstract | Download Original | Original Source | Check in Google Scholar

Abstract

The Sodium-Glucose co-transporter-2 (SGLT2) inhibitor represents a novel agent for the treatment of type 2 diabetes. Drugs of this class function by inhibiting glucose reabsorption in the kidneys, thereby controlling blood glucose levels. It is known that SGLT2 inhibitors activate the AMPK signaling pathway by increasing the expression and activity of AMP-activated protein kinase (AMPK). In vivo tests have demonstrated that ethanolic and aqueous extracts of Welsh onion leaves (Allium fistulosum L) can reduce body weight, liver weight, adipocyte size, and enhance AMP-activated protein kinase (AMPK) expression. In this study, the inhibitory activity (IC50) of compounds within Allium fistulosum against SGLT2 was predicted using the Support Vector Regression (SVR) predictive model and the SkelSpheres descriptor. The results of the predicted IC50 measurements for compounds present in the 70% ethanol extract of Allium fistulosum in silico indicate that 4 tyramine derivatives and 1 decursidate compound exhibit Excellent or Potent inhibitor activity criteria (IC50 < 1 µM). Among these, the four tyramine group compounds are the isomers N-trans-feruloyltyramine and N-cis-feruloyltyramine, as well as the isomers N-trans-feruloyl-3'-methoxytyramine and N-cis-feruloyl-3'-methoxytyramine. The findings of this study suggest that the ability of Allium fistulosum to enhance AMPK expression is possibly achieved through the inhibition of SGLT2.
Co-Authors Ade Arsianti Akmal P. Suprapto Anis Karuniawati Anwar S. Ibrahim Anwar S. Ibrahim Anwar S. Ibrahim Anwar S. Ibrahim Aprilliyani, Ifana Azizah, Norma N. Berna Elya Dendi Priyanto Derry Permana Dimas Noor Dimas Ramadhian N Dondin Sajuthi Erfi Prafiantini Erlina, Linda Eti Rohaeti Fadilah Fadilah Fadilah Fadilah, Fadilah Fadillah Fadillah Fajarido, Ariski Fajrin, Ajeng M. Fariska, Andrias Bayu Hamdani Zain Hashim, Najihah BM. Heryanto, Rudy Irandi Putra Pratomo Kezia, Immanuelle Kusmardi Kusmardi Kusmardi1 Latifah K. Darusman Latifah Kosim Darusman Linda Erlina Linda Erlina Megawati, Ajeng Mohamad Rafi Noor, Dimas Noor, Dimas Ramadhian Nur Ayu Ramadanti Peni Kistijani Samsuria Prawoto Prawoto Rafika Indah Paramita Ramadanti, Nur A. Ratnaningayu, Nindhyana Diwaratri Rino Patiatta Rosmalena, Rosmalena Rudi Heryanto Siti Nurbaya Sonar Soni Panigoro Subari A. Riyanto Subari A. Riyanto Surya Dwira Surya Dwira Wawaimuli Arozal