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Ade Arsianti
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INDONESIA
Indonesian Journal of Medical Chemistry and Bioinformatics
Published by Universitas Indonesia
ISSN : -     EISSN : 29633818     DOI : -
Core Subject : Science,
Chemistry Computer Science & IT
The Indonesian Journal of Medical Chemistry and Bioinformatics (IJMCB) provides a forum for disseminating information on both the theory and the application of in silico, in vitro, and in vivo methods in the analysis and design of molecules, phytochemistry, medicinal chemistry and bioinformatics. Indonesian Journal of Medical Chemistry and Bioinformatics was published by Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia. This peer-reviewed academic open access journal has its first publish in in August 2022 and formerly publish every March and August. The scope of the journal encompasses papers which report new and original research and applications in the following areas: 1. Phytochemical and Medicinal chemistry (identification of targets, design, synthesis and evaluation of biological target) 2. Bioinformatics (genomic profiling, mutation analysis) 3. Molecular modeling (pharmacophore, molecular docking, molecular dynamic simulation) 4. Protein Modeling 5. Network Pharmacology and protein-protein interaction 6. Genomic 7. Metagenomics
Arjuna Subject : Kedokteran - Kedokteran (Lain-Lain)
Articles 35 Documents
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Pharmacophore-Based Virtual Screening from Indonesian Herbal Database to Find Putative Selective Estrogen Receptor Degraders Prawiningrum, Aisyah F; Paramita, Rafika Indah; Erlina, Linda
Indonesian Journal of Medical Chemistry and Bioinformatics
Publisher : UI Scholars Hub

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Abstract

Most breast cancer cases are luminal subtypes which are estrogen receptor-sensitive or progesterone receptor-sensitive. Common treatments include surgery and adjuvant endocrine therapy by prescribing selective estrogen receptor degraders (SERD). SERD is a type of medication that inhibits estrogen receptor (ER) activity by degrading it, and as a result, downregulating it. The current FDA-approved SERD can only be administered through intramuscular injection. The aim of this study is to find orally non-toxic and bioavailable herbal alternatives of SERDs in Indonesian Herbal Database by doing virtual screening using LigandScout. The hit compounds were further analyzed using a molecular docking tool, AutoDock. Three compounds that gave the best results in molecular docking, namely kuwanon T, mulberrin, and curcumin, were analyzed in terms of their toxicity and drug-likeness. Based on toxicity and drug-likeness study, curcumin is considered to be the best candidates for SERD alternatives. This result is further supported by molecular dynamic simulation outcome in which curcumin is the most stable while binding with estrogen receptors.
Analysis and Visualization Of Molecular Docking 2hi4 Protein widiasti, innas
Indonesian Journal of Medical Chemistry and Bioinformatics
Publisher : UI Scholars Hub

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The crystal structure of the human microsomal complex P450 1A2 with alpha-naphthoflavone, a cytochrome P450 (CYP) enzyme is particularly important, as it is abundant in the human liver and alters a more diverse xenobiotic array than any other group of metabolic enzymes. CYP1A2 is abundantly found in the liver and involved in the metabolism of about 10% of clinically used drugs metabolized by CYP enzymes. The current drug discovery and development mostly uses high-throughput screening (HTS). However, this regular method is time-consuming and costly. To address the issue, an advanced drug discovery and development method namely chemical compound database screening through computational methods used in this study as a promising method for chemical compound identification. Molecular docking predicts the conformation and orientation of the ligand in the binding site of the target protein. The results of molecular bonding of 2hi4 protein with 15 chemical compounds showed that three chemical compounds, benzo(a)pyrene, pteryxine, and quinine had satisfactory binding energy levels. A comparison of amino acids seen from 2D visualization shows that there are 7 amino acids in common, namely ALA317, GLY316, ASP313, ASP320, PHE260, PHE226, and THR118.
Phytochemical Analysis, Antioxidant and Anticancer Effects of Clitoria ternatae Extract on Breast T47D Cancer Cells Arsianti, Ade; Mahindra, Shahjahan Pasha; Azizah, Norma Nur; Fajrin, Ajeng Megawati; Nadapdap, Lince Dameria
Indonesian Journal of Medical Chemistry and Bioinformatics
Publisher : UI Scholars Hub

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Abstract

Background: Breast cancer is one of the most common and deadly forms of cancer in the world. Cancer is a multi-factorial disease. Genetic factors, environment and lifestyle have a role in the development of cancer. One of the mechanisms of cancer development is when an imbalance between free radicals and antioxidants in the human body occurs. Uncontrolled and excessive amount of free radicals and cause cell damage and uncontrolled cell growth. Clitoria ternate is a plant that is often found in Asia and many of the benefits of this flower have been studied. This study aims to determine the phytochemical constituents, antioxidant activity, and cytotoxic activity of Clitoria ternatea against T47D breast cancer cells. Method: Clitoria ternatea in the form of dry powder is macerated in a multi-level manner with n-hexane, ethyl acetate, and ethanol as solvents, producing a Clitoria ternatea extract of the respective solvents. Each extract is then evaluated for its phytochemical constituents, antioxidant activity, and cytotoxic activity using phytochemical test, thin layer chromatography (TLC), DPPH assay, and MTT assay respectively. Results: Phytochemical analysis of Clitoria ternatea shows the presence of glycosides, flavonoids, tannins and triterpenoids with TLC revealing the presence of ten phytochemical constituents. DPPH assay reveals that Clitoria ternatea exhibits a very active antioxidant activity. MTT assay revels Clitoria ternatea has a high cytotoxic activity towards T47D breast cancer cell line with IC50 value ranging from 1.27 μg/mL to 32.38 μg/mL. Conclusion: Chemical constituents of Clitoria ternatea is responsible for the antioxidant and cytotoxic activity towards T47D breast cancer cell line.
Phytochemical Screening and In-Vitro α-Glucosidase Inhibitory Activity Analysis of Ethanol Extract of Mangifera quadrifida Fadilah, Fadilah
Indonesian Journal of Medical Chemistry and Bioinformatics
Publisher : UI Scholars Hub

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Abstract

Abstract Introduction: Type 2 Diabetes Mellitus (DM) is a metabolic disorder characterized by hyperglycemia caused by B cell dysfunction, insulin resistance, or both. Indonesia and worldwide have an increasing incidence that leads to a significant socio-economic burden. The effective treatment of Type 2 DM with minimal side effects is still challenging. This research aims to identify phytochemical properties in ethanol extract of Mangifera quadrifida and the effectivity as an alfa-glucosidase inhibitor beneficial to research on the treatment of type 2 DM. Method: Mangifera quadrifida was extracted by ethanol as solvent. The phytochemical analysis is conducted by phytochemical screening methods and thin-layer chromatography (TLC). The antidiabetic properties in ethanol extract of Mangifera quadrifida is tested by inhibitory activity on alpha-glukosidase. Result: The ethanol extract of Mangifera quadrifida contains tanin, triterpenoid, flavonoid, and glycoside. TLC test on the ethanol extract of Mangifera quadrifida was detected 4 points (Rf 0,15; 0,464, 0,511; and 0,63). The IC50 to α-glucosidase of Mangifera quadrifida and the acarbose as positive control are 18,19 ppm and 4,88 ppm respectively. Discussion: Tanin, triterpenoid, flavonoid, and glycoside of Mangifera quadrifida have antidiabetic properties. The result on IC50 value in ethanol extract of Mangifera quadrifida is among the active class of antidiabetic group although the value is higher the acarbose. Conclusion: Ethanol extract of the Mangifera quadrifida has phytochemical compunds that have antiadiabetic potential. Acarbose has better IC50 to α-glucosidase compared to Ethanol extract of Mangifera quadrifida.
Molecular docking of Vitamin D3 Receptor (VDR) with potential herbal substance as ligand to prevent excessive hair loss in menopausal women Parawangsa, Aditya; Sugito, Syailendra Karuna; Ayu Ananda Latifa, Ariestiana; Dinda Safira, Nadya; Ayuthaya, Shafa; Rahmalia Az Zahra, Raissa
Indonesian Journal of Medical Chemistry and Bioinformatics
Publisher : UI Scholars Hub

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Abstract

Hair loss is commonly found in menopausal women. Hair loss is one of the consequences of hormonal dynamics when a woman stops having menstrual cycle, which affect calcium and vitamin D level in the body. Although it is clear enough that hormonal adjustment is required, older people and another sociodemographic factor prefer herbal-based therapeutic rather than synthetic-based due to tradition and positive experience factors. This study is an in-silico study which aims to point out the possible ligand candidates that can work as Vitamin D Receptor (VDR) agonists. We perform molecular docking using Autodock version 4.2 with the criteria of Lamarckian GA. VDR (PDB ID: 1TXI) was docked with ten compounds and one native ligand, then analyzed using Autodock 4.2. Dolichosterone, Gartanin, and (-)-Matairesinol, Luteolin, 5-HETE, Sinapyl glucoside, and geraniol, in order shows smallest to bigger binding energy when simulated in the software (-9.72, -7.70, -7.20, -6.88, -5.76, -5.71 kcal/mol). Thus, we found that these compounds are potential to become VDR agonist. Further research is still required to determine each compound drug potential and maximize therapeutic concentration for medicinal purposes.
Comparison of Serum Albu-min Levels in The Breast Milk of Breastfeeding Infants Aged 1-3 Months and 4-6 Months Mudjihartini, Ninik
Indonesian Journal of Medical Chemistry and Bioinformatics
Publisher : UI Scholars Hub

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Abstract

Abstract: Background: Serum albumin is the most abundant plasma protein in the blood, contributing to maintaining colloid osmotic pressure and binding substances that are poorly soluble in plasma so that they can be distributed throughout the body. Serum albumin levels in breast milk can vary, influenced by various factors such as the lactation phase (age of the baby), number of parities, age and body mass index (BMI) of the mother. This study aims to determine the comparison of serum albumin levels in breast milk of mothers who breastfeed infants aged 1-3 months and 4-6 months and to find the relationship with the number of parities, age and BMI of the mother. Method: Cross-sectional design experimental study, breast milk samples as stored biological fluids were obtained from 58 mothers at the Petamburan and Cilincing Health Centers. Serum albumin levels were measured with the Bromocresol Green (BCG) kit. Results: The results showed that breast milk in the earlier lactation period, namely at 1-3 months, had significantly higher serum albumin levels compared to the serum albumin levels in the 4-6 months age group (p=0.002). Serum albumin levels in breast milk for infants aged 1-3 months did not correlate with mother's parity (p=0.428) and mother's age (p=0.881), but had a significant positive correlation with mother's BMI (p=000). Serum albumin levels in breast milk in the 4-6 months age group did not correlate with mother's parity (p=0.823) and mother's age (p=0.581) but had a strong positive correlation with maternal BMI (p=0.000). Conclusion: Breast milk serum albumin levels are affected by the lactation phase (age of the baby), namely at the age of 1-3 months the baby increases significantly compared to the age of 4-6 months. The level of serum albumin in breast milk is related to the mother's BMI, which increases with increasing mother's BMI.
Virtual Screening on Indonesian Herbal Compounds as SARS-CoV-2 Spike (S2) Glycoprotein Inhibitors: Pharmacophore Modelling & Molecular Docking Approaches
Indonesian Journal of Medical Chemistry and Bioinformatics
Publisher : UI Scholars Hub

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Abstract

Background: There are still no specific treatments for coronavirus disease (COVID-19) until present days. Several studies have been conducted to determine whether herbal medicine can be an option to be used as a definitive medicine for COVID-19. S2 subunit of spike protein which is responsible for SARS-CoV-2 entry to the host cell, is a potential drug target to inhibit the viral infection. In this study, we aimed to find some compounds from the HerbalDB database that have potential as SARS-CoV-2 spike (S2) glycoprotein inhibitor. Methods: The 6LXT protein was used as the target protein. The procedure in this study consisted of these following steps: protein and ligand preparation, pharmacophore modelling and compound screening, molecular docking, ADME, and toxicity analysis. The docking of hit compounds to the target protein were compared to arbidol and quercetin as positive controls. Results: Four hit compounds were screened from HerbalDB compounds. Two of them, octopamine and L-noradrenaline, showed lower binding energies (respectively, -5.19 and -4.98 kcal/mol) than positive controls whereas the other two compounds, mimosine and L-theanine, showed higher binding energies (respectively, -3.99 and -3.62 kcal/mol) compared to positive controls. Mimosine, L-noradrenaline, octopamine, and L-theanine had toxicity classes of IV, II, IV, and IV, respectively. Conclusion: Octopamine shows the best potential as SARS-CoV-2 spike (S2) glycoprotein inhibitor. However, this compound also poses several toxicity risks and therefore, needs a more elaborate considera-tion upon using. There are still no specific treatments for coronavirus disease (COVID-19) until present days. Several studies have been conducted to determine whether herbal medicine can be an option to be used as a definitive medicine for COVID-19. S2 subunit of spike protein which is responsible for SARS-CoV-2 entry to the host cell, is a potential drug target to inhibit the viral infection. In this study, we aimed to find some compounds from the HerbalDB database that have potential as SARS-CoV-2 spike (S2) glycoprotein inhibitor.
Therapeutic Options for COVID-19: Drug Repurposing of Serine Protease Inhibitor Against TMPRSS2
Indonesian Journal of Medical Chemistry and Bioinformatics
Publisher : UI Scholars Hub

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Abstract

The SARS-Coronavirus 2 (SARS-CoV-2) outbreak is a serious global public health threat. Researchers around the world are conducting mass research to control this epidemic, starting from the discovery of vaccines, to new drugs that have specific activities as antivirals. Drug repurposing is a potential method of using drugs with known activity for reuse as COVID-19 therapy. This method has the advantage that it can reduce costs and also the duration in the development of potential drugs. The initial step in drug repurposing can be done computationally to determine the effectiveness and specificity of the drug on the target protein. Molecular docking analysis can see the specific interactions of potential compounds with target proteins by analyzing the energy of the bonds formed. The spike protein of SARS-CoV-2 is a major target in the design and discovery of new drugs for the treatment of Covid-19 disease. In addition, transmembrane protein serine protease (TMPRSS2) from host cells has been shown to have an important role in the proteolytic cleavage of viral spike protein to the ACE2 receptor present in human cells. Based on screening studies, it is known that there are several drugs that have been established that have the potential to inhibit the SARS-CoV-2 transfection mechanism into host cells. 10 potential drug candidates used in this study namely Arbecacin, Bromhexine hydrochloride, Hydroxychloroquine, Camostat mesylate, Darunavir, Dequalinium, Fleroxacin, Lopinavir, Remdesivir, and Octopamine were used in molecular docking. Docking analysis revealed that there were three potential compounds, namely Bromhexine hydrochloride, Camostat mesylate and Octopamine with low binding affinity and inhibition constants. Based on the docking result, Camostat mesylate as the best candidate has a high specific binding affinity for the Ser441 and Asp435 residues present in the TMPRSS2 catalytic triad. Thus, these results reveal the mechanism of inhibition of TMPRSS2 by the known inhibitor Camostat mesylate in detail at the molecular level. Where, Camostat mesylate has a strong bond. This structural information could also be useful for designing and discovering new inhibitors of TMPRSS2, which may be useful for preventing the entry of SARS-CoV 2 into human cells.
Biomarker Metabolite Discovery for Pancreatic Cancer using Machine Learning
Indonesian Journal of Medical Chemistry and Bioinformatics
Publisher : UI Scholars Hub

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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
Potential of Dietary Flavonoids in The Prevention and Therapy of COVID-19 : Focusing in Mast Cell - Calcium Ion Channel Axis
Indonesian Journal of Medical Chemistry and Bioinformatics
Publisher : UI Scholars Hub

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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.

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