Introduction: Malaria is a serious tropical disease with Plasmodium falciparum as its most well-known causative parasite for producing higher levels of late stage parasites that leads to sequestration in vital organs which could lead to death. There is a growing trend of antimalarial drugs resistance against Plasmodium falciparum. Molecular assessment using polymerase chain reaction could trace the presence of mutation and also determine single-nucleotide polymorphism (SNP) in Plasmodium falciparum genes. This SNP can determine the particular population’s response to antimalarial drugs. Objectives: This study aims to examine the relationship between SNP in Plasmodium falciparum genes and antimalarial drugs resistance. Methods: Literature searches were carried out through various databases which were then collected and analyzed. Result: We identified various SNPs from eleven known genes in Plasmodium falciparum, each SNPs causes a different mechanism which contributes to antimalarial drug resistance. Mechanisms varying from slower drug clearance to drug transport activity alteration. Conclusion: Results from most studies included in this review suggest that SNPs in Plasmodium falciparum genes participate in the resistance against various antimalarial drugs via several mechanisms and may be necessary for parasite survival when stressed.
{"title":"Single Nucleotide Polymorphisms in Plasmodium falciparum Genes: Their Roles in Antimalarial Drugs Resistance and Recent Detection Strategies","authors":"","doi":"10.7454/ijmcb.v2i1.1005","DOIUrl":"https://doi.org/10.7454/ijmcb.v2i1.1005","url":null,"abstract":"Introduction: Malaria is a serious tropical disease with Plasmodium falciparum as its most well-known causative parasite for producing higher levels of late stage parasites that leads to sequestration in vital organs which could lead to death. There is a growing trend of antimalarial drugs resistance against Plasmodium falciparum. Molecular assessment using polymerase chain reaction could trace the presence of mutation and also determine single-nucleotide polymorphism (SNP) in Plasmodium falciparum genes. This SNP can determine the particular population’s response to antimalarial drugs. Objectives: This study aims to examine the relationship between SNP in Plasmodium falciparum genes and antimalarial drugs resistance. Methods: Literature searches were carried out through various databases which were then collected and analyzed. Result: We identified various SNPs from eleven known genes in Plasmodium falciparum, each SNPs causes a different mechanism which contributes to antimalarial drug resistance. Mechanisms varying from slower drug clearance to drug transport activity alteration. Conclusion: Results from most studies included in this review suggest that SNPs in Plasmodium falciparum genes participate in the resistance against various antimalarial drugs via several mechanisms and may be necessary for parasite survival when stressed.","PeriodicalId":126496,"journal":{"name":"Indonesian Journal of Medical Chemistry and Bioinformatics","volume":"15 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136360148","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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.
{"title":"In silico Prediction of Sodium-Glucose Co-Transporter-2 (SGLT2) Inhibition Activity by Allium Fistulosum Compound Based on SkelSpheres Molecular Descriptor","authors":"","doi":"10.7454/ijmcb.v2i1.1023","DOIUrl":"https://doi.org/10.7454/ijmcb.v2i1.1023","url":null,"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.","PeriodicalId":126496,"journal":{"name":"Indonesian Journal of Medical Chemistry and Bioinformatics","volume":"3 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136360147","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The lung parenchyma is largely impacted by the infectious condition known as pulmonary tuberculosis (pulmonary TB) when the immune system creates a wall around the germs in the lungs, a tiny, hard bulge known as a tubercle develops, earning the disease the name tuberculosis. Although the majority of TB germs target the lungs, they can also harm other bodily organs. The identification of TB biomarkers, which are crucial for diagnosis, treatment monitoring, risk analysis, and prognosis, has been the subject of extensive research. Differences in metabolites between normal cells and tuberculosis are considered to be able to support the diagnosis of tuberculosis. Metabolite data was taken from the Metabolomic workbench and further identification and prediction were carried out in silico. A total of 44 samples found 69 metabolites which were then carried out further analysis. Found as many as 5 metabolites that play an important role in tuberculosis. Of the 5 metabolites, 2 candidate biomarkers were found which are known to have potential as biomarkers. The candidate biomarkers for these metabolites are trans-3-methyluric acid and nicotinic acid. However, this simulation needs further testing to obtain more accurate biomarkers and support the diagnosis.
{"title":"Metabolomic Insights into Tuberculosis: Machine Learning Approaches for Biomarker Identification","authors":"","doi":"10.7454/ijmcb.v2i1.1020","DOIUrl":"https://doi.org/10.7454/ijmcb.v2i1.1020","url":null,"abstract":"The lung parenchyma is largely impacted by the infectious condition known as pulmonary tuberculosis (pulmonary TB) when the immune system creates a wall around the germs in the lungs, a tiny, hard bulge known as a tubercle develops, earning the disease the name tuberculosis. Although the majority of TB germs target the lungs, they can also harm other bodily organs. The identification of TB biomarkers, which are crucial for diagnosis, treatment monitoring, risk analysis, and prognosis, has been the subject of extensive research. Differences in metabolites between normal cells and tuberculosis are considered to be able to support the diagnosis of tuberculosis. Metabolite data was taken from the Metabolomic workbench and further identification and prediction were carried out in silico. A total of 44 samples found 69 metabolites which were then carried out further analysis. Found as many as 5 metabolites that play an important role in tuberculosis. Of the 5 metabolites, 2 candidate biomarkers were found which are known to have potential as biomarkers. The candidate biomarkers for these metabolites are trans-3-methyluric acid and nicotinic acid. However, this simulation needs further testing to obtain more accurate biomarkers and support the diagnosis.","PeriodicalId":126496,"journal":{"name":"Indonesian Journal of Medical Chemistry and Bioinformatics","volume":"262 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136360144","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Background: Colorectal cancer is one of the deadliest diseases with a high prevalence worldwide and is characterized by the appearance of adenomatous polyps in the colon mucosa which are at high risk of developing into colorectal cancer. This study aims to use serum metabolites as promising non-invasive biomarkers for colorectal cancer detection and prognostication. Differences in serum metabolites in patients with adenomatous polyps, colorectal cancer, and healthy controls are considered to be able to support the prognosis of colorectal cancer. Methods: Metabolite dataset is taken from the Metabolomic Workbench. Analysis and validation are carried out in silico using machine learning methods. Results: From a total of 234 samples, 113 metabolites were found and 5 metabolites; histidine, lysine, glyceraldehyde, linolenic acid, and aspartic acid were identified as the most significant in differentiating the sample groups. CTD analysis showed that aspartic acid and histidine are associated with the biological pathways of colorectal cancer progression and significant metabolites are associated with cancer-related phenotypes. Conclusion: The serum metabolites differ in colorectal cancer and healthy control. The significant metabolites can be used as a consideration in selecting colorectal cancer biomarkers, but improvisation is needed to obtain more accurate biomarkers.
{"title":"Serum Metabolomic Profiling for Colorectal Cancer using Machine Learning","authors":"","doi":"10.7454/ijmcb.v2i1.1021","DOIUrl":"https://doi.org/10.7454/ijmcb.v2i1.1021","url":null,"abstract":"Background: Colorectal cancer is one of the deadliest diseases with a high prevalence worldwide and is characterized by the appearance of adenomatous polyps in the colon mucosa which are at high risk of developing into colorectal cancer. This study aims to use serum metabolites as promising non-invasive biomarkers for colorectal cancer detection and prognostication. Differences in serum metabolites in patients with adenomatous polyps, colorectal cancer, and healthy controls are considered to be able to support the prognosis of colorectal cancer. Methods: Metabolite dataset is taken from the Metabolomic Workbench. Analysis and validation are carried out in silico using machine learning methods. Results: From a total of 234 samples, 113 metabolites were found and 5 metabolites; histidine, lysine, glyceraldehyde, linolenic acid, and aspartic acid were identified as the most significant in differentiating the sample groups. CTD analysis showed that aspartic acid and histidine are associated with the biological pathways of colorectal cancer progression and significant metabolites are associated with cancer-related phenotypes. Conclusion: The serum metabolites differ in colorectal cancer and healthy control. The significant metabolites can be used as a consideration in selecting colorectal cancer biomarkers, but improvisation is needed to obtain more accurate biomarkers.","PeriodicalId":126496,"journal":{"name":"Indonesian Journal of Medical Chemistry and Bioinformatics","volume":"30 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136360142","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Oxidative stress is a condition in which there is an imbalance between production of free radicals and protective response via antioxidant system. There are endogenous and exogenous antioxidants, however as age increases, there is a reduction in endogenous antioxidant, thus the search for potential exogenous antioxidants which could be derived from natural resources are needed. Indonesia is a megabiodiversity country which has more than 30,000 species of plants and animals. Red seaweed Eucheuma sp. is one of marine macroalgae species which shows potent biological activities. This study aims to determine the phytochemical constituent and to evaluate the antioxidant activity of red algae Eucheuma sp. Seaweed Eucheuma sp. obtained from Lombok, Nusa Tenggara Barat, Indonesia, were extracted by maceration process using three solvents, n-hexane, ethyl acetate, and ethanol, sequentially. Each extract was analyzed for its phytochemical constituents by phytochemistry screening, thin layer chromatography, total phenolic content, total flavonoid content, and total triterpenoid content. Evaluation of antioxidant activity for ethyl acetate extract and ethanol extract were done using DPPH method. Phytochemical analysis of Eucheuma sp. shows positive result for steroid and triterpenoid. Thin layer chromatography analysis of the Eucheuma sp. extracts showed total of 11 phytochemical constituents. Quantitative analysis revealed that the highest value in ethyl acetate extract, with total phenolic content of 29.57 mg gallic acid equivalent/g extract, total flavonoid content of 0.54 mg quercetin equivalent/g extract, and total triterpenoid content of 1.08 mg ursolic acid equivalent/g extract. Moreover, ethylacetate extract of Eucheuma sp. demonstrated an active antioxidant activity against DPPH free radical with IC50 value of 27.96 µg/mL. Thus, ethylacetate extract of Eucheuma sp. derived from Lombok, Indonesia, has a potential to be developed as a natural antioxidant.
{"title":"Phytochemical Constituent and Antioxidant Activity Evaluation of Red Seaweed Eucheuma sp.","authors":"","doi":"10.7454/ijmcb.v2i1.1019","DOIUrl":"https://doi.org/10.7454/ijmcb.v2i1.1019","url":null,"abstract":"Oxidative stress is a condition in which there is an imbalance between production of free radicals and protective response via antioxidant system. There are endogenous and exogenous antioxidants, however as age increases, there is a reduction in endogenous antioxidant, thus the search for potential exogenous antioxidants which could be derived from natural resources are needed. Indonesia is a megabiodiversity country which has more than 30,000 species of plants and animals. Red seaweed Eucheuma sp. is one of marine macroalgae species which shows potent biological activities. This study aims to determine the phytochemical constituent and to evaluate the antioxidant activity of red algae Eucheuma sp. Seaweed Eucheuma sp. obtained from Lombok, Nusa Tenggara Barat, Indonesia, were extracted by maceration process using three solvents, n-hexane, ethyl acetate, and ethanol, sequentially. Each extract was analyzed for its phytochemical constituents by phytochemistry screening, thin layer chromatography, total phenolic content, total flavonoid content, and total triterpenoid content. Evaluation of antioxidant activity for ethyl acetate extract and ethanol extract were done using DPPH method. Phytochemical analysis of Eucheuma sp. shows positive result for steroid and triterpenoid. Thin layer chromatography analysis of the Eucheuma sp. extracts showed total of 11 phytochemical constituents. Quantitative analysis revealed that the highest value in ethyl acetate extract, with total phenolic content of 29.57 mg gallic acid equivalent/g extract, total flavonoid content of 0.54 mg quercetin equivalent/g extract, and total triterpenoid content of 1.08 mg ursolic acid equivalent/g extract. Moreover, ethylacetate extract of Eucheuma sp. demonstrated an active antioxidant activity against DPPH free radical with IC50 value of 27.96 µg/mL. Thus, ethylacetate extract of Eucheuma sp. derived from Lombok, Indonesia, has a potential to be developed as a natural antioxidant.","PeriodicalId":126496,"journal":{"name":"Indonesian Journal of Medical Chemistry and Bioinformatics","volume":"35 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136360139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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.
{"title":"Comparison of Serum Albu-min Levels in The Breast Milk of Breastfeeding Infants Aged 1-3 Months and 4-6 Months","authors":"N. Mudjihartini","doi":"10.7454/ijmcb.v1i2.1015","DOIUrl":"https://doi.org/10.7454/ijmcb.v1i2.1015","url":null,"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.","PeriodicalId":126496,"journal":{"name":"Indonesian Journal of Medical Chemistry and Bioinformatics","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128652980","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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.
{"title":"Potential of Dietary Flavonoids in The Prevention and Therapy of COVID-19 : Focusing in Mast Cell - Calcium Ion Channel Axis","authors":"A. Tedjo","doi":"10.7454/ijmcb.v1i2.1016","DOIUrl":"https://doi.org/10.7454/ijmcb.v1i2.1016","url":null,"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.","PeriodicalId":126496,"journal":{"name":"Indonesian Journal of Medical Chemistry and Bioinformatics","volume":"52 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115966690","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Syailendra Karuna Sugito, Artha Uli Cristina, Putri Saskia Harimurti, Gabriella Regita Cendani, Fauzi Azhar Insani, L. Erlina, R. I. Paramita, Fadilah Fadilah
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.
{"title":"Virtual Screening on Indonesian Herbal Compounds as SARS-CoV-2 Spike (S2) Glycoprotein Inhibitors: Pharmacophore Modelling & Molecular Docking Approaches","authors":"Syailendra Karuna Sugito, Artha Uli Cristina, Putri Saskia Harimurti, Gabriella Regita Cendani, Fauzi Azhar Insani, L. Erlina, R. I. Paramita, Fadilah Fadilah","doi":"10.7454/ijmcb.v1i2.1006","DOIUrl":"https://doi.org/10.7454/ijmcb.v1i2.1006","url":null,"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.","PeriodicalId":126496,"journal":{"name":"Indonesian Journal of Medical Chemistry and Bioinformatics","volume":"18 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132695420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Immanuelle Kezia, L. Erlina, A. Tedjo, Fadilah Fadilah
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.
{"title":"Biomarker Metabolite Discovery for Pancreatic Cancer using Machine Learning","authors":"Immanuelle Kezia, L. Erlina, A. Tedjo, Fadilah Fadilah","doi":"10.7454/ijmcb.v1i2.1017","DOIUrl":"https://doi.org/10.7454/ijmcb.v1i2.1017","url":null,"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.","PeriodicalId":126496,"journal":{"name":"Indonesian Journal of Medical Chemistry and Bioinformatics","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123358222","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mohammad Wildan Abiyyi, S. Dwira, A. Bustami, L. Erlina
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.
{"title":"Therapeutic Options for COVID-19: Drug Repurposing of Serine Protease Inhibitor Against TMPRSS2","authors":"Mohammad Wildan Abiyyi, S. Dwira, A. Bustami, L. Erlina","doi":"10.7454/ijmcb.v1i2.1001","DOIUrl":"https://doi.org/10.7454/ijmcb.v1i2.1001","url":null,"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.","PeriodicalId":126496,"journal":{"name":"Indonesian Journal of Medical Chemistry and Bioinformatics","volume":"180 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133562069","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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