Indonesia Conference Directory

Corresponding Author
Sheilla Rachmania

Institutions
a) Graduate School of Biotechnology, University of Jember;
*sheilla.dr.fk[at]unej.ac.id
b) Faculty of Medicine, University of Jember;
c) Center for Development of Advance Science and Technology (CDAST), University of Jember,
d) Faculty of Mathematics and Natural Sciences, University of Jember

Abstract
Combatting malaria, as one of the world health burdens requires effective vaccine development, but high polymorphism in one protein vaccine candidate, Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1), is a major hurdle. One domain in its head structure, Duffy-binding like (DBL) domain, has a binding area to ICAM-1 receptor found in cerebral malaria patient, hence making this domain as a key to develop a malaria vaccine. Identify the epitopes within this protein is pivotal before formulating a peptide-based vaccine development strategy. This study aimed to identify the conserved epitopes by using an immunoinformatic approach. The protein was subjected to hydrophobicity attributes, Th-cell epitopes, and B-cell epitopes by using NN-align algorithm, Bepipred 2.0, and Kolaskar Tangaonkar methods combined with K-means clustering method to identify overlapping epitope. The result showed that the hydrophobicity value was 32.62 indicating that this protein is soluble and potentially fit into HLA alleles active site, but further NN-align algorithm showed no overlapping of Th-cell epitope positions for three Indonesian alleles. Three B-cell conserved epitopes in the position of 77-89, 236-254, and 360-377 amino acids were identified with one cluster overlapping with ICAM-1 determinant binding area. This information is valuable in constructing a subunit peptide-based malaria vaccine candidate.

Keywords
DBL2β, PfEMP1, epitope, immunoinformatic

Topic
Bioinformatics

Link: https://ifory.id/abstract/JGBtZpPF3hxK

Corresponding Author
Kennis Rozana

Institutions
Biology FMIPA Universitas Negeri Malang

Abstract
Bacillus subtilis is one of the microbes that is known very potential to degrade heavy oil because it can produce biosurfactants. The presence of biosurfactant makes Bacillus subtilis able to degrade the chains of carbon atoms in heavy oils that are very long and complex. The ability of Bacillus subtilis to produce biosurfactants is caused by the sfp gene which is required to produce Sfp 4-phosphopantetheinyl transferase protein. To know the characteristics and pathway of the sfp gene in producing biosurfactants, molecular analysis was carried out by using bioinformatics. The analysis carried out includes an analysis of the primary structure, secondary structure, and tertiary structure of the protein produced. Further analysis using EcoCyc was conducted to determine the Sfp 4-phosphopantetheinyl transferase protein metabolism pathway. Based on the results of the analysis carried out related to the sfp gene, it has a conserved protein motif associated with a fairly low similarity with some EntD proteins from Escherichia coli. Based on the EcoCyc analysis known that AccS as a group of genes that produce 4-phosphopantetheinyl transferase Sfp and Associated EntD proteins play an important role in maintaining membrane cell function. The expression of the sfp gene is controlled by the Crp and Fur transcription activator. Excessive expression of the SFP gene will help the secretion of secondary metabolites capable of breaking complex carbon atom chains in the heavy oil.

Keywords
Bacillus subtilis , biosurfactant, sfp gene, bioinformatics

Topic
Bioinformatics

Link: https://ifory.id/abstract/zNjXEcPAmJn2

Corresponding Author
Husnul Khotimah

Institutions
1Departement of Pharmacology, Faculty of Medicine, Universitas Brawijaya, Indonesia
2Laboratory of Biomoleculer, Faculty of Mathematics and Natural Sciences, Universitas Brawijaya, Indonesia

Abstract
Parkinsons disease (PD) the most common movement disorder and the second most common neurodegenerative disease after Alzheimers disease, is characterized primarily by the loss of dopaminergic neurons in the substantia nigra pars compacta leading to a dopamine deficit in the striatum. The standard therapy for Parkinson-s was levodopa (dopamine agonist) administration, but extended levodopa treatment often end up with dyskinesia. So, it-s needed the emerging alternative therapy for Parkinson-s. one of the most promising therapy is herbal remedies. Centella asiatica (CA) is one of popular herbs that has been used for many centuries for cure many disease such as bronchitis, memory improvement and neurotonic. In this study we explore the mechanism of CA to protect from Parkinson-s disease. We used SuperPred server to predict kinds of molecules that could bind to the certain protein. Four major active compound of CA (Asiaticoside, mdecassoside, madecassic acid and Asiatic acid) were docked using PatchDock and continuous using FireDock. One of interesting active compound was Asiatic acid, continued to further analyzed using Autodick Vina on PyRx 0.8, Molecular interaction (Ligand Scout V.2.0), Molecular visualization (chimera 1.8.1). Results showed that asiaticoside and madecassoside have strong anti-inflammatory activities due to their binding to the cyclooxygenase enzymes. While Asiatic acid and madecassic acid have specific binding to protein tyrosine phosphatase (PTP). FireDock analysis using 2F71 (protein tyrosine phosphatase 1b as receptor) and Asiatic acid as ligand (DSAsisticAcisCID119024.pdb) we found energy binding -6.62 kj/mol. Its known that if PTP 1b bound to certain molecule, the BDNF signalling will more strength. Because PTP 1b attenuate BDNF signaling. We can conclude that CA could protect Parkinson-s through the anti-inflammatory activities and strengthen the BDNF signaling.

Keywords
Centella asiatica, BDNF, Asiatic acid, PTP 1b

Topic
Bioinformatics

Link: https://ifory.id/abstract/vgDTBzmJ7jcL

Corresponding Author
Hendra Susanto

Institutions
1) Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Negeri Malang, Indonesia
2) Faculty of Medicine, Universitas Gadjah Mada, Indonesia
3) Department of Digestive Surgery, Dr. Sardjito Hospital, Yogyakarta, Indonesia
4) Department of Nursing Sciences, Tribhuwana Tunggadewi University, Indonesia

*Corresponding Author-s email: hendrabio[at]um.ac.id

Abstract
Hepatocellular carcinoma is cancer, which is a significant problem in several countries in the world, one of which is Indonesia. The presence of hepatocellular carcinoma is often accompanied by the occurrence of the metabolic syndrome and infection of the HBV virus. Lipoprotein lipase (LPL) is an enzyme that is thought to be a key factor of metabolic syndrome occurrence and also HBV infection. This computational study aims to see the interaction between ANGPTL8 and HBV virus particles against LPL as a target. Our study shows that HBV and ANGPTL8 have different binding regions in the LPL enzyme so that they can bind simultaneously. Computationally HBV has stronger energy bonds than ANGPTL8. To sum up, this study can be the hallmark of another research to find out the role of LPL to the occurrence of Hepatocellular carcinoma by the binding of ANGPTL8 and HBV.

Keywords
Hepatocellular carcinoma, HBV, Betatrophin, Metabolic syndrome.

Topic
Bioinformatics

Link: https://ifory.id/abstract/C7X8JADzTmge

Corresponding Author
Rulyana Salma Rosadha

Institutions
Department of Biology, Faculty of Mathematics and Sciences, Universitas Negeri Malang, Indonesia

Corresponding author: mohamad.amin.fmipa[at]um.ac.id

Abstract
Nephrolithiasis is the most common kidney disease in Indonesia. One of the natural treatments for nephrolithiasis that is by using Sonchus arvensis plant. The purpose of this study was to determine the potential of Sonchus arvensis natural compounds in the nephrolithiasis treatment using reverse docking analysis. The reverse docking method is used to prove the potential of a compound through several databases and softwares. The results of reverse docking showed interaction of predictive compounds with target proteins, binding affinity, and predictive compounds- binding sites with target proteins. The predicted compounds results of reverse docking were tested for toxicity using Toxtree v2.6.13 software and bio oral potential with the Rule of Five Lipinski. The results showed that one of predicted compounds named Apigenin 7 glucoside has potential as an anti-nephrolithiasis-s candidate.

Keywords
apigenin 7 glucoside, nephrolithiasis, reverse docking, Sonchus arvensis

Topic
Bioinformatics

Link: https://ifory.id/abstract/Q8gtAVGrEUDj

Corresponding Author
Wira Eka Putra

Institutions
1Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Negeri Malang
2Division of Genetics and Molecular Biology, Generasi Biologi Indonesia Foundation
3Department of Biology, Faculty of Mathematics and Natural Sciences, Brawijaya University

*Corresponding Email: hendrabio[at]um.ac.id

Abstract
This study aims to assess Moringa oleifera bioactive compounds as potential inhibitor against the human α-3 NAchR. The 2D structure of bioactive compounds were retrieved from PubChem chemical structure data base. Whereas, the 3D structure of protein was obtained from PDB. After finish protein and ligands preparation, the molecular screening through in silico approach was performed. The last step for this compounds screening was visualization and molecular interaction analysis. Based on the docking simulation, we found several potential bioactive compounds that can properly interact with the α-3 NAchR. In this study, we showed the top three ligands with the greatest energy binding to the α-3 NAchR, i.e. Ellagic acid (-9.0 kcal/mol), Quercetin (8.5 kcal/mol), and Glucosinolates (8.1 kcal/mol). This study suggest that Moringa oleifera bioactive compounds may have potential as α-3 NAchR inhibitor.

Keywords
In silico, Moringa oleifera, NAchRs

Topic
Bioinformatics

Link: https://ifory.id/abstract/96nUuW3tDEzm

Corresponding Author
Aulia Fahira

Institutions
1Department of Parasitology, Faculty of Medicine, Brawijaya University, Malang, East Java, Indonesia.
2Department of Anatomical Pathology, Faculty of Medicine, Brawijaya University, Malang, East Java, Indonesia.
3Medical Degree Program, Faculty of Medicine, Brawijaya University, Malang, East Java, Indonesia.

Abstract
RAS gene mutations, especially KRAS, are most common mutation in colorectal cancer. Mutations cause changes in conformation of KRAS protein, makes it unable to bind with RASGAP that works to turn KRAS off. The main chemotherapy drug for colorectal cancer is 5-fluorouracil (5-FU) which inhibits thymidylate synthase. 5-FU has many side effects, therefore it is necessary to consider a combination therapy with natural chemotherapy agents, one of which is lysenin, found in coelomic fluid from Lumbricus rubellus. The aim of this study was to determine the potential of lysenin bond with KRAS as a way of inhibiting the cancer pathway. This research is an in silico experimental study using PatchDock, FireDock, PyMOL, and LigPlot, while the molecular structures are taken from Pubchem and Uniprot databases. Result from molecular docking indicates that there was a bond between lysenin and KRAS with binding affinity score -14.51 kcal/mol, while RASGAP and KRAS has a binding affinity score 4.32 kcal/mol, but after lysenin binds to KRAS, the binding affinity score of this complex with RASGAP becomes -20.47 kcal/mol which was stronger. In conclusion, it was estimated that lysenin was able to become a bond stabilizer between KRAS and RASGAP, consequently KRAS can be turned off. This mechanism of lysenin which was different from 5-FU was expected to have a synergistic effect in inhibiting colorectal cancer.

Keywords
Colorectal cancer, KRAS, 5-fluorouracil (5-FU), lysenin, Lumbricus rubellus, molecular docking

Topic
Bioinformatics

Link: https://ifory.id/abstract/JbRQ86HVjxvG

Corresponding Author
Nor Azlina Ahmad

Institutions
Department of Biosciences,
Faculty of Science,
Universiti Teknologi Malaysia (UTM),
81310 UTM Johor, Malaysia

Abstract
Current analytical characterization of phytochemical is expensive and laborious. Alternatively, techniques such as biosensor with high binding affinity and specificity to the target such as aptamer emerged recently. Aptamers are oligonucleotides with structured molecules that can bind to their targets by specific 3-D conformation. Though aptamer technology have taken place for the past 30 years, little works have been conducted on its capacity to bind phytochemical compounds. Here, DNA aptamers named APT1 to APT30 3-D structures and possible binding mechanism of the aptamers-quercetin complex were evaluated in-silico. Secondary and tertiary structure of 28 potential DNA aptamers candidates were modelled adopting MFold and RNA Composer, respectively. The correspond sequence further modified from RNA to DNA by Discovery Studio Visualizer software. Applying AutoDock Vina, the aptamer-quercetin interactions were predicted. Amongst the aptamers, APT14, APT15 and APT1 displayed highest binding affinity with -9.4, -9.3 and -9.3 kcal/mol, respectively. Upon structure analysis, most of the binding sites that possess high docking energy were positioned at loops and stem conformation. The later plays an important role in stabilization while the bases within the loop motifs responsible in supporting the binding. The stability of potential aptamers-quercetin complex will be further explored for their specific intermolecular interaction using molecular dynamics simulation.

Keywords
DNA aptamers, 3-D structure, quercetin, binding affinity, molecular interaction

Topic
Bioinformatics

Link: https://ifory.id/abstract/YK6kFyNfaBpU

Corresponding Author
Yuslinda Annisa

Institutions
Universitas Negeri Malang

Abstract
The tribes in Indonesia are vary. Tengger tribe is one of the Indonesian tribes that located in Bromo Tengger Semeru NationalPark (BTSNP). BTSNP area has a very high diversity of plants. Various types of plants were used by Tengger Tribe in any field such as medicine, food sources including animal feed, industry and households, building materials, ecology, and traditional rituals. Based on interview with key informant called ‘Dukun- and Tengger tribe local people were found that Physalis angulata (local name: Ciplukan gunung) is the most used within Tengger tribe. They used P. angulata to treat any kind of diseases especially keep heart and lung in healthy condition. Tengger tribe used P. angulate by boiling in certain time then drink it as a tonic. The aims of this research were to analyze active compound from decoction of P. angulate that has anti-inflammatory agent. High Performance Liquid Chromatography (HPLC) result showed that decoction of P. angulate contained with active compound, one of them was Benzaldehyde. In silico study between benzaldehyde and cyclooxygenase 1 (COX-1) resulted that benzaldehyde has potency as inhibitor for COX-1. COX-1 is involved in inflammatory pathway. The inhibition towards COX-1 resulted on decreasing of inflammation. P. angulate has function as anti-inflammation.

Keywords
Tengger tribe, Bromo Tengger Semeru National Park (BTSNP), Physalis angulata, anti-inflammation, Cyclooxygenase 1 (COX-1)

Topic
Bioinformatics

Link: https://ifory.id/abstract/83VEhDkXzmru

Corresponding Author
Hendra Susanto

Institutions
1) Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Negeri Malang, Indonesia
2) Faculty of Medicine, Universitas Gadjah Mada, Indonesia
3) Department of Digestive Surgery, Dr. Sardjito Hospital, Yogyakarta, Indonesia
4) Department of Nursing Sciences, Tribhuwana Tunggadewi University, Indonesia

*Corresponding Author-s email: hendrabio[at]um.ac.id

Abstract
Liver fibrogenesis can turn out into liver cirrhosis and being a fatal failure. Infection of HBV and metabolic syndrome is the major causes of liver fibrogenesis. ANGPTL8 is the hormones that interact with many factors related to HBV infection and metabolic syndrome. The purpose of this study was to crosscheck computational based interaction of ANGPTL8 and TGFβ1 on TGFβR1 as the pathological signal that related to liver fibrogenesis. Our study shows that ANGPTL8 bind better onto TGFβ1R than TGFβ1 so that ANGPTL8 may implicate with fibrogenesis through simultaneous binding into TGFβ1R with TGFβ1. This study work as an initial study that can be used as the basis of the next study to determine the role of ANGPTL8 in the occurrence of liver fibrogenesis due to metabolic syndrome and HBV infection.

Keywords
ANGPTL-8, liver fibrinogenesis, TGFβ1R, hepatocellular carcinoma

Topic
Bioinformatics

Link: https://ifory.id/abstract/WbUYpk3m6hgr

Corresponding Author
Wira Eka Putra

Institutions
1Departement of Biology, Faculty of Mathematic and Natural Sciences, Universitas Negeri Malang
2Departement of Biology, Faculty of Mathematic and Natural Sciences, Universitas Brawijaya
3Division of Genetics and Molecular Biology, Yayasan Generasi Biologi Indonesia (Genbinesia)

*Corresponding Email: hendrabio[at]um.ac.id

Abstract
Nuclear factor kappa B (NF-κB) is known as master of regulation due to its multiple roles in biological system including metabolism, inflammation, or even diseases like cancer. The downstream phosphorylation of NF-κB complex is affected by the activity of IKK-B. Thus, in this study we aims to evaluate the bioactive compounds of Zingeber officinale as inhibitor agent against the IKK-B. The virtual screening evaluation was based on the interaction activity and binding free energy among the protein and the ligands. The virtual chemical structure and protein structure were obtained from pubchem web server and PDB respectively. Molecular docking, visualization, and data analysis were performed by computation approach. In this study, we found that 6-Shogaol might potential as drug like molecule for anti-inflammation compared to other compounds. Importantly, further study needed to evaluate the biological mechanism of 6-Shogaol inhibit the IKK-B activity.

Keywords
Anti-inflammation, IKKB, virtual screening, Zingiber officinale

Topic
Bioinformatics

Link: https://ifory.id/abstract/eqkjmdB3hELr

Corresponding Author
ATIKAH AMALIA

Institutions
Biology Department, Faculty of Mathematics and Natural Sciences, Universitas Negeri Malang, Indonesia

Abstract
It has been investigated that the prevalence of Rheumatoid Arthtritis (RA) is 0.5% -1.0% in general population worldwide. Inflammation arises because of prostaglandins, which are proinflammatory mediators enacted by the stimulus. The key enzyme in inflammation is cyclooxygenase-2. Flavonoids have various biological effects in mammalian cells carried out both in vitro and in vivo. This study was carried out to predict the potential of flavonoid group compounds as anti-inflammatory agents for rheumatoid arthritis through virtual screening using molecular docking methods. This method was employed to predict the potential of flavonoid compounds using web server PASS SERVER, predictions of the pharmacokinetic properties of flavonoid compounds including absorption, distribution, metabolism, excretion, and toxicity using pkCSM and molecular docking web servers to determine the interaction of COX-2 enzyme flavonoid compounds which was compared with control drugs. The results of this study indicated that flavonoid compounds (kaempferitrin, afzelin, and routine) could potentially replace the drug rofecoxib based on potential compounds, namely as anti-inflammatory, non-steroidal anti-inflammatory agents, antioxidants, and anti-carcinogenic. Flavonoid compounds had a decent ADMET profile. The compound had considerable activity as an anti-inflammatory agent based on its interaction with the COX-2 enzyme as indicated by the binding affinity value of ± -8.5 kcal/mol.

Keywords
Flavonoids, Inflammation, Molecular Docking

Topic
Bioinformatics

Link: https://ifory.id/abstract/NAByGmCu8Xxc

Corresponding Author
Maghfiroh Gesty Maharani

Institutions
1) Biology Departement, Faculty Mathematics and Science
Universitas Negeri Malang, St. Semarang 5 Malang, 65145, Indonesia
* srirahayulestari[at]um.ac.id

Abstract
Hypercholesterolemia is the highest risk of CVD which is the biggest disease leading death. One of the Indonesian medicinal plants is single bulb garlic with high flavonoids concentration. Lanosterol synthase, an enzyme on the final stage of cholesterol synthesis are the appropriate inhibition stage for drug. The purpose of this study was to analyze the potential of single bulb garlic flavonoids (quercetin, isoquercetin, and kaempferol) in inhibiting lanosterol synthase. Computational docking analysis was performed using Pyrx, Pymol, Discovery studio, also webserver to predict ADMET and biological activity. Lanosterol synthase was obtained from PDB (PDB ID: IW6J) with RO 48-8071 as native ligand used for control. The results showed binding energy RO 48-8071 (-10,3 kcal / mol), quercetin (-9.8 kcal / mol), isoquercetin (-6.8 kcal / mol ), and kaempferol (-9.9 kcal / mol). Based on interaction and bonding distance, flavonoids have more stable than control. Flavonoids also have potential as APOA1, HMOX1 enhancers, lipid peroxidase inhibitors, cardioprotectant and hepatoprotectant, had high distribution volumes, low toxicity and clearance. This result indicated that quercetin, isoquercetin, and kaempferol from single bulb garlic could be potential ligand to treat hypercholesterolemia, and could proceed to in vitro and in vivo study by improve the absorption.

Keywords
Antihypercholesterolemia, Single Bulb Garlic, Flavonoids, Molecular docking

Topic
Bioinformatics

Link: https://ifory.id/abstract/xJjUPThvgBfM

Corresponding Author
Lusi Suciati

Institutions
a) Biology Departement, Faculty Mathematics and Science
Universitas Negeri Malang, St. Semarang 5 Malang, 65145, Indonesia
*srirahayulestari[at]um.ac.id

Abstract
Cardiovascular disease is closely related to hypercholesterolemia (increased levels of total cholesterol in the blood). One effort to inhibit cholesterol biosynthesis is by inhibiting the enzyme squalene synthase. The inhibition of the enzyme squalene synthase does not interfere with the biosynthesis of other important biological molecules and thus better side effects are expected for this inhibitor. The purpose of this study was to analyze geraniin, corilagin, and elagic acid compounds of rambutan (Nephelium lappaceum L.) peel extract as squalene synthase inhibitors. Docking simulation has been performed using PyRx. Data from software and web tools were analyzed descriptively and compared with lapaquistat, a control drug that was proven to inhibit squalene synthase clinically. The docking results indicate that all ligands bind to squalene synthase active site and it has more stable bonds. Geraniin is the compound that has the lowest binding free energy (-12.2 kcal/mol). ADMET results show that on average 80% of geraniin, corilagin and ellagic acid compounds are absorbed by human digestion, well distributed, and don-t cause liver toxicity. The overall results indicated that the compounds could be potential as candidates for the structure-based drug design and the development of the pharmaceutical agents to treatment of cardiovascular disease.

Keywords
Geraniin, Corilagin, Ellagic acid, Squalene Syntase, Rambutan Peel, in silico

Topic
Bioinformatics

Link: https://ifory.id/abstract/FEPxfmAJ9yYa

Corresponding Author
Siti Imroatul Maslikah

Institutions
Universitas Negeri Malang

Abstract
Breast cancer is the second leading cause of cancer deaths among women. The most common triggers for breast cancer are excessive expression of estrogen-α receptors (ER-α) which play an important role in the growth, development and pathophysiology of the breast, so that ER-α is an attractive drug target. Tamoxifen is one of the Selective Estrogen Receptor Modulators (SERMs) to treat breast cancer patients, but this drug has a detrimental effect on the uterus, so a safe alternative is needed to use herbal ingredients such as Red Betel which is used by Indonesian people as traditional medicine. This study aims to predict the potential of compounds Kaempferitin, β-amyrin, Piperbetol, Piperine and Sesamin Sirih Merah as inhibitors of α-Estrogen Receptors (ER-α) through Molecular docking method, Potency Activity test and ADMET test using several software and web server. The docking results between the five red betel compounds and ER-α were at the same site as the Thamoxifen drug, through alkyl and hydrogen bonds with the affinity value of the red betel compound lower than the control drug. The results showed that red betel active compounds have the potential to be antineoplastic and antioxidant. Red betel active compounds have a good ADMET profile. The conclusions of this study are red betel compounds namely Kaempferitin, β-amyrin, Piperbetol, Piperine and Sesamin as potential candidates for breast anticancer drugs.

Keywords
Breast Cancer, Estrogen-α Receptor (ER-α), Virtual screening

Topic
Bioinformatics

Link: https://ifory.id/abstract/xudtYymBjZ8n

Corresponding Author
Wira Eka Putra

Institutions
1Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Negeri Malang
2Division of Genetics and Molecular Biology, Generasi Biologi Indonesia Foundation
3Department of Biology, Faculty of Mathematics and Natural Sciences, Brawijaya University

*Corresponding Email: hendrabio[at]um.ac.id

Abstract
The effect of the smoking alter the broad biological system and causing the negative effect including cardiovascular diseases, immune and metabolic disorders, and cancer. On the other hand, numerous strategies to suppress the dependency to the cigarette has come to its limit. Therefore, the new approach to face the undesired outcome is necessary. This study aims to evaluate the pharmaceutics potencies of bioactive compounds from several Indonesian medicinal plants. The 2D structure of poliherbal compounds were collected and prepared for the docking processes. On the other hand, the 3D structure of human α-3 NAchRs protein was retrieved from PDB. Virtual screening approach was occupied to observe the molecular interaction among ligands and the targeted protein. The value of binding energy was used to determine the potency of poliherbal compounds as inhibitor candidates against α-3 NAchRs protein. The result of this study showed several compounds that might possible as inhibitor against α-3 NAchRs. Here, we classified the top three compounds that have minimum energy binding, namely Asiaticoside (-12.2 kcal/mol), Orthosiphol B (-9.8 kcal/mol), and Panduratin A (9.0 kcal/mol). Our finding suggests that the poliherbal might potential as complementary supplement for smoker to avoid the adverse effect of cigarettes.

Keywords
Cigarette, human α-3 AchRs, poliherbal compounds

Topic
Bioinformatics

Link: https://ifory.id/abstract/WL7U6JRDkpYr

Corresponding Author
Nur Fitriana

Institutions
Biology Department, Faculty of Mathematics and Natural Science, Brawijaya University, Malang, Indonesia

Abstract
Current breast cancer treatment has shifted to using natural ingredients such as C. zedoaria high potential and low side effect. Previous studies have identified that compounds in C. zedoaria are capable as anti-proliferative, increasing apoptosis and anti-metastasis. However, information the mechanism of roles its active compound for CXCR4 inhibition in the carcinogenesis process unknown. C_X_C chemokine receptor type 4 (CXCR4) is an alpha-chemokine receptor specific for stromal-derived-factor-1 (SDF-1/CXCL12). CXCR4 has been reported to play an important role for prognosis and potential drug target in breast cancer. This study aimed to analyze the potential effect of active compound from C. zedoaria as breast cancer chemotherapeutic agents through CXCR4 inhibition. Binding affinity analysis through molecular docking shows that 11 active compounds have the potential inhibiting CXCR4 with smallest binding affinity and same binding site with Chalcone and Epirubicin. However, Stigmasterol, Campesterol, and β-sitosterol have lowest binding affinity than the other active compound. Protein interaction analysis illustrates that CXCR4 can interact with various protein, including CXCL12, STAT3, and JAk2, used as a diagnostic marker and poor prognosis factor for cancer. These data indicate that active compounds from C. zedoaria highly potential as anti-breast cancer. Additional research is needed to validate above data.

Keywords
Breast cancer, C. zedoaria, CXCR4

Topic
Bioinformatics

Link: https://ifory.id/abstract/zpK8xFhA9nuq

Corresponding Author
Qurin Nikmaturrohana

Institutions
a) Biology Department, Faculty of Mathematics and Science, Universitas Negeri Malang, Jl. Semarang 5 Malang, 65145, Indonesia
*srirahayulestari[at]um.ac.id

Abstract
Obesity is a chronic condition of excess body fat accumulated which can interference healthy. Indonesian prevalence of obesity at the 2018 is 31,0% and can increase every year. Obesity caused by excess calories and sugar which affect high 11β-HSD1 activity in sugar metabolism regulated by glucocorticoids, however that activity can be inhibited by providing a 11β-HSD1 inhibitor. Alliin, allicin, and ajoene from single bulb garlic (Allium sativum) is indicated able to inhibit 11β-HSD1. The aim of the research is predict alliin, allicin, and ajoene as 11β-HSD1 inhibitor for obesity drugs candidate using in silico method. The research performed with physicochemical properties analyze, PA test, pharmacokinetics test and molecular docking of alliin, allicin, ajoene and control drug BVT-2733. The results showed that alliin, allicin, and ajoene have a good oral bioavailability, antioxidant potential, lipoprotein disorders treatment, and lipid metabolism regulator. Based on pharmacokinetics test absorption, distribution and excretion is high and the toxicity is low. The molecular docking show the same binding site and amino acid residue with control drug BVT-2733, the type of bond formed is a hydrogen and hydrophobic bond. The conclusion showed that single bulb garlic has potential to be an oral drug candidate for treating obesity.

Keywords
Obesity, 11β-HSD1, Alliin, Allicin, Ajoene, and In Silico

Topic
Bioinformatics

Link: https://ifory.id/abstract/Zm6WrMjRzGVF

Corresponding Author
Muhammad Badrut Tamam

Institutions
a) Division Genetic and Molecular Biology, Generasi Biologi Indonesia (Genbinesia) Foundation, Gresik, Indonesia

b) Department of Biology, Faculty of Mathematics and Natural Sciences, Brawijaya University

c) Department of Biology, Faculty of Natural Sciences and Technology, Universitas Muhammadiyah Lamongan

d) Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Negeri Malang

*Corresponding author: violdhea[at]gmail.com

Abstract
Abstract. This research aims to reveal the potency of bioactive compound contained in Iponema batatas leaf as inhibitory agent to protease dengue virus through computational study. The target protein in this study is NS2B/NS3 serine protease. Furthermore, the 3D structure was obtained from PDB. In the same way, the 2D structure of several bioactive compounds of Iponema batatas leaf were collected from PubChem. The visualization and data analysis were performed by using the pymol software. Iponema batatas bioactive compounds have potency as inhibitor NS2/NS3 serine protease. According to the in silico analysis, dehydroabietinol have lowest free energy binding, but refer to the result of analysis of protein-ligand domain interaction of the all compounds showing that the protein-ligands have two type of chemical interaction namely hydrogen bond and hydrophobic. All of the compounds have hydrogen bond cannot be interacted with catalytic domain, but hydrophobic interaction can be interacted to target domain, via Ser135 by δ-Selinene and His51 by α-Caryophyllene. Finally, we conclude that δ-Selinene and α-Caryophyllene might have potencies as therapeutical drug for dengue.

Keywords
α-Caryophyllene, δ-Selinene, Ipomea batatas, NS2/NS3 serine protease.

Topic
Bioinformatics

Link: https://ifory.id/abstract/2CvYyug6H9dN

Corresponding Author
Dini Sri Damayanti Damayanti

Institutions
Universitas Islam Malang

Abstract
Soursop leaves (Annona muricata Linn.) as an anti-inflammatory substance: an in silico study Damayanti D.S, Firdaus R.S, Hanum S. Faculty of Medicine, Islamic University of Malang dinisridamayanti@unisma.ac.id Googlescholar ID: E3KD1GEAAAAJ ABSTRACT Soursop leaf essential oils and ethanol extract are known to have anti-inflammatory effects, but it is unclear how these effects work. This study aims to analyze the anti-inflammatory potential of soursop leaf essential oils and ethanol extract by the inhibition of COX-1 (Cyclooxygenase-1) and COX-2 (Cyclooxygenase-2) using an in silico study. Molecular docking between the active ingredients of soursop leaf (Annona muricata Linn) essential oils and ethanol extract against the target protein (COX-1 and COX-2) was done computationally. We measured free bond energy (ΔG) and hydrogen bonds on the amino acid residues. Inhibition potential was indicated by low free bonding energy and the presence of hydrogen bonds on the same amino acid, compared to the control, indomethacin. β-caryophyllene, trans-caryophyllene and linalool were predicted to have a weak potential to inhibit the COX-1 protein, in a manner similar to the control. Linolool was predicted to have the ability to inhibit COX-2, in a manner that was almost the same as the control. Rutin, nicotiflorin and quercetin had a weak potential to inhibit the COX-1 protein. Anonaine had the ability to inhibit the COX-2 protein in a manner close to that of the control. In conclusion, soursop leaf essential oils and ethanol extracts have a weaker ability to inhibit COX-1, but have the capability to control and inhbit COX-2.

Keywords
Annona muricata Linn., COX-1 enzyme, COX-2 enzyme

Topic
Bioinformatics

Link: https://ifory.id/abstract/8Qv3VYXgUkZE

Corresponding Author
Wiko Arif Wibowo

Institutions
a) Laboratory of Genetics and Breeding, Faculty of Biology, Universitas Gadjah Mada
b) Laboratory of Animals Physiology, Faculty of Biology, Universitas Gadjah Mada

Abstract
One of the common symptoms of cancer is the cells growth abnormaly. Currently, cancer treatment was conducted by chemotherapy. Doxorubicin was commonly used for chemotherapy through the TOP2A inhibition pathway. However, long-term use of Doxorubicin is thought to have a negative impact in the form of cardiotoxicity and multi drug resistance. Cucurbitacin compounds are natural ingredients which are generally produced by the Cucurbitaceae family plant. There are various types of Cucurbitacin compounds which are generally believed to have anti-cancer activity. The aim of this study was to explore the potential for anti-cancer in various types of Cucurbitacin compounds using in silico approach. DNA topoisomerase 2-alpha protein (TOP2A) was obtained from Protein Database (GDP) while a model of the compounds Doxorubicin and Cucurbitacin A, B, C, D, E, F, and I was collected from the chemical molecule database (PubChem). Molecular docking analysis was carried out using PyRx, while the analysis of DNA topoisomerase 2-alpha interaction with each ligand was analyzed by PyMol. The results showed that in general the whole Cucurbitacin compound tested had potential as an anti-cancer compound, with the highest bond energy value of -9.0 in Cucurbitacin I. Those value was higher than the control which was only -8.9.

Keywords
Cucurbitacin; Doxorubicin; TOP2A; Bioactive compound

Topic
Bioinformatics

Link: https://ifory.id/abstract/BN6edMHLfutG

Corresponding Author
Wira Eka Putra

Institutions
1Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Negeri Malang
2Division of Genetic and Molecular Biology, Yayasan Generasi Biologi Indonesia (Genbinesia)
3 Department of Biology, Faculty of Mathematics and Natural Sciences, Brawijaya University

*Corresponding Email: hendrabio[at]um.ac.id

Abstract
Recent trend in health care demonstrates the significant use of herbal as preventive or therapeutic strategy against multiple type of diseases including respiratory disorder. Thus, in this present study we aims to explore the potential of black tea phytochemical compounds as inhibitor against human α-3 nicotinic acetylcholine receptors. The 2D structure of black tea compounds were retrived online from PubChem data base. On the other hand, the 3D protein structure of human α-3 nicotinic acetylcholine receptors (NAchR) was obtained from protein data base. Protein-ligand preparation were proceed to optimize the molecular interaction results. The final step of this screening is performed data visualization and analysis. In this study, we found that there are three potential compounds that might be act as inhibitor for α-3-NAchR considering of its energy free binding. Thus, this results indicate that the black tea bioactive compounds might be potential to develop as inhibitory agents for α-3-NAchR to minimize the negative effect of nicotine.

Keywords
α-3 nicotinic acetylcholine receptors, black tea, nicotine

Topic
Bioinformatics

Link: https://ifory.id/abstract/gxRKjavJPWk7

Corresponding Author
Solichatul Afifah

Institutions
Department of Biology, Faculty of Mathematics and Natural Sciences, University of Malang

Abstract
Rheumatoid Arthritis (RA) is an inflammatory disease of the synovium. The key enzyme which role in RA is mPGES-1, which catalyzes conversion PGH2 into PGE2. PGE2 is the primary prostaglandin in inflammation when PGE2 binds to receptors PGE2, and it can activate the transcription factor. Data from WHO in 2010 depict that the prevalence of RA sufferers is relatively high. The synthetic drugs for RA commonly used are piroxicam and meloxicam, but has effect due to hepatoxics, so that a safe alternative which using an herbal madicine such as red betel. Red betel leaves contains terpenoid compounds such as β-amyrin, Spathulenol, Caryophyllene, and Humulene. Several previous studies reveal that terpenoid can inhibit prostaglandin biosynthesis such as terpenoid in Boswellia species and Salvia officinalis, which can inhibit mPGES-1. The purpose of this study is to predict potential of β-amyrin, Spathulenol, Caryophyllene, and Humulene terpenoid compounds in Red Betel as mPGES-1 inhibitor through Molecular docking, PA test, and ADMET test using software and web servers. The results showed four terpenoid compounds and mPGES-1 were on same binding site as drugs, and bound with enzyme through alkyl bond, while β-amyrin bound not only with alkyl bond but also hydrogen bond. The binding affinity of four terpenoid compounds were not significantly different from drugs. The potentials of antiinflammatory, antiarthritic, NSAID, transcription factor inhibitor and pharmacokinetic better than drugs. Based on the generated results, it can be concluded that β-amyrin, Spathulenol, Caryophyllene, and Humulene in Red Betel are potential for an antiinflammatory RA drug candidate.

Keywords
Rheumatoid Arthritis, mPGES-1, Virtual Screening

Topic
Bioinformatics

Link: https://ifory.id/abstract/ZmrWJwqt4MFG