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All Journal The Indonesian Biomedical Journal Eksakta : Berkala Ilmiah Bidang MIPA Indonesian Journal of Medical Chemistry and Bioinformatics Eduvest - Journal of Universal Studies
Dwira, Surya
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Phytochemical Assay and in – Vitro Cytotoxicity Assessment of Cassava Peel (Manihot esculenta) from Ethanol and Ethyl Acetate Extract Against Cervical Cancer Cells (HeLa) Soejono, Alice Hari; Dwira, Surya; Sari, Puji
Indonesian Journal of Medical Chemistry and Bioinformatics Vol. 2, No. 2
Publisher : UI Scholars Hub

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Abstract

Introduction: Cervical cancer is a type of cancer that develops in a woman’s cervix. It is a result of HPV (Human Papilloma Virus) and is one of the deadliest types of cancer. Some cervical cancer management including chemotherapy, which until recently continues to develop to cure the condition, is relatively expensive and comes with multiple different side effects. Method: Manihot esculenta undergoes multilevel maceration with the solvent of ethanol and ethyl acetate. This leads to the formation of ethanol extract and ethyl acetate extract of Manihot esculenta that is analyzed through phytochemical assay and thin layer chromatography (TLC) to determine the phytochemical components present. This is then followed by cytotoxicity assessment against Hela cervical cancer cells using MTT test. Result: Manihot esculenta peel contains secondary metabolites including tannin, flavonoid, alkaloid, and triterpenoid. Cytotoxicity activity evaluation for ethanol shows moderate cytotoxicity with IC50 value of 228.26 μg/mL. While ethyl acetate shows active cytotoxicity activity with IC50 value of 56.47 μg/mL. The data distribution of IC50 value of all extracts is normal (p>0.05). There was a statistically insignificant difference in IC50 value between extracts based on one-way ANOVA. Conclusion: Manihot esculenta peel contains phytochemical components that are cytotoxic towards HeLa cervical cancer cells.
Prothrombin Time (PT), Activated Partial Thromboplastin Time (APTT), Fibrinogen, and D-dimer in Coronavirus Disease 2019 Outcome Atmaja, Fredy Wirya; Adiyanti, Sri Suryo; Kristanty, Diyah; Dwira, Surya; Kusmardi, Kusmardi
Indonesian Journal of Medical Chemistry and Bioinformatics Vol. 3, No. 1
Publisher : UI Scholars Hub

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COVID-19, caused by SARS-CoV-2 has been reported to be associated with coagulopathy and DIC. This study aimed to investigate the profiles and differences of PT, APTT, fibrinogen, and D-dimer in COVID- 19 outcome. This retrospective cohort was conducted at Central Laboratory Clinical Pathology Department of dr. Cipto Mangunkusumo Hospital from July – December 2020. Demographic, clinical, and laboratory data were extracted from EHR and compared between poor and good outcome. Ninety-seven subjects were confirmed positive COVID-19, 45 of whom (46.4%) were in poor outcome group, while 52 subjects (53.6%) were in good outcome group. Median of PT 11.0” (9.7-28.3), APTT 38.4” (23.9-121), fibrinogen 484.8 mg/dL (51.2-940.9), and D-dimer 1,800 µg/L (190-35,200). Longer PT, APTT, and higher D-dimer (p < 0.05), while lower fibrinogen (p > 0.05) was found in poor outcome group. There were significant differences of PT, APTT and D-dimer in COVID-19 outcome.
Phytochemical Profile and Cervical Anticancer Activity of an In Vitro n-Hexane Extract of Kunto Dewo Fruit (Kigelia pinnata) Peel and Flesh Isbandiputri, Swarnasari Nurandita; Dwira, Surya; kristanty, diyah
Indonesian Journal of Medical Chemistry and Bioinformatics Vol. 2, No. 1
Publisher : UI Scholars Hub

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Cervical cancer is the fourth highest cancer occurring and causes death in women. Therefore, adequate management is needed to prevent its development. Currently, the treatment has a variety of adverse side effects, so it needs alternative treatments that are supportive and with minimal side effects. One way is to use herbal plants, such as the Kunto Dewo (Kigelia pinnata) plant which is often used as traditional medicine. This plant has antimicrobial and cytotoxic effects on cancer cells. Knowing the phytochemical profile and in-vitro anticancer activity of the n-hexane extract of peel and flesh of Kunto Dewo (Kigelia pinnata) fruit against cervical cancer HeLa cells. The peel and flesh of Kigelia pinnata fruit are macerated in n-hexane solvent then the resulting filtrate is evaporated to become an extract. The extract is used for phytochemical profile, carry out through phytochemical screening, thin layer chromatography, calculation of total phenol, and total flavonoids. The extract was also tested for cytotoxic activity against cervical cancer HeLa cells using MTT assay. The n-hexane extract of the peel and flesh of the kigelia pinnta fruit contains triterpenoids. In TLC analysis, there were found 4 components in the n-hexane extract of Kigelia pinnata fruit peel and 8 components in the n-hexane extract of Kigelia pinnata fruit flesh. The cytotoxic activity of the n-hexane extract of the peel and flesh of Kigelia pinnata fruit is included in the moderately active category. The n-hexane extract of the peel and flesh of the kigelia pinnata fruit has potential as an anti-cervical cancer.
Structure-Based Virtual Screening and Molecular Docking on the Indonesian Herbal Compound as a Promising Insulin Receptor (INSR) Inhibitor to Suppress Tumor Growth Candraningrum, Veronica Hesti; Erlina, Linda; Paramita, Rafika Indah; Fadillah, Fadillah; Dwira, Surya; Fatriansyah, Jaka Fajar
EKSAKTA: Berkala Ilmiah Bidang MIPA Vol. 24 No. 04 (2023): Eksakta : Berkala Ilmiah Bidang MIPA (E-ISSN : 2549-7464)
Publisher : Faculty of Mathematics and Natural Sciences (FMIPA), Universitas Negeri Padang, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/eksakta/vol23-iss04/452

Abstract

A healthy cell maintains a homeostasis condition of glucose level, whereas cancer cells do not. Increased glucose uptake is a hallmark of cancer cells that helps them survive, proliferate, and spread. INSR is one of key feature that take part in glucose metabolism through insulin signaling. To block the entry of glucose into cells, researchers were aiming to disrupt the insulin signaling pathway as the upstream activation in glucose metabolism by inhibiting insulin receptor (INSR) using Indonesian herbal compounds. The approach during the screening was structure-based drug discovery (SBDD) method where INSR was determined as the macromolecules. Some parameters such as binding affinity, constant inhibition, drug-likeness, pharmacokinetics, and toxicity were applied to help the search of potential inhibitor. According to the test results, Heterophylin, Sanggenofuran A, and Epigallocatechin-3-O-caffeate had the strongest molecular binding activity against the INSR protein. Heterophylin is discovered in jackfruit fruit trees and Sanggenofuran A is present in mulberry trees. While Epigallocatechin-3-O-caffeate, is abundantly found in green tea plant
In Silico Analysis of CD40 Mutations and Their Implications for Quinoline-benzoic acid derivatives Based Therapy in Graves' Disease Yunaini, Luluk; Kristanty, Diyah; Sari, Puji; Dwira, Surya; Suryandari, Dwi Anita; Bustami, Arleni
Indonesian Journal of Medical Chemistry and Bioinformatics Vol. 3, No. 2
Publisher : UI Scholars Hub

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Graves' disease is an autoimmune disorder in which the CD40-CD154 interaction plays a critical role in T-cell activation. In this study, in silico methods were employed to analyze the binding interactions of quinoline-benzoic acid derivatives (NSB, FSB, and NQB) with the CD40 receptor and to investigate the implications of specific CD40 mutations for drug efficacy. In this reseach conducted by molecular simulation approach with molecular docking Results Mutation analysis of CD40 identified alterations in key residues, such as R203C, which may impact ligand-independent activation and downstream TRAF binding, crucial for signal transduction. These findings highlight the therapeutic potential of quinoline-benzoic acid derivatives for targeting CD40 in Graves' disease, particularly in the context of receptor mutations. The integration of molecular docking, mutation analysis, and pharmacokinetic profiling provides a comprehensive framework for designing effective CD40-targeted therapies.
Targeting Detoxifying Enzymes in the Lymphatic Filariasis Vector: An In Silico Study on Curcumin, Camphor, and Menthol Subahar, Rizal; Winita, Rawina; Dwira, Surya; El Bayani, Gulshan Fahmi
Indonesian Journal of Medical Chemistry and Bioinformatics Vol. 4, No. 1
Publisher : UI Scholars Hub

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Abstract

Vector control remains a critical component in the prevention of lymphatic filariasis, a disease transmitted by insect vectors. Natural compounds such as curcumin, camphor, and menthol are being explored for their bio-insecticidal properties due to their potential to inhibit key detoxification and neurological enzymes in insects, including acetylcholinesterase (AChE), glutathione S-transferase (GST), and cytochrome P450 oxidases (CYP450). A molecular docking study using SwissDock was conducted to evaluate the interaction of curcumin, camphor, and menthol with AChE, GST, and CYP450 enzymes. Binding affinity (ΔG), hydrogen bonding, and active site interactions were analyzed to assess the inhibitory potential of each compound. Curcumin showed the highest binding affinity across all target enzymes. AChE (-8.2 kcal/mol), GST (-7.9 kcal/mol), and CYP450 (-7.5 kcal/mol). It formed strong hydrogen bonds with key catalytic residues, suggesting effective inhibition of neurotoxicity and detoxification pathways. Camphor displayed moderate binding affinities with AChE (-7.1 kcal/mol), GST (-6.5 kcal/mol), and CYP450 (-7.2 kcal/mol), primarily through hydrophobic interactions. Menthol exhibited the weakest binding, with limited hydrogen bonding and lower affinities (AChE: -6.4 kcal/mol, GST:-5.9 kcal/mol, CYP450: -6.3 kcal/mol). The findings suggest that curcumin is a promising candidate for insect vector control through inhibition of critical enzyme systems involved in neurotransmission and detoxification. Camphor may offer moderate bioactivity, while menthol appears less potent. These insights support further exploration of phenolic compounds as environmentally friendly, natural insecticidal agents against vectors of lymphatic filariasis.
Therapeutic Options for COVID-19: Drug Repurposing of Serine Protease Inhibitor Against TMPRSS2 Abiyyi, Mohammad Wildan; Dwira, Surya; Bustami, Arleni; Erlina, Linda
Indonesian Journal of Medical Chemistry and Bioinformatics Vol. 1, No. 2
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.
Identification of Novel Intronic Variants Implicating L3MBTL4 and AOAH in Indonesian Ovarian Endometriosis Trijayani, Trijayani; Dwira, Surya; Muharam, Raden; Paramita, Rafika Indah
The Indonesian Biomedical Journal Vol 17, No 6 (2025)
Publisher : The Prodia Education and Research Institute (PERI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18585/inabj.v17i6.3732

Abstract

BACKGROUND: Genetic factors are contributing substantially to endometriosis risk, however, there is limited data on genetic variant associations specific to ovarian endometriosis, especially in Indonesian populations. Understanding the genetic variants associated with this condition is essential for improving diagnosis and identifying potential therapeutic targets. Therefore, this study was conducted to analyze the association of genetic variants with ovarian endometriosis in Indonesian women using the single nucleotide polymorphisms (SNP)-array method, followed by an in-silico functional enrichment and gene expression analysis to explore their biological context.METHODS: This case-control study utilized the Infinium Asian Screening Array microarray platform to examine 46 samples, consisting of 22 ovarian endometriosis and 24 controls. The analysis included quality control, genetic association testing, and enrichment analysis. Genotypes were analyzed under dominant and recessive inheritance models, and functional insights were explored using gene expression databases.RESULTS: Ten intronic SNPs were significantly associated with endometrioma (p<0.05). Eight variants conferred increased risk (OR>1): rs77360595 (IFNLR1), rs2325558 (KLF12), rs1654499 (NLRP2), rs4809494 (LOC105376996), rs168482 (TMPRSS11A), rs17026725 (STPG2-AS1), rs59330070 (GFOD1), and rs58909364 (AOAH). Two variants were protective (OR<1): rs180732 (L3MBTL4) and rs7356507 (CRMP1). Notably, AOAH variant showed the highest odds ratio among risk variants, while L3MBTL4 variant showed the strongest statistical significance among protective variants in the dominant model. In-silico expression analysis confirmed that key implicated genes (KLF12, L3MBTL4, AOAH, and GFOD1) are expressed in relevant female reproductive tissues, generally at low-to-moderate levels.CONCLUSION: Ten novel genetic variants associated with ovarian endometriosis in Indonesian were identified. In particular, variants in L3MBTL4 and AOAH represent promising candidates that may play roles in disease pathophysiology of endometriosis, suggesting the importance of population-specific genetic studies and these specific loci as potential biomarkers or therapeutic targets.KEYWORDS: ovarian endometriosis, SNP, microarray, genetic association, plink, bioinformatics
In Silico Study: Metabolite Compounds of Zingiber Officinale Var. Rubrum as Potential E2F2 Inhibitor Agents in Breast Cancer Signaling Pathway Purwamita Budiutami, Khoirunnisa; Tedjo, Aryo; Fadilah, Fadilah; Dwira, Surya; Fajrin, Ajeng M.
Eduvest - Journal of Universal Studies Vol. 6 No. 1 (2026): Eduvest - Journal of Universal Studies
Publisher : Green Publisher Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.59188/eduvest.v6i1.52614

Abstract

Breast cancer ranks among the leading causes of death in women, linked to disruptions in signaling pathways regulating cell proliferation and survival, particularly E2F2 gene activity. E2F2 regulation falters when pRB is phosphorylated by Cyclin D–CDK4/6 or Cyclin E–CDK2 complexes, freeing E2F2 to activate cell cycle genes. This study, "In Silico Study: Metabolite Compounds of Zingiber officinale var. rubrum as Potential E2F2 Inhibitor Agents in Breast Cancer Signaling Pathway," assesses red ginger (Zingiber officinale var. rubrum) metabolites as CDK4/CDK6 inhibitors via molecular docking in silico. Target protein structures came from the Protein Data Bank; metabolites were chosen for reported anticancer effects and 3D-modeled. Docking used Molegro Virtual Docker to gauge ligand affinity and interactions at active sites. Results highlighted [12]-shogaol, (E,E)-α-farnesene, and 1-dehydro-[6]-gingerdione as CDK4 inhibitors; azafrin, [8]-shogaol, and [12]-shogaol for CDK6. These exhibit strong binding via hydrogen bonds and hydrophobic interactions at key residues. Red ginger metabolites show promise as CDK4/CDK6 inhibitors for breast cancer therapy, pending in vitro/in vivo validation.
Prediction of Structure and Function of a Novel β-Lactamase Protein in Gram-Negative Bacteria Using Homology Modeling and Molecular Docking Kiranasari, Ariyani; Dwira, Surya; Merizka, Engla
Indonesian Journal of Medical Chemistry and Bioinformatics
Publisher : UI Scholars Hub

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The emergence of β-lactamase–producing Gram-negative bacteria represents a major global challenge due to increasing resistance to β-lactam antibiotics. In this study, we performed in silico structural and functional prediction of a newly identified β-lactamase protein sequence obtained from a Gram-negative bacterial isolate. Homology modeling was used to construct a reliable 3D model of the protein based on structurally resolved β-lactamases. The model was further evaluated using stereochemical validation parameters. Molecular docking was conducted to assess binding affinity and interaction patterns between the predicted β-lactamase and clinically relevant β-lactam antibiotics, including ampicillin, cefotaxime, and imipenem. The results revealed conserved catalytic residues typical of class A β-lactamases, strong binding affinities toward penicillin and cephalosporin substrates, and key hydrogen bond interactions within the active site. This study provides a structural framework for understanding the function of the new β-lactamase and offers insights for developing β-lactamase inhibitors targeting resistant Gram-negative pathogens.
Co-Authors Abiyyi, Mohammad Wildan Ariyani Kiranasari Arleni Bustami Aryo Tedjo Atmaja, Fredy Wirya Candraningrum, Veronica Hesti Dwi Anita Suryandari El Bayani, Gulshan Fahmi Erlina, Linda Fadilah Fadilah, Fadilah Fadillah Fadillah Fajrin, Ajeng M. Fatriansyah, Jaka Fajar Isbandiputri, Swarnasari Nurandita Kristanty, Diyah Kusmardi Kusmardi Luluk Yunaini Merizka, Engla Paramita, Rafika Indah Puji Sari Purwamita Budiutami, Khoirunnisa Raden Muharam Natadisastra Rawina Winita Rizal Subahar Soejono, Alice Hari Sri Suryo Adiyanti, Sri Suryo Trijayani, Trijayani