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All Journal Eksakta : Berkala Ilmiah Bidang MIPA Indonesian Journal of Medical Chemistry and Bioinformatics Eduvest - Journal of Universal Studies
Surya Dwira
Department Of Medical Chemistry, Faculty Of Medicine, Universitas Indonesia, Jakarta, Indonesia
Aerospace Engineering Agriculture, Biological Sciences & Forestry Astronomy Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Civil Engineering, Building, Construction & Architecture Computer Science & IT Energy Engineering Environmental Science Health Professions Materials Science & Nanotechnology Mathematics Mechanical Engineering Neuroscience Social Sciences

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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 Vol. 4, No. 2
Publisher : UI Scholars Hub

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Abstract

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.
Larvicidal activity of β-asarone and Acorus calamus Linn. (sweet flag) extract against Aedes aegypti (Dipotera: Culicidae): Enzyme inhibition, midgut histopathology, and in silico analysis Subahar, Rizal; Dwira, Surya
Indonesian Journal of Medical Chemistry and Bioinformatics Vol. 4, No. 2
Publisher : UI Scholars Hub

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Aedes aegypti (Diptera: Culicidae), the primary vector of dengue, poses a significant public health threat in tropical and subtropical regions. Botanical insecticides and phytochemicals such as β- asarone, derived from essential oils,offer a promising alternative to synthetic larvicides. The rhizome of Acorus calamus L. (sweet flag), traditionally known for its neuroprotective and antioxidant properties, contains β-asarone as its principal bioactive constituent.This study evaluated the larvicidal efficacy of β-asarone and A. calamus rhizome extract against Ae. aegypti larvae, focusing on detoxification enzyme inhibition, midgut histopathology, and in silico molecular interactions.Third- and fourth-instar larvae were exposed to β-asarone and crude extract at concentrations ranging from 0.25 to 24.25 μg/mL. Larval mortality was recorded at 24, 48, and 72 hours post-exposure following WHO guidelines. Activities of acetylcholinesterase (AChE), glutathione-S-transferase (GST), and oxidase were measured using biochemical assays. Midgut histopathological changes were assessed via hematoxylin and eosin staining. Molecular docking (CB-Dock2) was used to evaluate β-asarone interactions with AChE, GST, and oxidase. β-asarone showed significantly higher larvicidal potency (LC₅₀ = 6.768 μg/mL) than the crude extract (LC₅₀ = 54.566 μg/mL). Both treatments markedly inhibited AChE and oxidase and caused extensive midgutdamage, including epithelial degeneration, ruptured peritrophic membrane, and loss of microvilli. These results demonstrate the potential of β-asarone as plant-derived larvicides acting through enzymatic inhibition and midgut disruption, offering a promising strategy for mosquito control.
In Silico Molecular Docking Study Of Antidiabetic Bioactive Compounds From Brotowali (Tinospora cordifolia) Targeting GLUT4 In Type II Diabetes Mellitus Tarigan, Gita Euaggelion; Dwira, Surya
Indonesian Journal of Medical Chemistry and Bioinformatics Vol. 4, No. 2
Publisher : UI Scholars Hub

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Abstract

Type 2 diabetes mellitus (T2DM) is a global metabolic disorder characterized by insulin resistance and impaired glucose uptake. Despite the availability of pharmacological therapies, limitations such as adverse effects and high costs highlight the need for alternative therapeutic candidates. Tinospora cordifolia has been widely reported to contain bioactive compounds with antidiabetic potential; however, comparative evaluation of their interaction with glucose transporter type 4 (GLUT4) remains limited. This study aimed to identify the most promising bioactive compounds from Tinospora cordifolia targeting GLUT4 using an in silico molecular docking approach, followed by pharmacokinetic and toxicity (ADMET) prediction. Molecular docking was performed using Molegro Virtual Docker with GLUT4 (PDB ID: 7WSM), and six ligands retrieved from the PubChem database. Model validation was conducted using redocking with RMSD < 2 Å. The results demonstrated that hesperetin 7-rhamnoglucoside, verbascoside, and cyanidin 3-O-sambubiosyl 5-O-glucoside exhibited stronger binding affinities than the native ligand, with rerank scores of −137.228, −132.756, and −131.726 kJ/mol, respectively. These compounds formed stable hydrogen bonds with key residues, including Asn176, Gln298/Gln299, and Trp404/Trp428. ADMET analysis indicated that hesperetin 7-rhamnoglucoside and verbascoside possessed more favorable pharmacokinetic profiles with relatively low toxicity risks. In conclusion, hesperetin 7-rhamnoglucoside and verbascoside are identified as the most promising candidates for GLUT4-targeted antidiabetic therapy. These findings provide a computational basis for further experimental validation in the development of novel antidiabetic agents.
Co-Authors Abiyyi, Mohammad Wildan Anwar S. Ibrahim 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 Fadillah Fadillah Fajrin, Ajeng M. Fatriansyah, Jaka Fajar Isbandiputri, Swarnasari Nurandita Kristanty, Diyah Kusmardi Kusmardi Linda Erlina Luluk Yunaini Merizka, Engla Nur Ayu Ramadanti Paramita, Rafika Indah Puji Sari Purwamita Budiutami, Khoirunnisa Rafika Indah Paramita Rawina Winita Rino Patiatta Rizal Subahar Soejono, Alice Hari Sri Suryo Adiyanti, Sri Suryo Tarigan, Gita Euaggelion Windy Dwininda