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All Journal Biology, Medicine, & Natural Product Chemistry Journal of Natural Sciences and Mathematics Research Abdimas Galuh: Jurnal Pengabdian Kepada Masyarakat Jurnal Abdimas Ilmiah Citra Bakti (JAICB) SIMBIOSA Jurnal Pijar MIPA BIO-CONS: Jurnal Biologi dan Konservasi Jurnal Bioteknologi & Biosains Indonesia (JBBI) Jurnal Bioteknologi & Biosains Indonesia
Rochmad Krissanjaya
Department Of Medical Laboratory Technology, Faculty Of Health Sciences, Kadiri University, Jalan Selomangleng No. 1, Kediri, East Java, Indonesia
Agriculture, Biological Sciences & Forestry Arts Humanities Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Computer Science & IT Decision Sciences, Operations Research & Management Economics, Econometrics & Finance Education Energy Environmental Science Health Professions Languange, Linguistic, Communication & Media Law, Crime, Criminology & Criminal Justice Materials Science & Nanotechnology Mathematics Medicine & Pharmacology Nursing Physics Public Health Social Sciences

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In Silico Molecular Docking and ADMET Evaluation of Active Compounds from Acalypha indica L. Against the HER2 Breast Cancer Target Lisa Savitri; Kharisul Ihsan; Elfred Rinaldo Kasimo; Rochmad Krissanjaya
Biology, Medicine, & Natural Product Chemistry Vol 15, No 1 (2026)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14421/biomedich.2026.151.45-51

Abstract

Breast cancer is one of the leading causes of cancer-related mortality in women worldwide, and overexpression of human epidermal growth factor receptor 2 (HER2) is associated with aggressive tumor progression, poor prognosis, and treatment resistance. Natural compounds are increasingly explored as safer anticancer candidates due to their structural diversity and lower toxicity profiles. Acalypha indica L., a traditional medicinal plant widely used in Asia, contains numerous phytochemicals with reported antioxidant and cytotoxic activities. This study investigates the binding affinity and pharmacokinetic potential of major A. indica phytochemicals against HER2 using in silico molecular docking and ADMET predictions. Twelve bioactive compounds were selected: quercetin, kaempferol, luteolin, rutin, isoquercitrin, caffeic acid, ferulic acid, esculetin, lupeol, beta-sitosterol, stigmasterol, and acalyphin. Docking was performed using AutoDock Vina against HER2 (PDB ID: 3PP0). Kaempferol (-10.2 kcal/mol), quercetin (-9.8 kcal/mol), and luteolin (-9.3 kcal/mol) showed the highest affinity, interacting strongly with key residues within the HER2 ATP-binding pocket. ADMET analysis indicated that kaempferol, quercetin, and luteolin possessed favorable oral bioavailability and safety characteristics. These findings suggest that A. indica contains promising HER2-targeting phytochemicals that warrant further investigation through in vitro and in vivo studies.
In Silico Discovery of Potent LpxC-Binding Compounds from Paederia foetida (Daun Kentut) as Promising Candidates against Gram-Negative Bacterial Infections Lisa Savitri; Kharisul Ihsan; Elfred Rinaldo Kasimo; Rochmad Krissanjaya
Biology, Medicine, & Natural Product Chemistry Vol 15, No 1 (2026)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14421/biomedich.2026.151.749-755

Abstract

The increasing prevalence of multidrug-resistant Gram-negative bacteria necessitates the discovery of novel antibacterial agents targeting essential bacterial enzymes. Lipopolysaccharide biosynthesis enzyme LpxC represents a promising target due to its critical role in maintaining bacterial outer membrane integrity and its absence in mammalian cells. This study aimed to identify potential LpxC inhibitors derived from Paederia foetida (Daun Kentut) using an integrated in silico approach. Bioactive compounds reported from P. foetida were subjected to molecular docking against LpxC, followed by protein–ligand interaction analysis, molecular dynamics simulations, binding free energy calculations, and ADMET prediction. Docking results revealed that several compounds exhibited strong binding affinity toward the LpxC active site, with PF-01 showing the most favorable binding energy (-9.2 kcal/mol) and stable zinc coordination. Molecular dynamics simulations confirmed the structural stability of the PF-01–LpxC complex, as indicated by low RMSD and RMSF values throughout 100 ns simulation. MM/PBSA analysis demonstrated that van der Waals and electrostatic interactions were the dominant contributors to binding stability. ADMET prediction suggested that while PF-01 showed slightly limited drug-likeness due to molecular size, it remained non-toxic and pharmacologically acceptable. Overall, this study provides molecular-level evidence supporting P.foetida as a promising natural source of LpxC-targeting compounds and proposes PF-01 as a potential lead candidate for further experimental validation against Gram-negative bacterial infections.
Molecular Interaction Mapping of Paederia foetida Phytochemicals against NF-kB p65 Highlights Their Potential in Modulating Systemic Inflammation Lisa Savitri; Kharisul Ihsan; Elfred Rinaldo Kasimo; Rochmad Krissanjaya
Biology, Medicine, & Natural Product Chemistry Vol 15, No 1 (2026)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14421/biomedich.2026.151.757-762

Abstract

Systemic inflammation is a fundamental pathological process involved in the development of various chronic diseases, with nuclear factor kappa B (NF-kB) p65 acting as a central transcriptional regulator of inflammatory responses. Paederia foetida L., commonly known as Daun Kentut, has been traditionally used as an anti-inflammatory medicinal plant; however, its molecular mechanisms of action remain poorly understood. This study aimed to investigate the molecular interactions between selected P. foetida phytochemicals and the NF-kB p65 protein using an in silico approach. Molecular docking was performed to evaluate binding affinity and interaction profiles of major phytochemical constituents, including flavonoids, iridoid glycosides, and phenolic acids. The docking results revealed that several compounds exhibited favorable binding energies and stable interaction patterns with key amino acid residues of NF-kB p65, such as Lys221, Arg246, Ser276, and Glu279. Among the tested compounds, quercetin and asperuloside demonstrated strong binding affinity and multiple hydrogen bonds within the transcriptionally active region of NF-kB p65. These interaction profiles were comparable to those of a reference inhibitor. The findings suggest that P. foetida phytochemicals have the potential to modulate NF-?B–mediated inflammatory signaling at the molecular level. This study provides mechanistic support for the traditional use of P. foetida as an anti-inflammatory agent and highlights its potential as a source of natural compounds for the development of inflammation-modulating therapeutics.
Computational Evaluation of Antibacterial Activity of Acalypha indica L. Phytochemicals Against Staphylococcus aureus DNA Gyrase Lisa Savitri; Kharisul Ihsan; Elfred Rinaldo Kasimo; Rochmad Krissanjaya
Biology, Medicine, & Natural Product Chemistry Vol 15, No 1 (2026)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14421/biomedich.2026.151.451-455

Abstract

This study investigated the antibacterial potential of phytochemical compounds derived from Acalypha indica L. against the DNA gyrase of Staphylococcus aureus using an in silico computational approach. Phytochemical structures were collected from established compound databases and subjected to geometry optimization to ensure conformational stability before molecular docking analysis. Docking simulations were carried out using AutoDock Vina to evaluate the binding affinity and interaction profiles of each ligand with the ATP-binding domain of DNA gyrase, a critical enzyme involved in bacterial DNA replication. The three-dimensional structure of S. aureus DNA gyrase was obtained from the Protein Data Bank and prepared through removal of water molecules, addition of polar hydrogens, and refinement of active-site residues. Among the screened ligands, five compounds exhibited strong predicted affinities, with binding energies ranging from -6.8 to -9.1 kcal/mol. Compound C demonstrated the most favorable interaction, forming stable hydrogen bonds and extensive hydrophobic contacts within the catalytic pocket, suggesting a strong inhibitory potential. Compound E also showed a high affinity, although its orientation within the binding site was slightly less optimal. ADMET predictions indicated that all top candidates satisfied drug-likeness criteria, showed good absorption potential, and presented low toxicity risks. Overall, the findings highlight that Acalypha indica L. contains bioactive constituents with promising inhibitory activity against bacterial DNA gyrase. These results support the traditional use of the plant in antimicrobial applications and provide a foundation for further experimental validation through in vitro enzyme inhibition assays and in vivo studies to confirm their therapeutic relevance.
The Role of the NF-kB Pathway and Oxidative Stress Markers in the Protective Effects of Peperomia pellucida in a Gastroenteritis Model Lisa Savitri; Fendy Prasetyawan; Yuneka Saristiana; Elfred Rinaldo Kasimo; Rochmad Krissanjaya; Cornelia Amanda; Konradus Klala Mebung
Biology, Medicine, & Natural Product Chemistry Vol 15, No 1 (2026)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14421/biomedich.2026.151.803-808

Abstract

Gastroenteritis is a common gastrointestinal disorder characterized by intestinal inflammation, epithelial damage, and oxidative stress. Activation of the nuclear factor kappa B (NF-kB) signaling pathway and excessive production of reactive oxygen species play key roles in its pathogenesis. Peperomia pellucida is a medicinal plant traditionally used for inflammatory and gastrointestinal conditions; however, its molecular mechanisms of action remain poorly understood. This study aimed to investigate the protective effects of P. pellucida extract in an experimental gastroenteritis model, with a particular focus on NF-kB pathway modulation and oxidative stress markers. Gastroenteritis was induced in experimental animals, followed by oral administration of P. pellucida extract at different doses. NF-kB p65 expression was assessed using molecular analysis, while oxidative stress was evaluated through malondialdehyde levels and antioxidant enzyme activities, including superoxide dismutase and catalase. Histopathological examination of intestinal tissue was also performed. The results demonstrated that P. pellucida treatment significantly suppressed NF-kB p65 activation, reduced lipid peroxidation, restored antioxidant enzyme activities, and improved intestinal histopathological features compared to the untreated gastroenteritis group. These findings indicate that P. pellucida confers intestinal protection by attenuating inflammation and oxidative stress, supporting its potential as a natural therapeutic agent for gastroenteritis.
Prediction of Interaction and Stability of Bioactive Compounds from Acalypha indica L. with Acetylcholinesterase as Alzheimer’s Drug Candidates: A Docking and Molecular Dynamics Study Lisa Savitri; Kharisul Ihsan; Rochmad Krissanjaya; Elfred Rinaldo Kasimo
Biology, Medicine, & Natural Product Chemistry Vol 15, No 1 (2026)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14421/biomedich.2026.151.679-684

Abstract

Alzheimer’s disease remains one of the most challenging neurodegenerative disorders, with acetylcholinesterase (AChE) inhibition serving as a key therapeutic strategy. This study evaluated the interaction profiles and dynamic stability of bioactive compounds from Acalypha indica L. as potential AChE inhibitors using molecular docking and molecular dynamics simulations. Candidate compounds were screened for drug-likeness through SwissADME and toxicity predictions using ProTox-II. Docking results identified Compound A as the strongest binder, showing a favorable binding energy of -9.2 kcal/mol and forming stable interactions with catalytic and peripheral residues of AChE. A 100-ns molecular dynamics simulation demonstrated the stability of the protein-ligand complex, supported by consistent RMSD and radius of gyration values. Residue-level flexibility analysis revealed minimal fluctuations in the active site, and hydrogen-bond monitoring indicated persistent interactions throughout the simulation. MM-PBSA calculations yielded a binding free energy of -32.4 ± 3.1 kcal/mol, with van der Waals contributions dominating the interaction. These findings suggest that Compound A is a promising lead candidate for further experimental validation as an AChE inhibitor and may contribute to the development of new therapeutic agents for Alzheimer’s disease.
Computational Profiling of Sapindus rarak (Lerak) Phytochemicals as Potential Antibacterial and Immunomodulatory Agents against Escherichia coli Lisa Savitri; Kharisul Ihsan; Elfred Rinaldo Kasimo; Rochmad Krissanjaya
Biology, Medicine, & Natural Product Chemistry Vol 15, No 1 (2026)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14421/biomedich.2026.151.639-644

Abstract

Antibiotic resistance in Escherichia coli continues to rise, creating an urgent need for new antibacterial candidates with novel mechanisms of action. Sapindus rarak contains diverse phytochemicals, including saponins, flavonoids, and triterpenoids, yet the molecular basis of their biological activity remains poorly understood. This study aimed to profile the antibacterial and immunomodulatory potential of major S. rarak compounds using a computational approach. Twenty phytochemicals were collected from public databases and evaluated against three targets: E. coli DNA gyrase and DHFR, and human TLR4. Docking analysis identified rarasaponin A and B as the strongest gyrase binders, with binding energies of -9.8 and -9.6 kcal/mol. A 100-ns molecular dynamics simulation demonstrated stable interactions between rarasaponin A and gyrase, supported by consistent RMSD values and an MM–GBSA energy of approximately -42 kcal/mol. Flavonoids such as quercetin-3-O-glucoside showed preferential binding to TLR4 and were predicted to promote IL-10 induction with minimal TNF-alpha activation. ADMET predictions indicated more favorable pharmacokinetic properties for flavonoids than saponins. These findings support a dual-mechanism therapeutic model in which saponins act as antibacterial agents and flavonoids contribute to balanced immune modulation. Further experimental validation through in vitro and in vivo assays is recommended.
In Vivo Evaluation of the Antibacterial Activity of Sapindus rarak (Lerak) and Host Immunological Profiles in an Escherichia coli Infection Model Lisa Savitri; Kharisul Ihsan; Elfred Rinaldo Kasimo; Rochmad Krissanjaya
Biology, Medicine, & Natural Product Chemistry Vol 15, No 1 (2026)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14421/biomedich.2026.151.319-324

Abstract

This study evaluated the in vivo antibacterial activity of Sapindus rarak (lerak) extract and its effects on host immune responses during Escherichia coli infection. Lerak contains saponins and other bioactive compounds that have shown promising antimicrobial effects in vitro, but in vivo evidence remains limited. Male BALB/c mice were assigned to healthy, infected control, and three treatment groups receiving low, medium, or high doses of lerak extract. All infected groups were orally challenged with pathogenic E. coli and treated for seven days. Clinical signs, bacterial load, cytokines, immunoglobulin levels, and tissue histopathology were assessed. Mice in the infected control group developed weight loss, diarrhea, and systemic signs of infection, whereas those receiving lerak extract showed milder symptoms, especially at higher doses. Lerak significantly reduced bacterial counts in intestinal and systemic tissues, with the strongest effect in the high-dose group. Treatment also decreased pro-inflammatory cytokines (TNF-alpha, IL-6) and increased IL-10, indicating a shift toward controlled inflammation. Serum IgA levels were elevated in treated mice, suggesting enhanced mucosal protection. Histopathology confirmed reduced epithelial damage and inflammatory infiltration in the intestine, liver, and spleen. These findings suggest that lerak extract exerts both antibacterial and immunomodulatory effects in vivo. Its dual activity highlights its potential as a plant-derived therapeutic candidate for managing enteric infections caused by E. coli. Further fractionation and mechanistic studies are warranted to identify active compounds and clarify biological pathways involved.
Regulation of CD4+ and CD8+ T Cell Responses by Extract of Male Papaya Leaves (Carica papaya L.) in Experimental Autoimmune Disease Lisa Savitri; Kharisul Ihsan; Elfred Rinaldo Kasimo; Rochmad Krissanjaya
Biology, Medicine, & Natural Product Chemistry Vol 15, No 1 (2026)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14421/biomedich.2026.151.809-813

Abstract

Autoimmune diseases are characterized by dysregulated adaptive immune responses, particularly involving CD4+ and CD8+ T lymphocytes. Current therapeutic strategies often rely on broad immunosuppression, which may lead to adverse effects and increased susceptibility to infections. Therefore, the exploration of natural immunomodulatory agents remains an important research focus. This study aimed to evaluate the regulatory effects of male papaya leaf extract (Carica papaya L.) on CD4+ and CD8+ T cell responses in an experimental autoimmune disease model. Male papaya leaves were extracted using 70% ethanol and administered orally to autoimmune disease-induced mice at different dosage levels. T cell populations were analyzed using flow cytometry, focusing on CD4+ and CD8+ T cell proportions in splenocytes. The results showed that experimental autoimmune disease significantly increased CD4+ T cell levels and reduced CD8? T cell proportions compared to normal controls. Treatment with male papaya leaf extract led to a dose-dependent reduction in CD4+ T cells and restoration of CD8+ T cell levels. The highest dose produced a T cell profile comparable to that of healthy animals. These findings indicate that male papaya leaf extract modulates adaptive immune responses by rebalancing CD4+ and CD8+ T cell populations rather than inducing broad immunosuppression. The study highlights the potential of male papaya leaf extract as a natural immunomodulatory agent for the management of autoimmune diseases and supports further investigation into its underlying mechanisms and clinical relevance.
In Silico Study of Bioactive Compounds from Acalypha indica L. Interacting with the COX-2 Receptor as Potential Anti-Inflammatory Candidates Lisa Savitri; Kharisul Ihsan; Rochmad Krissanjaya; Elfred Rinaldo Kasimo
Biology, Medicine, & Natural Product Chemistry Vol 15, No 1 (2026)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14421/biomedich.2026.151.31-37

Abstract

Acalypha indica L. is a medicinal herb traditionally used across Asia for treating inflammation-related conditions. Although several studies report anti-inflammatory activity in its extracts, little is known about the molecular interaction of its individual phytochemicals with cyclooxygenase-2 (COX-2)—a validated therapeutic target for inflammatory diseases. This study fills this gap by performing a comprehensive in silico analysis of 20 major bioactive compounds of A. indica using molecular docking, binding interaction profiling, and ADMET predictions. Docking against the COX-2 receptor (PDB: 3LN1) using AutoDock Vina revealed that rutin (-10.4 kcal/mol), kaempferol-3-O-rutinoside (-10.1 kcal/mol), quercetin (-9.6 kcal/mol), and luteolin (-9.3 kcal/mol) demonstrated strong predicted affinity and stable interactions with key residues Arg120, Tyr355, and Tyr385, comparable to celecoxib (-10.8 kcal/mol). ADMET profiling showed that aglycone flavonoids possessed more favorable drug-likeness properties than glycosides. These results suggest that A. indica contains multiple promising lead compounds for future COX-2 inhibition studies and highlight the molecular mechanisms supporting its ethnomedicinal use as an anti-inflammatory agent.
Co-Authors Akbar Nur Kholis Alves, Silvina Sandra X. Amanda, Cornelia Anjarwati, Aprilia Antoro, Ester Lianawati Apriana, Dita Cornelia Amanda Datin An Nisa Sukmawati Datin An Nisa Sukmawati Dhony Hermanto Elfred Rinaldo Kasimo Elfred Rinaldo Kasimo Elfred Rinaldo Kasimo Elfred Rinaldo Kasimo Elfred Rinaldo Kasimo, Elfred Rinaldo Ester Lianawati Antoro Fendy Prasetyawan Fitri, Devi Nor Freitas, Maria Do Carmo Da Costa Hilmi, Mochammad Hanif Ida Septika Wulansari Ihsan, Kharisul Juwita, Syntia Tanu Kharisul Ihsan Kholis, Akbar Nur Konradus Klala Mebung Laili, Nur Fahma Lisa Savitri Loviana, Novi Masyhuri, Aga Adi Mebung, Konradus Klala Mochamad Hanif Hilmi Mochamad Hanif Hilmi Mosse1, Yosep Muttaqin, Saiful Neni Probosiwi Novirma Yanti Novirma Yanti Nurul Ismillayli Rasyadan Taufiq Probojati Retnowati, Ana Syntia Tanu Juwita Syntia Tanu Juwita Tiyas, Eka Wahyuning Tsamrotul Ilmi Wulansari, Ida Septika Yosep Mosse1 Yuneka Saristiana