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All Journal Journal of the Medical Sciences (Berkala Ilmu Kedokteran) The Journal of Pure and Applied Chemistry Research Biology, Medicine, & Natural Product Chemistry Majalah Obat Tradisional Public Health of Indonesia Jurnal Surya Medika Jurnal SOLMA JMM (Jurnal Masyarakat Mandiri) Pharmacology and Clinical Pharmacy Research Jurnal Ilmu Kefarmasian Indonesia Science Midwifery Jurnal Mandala Pengabdian Masyarakat Journal SAGO Gizi dan Kesehatan Journal of Experimental and Clinical Pharmacy (JECP) Sasambo Journal of Pharmacy Jurnal Pengabdian Ilung (Inovasi Lahan Basah Unggul)
Ysrafil, Ysrafil
Departemen Farmakoterapi, Fakultas Kedokteran, Universitas Palangka Raya
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siRNAs targeting icaD Gene of Staphylococcus aureus to Inhibit Biofilm Formation: Structural Analysis and Efficacy Dinda Ananda Sulistina; Rian Ka Praja; Margaretha Yayu Indah Anugerahny; Hanasia Hanasia; Ysrafil Ysrafil
Biology, Medicine, & Natural Product Chemistry Vol 14, No 2 (2025)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14421/biomedich.2025.142.921-926

Abstract

Antibiotic resistance in Staphylococcus aureus infections, especially those involving biofilm formation, is a global health issue. Biofilm protects bacteria from the immune system and antibiotic treatment, making them 10 to 1000 times more resistant. The icaD gene, part of the ica operon, is crucial for biofilm synthesis by enhancing the enzymes responsible for forming the biofilm matrix. The icaD gene sequence of Staphylococcus aureus was obtained from the GenBank NCBI database with the accession code CP140612.1, with a gene sequence length of 306 bp and employed several bioinformatics methods, including siDirect for designing and evaluating effective siRNA sequences to select the most promising candidates. Additionally, siRNA Scales, MaxExpect, Duplex Fold, and siPred were employed to analyze the siRNA sequence length, secondary structure, binding energy, and efficacy predictions of siRNAs targeting the icaD gene. The study found that out of 54 siRNA candidates, siRNA22, siRNA50, and siRNA25 achieved inhibition rates of 93.69%, 92.82%, and 92.52%, respectively. These results bioinformatically demonstrated their potential to suppress the expression of the icaD gene and highlight their promise as siRNA-based antibacterial therapies to combat biofilm-related infections. The designed siRNA computationally shows potential as an innovative therapy to combat biofilm infections caused by Staphylococcus aureus.
The Antivirulence Mechanisms of Phytate Against Pathogenic Bacteria in Skin Infections Nabilatul Zhofiroh; Rian Ka Praja; Elsa Trinovita; Ysrafil Ysrafil; Ranintha BR Surbakti
Biology, Medicine, & Natural Product Chemistry Vol 14, No 2 (2025)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14421/biomedich.2025.142.731-738

Abstract

Skin infections caused by the bacteria Staphylococcus aureus, Streptococcus pyogenes, and Propionibacterium acnes are often a common health problem. One treatment is antibiotics, but the cases of antibiotic resistance are increasing. Thus, new treatment alternatives are needed. This study aimed to analyze the molecular mechanism of phytate antivirulence against pathogenic bacteria of skin infection. This study used a bioinformatics approach involving analysis of phytate interactions with bacterial virulent proteins via STITCH, functional classification of proteins with VICMpred, and prediction of virulence properties using VirulentPred. B-cell and MHC epitopes were analyzed using IEDB, while protein subcellular location was determined through PSORTb. The results showed that phytate interacted specifically with virulent proteins in all three bacteria, most of which functioned in cellular and metabolic processes. These virulent proteins also have immunologically relevant epitopes. Subcellular location analysis showed that phytate protein targets were dispersed in the cytoplasmic membrane and cytoplasm. These findings indicated that phytate has a significant antivirulence mechanism by targeting virulent proteins of skin pathogenic bacteria, thus potentially becoming a therapeutic agent to treat skin infections while reducing antibiotic resistance.
Bioinformatics Analysis of Quercetin and Morin Bioactivity from Morinda citrifolia L. Targeting Streptococcus mutans Virulence Factors In Dental Caries Cases Astrid Ekklesia Saputri; Rian Ka Praja; Agnes Frethernety; Oktaviani Naulita Turnip; Ysrafil Ysrafil
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.2026.151.535-553

Abstract

Dental caries remains one of the most neglected oral diseases, particularly among populations living far from healthcare services. Its pathogenesis is largely triggered by poor oral hygiene and the activity of Streptococcus mutans. The use of synthetic antimicrobial agents often leads to prolonged side effects and a higher risk of antibiotic resistance. As an alternative, Morinda citrifolia L. extract shows high potential due to its good public acceptance, minimal side effects, and proven in vitro efficacy in inhibiting S. mutans growth. This study aimed to investigate the bioactivity factors of S. mutans in relation to specific components of Morinda citrifolia L. as an alternative therapeutic agent for dental caries using a bioinformatics-based approach. A descriptive-exploratory bioinformatics method was employed using computational analysis. The bacterial FASTA sequence of Streptococcus mutans UA159 was retrieved from the National Center for Biotechnology Information (NCBI) database and analyzed using several software tools, including STITCH v5.0, VICMPred, VirulentPred, BepiPred v1.0, MHC I and MHC II BindingPred, and PSORTb v3.0. The analysis revealed notable interactions in bioactivity between S. mutans proteins and the phytocompounds quercetin and morin. Seven virulent proteins PknB, SMU_1806, SMU_1213c, SMU_922, SMU_906, SMU_525, and SMU_1078c, contribute to cellular process, metabolism, virulence factors, and information & storage. Five proteins were identified in the cytoplasmic membrane, one in cell wall, and also cytoplasm. Quercetin and morin demonstrated strong antibacterial potential against S. mutans through interactions with virulent proteins. PknB, SMU_906, and SMU_1078c stand out in epitope T cell analysis with high affinity, demonstrating the ability to provoke an adaptive immune system response. Location complexity of 5’-nucleotide enzyme targeted by strategic antimicrobials leads to bacterial mortality.
Co-Authors Agnes Frethernety Agnes Frethernety Ahmad Sukrianur Alayya Adistia Putri Alexandra, Francisca Diana Andra Ari P., Eko Marwanto Heru Mulyantoro Dwi Hermayantiningsih Angeline Novia Toemon, Angeline Novia Ardi Sandriya Astrid Ekklesia Saputri Dali Dali Damiti, Sukmawati A Damiti, Sukmawati Ahmad Denny Indra Setiawan Desyandri Desyandri Dinda Ananda Sulistina Elsa Trinovita Erwin Prasetya Toepak Erwin Prasetya Toepak Fariz Noorrahman, Nabil Fatmaria Fatmaria Fatmaria, Fatmaria Fihrina Mohamad Francisca Diana Alexandra Frethernety, Agnes Hakim, Muh. Supwatul Halisa, Nida Hanasia , Hanasia Hanasia Hanasia Hanasia Hanasia Hanasia, Hanasia Harlyanti Muthma'innah Mashar Hartati Hartati Hartati Hartati Havid, Husnul Indwiani Astuti Irmawan, Muhammad Ishak, Pratiwi Ismail Ismail Komara, Nisa Kartika Margaretha Yayu Indah Anugerahny Marvin Horale Pasaribu Mashar, Harlyanti Muthma’innah Miranti Maya Sylvani Muhammad Irmawan Nabilatul Zhofiroh Natalia Sri Martani Oktaviani Naulita Turnip Oktriani R Permatasari, Silvani PRISCA SAFRIANI WICITA Rahman, Sudarman Rahmawati Halim Rahmawati, Rahmawati Ranintha BR Surbakti Remi Ayu Pratika Rian Ka Praja Sari, Meiyanti Ratna Kumala Sa’adah N Sinuhaji, Masira Sony Crespo Sirait, Christine Sofia Mubarika Haryana Stevin Carolius Angga Sukmawati A. Damiti Sukmawati Damiti Syamsul Thalib Teguh Aryandono Tesalonika, Lidya Toemon, Agnes Immanuela Torizal GF Turnip, Oktaviani Naulita Valencia, Regina Vyani Kamba Wardana T Yuliana Yusuf, Ghaitsa Zahira Sopha Zaenal Abidin