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All Journal HAYATI Journal of Biosciences Microbiology Indonesia BIOTROPIA - The Southeast Asian Journal of Tropical Biology Pharmaciana: Jurnal Kefarmasian Indonesian Journal of Biotechnology Sari Pediatri Paediatrica Indonesiana Belitung Nursing Journal Indonesian Journal of Chemistry Biota Jurnal Ilmu Kefarmasian Indonesia Pharmaceutical Sciences and Research (PSR) Makara Journal of Science
Amarila Malik
Faculty Of Pharmacy, Universitas Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Earth & Planetary Sciences Education Environmental Science Health Professions Immunology & microbiology Materials Science & Nanotechnology Medicine & Pharmacology Nursing Public Health Veterinary

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The development of papain‐like protease from SARS‐CoV‐2, a potential drug target for antiviral screening: A review Riswanto Napitupulu; Is Helianti; Maimunah Maimunah; Fairuz Andini Fatiningtyas; Amarila Malik
Indonesian Journal of Biotechnology Vol 28, No 3 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.83376

Abstract

The SARS‐CoV‐2 outbreak caused a global pandemic, claiming numerous lives and becoming this century’s most widespread life‐threatening disease. The virus relies on two specific enzymes to facilitate replication, 3‐chymotrypsin‐like protease (3CLPro) and papain‐like protease (PLpro). These enzymes are crucial in breaking down nonstructural polypeptides into functional proteins. PLpro with LXGG↓X recognition and cleavage sites also play a role in deubiquitylase (DUB) and delSGylase by cleaving after the double glycine residue of ubiquitin (Ub) and ISG15 as a mechanism to suppress the host’s innate immune response. Despite its important role in the viral infection cycle and the potential for drug discovery, no antivirals have been approved as PLpro inhibitors. Therefore, this review focuses on PLpro protein, its recombinant product development and purification, and its application as a protein target in drug discovery for COVID‐19 screening to develop effective COVID‐19 drugs.
Clinical profile, treatment, and outcomes of patients with COVID-19 in a tertiary referral hospital in South Sumatera, Indonesia: A retrospective single-center study Deli Marteka; Amarila Malik; Ingrid Faustine; Nadia Farhanah Syafhan
Belitung Nursing Journal Vol. 8 No. 6 (2022): November - December
Publisher : Belitung Raya Foundation, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33546/bnj.2302

Abstract

Background: Although there are fewer COVID-19 cases in Indonesia, the pandemic is still ongoing. COVID-19 has a significant death rate in Indonesia, but lack of information on the effect of different clinical and demographic factors on COVID-19-related grimness and mortality in Indonesia. Objective: This study examined the clinical profile, treatment, and outcomes of patients with COVID-19 at Lahat Regency Hospital in South Sumatera, Indonesia, to find relevant markers that might be utilized to predict the prognosis of these patients. Methods: This was a retrospective single-center study of all medical record files of confirmed patients with COVID-19 admitted to Lahat Hospital from September 2020 to August 2021 (n = 285). Descriptive statistics, Chi-square, Mann-Whitney, Multiple Logistic Regression, and Cox's proportional hazards model were used for data analyses. Results: This study included 65 non-hospitalized and 220 hospitalized patients. Hospitalized patients were divided into dead and alive groups. The median age was lower in the non-hospitalized group without gender discrimination, and most hospitalized patients had comorbidities. Vital signs and clinical features were significantly different in hospitalized patients compared to non-hospitalized. The survival patients in the hospitalized group showed lower white blood cell (WBC), neutrophil percentages, and neutrophil-lymphocyte ratio (NLR) but higher lymphocyte and eosinophil. Non-survival patients had elevated alanine aminotransferase (ALT), blood urea nitrogen (BUN), creatinine, blood glucose, and potassium. The use of Favipiravir and Remdesivir was significant between the alive and dead groups. The mean hospital stay for all patients was 9.49 ± 4.77 days, while the median duration of hospital time was 10.73 ± 4.33 days in the survival group and 5.39 ± 3.78 days in the non-survival group. Multiple logistic regression analysis determined respiration rate, WBC, and BUN as predictors of survival. Conclusions: Age and comorbidities are significant elements impacting the seriousness of COVID-19. Abnormal signs in laboratory markers can be used as early warning and prognostic signs to prevent severity and death. Potential biomarkers at various degrees in patients with COVID-19 may also aid healthcare professionals in providing precision medicine and nursing.
PRODUKSI BETA-1,3 GLUKAN DARI Agrobacterium DAN AKTIVITAS PENYEMBUHAN LUKA TERBUKA PADA TIKUS PUTIH Kusmiati, Kusmiati; Rachmawati, Fitria; Siregar, Syafrida; Nuswantara, Sukma; Malik, Amarila
Makara Journal of Science Vol. 10, No. 1
Publisher : UI Scholars Hub

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Abstract

Production of beta-1,3 glucan from Agrobacterium and its wound healing activity on white rat. The objective of this study was to determine the activity of beta-1,3 glucan product extracted from local Agrobacterium sp Bro 1.2.1, both wild-type and mutant-type, on opened-wound healing process. Beta-1,3 glucan product was extracted by precipitation, and the purification was carried out by column chromatography as KCl gradient fractions. In this study, white Sprague Dawley rats were employed, and have been treated for opened-wound condition. Seven groups were performed in this experiment, i.e. the negative control, the positive control employing povidone iodine, the two groups of two commercial beta-1,3 glucan with 0,02 mg/4 cm2 each, and the last three groups of beta-1,3 glucan as the test group with 0,02 mg/4 cm2, 0,10 mg/4 cm2 and 0,50 mg/4 cm2, respectively. The result showed significant differences of wound-healing activity performing statistical analysis of the least significance between the negative control, the positive control, as well as the highest dose of the test group of beta-1,3 glucan, at the dose of 0,5 mg/4 cm2 (p<0.05).
ISOLASI DAN SKRINING MOLEKULER BAKTERI ASAM LAKTAT PEMBAWA GEN GLUKANSUKRASE DARI MAKANAN DAN MINUMAN MENGANDUNG GULA Malik, Amarila; Hermawati, Ajitya Kurnia; Hestiningtyas, Mahardhika; Radji, Maksum
Makara Journal of Science Vol. 14, No. 1
Publisher : UI Scholars Hub

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Abstract

Isolation and Molecular Screening of Glucansucrase Gene Harboring-Lactic Acid Bacteria. Exopolysaccharides (EPS) have been possessed to be used in pharmaceutical, cosmetic and food industries. Lactic acid bacteria (LAB) produce a wide variety of exopolysaccharides and carries sucrase genes glucansucrase/glucosyltransferase (gtf) and fructansucrase/fructosyltransferases (ftf) for EPS production. In this study, the isolation and screening of EPS producing-LAB (EPS-LAB) were carried out on modified de Mann-Rogosa-Sharpe (MRS) agar medium supplemented with 10% of sucrose on LAB isolated from various unique sugar containing-foods and -beverages originated from local sources. Besides obtaining EPS-LAB, this study aimed to screen for gtf gene as well as to molecular identify strains by using PCR technique. Degenerate primer pairs DegFor and DegRev which targeted the conserved region of gtf genes catalytic domain were used, whereas LABfw and LABrv were used to molecular identify strains using 16S rRNA gene. An approximately 660 base pairs (bp) amplicons which targeted gtf gene were obtained from 13 out of 16 srains chosen. Result from PCR of 16S rRNA gene identification on gtf positive strains revealed that all strains were molecular identified as LAB after DNA sequencing analysis by using blastn. A rare EPS-producing LAB were obtain i.e. Weissella. Strains obtained in this study are potential sources for exploring novel sucrase gene/s and obtain unique EPS polymer product/s.
Karakteristik Sel Punca Mesenkim yang Berasal dari Tali Pusat (Umbilical Cord Derived Mesenchymal Stem Cell/UCMSC) dari Macaca fascicularis dan Sekretomnya dalam Kondisi Hipoksia Dumingan, Alvian; Malik, Amarila; Rinendyaputri, Ratih; Utama, Hieronimus Adiyoga Nareswara; Sunarno, Sunarno; Purwaningtyas, Yoggi Ramadhani; Idrus, Hasta Handayani; Noverina, Rachmawati; Huda, Fathul; Faried, Ahmad
Biota Vol 17 No 1 (2024)
Publisher : Universitas Islam Negeri Mataram

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20414/jb.v17i1.492

Abstract

Mesenchymal Stem Cell (MSC) secretome has potential as a neuroprotective and neuroregenerative agent. It can have effects due to its paracrine factors, such as Brain Derived Neurotrophic Factor (BDNF) and Stromal-Cell Derived Factor-1 (SDF-1) which can be induced with hypoxia preconditioning. This compound may play a role in the treatment of neurological diseases. Stroke has become a neurological disease that contributes to high rates of mortality and morbidity worldwide. There have been several pre-clinical trials on animal stroke models using MSC secretomes from rats and humans, but no studies have been conducted on Non-Human Primate, such as Macaca fascicularis. This species has been widely used in biomedical research and part of it can be utilized for such studies which will reduce the cost of using human MSC. The results of this study, Umbilical Cord (UC)-MSCs of Macaca fascicularis have been successfully cultured and characterized in terms of phenotypic and differentiation. Hypoxia precondition was able to induce BDNF secretion up to 264 pg/mL and SDF-1 up to 666 pg/mL in the UCMSC secretome. Hypoxic preconditioning with 3% oxygen can induce the most optimal BDNF and SDF-1 secretion, compared to 1% and 5% hypoxia.
In Silico and In Vitro Inhibitory Activity of Indonesian Herbal Compound Extracts against SARS-COV-2 Recombinant Papain-Like Protease Fatiningtyas, Fairuz Andini; Napitupulu, Riswanto; Malik, Amarila; Helianti, Is
HAYATI Journal of Biosciences Vol. 32 No. 2 (2025): March 2025
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.32.2.356-366

Abstract

The SARS-CoV-2 papain-like protease (PLpro) is essential for viral replication and a promising target for drug discovery. This study explored the inhibitory potential of compounds from Indonesia herbals Butterfly pea flower (Clitoria ternatea L), Star fruit leaves (Averrhoa carambola L.), and Java plum leaves (Syzygium cumini (L.) Skeels) against PL pro through molecular docking and in vitro assays. The molecular docking method utilized the target protein PLpro (PDB ID: 7CMD), with the native ligand obtained from compounds identified in these plant extracts. The compounds were identified using the KNApSAcK database and analyzed for drug-likeness based on Lipinski's Rule of Five. The physicochemical characteristics affecting absorption, distribution, metabolism, excretion, and toxicity (ADMET) were determined using the pkCSM descriptor algorithm protocol. Validation was performed using the redocking method, achieving an RMSD score of 0.728 Å, which indicated validity (RMSD <2.0 Å). The results identified four ligands with the lowest binding affinities from these extracts: (-)-Epicatechin 3-O-gallate, folic acid, petunidin 3-glucoside, and ellagic acid, with binding scores of -8.6, -8.3, -7.1, and -7.1 kcal/mol, respectively. Prior to conducting the PLpro in vitro inhibition assay, a fluorescence-based inhibition assay was performed using Z-RLRGG-AMC as the substrate and GRL0617as the control inhibitor. All extracts were subjected to 70% ethanol maceration. The IC50 value of GRL0617 was 3.38 μM, while fluorescence tests showed that Java plum leaf extract exhibited the highest inhibition percentage at 66.10±3.22%. These findings indicate that all three plant extracts contain compounds capable of inhibiting PLpro activity.
Biotechnology-based therapy for stroke treatment: review Utama, Hieronimus Adiyoga Nareswara; Mariya, Sela Septima; Dumingan, Alvian; Putri, Ratih Rinendya; Sunarno, Sunarno; Malik, Amarila
JURNAL ILMU KEFARMASIAN INDONESIA Vol 22 No 2 (2024): JIFI
Publisher : Faculty of Pharmacy, Universitas Pancasila

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.35814/jifi.v22i2.1613

Abstract

Various therapeutic agents have been used to treat stroke. However, currently there is extensive exploration of new potential therapies for stroke involving novel signaling pathways and development of therapeutic agents through biotechnological approaches. This article examines the recent advances in stroke therapy using biotechnology-based drugs. We conducted a comprehensive search using specific keywords relating to Ischemic Stroke, ATMP, Peptide, Antibody, Stem Cells, and connected topics in the databases of Medline, Scopus, Web of Science, and Pubmed. The main focus of the selection criteria was on English-language literature that explored the relationship between Ischemic Stroke, ATMP, Peptide, Antibody, Stem Cells, and related factors. This article exhibits that numerous studies are being conducted and have demonstrated the use of biotechnology-based therapeutic agents for stroke, including tissue plasminogen activators, therapeutic peptides, microRNA, monoclonal antibodies, as well as stem cells. These therapeutic agents have not only been tested on test animals but have also been commenced to be tested in clinical studies or have obtained marketing approval for use in ischemic stroke patients. In conclusion, despite the limited number of approved drugs, advancements in biotechnology are poised to make them common adjunct treatments for stroke patients, not just for managing the disease but also for its cure and regenerative effects in survivors.
A NOVEL INTEGRON IN THE GENOME OF ESCHERICHIA COLI ISOLATED FROM INDONESIAN MONITOR LIZARD (VARANUS SPP). ESTI PUSPITASARI; ANTONIUS SUWANTO; AMARILA MALIK; WALTER ERDELEN
BIOTROPIA No. 16 (2001)
Publisher : SEAMEO BIOTROP

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (97.942 KB) | DOI: 10.11598/btb.2001.0.16.163

Abstract

The genotype of antibiotic resistance  in natural isolates of Escherichia coli was determined  through integron detection and  characterization of the associated antibiotic  resistance. E. coli SG2 isolated from Varanus salvator  of Java demonstrated  resistance  to spectinomycin (50ng/ml)  and streptomycin (SOng/ml). Integron detection indicated  that eight isolates out of nine E. coli  isolates possessed a conserved segment of the integron. Amplification of  the inserted cassette of the integron in this SG2 isolate yielded a 1-kb DNA fragment. Sequence analyses indicated that this fragment was homologous with aad gene, which confirmed  the resistance  to spectinomycin/streptomycin. This is the first report on the presence of integron in the E. coli isolated from the environment. Key words: Integron / antibiotic resistance / Escherichia coli
Three-dimensional microcarrier culture enhances secretome particle yield of human umbilical cord mesenchymal stem cells Utami, Emilia Rahmadaniah; Malik, Amarila; Rinendyaputri, Ratih; Kino-Oka, Masahiro; Yamamoto, Riku
Indonesian Journal of Biotechnology Vol 31, No 3 (2026)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.117286

Abstract

Human umbilical cord–derived mesenchymal stem/stromal cell (UC-MSC) secretome represents a promising cell-free approach for regenerative therapy; however, achieving a high-potency and a high-yield secretome in sufficient quantities remains a major challenge. This study compares conventional 2D monolayer culture with a 3D microcarrier-based system to evaluate their effects on secretome yield and characteristics. Secretome profiling included analysis of extracellular vesicle (EV)-related gene expressions (RAB27A, RAB27B, and RAB7A), nanoparticle concentration, and size distribution using nanoparticle tracking analysis (NTA). The results showed that RAB gene expression was reduced in the 3D system (0.52–0.75-fold relative to 2D), along with decreased cell proliferation. Despite this downregulation and a concurrent reduction in cellular proliferation, NTA revealed a higher particle concentration in 3D cultures (1.74 × 109 particles/mL) compared to 2D (7.30 × 108 particles/mL), with a broader size distribution. Although the 3D microcarrier culture limited UC-MSC expansion, it resulted in a higher concentration of extracellular vesicle-sized particles, supporting its potential as a platform for scalable secretome production.
Co-Authors 'Alawiyyah, Raden Zulfa Achmad Fariz Ahmad Baikuni Ahmad Baikuni Ahmad Faried Ajitya Kurnia Hermawati Amin Soebandrio Anandayu Nurfachtiyani ANDI YEHUDA Andiani Wanda Putri Anis Karuniawati Antonius Suwanto Arry Yanuar Asmarinah ASTUTIATI NURHASANAH Astutiati Nurhasanah Atiek Soemiati Aulia Rizki Azminah Azminah Berna Elya CESILIA ANITA Deli Marteka Dewi Puspita Donna M. Ariestanti Dumingan, Alvian Endang Saepudin Endang W Bachtiar ESTI PUSPITASARI Fairuz Andini Fatiningtyas Fathan Luthfi Hawari Fathan Luthfi Hawari Fatiningtyas, Fairuz Andini HANIFAH RAHMI Hanita Omar HANS-JOACHIM FREISLEBEN HARALD HUBER Harry Ardiansyah Hermawati, Ajitya Kurnia Hestiningtyas, Mahardhika Huda, Fathul IMAN SANTOSO INDRIANI INDRIANI Ingrid Faustine Is Helianti IS HELIANTI Islamudin Ahmad Kambang Sariadji Kino-Oka, Masahiro Kusmiati . Kusmiati Kusmiati Kusmiati Kusmiati Larashintya Rulita LILIANA SARAGIH Mahardhika Hestiningtyas Maimunah Maimunah Maksum Radji Meidy Richky Wanyodiharjo Mohamad Sadikin Muhammad Hanafi MUHAMMAD IQBAL Murti Andriastuti, Murti Nadia Farhanah Syafhan Napitupulu, Riswanto Neneng Siti Silfi Ambarwati Nilam Sartika Noverina, Rachmawati NUNUK WIDHYASTUTI Nusaiba, Putri Oktaviyani, Devi Purwaningtyas, Yoggi Ramadhani Putri, Ratih Rinendya Radhian Amandito Radhian Amandito RAFIKA SARI RAMADON, DELLY Ratih Rinendyaputri Retnaningsih, Agustina Rina Mutiara Rinawati Rohsiswatmo Riswanto Napitupulu RIZKI AYU AMALIA Rosari Saleh S.Pd. M Kes I Ketut Sudiana . SAHLAN, MUHAMAD SELA SEPTIMA MARIYA Septelia I. Wanandi Septelia Inawati W SERUNI K.U. FREISLEBEN Sheilla Sheilla SISWA SETYAHADI Sri Wulandah Fitriani Stella Vania Sukma Nuswantara Sukma Nuswantara Sunarno Sunarno Sunarno Sunarno Susan Rahayu Sutriyo Syafrida Siregar Syafrida Siregar, Syafrida Tiodinar Theresia Tri Handayani Trismilah Margono TRISMILAH TRISMILAH Trismilah Trismilah Trismilah, Utama, Hieronimus Adiyoga Nareswara Utami, Emilia Rahmadaniah Wahono Sumaryono WALTER ERDELEN Wangi Firdausi Yamamoto, Riku Yuditya Artha YUKI DESIANDINI ZESSINDA LUTHFA