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Article ; Online: Exploring the potential of black cumin derived nanovesicles for miRNA drug delivery.

Khristiani Rahayu, Adelina / Fibriani, Azzania / Irasonia Tan, Marselina

European journal of pharmaceutics and biopharmaceutics : official journal of Arbeitsgemeinschaft fur Pharmazeutische Verfahrenstechnik e.V

2024 Volume 199, Page(s) 114275

Abstract: Liposomes is a non-viral vector drug delivery system. Nevertheless, the existing commercial liposomes are quite expensive and not always affordable, particularly in developing countries. To address this challenge, plant-derived nanoparticles offer a cost- ...

Abstract	Liposomes is a non-viral vector drug delivery system. Nevertheless, the existing commercial liposomes are quite expensive and not always affordable, particularly in developing countries. To address this challenge, plant-derived nanoparticles offer a cost-effective alternative while maintaining similar drug delivery capabilities. Hence, this study aimed to explore the potential of nanovesicles derived from black cumin (Nigella sativa) as a miRNA delivery system. Gradient sucrose-centrifugation was utilized to separate the nanovesicles derived from black cumin. Subsequently, these isolated nanovesicles, originating from black cumin, underwent centrifugation at a speed of 11,000 rpm. The miRNAs were encapsulated within these nanovesicles through the ethanol injection method. Morphological examinations of the nanovesicles derived from black cumin and DOTAP, as the positive control, were conducted using TEM and SEM. Furthermore, the cytotoxicity of the nanovesicles derived from black cumin was evaluated through the MTT assay on the MCF-7 cell line. Lastly, the process of internalization for both the black cumin-derived nanovesicles and DOTAP was visualized using a confocal microscope. Results demonstrated the successful isolation of nanovesicles from black cumin using the sucrose gradient method. These particles exhibited a spherical shape with diameters ranging from 100 nm to 200 nm, featuring a negative surface charge. When MCF-7 cells were exposed to black cumin-derived nanovesicles at a concentration of 12 mg/mL, cell viability reached 89.8 %, showing no significant difference compared to the positive control (p > 0.05). Furthermore, the MCF-7 cell line effectively internalized the black cumin-derived nanovesicles after a 45-minute incubation period. Notably, the encapsulation of miRNA within these nanovesicles demonstrated an impressive entrapment efficiency of 76.4 %. Subsequent transfection of miRNA-loaded black cumin-derived nanovesicles resulted in a substantial inhibition of MCF-7 cell viability, reducing it to 67 % after 48 h of treatment. These findings underscore the potential of black cumin-derived nanovesicles as potential nanovectors for the encapsulation and delivery of miRNA within drug delivery systems, offering a cost-effective and accessible solution for advanced drug delivery technologies, particularly in developing country.
MeSH term(s)	Humans ; MicroRNAs ; MCF-7 Cells ; Drug Delivery Systems/methods ; Nigella sativa/chemistry ; Nanoparticles/chemistry ; Cell Survival/drug effects ; Liposomes ; Plant Extracts/administration & dosage ; Plant Extracts/chemistry
Language	English
Publishing date	2024-04-04
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1065368-5
ISSN	1873-3441 ; 0939-6411
ISSN (online)	1873-3441
ISSN	0939-6411
DOI	10.1016/j.ejpb.2024.114275
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Article ; Online: Development of Moloney Murine Leukemia Virus Reverse Transcriptase Fused with Archaeal DNA-binding Protein Sis7a.

Simanjuntak, Goldyna M / Fibriani, Azzania / Fananda, Amalia A / Yamahoki, Nicholas

Recent patents on biotechnology

2023 Volume 18, Issue 1, Page(s) 71–83

Abstract: Introduction: Moloney Murine Leukemia Virus Reverse Transcriptase (MMLV RT) is a common enzyme used to convert RNA sequences into cDNA. However, it still has its shortcomings, especially in terms of processivity and thermostability. According to a ... ...

Abstract	Introduction: Moloney Murine Leukemia Virus Reverse Transcriptase (MMLV RT) is a common enzyme used to convert RNA sequences into cDNA. However, it still has its shortcomings, especially in terms of processivity and thermostability. According to a previous patent, the fusion of polymerase enzyme to an archaeal DNA-binding protein has been proven to enhance its performance. Furthermore, recent studies have also stated that the fusion of a polymerase enzyme to an archaeal DNA-binding protein is predicted to improve its thermostability and processivity. Aim: As an early stage of enzyme development, this study aimed to design, express, and purify enzymatically active MMLV RT fused with archaeal DNA-binding protein. Methods: RT fusion proteins were designed and evaluated using Results: This study showed that MMLV RT fusion with Sis7a protein at its C-terminal end using commercial linker (GGVDMI) produced the best Conclusion: This study shows that the designed MMLV RT Sis7a fusion can be expressed and purified, is enzymatically active, and has the potential to be developed as an improved RT enzyme. Further study is still needed to prove its thermostability and processivity, and further characterize, and plan production scale-up of the MMLV RT Sis7a fusion for commercial use.
MeSH term(s)	Animals ; Mice ; RNA-Directed DNA Polymerase/genetics ; RNA-Directed DNA Polymerase/chemistry ; RNA-Directed DNA Polymerase/metabolism ; Moloney murine leukemia virus/genetics ; Moloney murine leukemia virus/metabolism ; Carrier Proteins ; DNA, Archaeal ; Patents as Topic ; DNA-Binding Proteins/metabolism
Chemical Substances	RNA-Directed DNA Polymerase (EC 2.7.7.49) ; Carrier Proteins ; DNA, Archaeal ; DNA-Binding Proteins
Language	English
Publishing date	2023-04-03
Publishing country	United Arab Emirates
Document type	Journal Article
ISSN	2212-4012
ISSN (online)	2212-4012
DOI	10.2174/1872208317666230403104302
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Article ; Online: Construction and Cloning of Plastic-degrading Recombinant Enzymes (MHETase).

Janatunaim, Rifqi Z / Fibriani, Azzania

Recent patents on biotechnology

2020 Volume 14, Issue 3, Page(s) 229–234

Abstract: Background: Polyethylene terephthalate (PET) is the most widely produced polyester plastic in the world. PET is very difficult to catalyze or biological depolymerization due to the limited access to ester bonds. Consequently, plastic will be stockpiled ... ...

Abstract	Background: Polyethylene terephthalate (PET) is the most widely produced polyester plastic in the world. PET is very difficult to catalyze or biological depolymerization due to the limited access to ester bonds. Consequently, plastic will be stockpiled or flowed into the environment which is projected until hundreds of years. The most effective and environmental friendly plastic degradation method is biodegradation with microorganisms. Two specific enzyme for PET hydrolase, PETase and MHETase have been identified from Ideonella sakaiensis 201-F6. Recombinant genes are made to increase the effectiveness of enzymes in degrading PET. Previous studies of the PETase gene have been carried out, but to produce the final degradation PET product, the enzyme MHETase is needed. Thus, in this study the MHETase gene construction was carried out. Methods: The goal of this study is to construct MHETase gene in pUCIDT plasmid with native signal peptide from I. sakaensis 201-F6 and constitutive promoter J23106 was expressed in Escherichia coli BL21 (DE3) by heats shock. Expression analysis using SDS-PAGE and activity of enzyme is analyzed by spectrophotometry method and SEM. Results: MHETase gene protein was successfully constructed in pUCIDT +Amp plasmid with native signal peptide from Ideonella sakaensis 201-F6, T7 terminator and constitutive promoter J23106. PCR analysis showed that the gene successfully contained in the cells by band size (1813 bp) in electrophoresis gel. Analysis using Snap Gene, pairwise alignment using MEGA X, and NCBI was demonstrated that MHETase sequence the gene was in-frame in pUCIDT plasmid. Conclusion: MHETase gene was successfully constructed in plasmids by in silico method. Synthetic plasmids transformed in E. coli BL21 (DE3) contain MHETase gene sequences which were in frame. Hence, the E. coli BL21 (DE3) cells have the potential to produce MHETase proteins for the plastic degradation testing process. We will patent the construct of MHETase gene using constitutive promoter and signal peptide from native which expressed in E. coli BL21 (DE3). This patent refers to a more applicable plastic degradation system with a whole cell without the need for purification and environmental conditioning of pure enzymes.
MeSH term(s)	Amino Acid Sequence ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Biodegradation, Environmental ; Burkholderiales/chemistry ; Burkholderiales/enzymology ; Burkholderiales/genetics ; Cloning, Molecular/methods ; Environmental Pollutants/chemistry ; Environmental Pollutants/metabolism ; Enzyme Assays ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Gene Expression ; Humans ; Hydrolases/genetics ; Hydrolases/metabolism ; Industrial Microbiology/methods ; Kinetics ; Patents as Topic ; Plasmids/chemistry ; Plasmids/metabolism ; Polyethylene Terephthalates/chemistry ; Polyethylene Terephthalates/metabolism ; Promoter Regions, Genetic ; Protein Sorting Signals/genetics ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism
Chemical Substances	Bacterial Proteins ; Environmental Pollutants ; Polyethylene Terephthalates ; Protein Sorting Signals ; Recombinant Proteins ; Hydrolases (EC 3.-)
Language	English
Publishing date	2020-02-08
Publishing country	United Arab Emirates
Document type	Journal Article
ISSN	2212-4012
ISSN (online)	2212-4012
DOI	10.2174/1872208314666200311104541
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Article ; Online: The Use of Biomaterials in Three-Dimensional Culturing of Cancer Cells.

Hanasti, Novia / Faridah, Lia / Fibriani, Azzania / Wiraswati, Hesti Lina / Kusumawaty, Diah / Ekawardhani, Savira

Current issues in molecular biology

2023 Volume 45, Issue 2, Page(s) 1100–1112

Abstract: Cell culture is an important tool in biological research. Most studies use 2D cell culture, but cells grown in 2D cell culture have drawbacks, including limited cell and cell-extracellular matrix interactions, which make it inaccurate to model conditions ...

Abstract	Cell culture is an important tool in biological research. Most studies use 2D cell culture, but cells grown in 2D cell culture have drawbacks, including limited cell and cell-extracellular matrix interactions, which make it inaccurate to model conditions in vivo. Anticancer drug screening is an important research and development process for developing new drugs. As an experiment to mimic the cancer environment in vivo, several studies have been carried out on 3-dimensional (3D) cell cultures with added biomaterials. The use of hydrogel in 3D culture cells is currently developing. The type of hydrogel used might influence cell morphology, viability, and drug screening outcome. Therefore, this review discusses 3D cell culture research regarding the addition of biomaterials.
Language	English
Publishing date	2023-01-30
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2000024-8
ISSN	1467-3045 ; 1467-3037
ISSN (online)	1467-3045
ISSN	1467-3037
DOI	10.3390/cimb45020073
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Article ; Online: Translational Bioinformatics of HIV Peptide 2.0

Nugrahapraja Husna / Fauzi Alidza / Adi Sadewa Alfonsus / Fibriani Azzania / Giri-Rachman Ernawati A.

BIO Web of Conferences, Vol 41, p

From Dry To Wet Bench

2021 Volume 02002

Abstract: Infectious diseases have become part of human civilization as a constant phenomenon throughout time. The Human Immunodeficiency Virus (HIV) is a virus that can cause immune system weakness by attacking cells that have CD4 receptors and CCR5 or CXCR4 ... ...

Abstract	Infectious diseases have become part of human civilization as a constant phenomenon throughout time. The Human Immunodeficiency Virus (HIV) is a virus that can cause immune system weakness by attacking cells that have CD4 receptors and CCR5 or CXCR4 chemokine coreceptors, namely helper T cells macrophages and dendritic cells. Therefore, people infected with this virus will be vulnerable to opportunistic infections and cancer. Here we proposed the translational bioinformatics approach from dry to wet bench. From proof of concept to the applications will be highlighted and discussed further in diagnostic of HIV and vaccine candidate development based on reverse vaccinology approach. We performed sequence data analysis to find the best epitope for HIV strains in Indonesia and compatible with the MHC class 1, the linear core with MHC class 2, and the B cell epitope. Epitope compatible with the two cells is expected to have high immunogenicity and potentially produce a response to good T memory. The epitope was then tested using an indirect ELISA against the serum of HIV positive patients. In this study, a negative control is used in blood serum from healthy individuals originating from Stored Biological Material and carried out with a commercial ELISA kit for the negative controls. The epitope in PBS buffer solution was coated to a microplate with an incubation time of 16 hours and various concentrations. As a result, the epitope from the concentration range of 1-2500 ng epitope/well can be recognized by HIV patient antibodies. In summary, the epitope from the in silico prediction had antigenicity against anti-HIV antibodies in sera samples and could also be a promising candidate for the vaccine.
Keywords	b cell epitope ; diagnostic ; reverse vaccinology ; t cell epitope ; vaccine ; Microbiology ; QR1-502 ; Physiology ; QP1-981 ; Zoology ; QL1-991
Subject code	570
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	EDP Sciences
Document type	Article ; Online
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Article ; Online: The SARS-CoV-2 M

Giri-Rachman, Ernawati Arifin / Effendy, Vergio V / Azmi, Muhammad H S / Yamahoki, Nicholas / Stephanie, Rebecca / Agustiyanti, Dian F / Wisnuwardhani, Popi H / Angelina, Marissa / Rubiyana, Yana / Aditama, Reza / Ningrum, Ratih A / Wardiana, Andri / Fibriani, Azzania

ACS synthetic biology

2024 Volume 13, Issue 2, Page(s) 509–520

Abstract: The COVID-19 endemic remains a global concern. The search for effective antiviral candidates is still needed to reduce disease risk. However, the availability of high biosafety level laboratory facilities for drug screening is limited in number. To ... ...

Abstract	The COVID-19 endemic remains a global concern. The search for effective antiviral candidates is still needed to reduce disease risk. However, the availability of high biosafety level laboratory facilities for drug screening is limited in number. To address this issue, a screening system that could be utilized at lower biosafety levels remains essential. This study aimed to develop a novel SARS-CoV-2 main protease (M
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19 ; Saquinavir/pharmacology ; Molecular Docking Simulation ; Dimerization ; Antiviral Agents/pharmacology ; Antiviral Agents/chemistry ; Protease Inhibitors/pharmacology ; Protease Inhibitors/chemistry ; Protease Inhibitors/metabolism ; Synthetic Biology ; Molecular Dynamics Simulation
Chemical Substances	Saquinavir (L3JE09KZ2F) ; Antiviral Agents ; Protease Inhibitors
Language	English
Publishing date	2024-02-05
Publishing country	United States
Document type	Journal Article
ISSN	2161-5063
ISSN (online)	2161-5063
DOI	10.1021/acssynbio.3c00446
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Article: Cell-free fetal DNA as a non-invasive method using pyrosequencing in detecting beta-globin gene mutation: A pilot study from area with limited facilities in Indonesia.

Maskoen, Ani Melani / Rahayu, Nurul Setia / Laksono, Bremmy / Fibriani, Azzania / Soewondo, Willyanti / Mose, Johanes C / Sahiratmadja, Edhyana / Panigoro, Ramdan

Frontiers in pediatrics

2022 Volume 10, Page(s) 902879

Abstract: Background: Thalassemia is a monogenic, autosomal recessive, inherited disorder of the red blood cells caused by mutations or deletions in the globin gene. Approximately 6-10% of the Indonesian population carries the β-globin gene mutation; however, ... ...

Abstract	Background: Thalassemia is a monogenic, autosomal recessive, inherited disorder of the red blood cells caused by mutations or deletions in the globin gene. Approximately 6-10% of the Indonesian population carries the β-globin gene mutation; however, premarital screening is rarely conducted, and antenatal screening is optional. We explored the use of cell-free fetal DNA (cffDNA) as a potential non-invasive method of detecting the fetal β-globin gene mutation prenatally in pregnant women. Materials and methods: Pregnant mothers ( Results: In total, 7 out of 10 cffDNA successfully passed the maternal contamination test. The results of the allele quantification showed that six fetuses were predictive carriers of IVS1nt5 and one was predictive normal, in line with the allele quantification for the bio-archived DNA from patients with thalassemia major. The minimum threshold percentage for mutant A allele at cd26 was 32%, mutant T allele at IVS1nt1 was 23%, and mutant C allele at IVS1nt5 was 39%. Conclusion: Taking cffDNA from the mother's blood proved useful as a non-invasive means of detecting the β-globin gene mutation using pyrosequencing allele quantification. This non-invasive method is of great interest for prenatal diagnosis in settings with limited facilities, as it minimizes the risk of abortion. Further study of other mutations of the β-globin gene is needed.
Language	English
Publishing date	2022-08-04
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2711999-3
ISSN	2296-2360
ISSN	2296-2360
DOI	10.3389/fped.2022.902879
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Article ; Online: SARS-CoV-2 genetic variation and bacterial communities of naso-oropharyngeal samples in middle-aged and elderly COVID-19 patients in West Java, Indonesia.

Adzdzakiy, Muhammad M / Sutarno, Sutarno / Asyifa, Isnaini Z / Sativa, Alvira R / Fiqri, Ahmad R A / Fibriani, Azzania / Ristandi, Ryan B / Ningrum, Ratih A / Iryanto, Syam B / Prasetyoputri, Anggia / Dharmayanthi, Anik B / Saputra, Sugiyono

Journal of Taibah University Medical Sciences

2023 Volume 19, Issue 1, Page(s) 70–81

Abstract: Objective: The number of COVID-19 cases in Indonesia reflects the disease severity and rapid dissemination. In response to the mounting threat, SARS-CoV-2 genomic surveillance and the investigation of naso-oropharyngeal bacterial communities in West ... ...

Abstract	Objective: The number of COVID-19 cases in Indonesia reflects the disease severity and rapid dissemination. In response to the mounting threat, SARS-CoV-2 genomic surveillance and the investigation of naso-oropharyngeal bacterial communities in West Java were conducted, as dysbiosis of the upper respiratory tract microbiota might adversely affect the clinical condition of patients. Methods: We utilized the Oxford Nanopore sequencing platform to analyze genetic variation of 43 samples of SARS-CoV-2 and 11 selected samples for 16S rRNA gene sequencing, using samples collected from May to August 2021. Results: The prevalence of AY.23 (>82%) predominated among five virus lineages in the populations (AY.23, AY.24, AY.26, AY.42, B.1.1.7). The region in the SARS-CoV-2 genome found to have the highest number of mutations was the spike (S) protein (>20%). There was no association between SARS-CoV-2 lineages, mutation frequency, patient profile, and COVID-19 rapid spread-categorized cases. There was no association of bacterial relative abundance, alpha-beta diversity, and linear discriminant analysis effect size analysis with patient profile and rapid spread cases. MetagenomeSeq analysis showed eight differential abundance species in individual patient profiles, including Conclusions: The data demonstrated relevant AY.23 dominance (the Delta variant) in West Java during that period supporting the importance of surveillance program in monitoring disease progression. The inconsistent results of the bacterial communities suggest that a complex multifactor process may contribute to the progression of bacterial-induced disease in each patient.
Language	English
Publishing date	2023-09-13
Publishing country	Saudi Arabia
Document type	Journal Article
ZDB-ID	2817396-X
ISSN	1658-3612 ; 1658-3612
ISSN (online)	1658-3612
ISSN	1658-3612
DOI	10.1016/j.jtumed.2023.09.001
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Article: Curcumin-derived carbon-dots as a potential COVID-19 antiviral drug.

Fibriani, Azzania / Taharuddin, Audrey Angelina Putri / Stephanie, Rebecca / Yamahoki, Nicholas / Laurelia, Jessica / Wisnuwardhani, Popi Hadi / Agustiyanti, Dian Fitria / Angelina, Marissa / Rubiyana, Yana / Ningrum, Ratih Asmana / Wardiana, Andri / Iskandar, Ferry / Permatasari, Fitri Aulia / Giri-Rachman, Ernawati Arifin

Heliyon

2023 Volume 9, Issue 9, Page(s) e20089

Abstract: Even entering the third year of the COVID-19 pandemic, only a small number of COVID-19 antiviral drugs are approved. Curcumin has previously shown antiviral activity against SARS-CoV-2 nucleocapsid, but its poor bioavailability limits its clinical uses. ... ...

Abstract	Even entering the third year of the COVID-19 pandemic, only a small number of COVID-19 antiviral drugs are approved. Curcumin has previously shown antiviral activity against SARS-CoV-2 nucleocapsid, but its poor bioavailability limits its clinical uses. Utilizing nanotechnology structures, curcumin-derived carbon-dots (cur-CDs) were synthesized to increase low bioavailability of curcumin.
Language	English
Publishing date	2023-09-12
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2023.e20089
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Article ; Online: Porphyrin-derived carbon dots for an enhanced antiviral activity targeting the CTD of SARS-CoV-2 nucleocapsid.

Fibriani, Azzania / Taharuddin, Audrey Angelina Putri / Yamahoki, Nicholas / Stephanie, Rebecca / Laurelia, Jessica / Agustiyanti, Dian Fitria / Wisnuwardhani, Popi Hadi / Angelina, Marissa / Rubiyana, Yana / Ningrum, Ratih Asmana / Wardiana, Andri / Desriani, Desriani / Iskandar, Ferry / Permatasari, Fitri Aulia / Giri-Rachman, Ernawati Arifin

Journal, genetic engineering & biotechnology

2023 Volume 21, Issue 1, Page(s) 93

Abstract: Background: Since effective antiviral drugs for COVID-19 are still limited in number, the exploration of compounds that have antiviral activity against SARS-CoV-2 is in high demand. Porphyrin is potentially developed as a COVID-19 antiviral drug. ... ...

Abstract	Background: Since effective antiviral drugs for COVID-19 are still limited in number, the exploration of compounds that have antiviral activity against SARS-CoV-2 is in high demand. Porphyrin is potentially developed as a COVID-19 antiviral drug. However, its low solubility in water restricts its clinical application. Reconstruction of porphyrin into carbon dots is expected to possess better solubility and bioavailability as well as lower biotoxicity. Methods and results: In this study, we investigated the antiviral activity of porphyrin and porphyrin-derived carbon dots against SARS-CoV-2. Through the in silico analysis and assessment using a novel drug screening platform, namely dimer-based screening system, we demonstrated the capability of the antivirus candidates in inhibiting the dimerization of the C-terminal domain of SARS-CoV-2 Nucleocapsid. It was shown that porphyrin-derived carbon dots possessed lower cytotoxicity on Vero E6 cells than porphyrin. Furthermore, we also assessed their antiviral activity on the SARS-CoV-2-infected Vero E6 cells. The transformation of porphyrin into carbon dots substantially augmented its performance in disrupting SARS-CoV-2 propagation in vitro. Conclusions: Therefore, this study comprehensively demonstrated the potential of porphyrin-derived carbon dots to be developed further as a promisingly safe and effective COVID-19 antiviral drug.
Language	English
Publishing date	2023-10-06
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2637420-1
ISSN	2090-5920 ; 1687-157X ; 2090-5920
ISSN (online)	2090-5920
ISSN	1687-157X ; 2090-5920
DOI	10.1186/s43141-023-00548-z
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