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All Journal AGRIVITA, Journal of Agricultural Science Eksakta : Berkala Ilmiah Bidang MIPA Narra J Borneo Journal of Pharmacy Biosaintifika: Journal of Biology & Biology Education
Rebezov, Maksim
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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 Immunology & microbiology Materials Science & Nanotechnology Mathematics Mechanical Engineering Medicine & Pharmacology Public Health

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Genotype by Environment Interactions in Barley (Hordeum vulgare L.) Cultivars for Nutritional Quality Assessment Quddos, Abdul; Nadeem, Muhammad; Ahsan, Samreen; Khaliq, Adnan; Chughtai, Muhammad Farhan Jahangir; Rebezov, Maksim; Terent’ev, Sergei; Tryabas, Yulia; Ermolaev, Vladimir; Iskakova, Galiya; Konovalov, Sergey; Gayvas, Alexei; Shariati, Mohammad Ali
AGRIVITA, Journal of Agricultural Science Vol 43, No 3 (2021)
Publisher : Faculty of Agriculture University of Brawijaya in collaboration with PERAGI

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.17503/agrivita.v43i3.2925

Abstract

In current study twenty-five barley genotypes were grown under RCBD (randomized complete block design). Barley flour was analyzed for proximate composition, β-glucan content, soluble and insoluble dietary fiber. Based on the results of nutritional quality best line (4158) was selected for the preparation of wheat flour supplemented bread. The sensory evaluation of bread was carried out to assess its suitability for consumers. The data obtained from all the experiments was subjected to statistical analysis by CRD. The results indicated that the highest moisture content (13.47%), protein content (13.93%), fat content (3.39%), fiber content (7.08%), ash content (2.67%) and NFE (71.54%) were observed in lines 4220, 4158, 4149, 4193, 4233, 4220 respectively. Similarly, significant differences for β-glucan (4.99%), total dietary fiber (16.62%), soluble (6.23%) and insoluble dietary fiber contents (10.36%) were observed in barley line 4193, 4233, 4168 and 4233, respectively. The bread prepared with the addition of 5% flour to wheat flour was liked most by the judges after the control bread. The current study showed significant potential of flour to be used by baking industry for the preparation of bread and other food products by the addition of flour. 
Application of CRISPR-Cas9 genome editing technology in various fields: A review Ansori, Arif NM.; Antonius, Yulanda; Susilo, Raden JK.; Hayaza, Suhaila; Kharisma, Viol D.; Parikesit, Arli A.; Zainul, Rahadian; Jakhmola, Vikash; Saklani, Taru; Rebezov, Maksim; Ullah, Md. Emdad; Maksimiuk, Nikolai; Derkho, Marina; Burkov, Pavel
Narra J Vol. 3 No. 2 (2023): August 2023
Publisher : Narra Sains Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52225/narra.v3i2.184

Abstract

CRISPR-Cas9 has emerged as a revolutionary tool that enables precise and efficient modifications of the genetic material. This review provides a comprehensive overview of CRISPR-Cas9 technology and its applications in genome editing. We begin by describing the fundamental principles of CRISPR-Cas9 technology, explaining how the system utilizes a single guide RNA (sgRNA) to direct the Cas9 nuclease to specific DNA sequences in the genome, resulting in targeted double-stranded breaks. In this review, we provide in-depth explorations of CRISPR-Cas9 technology and its applications in agriculture, medicine, environmental sciences, fisheries, nanotechnology, bioinformatics, and biotechnology. We also highlight its potential, ongoing research, and the ethical considerations and controversies surrounding its use. This review might contribute to the understanding of CRISPR-Cas9 technology and its implications in various fields, paving the way for future developments and responsible applications of this transformative technology.
Detection of Pseudomonas aeruginosa pus wound isolate using a polymerase chain reaction targeting 16S rRNA and gyrB genes: A case from Indonesia Jamaluddin, Indra P.; Musa, Susan H.; Ethica, Stalis N.; Ansori, Arif NM.; Yosephi, Valensa; Atmaja, Peter Y.; Murtadlo, Ahmad AA.; Sahadewa, Sukma; Durry, Fara D.; Rebezov, Maksim; Derkho, Marina; Naw, Sin W.; Zainul, Rahadian; Rachmawati, Kadek
Narra J Vol. 4 No. 2 (2024): August 2024
Publisher : Narra Sains Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52225/narra.v4i2.774

Abstract

Infectious wounds on the skin surface are easily colonized by bacteria from pyogenic group that manifest as inflammation, such as Pseudomonas aeruginosa. P. aeruginosa is a Gram-negative bacterium and an opportunistic pathogen known for causing invasive state in critically ill and immunocompromised patients. The aim of this study was to detect the 16S rRNA and gyrB genes in P. aeruginosa using polymerase chain reaction (PCR) method. The sample in this study was pus isolate from a 5-year-old boy with leg wounds. The bacteria were isolated on brain heart infusion broth (BHIB) media and identified with molecular identification. Sequencing and BLAST analysis were carried out to determine the similarity of gene identity by comparing sample sequence with other isolate sequences on the Gene Bank. The results of molecular identification showed amplification DNA band of around 934 base pairs (bp) for 16S rRNA and 225 bp for gyrB gene. The BLAST program demonstrated that the sample had 99.89% similarity with P. aeruginosa strain XC4 (accession code ON795960.1) for the 16S rRNA gene. Meanwhile, the gyrB gene exhibited 99.10% similarity with the P. aeruginosa strain PSA-1.2 (accession code KP172300.1).
Molecular interaction analysis of ferulic acid (4-hydroxy-3-methoxycinnamic acid) as main bioactive compound from palm oil waste against MCF-7 receptors: An in silico study Herdiansyah, Mochammad A.; Rizaldy, Rafli; Alifiansyah, Mochamad RT.; Fetty, Amelia JT.; Anggraini, Dhea; Agustina, Niken; Alfian, Fariz R.; Setianingsih, Primanita NM.; Elfianah, Verah; Aulia, Halimatus S.; Putra, Justitia ERP.; Ansori, Arif NM.; Kharisma, Viol D.; Jakhmola, Vikash; Purnobasuki, Hery; Pratiwi, Intan A.; Rebezov, Maksim; Shmeleva, Svetlana; Bonkalo, Tatyana; Kovalchuk, Dmitriy F.; Zainul, Rahadian
Narra J Vol. 4 No. 2 (2024): August 2024
Publisher : Narra Sains Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52225/narra.v4i2.775

Abstract

Ferulic acid (4-hydroxy-3-methoxycinnamic acid) is a phytochemical compound that is commonly found in conjugated forms within mono-, di-, polysaccharides and other organic compounds in cell walls of grain, fruits, and vegetables. This compound is highly abundant in the palm oil waste. The aim of the study was to predict the anticancer activity of ferulic acid against the breast cancer cell lines (MCF-7) receptors through a computational analysis. MCF-7 receptors with PDB IDs of 1R5K, 2IOG, 4IV2, 4IW6, 5DUE, 5T92, and 5U2B were selected based on the SMILE similarity of the native ligand. Thereafter, the protein was prepared on Chimera 1.16 and docked with ferulic acid on Autodock Vina 1.2.5. The ligand-protein complex interaction was validated by computing the root mean square fluctuation (RMSF) and radius of gyration (Rg) through molecular dynamic simulation. In addition, an absorption, distribution, metabolism, excretion, and toxicity (ADMET) prediction was performed on ferulic acid using the pkCSM platform. The molecular docking revealed that the ferulic acid could interact with all receptors as indicated by the affinity energy <-5 kcal/mol. The compound had the most optimum interaction with receptor 2IOG (affinity energy=-6.96 kcal/mol), involving hydrophobic interaction (n=12) and polar hydrogen interaction (n=4). The molecular dynamic simulation revealed that the complex had an RMSF of 1.713 Å with a fluctuation of Rg value around 1.000 Å. The ADMET properties of ferulic acid suggested that the compound is an ideal drug candidate. In conclusion, this study suggested that ferulic acid, which can be isolated from palm oil waste, has the potential to interact with MCF-7 receptors.
In Silico Study of Cladosporol and Its Acyl Derivatives as Anti-Breast Cancer Against Alpha-Estrogen Receptor Herdiansyah, Mochammad Aqilah; Ansori, Arif Nur Muhammad; Kharisma, Viol Dhea; Alifiansyah, Mochamad Radika Tory; Anggraini, Dhea; Priyono, Qiara Amelia Putri; Yusniasari, Putri Antika; Fetty, Amelia Julia Tria; Zainul, Rahadian; Rebezov, Maksim; Kolesnik, Evgeniy; Maksimiuk, Nikolai
Biosaintifika: Journal of Biology & Biology Education Vol. 16 No. 1 (2024): April 2024
Publisher : Universitas Negeri Semarang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v15i1.949

Abstract

Breast cancer is a chronic health problem that causes 690,000 deaths worldwide. The development of secondary metabolite compounds from natural preparations through an in silico approach is needed as a predictive tool to prevent breast cancer, one of them is cladosporol from Cladosporium spp. This study aims to utilize an in silico approach to predict the potential of cladosporol against alpha-estrogen receptors. The alpha-estrogen receptor with code 6CBZ was selected based on group function as pharmacophore in ligand-receptor interaction. The methods used in this study are by using an in silico approach with Molegro Virtual Docker (MVD) Ver 5.5 for the docking process and CABS-flex 2.0 for identifying the stability of the complexes. ADMET properties analysis was also performed to know the pharmacokinetics attributes of cladosporol. Based on research conducted, stated that cladosporol octanoate has the lowest rerank score with a -84.3593 value and the RMSD value is 1.195 Å so it’s valid for molecular docking. Exploration of cladosporol for anti-breast cancer from Cladosporium spp fungi can be a novelty for the development of future pharmaceutical research. Thus, the development of anti-cancer drugs for early prevention can be carried out to reduce the number of breast cancer cases worldwide.
Computational Calculation and Molecular Docking of Thymol and O-Benzoyl Thymol as Inhibitor TYK2 Enzyme Maahury, Mirella Fonda; Baharudin, Muhammad Daswar A.; Zainul, Rahadian; Khalid, Ahmad Khudzairi; Jakmola, Vikash; Rebezov, Maksim
EKSAKTA: Berkala Ilmiah Bidang MIPA Vol. 24 No. 03 (2023): Eksakta : Berkala Ilmiah Bidang MIPA (E-ISSN : 2549-7464)
Publisher : Faculty of Mathematics and Natural Sciences (FMIPA), Universitas Negeri Padang, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/eksakta/vol23-iss03/405

Abstract

Thymol is the active ingredient in plants from Thymus vulgaris (thymus). The calculations and molecular docking have been done computationally for the thymol and o-benzoyl thymol. This computational calculation aims to obtain a stable structure and electronic properties of thymol and o-benzoyl thymol. The computational analysis used DFT for geometry optimization in the gas phase using B3LYP functional and 3-211G(d) as the basis set. The optimized structure of thymol and o-benzoyl thymol is not planar. The functional benzoyl decreases the bond length, increases the bond angle, and turns the dihedral. The electronic properties, such as atomic charge and density of HOMO-LUMO, show the difference between the two molecules. The optimized structure of thymol and o-benzoyl thymol is used for molecular docking with the TYK2 enzyme (tyrosine kinase). In this research, thymol and o-benzoyl thymol can inhibit TYK2 enzyme with the bond affinity is about -5.909 kcal/mol and -7.456 kcal/mol, respectively, for thymol o-benzoyl thymol. The primary molecular interaction is hydrophobic.
Molecular Docking Analysis of Flavonoids from Syzygium cumini (L.) Skeels: Proapoptotic Potential as an Anticancer Mechanism Aini, Nur Sofiatul; Ansori, Arif Nur Muhammad; Widyananda, Muhammad Hermawan; Kharisma, Viol Dhea; Murtadlo, Ahmad Affan Ali; Herdiansyah, Mochammad Aqilah; Rebezov, Maksim; Burkov, Pavel; Gudz, Petr; Derkho, Marina; Bezhinar, Tatyana; Maksimiuk, Nikolai; Sazali, Munawir; Purnobasuki, Hery; Rollando, Rollando; Khairullah, Aswin Rafif; Sucipto, Teguh Hari
Borneo Journal of Pharmacy Vol. 8 No. 3 (2025): Borneo Journal of Pharmacy
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33084/bjop.v8i3.9843

Abstract

Non-small cell lung cancer (NSCLC) presents a significant global health challenge, with its prevalence and mortality rates rising steadily. In Indonesia, Syzygium cumini (L.) Skeels, known for its flavonoid richness, has a long history in traditional medicine. However, its specific mechanisms of action against cancer, particularly in inducing apoptosis in NSCLC, have not been fully elucidated. This study utilized an in silico approach to evaluate the pro-apoptotic potential of S. cumini flavonoids against NSCLC by targeting key proteins: Bcl-2, Bax, and Caspase-3. We retrieved flavonoid structures from PubChem and protein data from the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB). The drug-likeness of these compounds was assessed using Swiss ADME, adhering to Lipinski's rule of five, while their anti-NSCLC probability was predicted using PASS Online. Molecular docking and screening were performed with PyRx, and the results were visualized using Discovery Studio. Our findings identified epigallocatechin 3-O-gallate and ellagic acid as the most promising anti-NSCLC candidates. Ellagic acid demonstrated the strongest binding affinity to Caspase-3, suggesting a potent pro-apoptotic effect. Epigallocatechin 3-O-gallate, on the other hand, exhibited the lowest binding energy across multiple target proteins, particularly Bcl-2 and Bax, indicating its broad pro-apoptotic potential. These results collectively suggest that flavonoids from S. cumini may hold significant promise as a source of novel anti-NSCLC agents, warranting further in vitro and in vivo investigations.
Co-Authors Adi Sofyan Ansori, Muhammad Agustina, Niken Ahsan, Samreen Aini, Nur Sofiatul Alfian, Fariz R. Alifiansyah, Mochamad Radika Tory Alifiansyah, Mochamad RT. Anggraini, Dhea Ansori, Arif NM. Antonius, Yulanda Atmaja, Peter Y. Aulia, Halimatus S. Baharudin, Muhammad Daswar A. Bezhinar, Tatyana Bonkalo, Tatyana Burkov, Pavel Chughtai, Muhammad Farhan Jahangir Derkho, Marina Durry, Fara D. Elfianah, Verah Ermolaev, Vladimir Ethica, Stalis N. Fetty, Amelia JT. Fetty, Amelia Julia Tria Gayvas, Alexei Gudz, Petr Hayaza, Suhaila Herdiansyah, Mochammad A. Herdiansyah, Mochammad Aqilah Hery Purnobasuki Iskakova, Galiya Jakhmola, Vikash Jakmola, Vikash Jamaluddin, Indra P. Kadek Rachmawati Khairullah, Aswin Rafif Khalid, Ahmad Khudzairi Khaliq, Adnan Kharisma, Viol D. Kharisma, Viol Dhea Kolesnik, Evgeniy Konovalov, Sergey Kovalchuk, Dmitriy F. Maahury, Mirella Fonda Maksimiuk, Nikolai Mohammad Ali Shariati Muhammad Nadeem, Muhammad Munawir Sazali Murtadlo, Ahmad AA. Murtadlo, Ahmad Affan Ali Musa, Susan H. Naw, Sin W. Parikesit, Arli A. Pratiwi, Intan A. Priyono, Qiara Amelia Putri Putra, Justitia ERP. Quddos, Abdul Rahadian Zainul Rizaldy, Rafli Rollando, Rollando Saklani, Taru Setianingsih, Primanita NM. Shmeleva, Svetlana Sukma Sahadewa, Sukma Susilo, Raden JK. Teguh Hari Sucipto, Teguh Hari Terent’ev, Sergei Tryabas, Yulia Ullah, Md. Emdad Widyananda, Muhammad Hermawan Yosephi, Valensa Yusniasari, Putri Antika