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All Journal Majalah Obat Tradisional Journal of Applied Pharmaceutical Research Narra J Makara Journal of Science Genbinesia Journal of Biology
Jakhmola, Vikash
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Health Professions Immunology & microbiology Medicine & Pharmacology Public Health

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Molecular Simulation of B-Cell Epitope Mapping from Nipah Virus Attachment Protein to Construct Peptide-Based Vaccine Candidate: A Reverse Vaccinology Approach Kharisma, Viol Dhea; Dian, Farida Aryani; Burkov, Pavel; Scherbakov, Pavel; Derkho, Marina; Sepiashvili, Ekaterina; Sucipto, Teguh Hari; Parikesit, Arli Aditya; Murtadlo, Ahmad Affan Ali; Jakhmola, Vikash; Zainul, Rahadian
Makara Journal of Science Vol. 27, No. 2
Publisher : UI Scholars Hub

Show Abstract | Download Original | Original Source | Check in Google Scholar

Abstract

There are no specific drugs or vaccines for Nipah virus (NiV), which is a new Paramyxovirus that infects swine and humans. This study was conducted to investigate B-cell epitope mapping of the NiV attachment glycoprotein and to construct peptide-based vaccine candidates using the reverse vaccinology approach. To generate the linear B-cell epitope, the NiV isolates were extractad from GenBank, NCBI, using the IEDB web server; peptide modeling was conducted using PEP-FOLD3; docking was conducted using PatchDock and FireDock; and in silico cloning was designed using SnapGene. Various peptides were successfully identified from the NiV attachment glycoprotein based on B-cell epitope prediction, allergenicity prediction, similarity prediction, and toxicity prediction. An in silico cloning design of the pET plasmic was also developed. The peptide “RFENTTSDKGKIPSKVIKSYYGTMDIKKINEGLLD” (1G peptide) is predicted to be a potential candidate for the NiV vaccine as it has several good vaccine characteristics. It increases the immune response of B cells through activation, differentiation into plasma cells, the formation of memory cells, and it may increase IgM/IgG antibody titres for viral neutralization. However, the results of this study should be further verified through in vivo and in vitro analyses
Sleep Disorder and its Treatment: From Nature to Laboratory Varshney, Mohit; Saha, Supriyo; Prinsa, Prinsa; Jakhmola, Vikash
Majalah Obat Tradisional Vol 29, No 1 (2024)
Publisher : Faculty of Pharmacy, Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/mot.86645

Abstract

Sleep is the natural cellular repair mechanism to improve and restore central neural mechanism, memory, hormonal imbalance, and finally, cell rejuvenation. Sleep disorder is characterized by insomnia, circadian rhythm disorder (CRD), sleep apnea, narcolepsy, parasomnia, and restless leg syndrome (RLS) or periodic limb movement disorder (PLMD). Both oversleeping and less sleeping are associated with sleep disorders (SD). Anxiety, schizophrenia, weight loss/gain, hypothyroidism, and oxidative stress are the most common outcomes of SD. There is also a genetic explanation behind circadian rhythmicity, circadian disorder, narcolepsy-cataplexy syndrome, fatal familial insomnia, and somnambulism. Excessive work pressure, stress, and consumption of caffeine and alcohol collectively push a person toward sleep deprivation. Anxiety, schizophrenia, weight loss/gain, hypothyroidism, and oxidative stress are the most common outcomes of SD. Adenosine, melatonin, dopamine, serotonin, gamma amino butyric acid (GABA), orexin, and histamine regulate SDs by various pathways. Among natural sources, Centella asiatica, Bacopa monnieri, Acorus calamus, Withania somnifera, Nardostachys jatamansi, Poria cocos is, Valeriana officinalis, Matricaria chamomilla, Lavandula angustifolia, Nelumbo nucifera, Melissa officinalis, Convolvulus pluricaulis, Camellia sinensis, Ziziphus jujube, Datura stramonium, Zhizhipus jujube, Passiflora incarnata, and Moringa oleifera showed remarkable effects on different forms of SDs through GABAA, serotonin, and melatonin receptors. Pramipexole, ropinirole, rotigotine, clonazepam, lorazepam, estazolam, zolpidem, lemborexant, daridorexant, and suvorexant showed its activity in the treatment of SDs as a dopamine agonist, inhibitor of GABAA receptor, dual orexin receptor antagonist, respectively. This article focused on the types of SDs, the effects of SDs on mental health, receptors involved in the sleep cycle, and the impact of natural molecules and synthetic molecules in the management of SDs.
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.
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.
Pharmacophore insights and molecular docking of ciprofloxacin analogues against 2XE1: strategies for reduced antibiotic resistance Katlaria, Sanjana; Chauhan, Ashish Singh; Kumar, Krishna; Kumar, Mohit; Chauhan, Bhumika; Jakhmola, Vikash
Journal of Applied Pharmaceutical Research Vol. 12 No. 6 (2024)
Publisher : Creative Pharma Assent

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.69857/joapr.v12i6.660

Abstract

Background: Antibiotic resistance is a silent pandemic disease that is growing and causing a global threat. Existing antibiotics are less effective against infectious diseases, so we must discover more potent and effective drugs. The latest report from the World Health Organization (WHO) underscores the global nature of the situation, revealing that high levels of antibiotic resistance in bacteria worldwide lead to life-threatening bloodstream infections and resistance to treatment. Methods: This study focuses on the Molecular Docking and Pharmacophore Modeling of Ciprofloxacin and its analogs to explore ligand-protein interactions and identify potent drugs against AMR. Twenty ciprofloxacin analogs, designed using ChemDraw Pro12.0, were docked with the 2XE1 protein. Molecular docking assessed the binding affinity, with Arguslab 4.0 scoring the lowest docking scores to indicate strong interactions and biological activity. Pharmacophore modeling identified essential molecular features like HBA, HBD, and AI for optimal biological activity. Results: The computational screening identified several compounds with improved binding properties, showing greater affinity towards ALA129, TYR149, and PHE88 amino acids, essential for biological activity. Conclusion: The study identifies the best analog of ciprofloxacin, which can effectively combat antibiotic resistance. Compound 13 showed promising docking scores and relevant pharmacophoric features, outperforming the parent ciprofloxacin in binding affinity, suggesting it could be a potent drug candidate against AMR.
Nanostructured lipid carriers (NLCs): A comprehensive review of drug delivery advancements Panwar, Pramesh; Kumar, Saurabh; Chand, Pallavi; Chauhan, Ashish Singh; Jakhmola, Vikash
Journal of Applied Pharmaceutical Research Vol. 13 No. 2 (2025)
Publisher : Creative Pharma Assent

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.69857/joapr.v13i2.676

Abstract

Background: Nano-structured lipid carriers (NLCs) have emerged as a significant advancement in lipid-based drug delivery systems. Compared to Solid Lipid Nanoparticles (SLNs), NLCs offer improved drug loading capacity, stability, and controlled release profiles. Objective: This review article explores the structural and functional benefits of NLCs, their enhanced bioavailability, and their potential in targeted therapeutic agent delivery. Methodology: We investigated the unique combination of solid and liquid lipids in NLCs, which creates an internal structure for improved drug encapsulation and sustained release. Various methods were analyzed for their contribution to NLC efficacy, including high-pressure homogenization and solvent emulsification. Results and Discussion: NLCs demonstrated encapsulation efficiency ranging from 85–95%, with particle sizes between 100–300 nm. Drug release was sustained over 24 hours, affirming their effectiveness in controlled drug delivery. Applications of NLCs were highlighted across diverse delivery modes, including topical, pulmonary, oral, parenteral, and ocular. Challenges such as scaling production, overcoming biological barriers, and ensuring regulatory compliance were also addressed. Conclusion: NLCs present a promising future in pharmaceutical sciences, with the potential to improve therapeutic outcomes in complex diseases like cancer and neurodegenerative disorders. Continued research into NLC formulations is critical for advancing patient outcomes and addressing global health challenges.
Advancements in formulations and technologies for colon-targeted drug delivery Rana, Ritik Singh; Ale, Yogita; Pant, Pankaj; Kukreti, Neha; Jakhmola, Vikash
Journal of Applied Pharmaceutical Research Vol. 13 No. 2 (2025)
Publisher : Creative Pharma Assent

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.69857/joapr.v13i2.825

Abstract

Background: Colonic administration of drugs may enhance drug absorption, reduce adverse reactions, and facilitate delivery to specific therapeutic targets. Objective: Delivering pharmaceuticals to the colon poses challenges that require innovative formulation strategies. Methodology: Various formulation approaches have been explored for colon-targeted drug delivery systems. These approaches target the colon using formulation components that interact with GI physiology parameters such as pH, colonic flora, and enzymes. Result and Discussion: The article discussed the various research studies conducted for colon targeting involving novel strategies such as pH-dependent, enzyme-dependent, Ligand-Receptor-based, new technologies, Phloral, and magnetically derived approaches. It also explored the translational technologies, such as in vivo, in vitro, and in silico, which expedite the transition from fundamental research to clinical application and enhance therapeutic outcomes. Conclusion: In conclusion, the most relevant preclinical studies, encompassing in vitro, in vivo, and in silico research, are delineated to facilitate the strategic advancement of novel colon-targeted therapeutics.
Development and evaluation of an amorphous solid dispersion-based probucol immediate-release tablet Adhikari, Vaibhav; Butola, Mansi; Jakhmola, Vikash; Ojha, Abhijeet; Negi, Arvind
Journal of Applied Pharmaceutical Research Vol. 13 No. 2 (2025)
Publisher : Creative Pharma Assent

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.69857/joapr.v13i2.997

Abstract

Background: In its crystalline form, probucol has an extremely low bioavailability and is a poor water-soluble drug. The main aim of this study was to enhance the solubility and dissolution rate of probucol by using a solvent evaporation method to develop a solid dispersion that contains polyvinyl pyrrolidone K30 (PVP-K30) and polyethylene glycol 6000 (PEG 6000). Methodology: The solvent evaporation method is considered superior to other techniques for preparing solid dispersions due to its ability to achieve uniform drug distribution at the molecular level. This method ensures homogeneity by dissolving the drug and carrier in a common solvent, reducing the risk of drug recrystallization and enhancing solubility and bioavailability. Result: The drug-to-carrier ratio is the determining factor for dissolution enhancement. The FTIR spectra do not suggest any chemical interaction between PVP-K30 or PEG 6000. The immediate release profiles of both formulations were favourable, with F3 releasing approximately 95.31% of the drug and F6 releasing around 86.77% within 2 hours. This indicates a rapid drug dissolution, which is beneficial for achieving a fast onset of action and enhancing bioavailability.  Conclusion: The solid dispersion formulations F3 & F6 successfully transformed crystalline probucol to an amorphous state, enhancing solubility & dissolving rates appropriate for immediate-release tablets.
Therapeutic potential of bioconstituents in the prevention and treatment of rheumatoid arthritis Morris, Srishti; Srivastava, Yashashvi; Kartikey Kumar; Jakhmola, Vikash
Journal of Applied Pharmaceutical Research Vol. 13 No. 3 (2025)
Publisher : Creative Pharma Assent

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.69857/joapr.v13i3.847

Abstract

Background: Rheumatoid arthritis (RA), a joint disease characterized by inflammation and an autoimmune response, affects approximately 1% of the global population. The disruption of immunological tolerance causes the immune system to attack self-molecules, resulting in autoimmune disease. RA is characterized by synovial swelling, accompanied by morning stiffness and joint soreness. Methodology: Herbal pharmacotherapy is now a meaningful focus in the treatment of rheumatoid arthritis. Medicinal plants contain strong active components like flavonoids, alkaloids, stilbenoids, tannins, and sesquiterpene lactones. Their anti-inflammatory and antioxidant qualities make them a potential treatment option for RA. Results and Discussion: Standard medication aims to prevent further deterioration of the affected joint. This treatment includes several antirheumatic medications, such as methotrexate, biological agents, cytotoxic drugs, immunosuppressants, and NSAIDs. Urinary and respiratory tract infections have been reported in patients treated with certolizumab pegol. Several concerns regarding anti-rheumatoid medication arise during a woman's pregnancy. Therefore, rheumatoid arthritis is now being effectively treated with herbal pharmacotherapy. Conclusion: RA is a chronic autoimmune disorder that primarily affects joints through persistent inflammation. Conventional treatment regimens for RA can lead to the occurrence of adverse effects, such as urinary and respiratory tract infections. Given these challenges, herbal pharmacotherapy is emerging as a safer and more sustainable approach. This review highlights a variety of phytochemicals with anti-inflammatory and antiarthritic properties, including flavonoids, alkaloids, stilbenoids, tannins, and sesquiterpene lactones. It underscores the need for further research to elucidate their mechanisms of action, assess their long-term safety and clinical utility, and compare their efficacy.
DNA damage, inflammation, and cellular senescence investigation in SARS-CoV-2 infection: A short review Kharisma, Viol Dhea; Ansori, Arif Nur Muhammad; Murtadlo, Ahmad Affan Ali; Turista, Dora Dayu Rahma; Tamam, Muhammad Badrut; Ullah, Md. Emdad; Jakhmola, Vikash
Genbinesia Journal of Biology Vol. 2 No. 3 (2023): July 2023
Publisher : Generasi Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.55655/genbinesia.v2i3.35

Abstract

SARS-2 infection is predicted to trigger DNA damage due to excessive inflammatory responses from the immune system such as cytokine storms. The cytokine storm leads to an increase in oxidative stress in cells, possibly triggering senescence through activation of the DNA damage response (DDR) signaling pathway. Alterations in the DDR pathway that induce cellular senescence have been identified due to the regulation of viral proteins that lead to impaired DNA repair. However, previous studies have not examined the relationship between DNA damage, inflammation, and cellular senescence. In this short review, we will discuss with a simple perspective why SARS-CoV-2 infection can accelerate the cellular senescence process and its relationship with the inflammatory response.
Co-Authors Adhikari, Vaibhav Adi Sofyan Ansori, Muhammad Agustina, Niken Ale, Yogita Alfian, Fariz R. Alifiansyah, Mochamad RT. Anggraini, Dhea Ansori, Arif NM. Antonius, Yulanda Arli Aditya Parikesit Aulia, Halimatus S. Bonkalo, Tatyana Burkov, Pavel Butola, Mansi Chand, Pallavi Chauhan, Ashish Singh Chauhan, Bhumika Derkho, Marina Dian, Farida Aryani Elfianah, Verah Fetty, Amelia JT. Hayaza, Suhaila Herdiansyah, Mochammad A. Hery Purnobasuki Kartikey Kumar Katlaria, Sanjana Kharisma, Viol D. Kharisma, Viol Dhea Kovalchuk, Dmitriy F. Kukreti, Neha Kumar, Krishna Kumar, Mohit Kumar, Saurabh Maksimiuk, Nikolai Morris, Srishti Murtadlo, Ahmad Affan Ali Negi, Arvind Ojha, Abhijeet Pant, Pankaj Panwar, Pramesh Parikesit, Arli A. Pratiwi, Intan A. Prinsa, Prinsa Putra, Justitia ERP. Rahadian Zainul Rana, Ritik Singh Rebezov, Maksim Rizaldy, Rafli Saha, Supriyo Saklani, Taru Scherbakov, Pavel Sepiashvili, Ekaterina Setianingsih, Primanita NM. Shmeleva, Svetlana Srivastava, Yashashvi Susilo, Raden JK. Tamam, Muhammad Badrut Teguh Hari Sucipto, Teguh Hari Turista, Dora Dayu Rahma Ullah, Md. Emdad Varshney, Mohit