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Assessment of bio-activities of the crude extract and components of Withania somnifera leaves by bioinformatics Nashi Widodo; Didik Priyandoko; Custer C. Deocaris; Renu Wadhwa; Sunil C. Kaul
Journal of Tropical Life Science Vol. 1 No. 1 (2010)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.1.1.%x

Traditional herbal medicines are now increasingly being appreciated with Western models of integrative health sciences and evidence-based approach both in the basic research and clinic scenario. Ashwagandha is a commonly used plant in Ayurvedic, Indian traditional medicine. Medicinal value of Ashwagandha (WithaniasomniferaDunal) extends from anti-inflammatory, anti-arthritic, anti-rheumatic, rejuvenation and anti-cancer. Based on the belief that holistic multi-site mechanism of action offers greater chance of success, the traditional Ayurvedicmedicine practices the use of whole herb or its crude extract. It opposes with the mainstream of pharmaceutical industry that uses single and purified molecules. In the present study, we used bioinformatics approach to reveal the mechanism of action of (i) crude extract of Ashwagandha leaf extract and its purified components, (ii) Withanone and (iii) Withaferin A. Whereas p53-p21 was identified as a common signaling pathway for the three kinds of reagents, specific signaling pathways for Withaferin-A and Withanone were identified. Whereas the crude extract and Withanone were selectively toxic to human cancer cells, Withaferin A showed cytotoxicity to the normal cells too. The study suggested that the crude extract or a combinational formulamay be a superior and safenatural reagent for cancer treatment.

Design of Epitope-Based Vaccine Against SARS-CoV-2: An Immuno-Informatics Study: Epitope-Based Vaccine Against SARS-CoV-2 Kusuma, Kavana Hafil; Widyananda, Muhammad Hermawan; Nafisah, Wirdatun; Grahadi, Rahmat; Christina, Yuyun Ika; Dwijayanti, Dinia Rizqi; Mustikaningtyas, Dewi; Widodo, Nashi; Djati, Muhammad Sasmito
Journal of Tropical Life Science Vol. 14 No. 3 (2024): In Press
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.03.07

This study aimed to develop an epitope-based vaccine of SARS-CoV-2 S protein through an immuno-informatics study. The whole genome of SARS-CoV-2 sequences was obtained from the GISAID database and then trimmed to obtain the S protein sequences. The alignment was done by Clustal-W of MEGA software. Epitope prediction and modeling were performed by Discotope BepiPred and the PepFold3 web server. The allergic responses and physicochemical characteristics of predicted epitopes were analyzed using the AlgPred and ProtParam from ExPASy. Molecular docking and dynamic stimulation were performed using AutoDock Vina and YASARA. Biovia Discovery Studio 2019 was used to visualize the molecular docking results. The study predicted 3 potential epitopes, including ‘GDEVRQIAPGQTGKIADYNYKLP’ (epitope 1), ‘YTMSLGAENSVAYSNN’ (epitope 2), and ‘VNNSYECDIPI’ (epitope 3) located in the spike head specifically RBD region. The epitopes did not show an allergen reaction based on IgE epitope mapping. The suitable overexpression for the host of epitopes was mammalian cells. Only epitopes 1 and 2 were stable (instability index above 40). Epitopes 1, 2, and 3 interacted with BCR with binding affinity values -6.6, -7.8, and -7.5 kcal/mol. Epitope 2 wasere stable when interacting with the BCR. Therefore, three epitopes were predicted to have high potency as the SARS-CoV-2 epitope-based vaccine.

Determination of Anticancer from EtOAc Fraction of Spatholobus Littoralis Hassk and of Molecular Structure Prediction Iskandar, Dodi; Widodo, Nashi; Warsito, Warsito; Masruri, Masruri; Rollando, Rollando; Afthoni, Muhammad Hilmi; Ichsan, Ichsan; Hermansyah, Adi
Majalah Obat Tradisional Vol 29, No 2 (2024)
Publisher : Faculty of Pharmacy, Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/mot.88894

In recent years, the search for new anticancer drugs from local plants in Indonesia has become an interesting topic for research. One of the typical Indonesian local plants that have been used by the community as an anticancer traditional medicine (jamu) is Spatholobus littoralis Hassk (SLH) or better known as Bajakah. The native Dayak people of Kalimantan have used it for years for the treatment of breast cancer. In this study, the separation of single compounds from the ethyl acetate fraction of SLH stems was carried out, their molecular structure was analyzed, and anticancer bioactivity was tested. The isolation used the preparative HPLC method. The elucidation of the isolates from the ethyl acetat fraction used LCMS-MS, FTIR, and NMR. Anticancer bioactivity was determined using the MTT bioassay. The result is the acquisition of two isolates; it has been predicted that both are pseudobaptinin. The anticancer IC50 of the pseudobaptinin was 62.85 ppm, and Pseudobaptinin with impurities was 145.60 ppm.

A hybrid feature selection on AIRS method for identifying breast cancer diseases Ridok, Achmad; Widodo, Nashi; Mahmudy, Wayan Firdaus; Rifa’i, Muhaimin
International Journal of Electrical and Computer Engineering (IJECE) Vol 11, No 1: February 2021
Publisher : Institute of Advanced Engineering and Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11591/ijece.v11i1.pp728-735

Breast cancer may cause a death due to the late diagnosis. A cheap and accurate tool for early detection of this disease is essential to prevent fatal incidence. In general, the cheap and less invasive method to diagnose the disease could be done by biopsy using fine needle aspirates from breast tissue. However, rapid and accurate identification of the cancer cell pattern from the cell biopsy is still challenging task. This diagnostic tool can be developed using machine learning as a classification problem. The performance of the classifier depends on the interrelationship between sample sizes, some features, and classifier complexity. Thus, the removal of some irrelevant features may increase classification accuracy. In this study, a new hybrid feature selection fast correlation based feature (FCBF) and information gain (IG) was used to select features on identifying breast cancer using AIRS algorithm. The results of 10 times the crossing (CF) of our validation on various AIRS seeds indicate that the proposed method can achieve the best performance with accuracy =0.9797 and AUC=0.9777 at k=6 and seed=50.

Oxidation of Cellulose and Nanocellulose Isolated from Paraserianthes falcataria by Potassium Permanganate Ikhtiarini, Nur; MASRURI, Masruri; Mariyah Ulfa, Siti; Widodo, Nashi
The Journal of Pure and Applied Chemistry Research Vol. 12 No. 3 (2023): September-December 2023
Publisher : Chemistry Department, The University of Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jpacr.2023.012.03.3331

A high crystallinity proportion of cellulose and nanocellulose in some points contribute to the solubility in polar solvent. This paper reports oxidation reaction study by using potassium permanganate of the cellulose and nanocellulose isolated from the soft wood of Paraserianthes falcataria. Â The reaction was conducted under acidic condition at 30 and 70Â°C for 12 and 24 hours. The product was characterized by FTIR, XRD, SEM, DTA-TGA, and solubility test. Oxidation of cellulose resulted in the opening of hemiacetal of glucopyranose chain, as indicated by carbonyl peak recorded in FTIR spectra. The particle size was determined and amorphous product of cellulose and nanocellulose was isolated. In addition, the DTA/TGA analysis indicate the oxidized cellulose give a more stable structure than the nanocellulose.

Evaluating SARS-CoV-2 Spike Protein Transfection in HEK-293T Cells for VLP Applications Rohmah, Ilmiana Nurur; Hafil Kusuma, Kavana; Ika Christina, Yuyun; Rizqi Dwijayanti, Dinia; Mustikaningtyas, Dewi; Widodo, Nashi; Sasmito Djati, Muhammad
The Journal of Experimental Life Science Vol. 14 No. 3 (2024)
Publisher : Graduate School, Universitas Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jels.2024.014.03.02

The spike protein in SARS-CoV-2 works mainly to initiate infections, especially for binding to host cells and fusing with cell membranes. Characterizing SARS-CoV-2 spikes protein transfection cells could optimize the production of VLP in HEK-293T cells. Therefore, the present study aimed to investigate the characteristics of SARS-CoV-2 spike protein expression in transfected HEK-293T cells. Characterization of spike protein in transfected-HEK 293T cells was used to determine VLP formation in SARS-CoV-2. The study was conducted by isolating DNA and protein from transfected HEK 293T cells and analyzing spike expression using Polymerase Chain Reaction (PCR) and Flow Cytometry. The success of the SARS-CoV-2 spike protein transfection in PCR analysis has yet to be confirmed because DNA band smears do not specifically indicate the spike protein's size. However, the SARS-CoV-2 spike protein was successfully confirmed using flow cytometry with the percentage of spike-EGFP by 30%. Therefore, the present study confirmed the presence of spike protein in transfected HEK 293T cells by flow cytometry analysis. Keywords: Coronavirus, Characterization, DNA, Spike, Virus-Like Particle (VLP)

Design of Epitope-Based Vaccine Against SARS-CoV-2: An Immuno-Informatics Study: Epitope-Based Vaccine Against SARS-CoV-2 Kusuma, Kavana Hafil; Widyananda, Muhammad Hermawan; Nafisah, Wirdatun; Grahadi, Rahmat; Christina, Yuyun Ika; Dwijayanti, Dinia Rizqi; Mustikaningtyas, Dewi; Widodo, Nashi; Djati, Muhammad Sasmito
Journal of Tropical Life Science Vol. 14 No. 3 (2024)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.03.07

This study aimed to develop an epitope-based vaccine of SARS-CoV-2 S protein through an immuno-informatics study. The whole genome of SARS-CoV-2 sequences was obtained from the GISAID database and then trimmed to obtain the S protein sequences. The alignment was done by Clustal-W of MEGA software. Epitope prediction and modeling were performed by Discotope BepiPred and the PepFold3 web server. The allergic responses and physicochemical characteristics of predicted epitopes were analyzed using the AlgPred and ProtParam from ExPASy. Molecular docking and dynamic stimulation were performed using AutoDock Vina and YASARA. Biovia Discovery Studio 2019 was used to visualize the molecular docking results. The study predicted 3 potential epitopes, including ‘GDEVRQIAPGQTGKIADYNYKLP’ (epitope 1), ‘YTMSLGAENSVAYSNN’ (epitope 2), and ‘VNNSYECDIPI’ (epitope 3) located in the spike head specifically RBD region. The epitopes did not show an allergen reaction based on IgE epitope mapping. The suitable overexpression for the host of epitopes was mammalian cells. Only epitopes 1 and 2 were stable (instability index above 40). Epitopes 1, 2, and 3 interacted with BCR with binding affinity values -6.6, -7.8, and -7.5 kcal/mol. Epitope 2 wasere stable when interacting with the BCR. Therefore, three epitopes were predicted to have high potency as the SARS-CoV-2 epitope-based vaccine.

Piper betle L. Leaves Extract Potentially Reduce the Nitric Oxide Production on LPS-Induced RAW 264.7 Cell Lines Dwijayanti, Dinia Rizqi; Puspitarini, Sapti; Widodo, Nashi
The Journal of Experimental Life Science Vol. 13 No. 2 (2023)
Publisher : Graduate School, Universitas Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jels.2023.013.02.02

Chronic inflammation can lead to several diseases that represent the leading causes of mortality worldwide. Conventional treatment of inflammation can carry some risks. Therefore, research on herbal medicine that are suspected of having anti-inflammatory effects, such as Piper betle L., is important. This study aims to investigate the effect of P. betle L. extract on nitric oxide as a pro-inflammatory mediator. The dried leaves of P. betle L. were extracted by ethanol. RAW 264.7 cells were treated with LPS and P. betle L. extract (PBE). Nitric oxide was measured by the Griess method. Antioxidant activity was determined using 2,2–Diphenyl-1-picrylhydrazyl (DPPH) method. Total flavonoids and phenolic content were also identified by aluminium chloride and Folin–Ciocalteu colorimetric assay, respectively. This study demonstrated that the PBE has excellent NO suppression activity with the IC50 56.22±16.41 μg.mL-1, without cytotoxicity. PBE also has DPPH inhibitory concentration IC50 values of 279.67±11.36 ppm. Interestingly, PBE has a flavonoid content of 50.17±3.14 mg QE.g-1 and phenolic content of 128.92±1.2 mg GAE.g-1. These compounds are thought to be responsible for its anti-inflammatory as well as antioxidant. This study proved that P. betle L. leaves extract could be used as a candidate for anti-inflammatory drugs. Nevertheless, further research about the biological activity mechanism and their bioactive compounds' purification is still required. Keywords: Inflammation, lipopolysaccharide, Macrophage, Nitric Oxide, Piper betle.

Effect of Combination of Different Antibiotics and Promoters for Expressing Recombinant Darbepoetin in Stable CHO K-1 Cell Line: Evaluating Antibiotic Combinations to Improve Yield and Quality of Darbepoetin Widekdo, Dwi purno; Widodo, Nashi; Rifa'i, Muhaimin; Jatmiko, Yoga Dwi
Journal of Tropical Life Science Vol. 15 No. 1 (2025)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/

Antibiotics are key for successful molecular cloning techniques. Different antibiotics have different mechanisms of action, which leads to cell heath and a viable number of passages. Moreover, the suitability of the promoter also plays an important role in achieving a higher level of protein titter in the stable cell platform. Therefore, with plenty of options of antibiotics and promoters available, we need to determine the best combination of antibiotics and promoters, particularly for specific proteins of interest. Darbepoetin is a recombinant therapeutics protein with extra glycosylation to increase the half-life in the blood; this drug is used for the administration of CKD and leukemia patients. Blasticidin-S and puromycin were used as antibiotics, and CMV and EF-1 promoters were used in this experiment to evaluate the expression of recombinant darbepoetin for the protein model. CHO K-1 cell line was transfected with a plasmid carrying a combination of promoter and antibiotics genes; after 14 days, the level of specific protein expression was evaluated using the western blot technique. A single clone cell was obtained using the serial dilution method to evaluate the clonality and expression of the protein of interest. This study successfully obtained a single clone from stable pool transfection. This result suggested that a combination of puromycin antibiotics and EF-1 promoter has promising expression compared to Blasticidin-S antibiotics with CMV promoter. For further conclusion, an analytical comparison of both combinations needed to be done.

Antioxidant Properties and Quantification of Phenolic and Flavonoid Compounds in Alpinia purpurata (Viell.) K. Schum Ethanol Extract Djati, Muhammad Sasmito; Azerlyn, Defiona Rensia Naomi; Kusuma, Kavana Hafil; Rosyadah, Nuraini; Kamila, Fairuz Sarah; Annisa, Yuslinda; Christina, Yuyun Ika; Dwijayanti, Dinia Rizqi; Widodo, Nashi
Biotropika: Journal of Tropical Biology Vol. 13 No. 1 (2025)
Publisher : Universitas Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.biotropika.2025.013.01.02

Phenolic and flavonoid compounds have been found to have positive benefits due to their antioxidant activity. Alpinia purpurata (Viell.) K. Schum, or lengkuas merah, is known to have aromatic rhizomes and is rich in active compounds such as flavonoids and phenolics. This research aimed to investigate the total phenolic and flavonoid content of A. purpurata ethanol extract and its antioxidant activity. A. purpurata was extracted using Microwave-Assisted Extraction (MAE) with 97% ethanol solvent. The ethanol extract of A. purpurata was then analyzed for the total phenolic and flavonoid content. The antioxidant activity and nitric oxide (NO) levels were determined by DPPH and NO scavenging assay, respectively. The results showed that A. purpurata ethanol extract had a high phenolic content (148.76 ± 1.03 mg GAE.g-1extract) but weak DPPH scavenging activity (IC50 of 219.06 ± 8.15 µg.mL-1), indicating that high phenolic content does not necessarily correlate with strong antioxidant properties. In contrast, the extract exhibited strong NO scavenging activity with an IC50 of 22.73 ± 7.57 µg.mL-1. Despite its high phenolic content, the weak DPPH activity indicates that total phenolic concentration alone is not always a reliable indicator of antioxidant strength. Further studies should include additional antioxidant assays to comprehensively evaluate the extract’s antioxidant potential.

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