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Assessment of bio-activities of the crude extract and components of Withania somnifera leaves by bioinformatics Widodo, Nashi; Priyandoko, Didik; Deocaris, Custer C.; Wadhwa, Renu; Kaul, Sunil C.
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.

in silico Study Reveals Potential Docking Sites of Î´ 2-isoxazolines derivates for Inhibiting Russellâ€™s Viper PLA2 Toxin Kholilah, Tsaniyah Nur; Widodo, Nashi; Kurniawan, Nia
Journal of Tropical Life Science Vol 11, No 1 (2021)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.11.01.06

Snake venom phospholipase A2s (svPLA2s) has been known as the most abundant component and predominant cause of Russellâ€™s viper envenomation. Limitation to serum therapy and considerable pharmacological interest led the researcher to synthesized multi-toxic PLA2 inhibitors, Î´2-isoxazolines derivate. Although Î´2- isoxazolines derivate already proved inhibitor activity in Group II svPLA2 with known IC50, their mechanism of action remains unveiled. Our recent study investigated their inhibitory activity via molecular docking. The virtual screening revealed that the ligand with diverse structures tied to the relatively same active site region. The result sheds light on the significance of His48 and Asp49 as part of the pro-inflammatory eliciting region. ADME analysis was also performed to filter and identify the best potential inhibitor acceptable for human use. This moiety leads to finding a better therapeutic strategy of svPLA2 inhibitors both as an alternative to serum anti-venom treatment.

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.

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.

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.

Daruju (Acanthus ilicifolius L.) May Exhibit Anti-Breast Cancer Activity Through Inhibition of Proliferation Regulators: A Computational Study: Daruju (Acanthus ilicifolius L.) as Anti-Breast Cancer Agent Rosyadah, Nuraini; Kamila, Fairuz Sarah; Hermanto, Feri Eko; Widyananda, Muhammad Hermawan; Grahadi, Rahmat; Dwijayanti, Dinia Rizqi; Widodo, Nashi; Ulfa, Siti Mariyah
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/

Breast cancer's increasing prevalence globally underscores the urgent need for effective and gentle therapies, positioning the exploration of herbal remedies as a critical pursuit. Daruju (Acanthus ilicifolius L.) emerges as a compelling candidate due to its inherent bioactive components. This research pioneers the application of advanced computational techniques to unveil the latent anti-breast cancer potential within A. ilicifolius. Our in-silico investigation commenced by cataloging A. ilicifolius compounds using the KNApSAcK database and existing literature. These compounds underwent rigorous screening for drug-like characteristics via SWISS-ADME and potential biological activity using PASS ONLINE. Protein targets relevant to breast cancer were predicted through SWISS Target and the STRING database, integrated with Cytoscape for network visualization. Molecular docking, performed with PyRx 0.8, assessed the binding strength between the identified compounds and target proteins, with the most promising interactions selected for further scrutiny. The stability of these crucial interactions was then evaluated through molecular dynamics simulations using YASARA. This comprehensive computational strategy aims to pinpoint potential anti-breast cancer agents derived from A. ilicifolius. Initial analysis of 17 compounds from A. ilicifolius, based on chromatography, databases, and prior studies, narrowed down to five that adhered to Lipinski’s Rule of Five for drug-likeness: 4-O-beta-D-glucosyl-4-coumaric acid, (-)-lyoniresinol, α-amyrin, adenosine, and p-coumaric acid. These compounds were predicted to directly interact with key breast cancer-related proteins across pathways like estrogen signaling, JAK/STAT, and PI3K/AKT. Notably, molecular docking revealed strong binding affinities for α-amyrin with CDK4, ER, and EGFR (-7.5 kcal/mol, -9.5 kcal/mol, and -8.7 kcal/mol, respectively), comparable to known inhibitors. Molecular dynamics simulations further corroborated the stability of these complexes, analyzing RMSD and binding affinity parameters. Consequently, α-amyrin stands out as a promising anti-breast cancer agent within A. ilicifolius, exhibiting potential to inhibit proteins crucial for breast cancer cell proliferation and survival, including CDK4, ER, and EGFR.

Design, Construction and Expression of Spike Highly Conserved Region (HCR) SARS-CoV-2 and Cholera Toxin Subunit B Fusion Protein in Lactococcus lactis NZ3900: Construction of recombinant plasmid in Lactococcus lactis Kesuma, Suryanata; Adianingsih, Oktavia Rahayu; Winarsih, Sri; Widodo, Nashi; Yurina, Valentina
Journal of Tropical Life Science Vol. 15 No. 2 (2025): In Press
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/2xf1qp96

Prevention of SARS-CoV-2 transmission has primarily been achieved through vaccination, which is generally administered via injection and may cause discomfort. No commercially available SARS-CoV-2 vaccines can be administered via the mucosal route. However, recent advancements have demonstrated that vaccination with Lactococcus lactis enables vaccine delivery through the mucosa. A promising target for SARS-CoV-2 vaccine materials is the highly conserved region (HCR) of the SARS-CoV-2 spike (SARS-CoV-2 HCR Spike). Vaccine efficacy is enhanced by adding Cholera Toxin Subunit B (CTB) as an adjuvant. HCR and CTB proteins were recombinantly fused using a synthetic gene with optimized codons. This study aimed to construct a fusion protein of the SARS-CoV-2 spike protein and CTB in L. lactis strain NZ3900. The construction and expression of fusion proteins were analyzed using sequencing and protein electrophoresis. Codon optimization resulted in a Codon Adaptation Index value of 0.93 and a GC content of 27.06%. The cloning results revealed the formation of L. lactis colonies expressing the Fusion protein of the SARS-CoV-2 HCR Spike and CTB, which formed yellow colonies on the selection Elicker medium. PCR and sequencing confirmed the presence of the hcr-ctb gene, with a length of 981 bp and 100% sequence similarity. The Fusion protein of the SARS-CoV-2 HCR Spike and CTB was successfully expressed with a molecular weight of >35 kDa. In conclusion, we successfully constructed a Fusion protein of the SARS-CoV-2 HCR Spike and CTB in L. lactis NZ3900 as a potential vaccine candidate for oral administration to prevent SARS-CoV-2 infection.

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