The effectiveness of UPA system to boost the bioinformatics learning process in limited time for pharmacy students at University of Surabaya, Indonesia

Bioinformatics is one of essential fields widely applied to various studies, especially in the exploration studies of the herbal medicine in drugs discovery. However, bioinformatics course at the Faculty of Pharmacy University of Surabaya still needs to be improved. This research aims to develop the efficient teaching system to optimize the bioinformatics course within limited time. The developed learning system: Understanding, Practicing, and Applying (UPA) system, was conducted. This study involved 95 pharmacist students which were given questionnaire I (before the class) and questionnaire II (after the class) to measure the success rate of learning process. UPA system was implemented by instructor through the explanation about basic concept, the guidance for practice, and the demonstration in research. Result showed that 72% student was lacked of knowledge about the bioinformatics in the beginning but they have a strong willingness to learn. It proved by high interest in bioinformatics (78%) and herbal exploration (72%), respectively. In the end, the interest rate of student to bioinformatics was 96%. It was in line with the understanding of the tools usage ratein advance research. UPA system was successfully boosting the interest and skill of student in bioinformatics, as well as the awareness of herbal conservation

Identification of Potential Ebola Virus Nucleoprotein (EBOV NP) Inhibitor Derivate from Various Traditional Medicinal Plants in Indonesia: in silico study

Ebola virus disease is caused by Ebolavirus infection. Within infection, Ebola nucleoprotein (EBOV NP) is essential part for virus proliferation. Recent report showed that the outbreak was happened in Congo on February 2021. Although million cases were reported, the drug is remain unavailable. However, Indonesia had a high diversity of plants as traditional drugs. This research aimed to identify the traditional drug plants as potential inhibitor for EBOV NP. The SMILE notation of 65 identified compounds were collected from PubChem and 3D structured of EBOV NP (PDB ID: 4Z9P) was obtained from PDB. Molecular docking was conducted between selected compounds and EBOV NP. Clabistrin C was selected as a control. Complex of compounds EBOV NP and its amino acid residues were depicted by using Chimera X and LigPlot. Several potential compounds were selected for pharmacological activity prediction by PASS Online, toxicity analysis by ProTox-II, and drug likeness analysis with SWISSADME. Result showed that among the docked compound, hesperidin, cucurbitacin, ginsenoside RH2, and ginsenoside RO had lower binding energy compared to control. Moreover, all of those compounds had comparable hydrogen and hydrophobic interactions with EBOV NP. Further analysis showed it has potential biological function for Ebola disease, such as antiviral, antioxidant, and immunostimulant. All those compounds had low toxicity. As conclusion, there are four promising compounds that potentially inhibited the Ebolavirus proliferation

Identification Of Potential Activity Of Volatile Compounds Derived From Pogostemon Cablin Benth As Antiviral Of Sars-Cov-2

Objective: Coronavirus disease-19 (COVID-19) is global pandemic which caused by SARS-CoV-2 infection. Mechanism of infection is initiated by attachment between viral glycoprotein with ACE2 receptor in human cells. Furthermore, Indonesia had a massive diversity of plants with a high potency of drugs, such as Pogostemon cablin Benth. In brief, it contained of various volatile compounds with many therapeutic properties. Therefore, this research aimed to identify the ability of volatile compounds from Pogostemon cablin Benth as a potential inhibitor of SARS-CoV-2 spike glycoprotein. Methods: SMILE notation of 22 volatile compounds of Pogostemon cablin Benth were collected from PubChem and the 3D structure of SARS-CoV-2 glycoprotein (PDB ID: 6VXX) was obtained from PDB database. Simulation of interaction between volatile compound and glycoprotein was conducted by using Pyrx molecular docking. Moreover, the complex of compounds-glycoprotein was depicted by using Chimera and the amino acid residue was analysed by using LigPlot. Selected potential compounds were identified for biological activity prediction, drug-likeness, and toxicity analysis. Results: Analysis showed that among those volatile compounds, only caryophyllene oxide (-6.3 kcal/mol) naturally bind specific into RBD site as compared to the control. Furthermore, it had comparable hydrogen and hydrophobic interactions with glycoprotein. Further analysis showed it has strong potential biological function for antiviral with low toxicity. Conclusion: Caryophyllene oxide is considered as promising candidate compounds that inhibited viral infection through SARS-CoV-2 glycoprotein

Molecular docking of active compounds from traditional medicinal plants as ACE-2 protein (1R4L) inhibitor in searching for COVID-19 drug

Coronavirus disease known as COVID-19 is a global pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). SARS-CoV-2 binds to the receptor binding-domain of ACE-2. By blocking it with a specific ligand, we can prevent SARS-CoV-2 binding and therefore prevent its cellular entry and injury. The number of COVID-19 cases is still increasing and yet only 2.5% of Indonesians are fully vaccinated. Moreover, up to now, a specific cure for COVID-19 has not been found yet. However, many traditional medicinal plants have the potency of becoming COVID-19 drugs. Therefore, this study aimed to examine various active compounds derivate from the traditional medicinal plant as an inhibitor of SARS-CoV-2 receptor in human cell termed as ACE2. The activity and drug-likeness of the active compounds were predicted and molecular docking were conducted to identify the interactions between ligands and ACE-2. Toxicity assay was also identified to predict the toxicity class, lethal dose, and organ toxicity. This study showed that indirubin has lower binding energy as compared to the sulabiroins A and MLN-4760 as comparative control and potent inhibitor control, respectively. Indirubin shared similar interaction with amino acid residue to ACE-2 as compared to control. Based on the research result, it was suggested that Indirubin could be developed as a promising compound for COVID-19 antiviral drugs. KEYWORDS: ACE-2 inhibitor, Antiviral drug, Coronavirus, Indirubin, Sulabiroins A

Improvement of Herbal Research with Bioinformatics in Pharmacy Student Faculty of Pharmacy University of Surabaya

Improvement of Herbal Research with Bioinformatics in Pharmacy Student Faculty of Pharmacy University of Surabaya Marisca Evalina Gondokesumo1, Yulanda Antonius2, Oeke Yunita1 1Faculty of Pharmacy, University of Surabaya, Surabaya, Indonesia 2Faculty of Biotechnology, University of Surabaya, Surabaya, Indonesia ABSTRACT Bioinformatics is a combination of biological study and information engineering. It can be widely applied to various studies, especially in the medicinal study to explore the herbal medicine towards drug delivery. By knowing the benefits of various herbs, especially Indonesian endemic plants or plants with lack of function, bioinformatics acts as a mediator to increase the awareness of plant conservation.The pharmaceutical studies are closely related to the process of exploration of natural compounds for drugs development. However, the bioinformatics topic at the Faculty of Pharmacy University of Surabaya still needs to be improved due to the limited number of the lecture. Moreover, this topic is highly needed for pharmacist.Therefore, applicable learning and fun approach through the three golden stages of the workshop was conducted. It consisted of introduction, practice course, and deepening research application. In brief, 95 pharmacist students were addressed as a subject in this research. They were handed by questionnaire I (before workshop) and questionnaire II (after workshop) to measure the success rate of learning. Result showed that 72% student never know about bioinformatics but they have strong courage to learn which proved by high interest rate in bioinformatics (78%) and herbal exploration (72%), respectively. Most of student was actively engaged in every step of workshop by asking questions and directly practice for using the tools that specially directed for herbal exploration. In the end of workshop, the interest rate of student to bioinformatics was reached 96%. It was in line with the understanding rate of the tools usage in advance research. Therefore, it concluded that the workshop with this three golden steps was successfully boosting not only the interest and skill of student in bioinformatics but also the awareness of herbal conservation

Immunobioinformatics analysis and phylogenetic tree construction of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Indonesia: spike glycoprotein gene

The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), has spread worldwide and as a result, the World Health Organization (WHO) declared it a pandemic. At present, there are no approved vaccines against SARS-CoV-2. Therefore, the aim of this study was to predict epitope-based vaccines using bioinformatics approaches and phylogenetic tree construction of SARS-CoV-2 against the backdrop of the COVID-19 pandemic. In this study, we employed 27 isolates of SARS-CoV-2 spike glycoprotein genes retrieved from GenBank® (National Center for Biotechnology Information, USA) and the GISAID EpiCoV™ Database (Germany). We analyzed the candidate epitopes using the Immune Epitope Database and Analysis Resource. Furthermore, we performed a protective antigen prediction with VaxiJen 2.0. Data for B-cell epitope prediction, protective antigen prediction, and the underlying phylogenetic tree of SARS-CoV-2 were obtained in this research. Therefore, these data could be used to design an epitope-based vaccine against SARS-CoV-2. However, the advanced study is recommended for confirmation (in vitro and in vivo)

The character of PA3235 virulence factors of Pseudomonas aeruginosa PAO1 – a preliminary study

Introduction:Many virulence factors ofPseudomonas aeruginosaPAO1 are regulated by temperature and host conditions upon infection. Based on microarray data, the PA3235 gene is one of the upregulated genes during cell growth at 37 °C. Until now, no information about its role in PAO1 pathogenicity.Methods:The PAO1∆PA3235 strain was constructed by overlapping polymerase chain reaction (PCR) method and through biparental mating. The deletion was confirmed by PCR and restriction analyses. The virulence factors of bothP. aeruginosa PAO1 wild type and ∆PA3235 mutant strains were examined, which consisted of the amount of pyocyanin and pyoverdine, swarming, swimming, and twitching motility, biofilm formation, 3-oxo-dodecanoyl-homoserine lactone concentration, and growth curve profile. Data were analyzed using Student’s t-tests to determine differences between treatments. P-value < 0.05 were considered significant.Results:The ∆PA3235 strain was successfully constructed. At 37 ºC, the mutant produced less pyocyanin (p-value 0.0004), pyoverdine (p-value 0.0009), and swarm area than the wild-type. The dendrites pattern of both strains was similar. The mutant and parental strains showed no differences in swimming and twitching motility when incubated at 22 ºC and 37 ºC. The mutant produced more biofilm compared to the wild-type strain (p-value 0.0013). The AHL was higher in the mutant than in wild type strain (p-value 0.0095) after 24 h incubation. Both the wild type and mutant strains exhibited similar growth patterns in LB broth. The mutant colonies also showed the same morphology as the wild type on the LB plate (not shown here).Conclusion:The deletion of the PA3235 gene from thePseudomonas aeruginosagenome caused some changes in virulence factors production, as the bacterium grew at body temperature 37°C. We predicted that the PA3235 gene might function to transport molecules involved in the early infection of this bacterium to human

Pelatihan Pertanian Secara Vertikultur di Kampung Mejoyo RT 03 RW 07 Surabaya

Kelompok warga RT 03 RW 07 Mejoyo Surabaya adalah masyarakat yang aktif dan rajin. Kampung ini selalu berprestasi khususnya dalam hal lingkungan hidup dan Usaha Mikro Kecil dan Menengah (UMKM). Program pengabdian masyarakat yang didanai DIKTI ini bertujuan untuk memberdayakan warga kampung dalam hal pertanian sayur organik dengan memanfaatkan lahan sempit yang merupakan sepetak tanah fasilitas umum dari Universitas Surabaya (UBAYA). Selain itu, hasil budidaya sayur diolah sehingga terdapat nilai tambah dan solusi jika panen berlebihan atau hasil panen tidak laku terjual. Agar rintisan usaha ini sukses, warga juga dibekali dengan manajemen keuangan dan pemasaran. Peningkatan kemampuan masyarakat dalam hal pertanian organik vertikultur diukur dengan memberikan pre test dan post test. Hasilnya adalah adanya peningkatan keterampilan warga, yaitu sebesar 16%. Sedangkan keterlibatan mahasiswa Merdeka Belajar Kampus Merdeka (MBKM) di dalam program ini dinilai sangat efektif untuk memperkaya pengalaman mahasiswa dalam mengabdi di masyarakat. Hal ini tertuang dalam nilai keterlibatan masing-masing siswa yaitu antara A dan B

Genetic Variant of SARS-CoV-2 Isolates in Indonesia: Spike Glycoprotein Gene

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a novel coronavirus and the primary causative agent of coronavirus disease 2019 (COVID-19), first occurred in China and rapidly spread worldwide. The government of the Republic of Indonesia confirmed its first two cases of COVID-19 in March 2020. COVID-19 is a serious illness with no efficacious antiviral medication or approved vaccine currently available. Therefore, there is a need to investigate the genome of SARS-CoV-2. In this study, we characterized SARS-CoV-2 spike glycoprotein genes from Indonesia to investigate their genetic composition and variability. Overall, ten SARS-CoV-2 spike glycoprotein gene sequences retrieved from GenBank (National Center for Biotechnology Information, USA) and the GISAID EpiCoV database (Germany) were compared. We analyzed nucleotide variants and amino acid changes using Molecular Evolutionary Genetics Analysis (MEGA) X and analyzed gene similarity using the LALIGN web server. Interestingly, we revealed several specific mutation sites, however, there were no significant changes in the genetic composition of SARS-CoV-2 spike glycoprotein genes, when compared to the WuhanHu-1 isolate from China. However, this is a preliminary study and we recommend that molecular epidemiology and surveillance programs against COVID-19 in Indonesia be improve

Concept of SARS-CoV-2 Vaccine Design to Fight COVID-19 Pandemic: A Review Insight

Cluster of pneumonia infection emerged in Wuhan, China due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Additionally, more than 190 countries have confirmed 82 million cases of SARS-CoV-2 infection. Currently, there is a SARS-CoV-2 epidemic, and no effective prophylactic methods are available. A vaccine is considered as an effective method to restrict an epidemic. Several vaccine designing techniques have been established, which is enabling researchers from various institutes for developing vaccine towards SARS-CoV-2 infections. In this review, we condense the development of vaccine research against SARS-CoV-