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All Journal Jurnal Teknologi Perikanan dan Kelautan Jurnal Pangan dan Gizi Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences JURNAL KIMIA SAINS DAN APLIKASI Interaksi Online Microbiology Indonesia Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati Pro-Life Jurnal Profesi Medika: Jurnal Kedokteran dan Kesehatan Jurnal Kimia Terapan Indonesia Indonesian Journal of Chemistry MITRA: Jurnal Pemberdayaan Masyarakat Warta Ikatan Sarjana Komunikasi Indonesia Journal of Tropical Biodiversity Jurnal Informasi Pengabdian Masyarakat Jurnal Pengabdian Kepada Masyarakat
Vivitri Dewi Prasasty
Faculty Of Biotechnology, Atma Jaya Catholic University Of Indonesia
Religion Agriculture, Biological Sciences & Forestry Humanities Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Computer Science & IT Decision Sciences, Operations Research & Management Economics, Econometrics & Finance Education Engineering Environmental Science Health Professions Immunology & microbiology Languange, Linguistic, Communication & Media Library & Information Science Materials Science & Nanotechnology Medicine & Pharmacology Public Health Social Sciences

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Structure-Based Design and Molecular Dynamics Simulations of Pentapeptide AEYTR as a Potential Acetylcholinesterase Inhibitor Vivitri Dewi Prasasty; Enade Perdana Istyastono
Indonesian Journal of Chemistry Vol 20, No 4 (2020)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (16.267 KB) | DOI: 10.22146/ijc.46329

Abstract

Structure-based virtual screening protocol to identify potent acetylcholinesterase inhibitors was retrospectively validated. The protocol could be employed to examine the potential of designed compounds as novel acetylcholinesterase inhibitors. In a research project designing short peptides as acetylcholinesterase inhibitors, peptide AEYTR emerged as one of the potential inhibitors. This article presents the design of AEYTR assisted by the validated protocol and guided by literature reviews followed by molecular dynamics studies to examine the interactions of the pentapeptide in the binding pocket of the acetylcholinesterase enzyme. The molecular dynamics simulations were performed using YASARA Structure in Google Cloud Platform. The peptide AEYTR was identified in silico as a potent acetylcholinesterase inhibitor with the average free energy of binding (DG) of -19.138 kcal/mol.
Computer-Aided Discovery of Pentapeptide AEYTR as a Potent Acetylcholinesterase Inhibitor Enade Perdana Istyastono; Vivitri Dewi Prasasty
Indonesian Journal of Chemistry Vol 21, No 1 (2021)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.55447

Abstract

One of the key targets in the drug development for potential Alzheimer’s disease (AD) therapeutics is the search for acetylcholinesterase enzyme (AChE) inhibitors. Very recently, a pentapeptide AEYTR was reported as a potential inhibitor for AChE. The peptide was identified in a retrospectively validated virtual screening campaign, which was subsequently followed by 10 ns molecular dynamics (MD) simulations. The study aimed to characterize the structure and identify in vitro of AEYTR peptide as a potent acetylcholinesterase inhibitor. This article presents the structure characterization and the in vitro examination of the peptide as an AChE inhibitor, followed by MD simulations for 100 ns. The results show that the pentapeptide is a potent AChE inhibitor with an IC50 value in the picomolar range and stabilizes the enzyme during MD simulations.
The Relationship Between Cervical Cancer Severity and miRNA-205 Expression in Bali Kartika Sari; Desak Putu Oki Lestari; Novitasari Novitasari; Yudhi Nugraha; Vivitri Dewi Prasasty; Septi Panca Sakti
Jurnal Profesi Medika : Jurnal Kedokteran dan Kesehatan Vol 16 No 2 (2022): Jurnal Profesi Medika : Jurnal Kedokteran dan Kesehatan
Publisher : Fakultas Kedokteran UPN Veteran Jakarta Kerja Sama KNPT

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33533/jpm.v16i2.4106

Abstract

Cervical cancer is the one of leading cause of death for women worldwide. It occurs due to infection with the human papilloma virus (HPV) which attacks the cervix in the female reproductive organs. The detecting cervical cancer method is by using pap smears and liquid based cytology (LBC) and vaccinations. However, both methods are limited in detecting cervical cancer quickly and accurately. This study aims to find potential biomarkers that will be used to quickly detect the development of cervical cancer. Large-scale studies have shown that microRNA-205 (miRNA) regulation has a very important role in various types of cancer including cervical cancer. The extraction and synthesis of cDNA from 26 preparations of cervical cancer paraffin blocks were measured by quantitative real time PCR to evaluate the expression of miRNA-205 as a biomarker of cervical cancer in cervical cancer samples. Statistical results showed that there was a significant difference in the expression of miRNA-205 which was relatively higher in cervical cancer patients (p<0.05) miRNA-205. In addition, the increased expression of miRNA-205 is associated with an increase in the severity of cervical cancer. We conclude that miRNA-205 is a potential candidate for cervical cancer molecular biomarker.
In Silico Screening and Designing Synthesis of Cinchona Alkaloids Derivatives as Potential Anticancer Muhammad Hanafi; Rosmalena Rosmalena; Vivitri Dewi Prasasty; Linar Zalinar Udin; Gian Primahana
Journal of Tropical Life Science Vol. 7 No. 2 (2017)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.07.02.06

Abstract

P-glycoprotein (P-gp) resistance in cancer cells decreases intracellular accumulation of various anticancer drugs. This multidrug resistance (MDR) protein can be modulated by a number of non-cytotoxic drugs. We have screened 30 chincona alkaloids derivatives as a potent P-gp inhibitor agent in silico. Hereby, we report the highest potential inhibitions of P-gp is Cinchonidine isobutanoate through molecular docking approach. with affinity energy -8.6 kcal/mol and inhibition constant, Ki is 4.89 x 10-7 M. Cinchonidine isobutanoate is also known has molecular weight below 500, Log P value 3.5, which is indicated violation free of Lipinski`s rule of five. Thus, Cinchonidine isobutanoate is the most potent compound as anticancer compare to other Cinchona alkaloids. Ultimately, we design Cinchonidine isobutanoate for further lead synthesis by using DBSA, act as a combined Brønsted acid-surfactant-catalyst (BASC) to obtain high concentration of organic product by forming micellar aggregates which is very powerful catalytic application in water environment.
Structural Stability of ADTC5 Peptide: Conformational Insights into Dynamics and Its Binding Mode Parsaoran Siahaan; Vivitri Dewi Prasasty; Bungaran David Simanjuntak; Suci Hildayani; Khairul Anam
Journal of Tropical Life Science Vol. 7 No. 2 (2017)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.07.02.09

Abstract

The cyclic structure of ADTC5 (Ac-CDTPPVC-NH2) peptide is known has ability to modulate homo dimer E-cadherin interactions to form adherens junction at the intercellular junction.  The ability to inhibit E-cadherin interaction has become important to increase paracellular porosity in delivering drug molecules to the target cell. There are two types of ADTC5 state: opened-cyclic state (OCS) and closed-cyclic state (CCS). OCS of ADTC5 is affected by distance constraint and CCS is formed by disulfide bond from terminal cysteines through force restraint. The aim of this research is to investigate the inhibition activity of ADTC5 peptide upon E-cadherin. Here we used molecular docking and molecular dynamics approaches. The structure of ADTC5 peptide was generated by PyMOL program. GROMACS v4.5.5 was utilized to simulate molecular dynamics. The optimized ADTC5 molecule was placed in aqueous or polar condition at physiological pH. Furthermore, ADTC5 was docked with EC1-EC2 coupled domain of E-cadherin using AutoDock 4.2 and be refined using molecular dynamic (MD). The result showed that CCS ADTC5 peptide has stronger affinity and more stable interaction with EC1-EC2 coupled domain than the OCS one.
Online Training on How to Produce Hygienic Tempeh during the Covid-19 Pandemic Tati Barus; Rory Anthony Hutagalung; Rianita Pramitasari; Vivitri Dewi; Alfonsus Samuel Satya Pradipta
MITRA: Jurnal Pemberdayaan Masyarakat Vol. 6 No. 2 (2022): Mitra: Jurnal Pemberdayaan Masyarakat
Publisher : Institute for Research and Community Services

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.25170/mitra.v6i2.2976

Abstract

One of the Indonesian government's strategies to control the spread of the Covid-19 virus is to restrict people’s mobility when going out, which is often called the Implementation of Restrictions on Social Activities (PPKM). As a consequence of this PPKM, access to sufficient food tends to be rather limited. One effort to help people meet their food needs was through online tempeh-making training. This training, conducted online using Zoom and WhatsApp groups, involved community members who were connected through several health-related WhatsApp groups. The participants were all Indonesian from various areas, including the Greater Jakarta area, Ambon, Makassar, Medan, Padang, and even the US. Most of them were over 40 years old and were either employees or college graduates. Considering the significance of tempeh as a food item in Indonesia and a relatively affordable source of protein, the training became relevant in helping the participants to produce their own tempeh at home amidst the Covid-19 pandemic. After the training, all participants were found to be able to make tempeh with good quality and hygiene, with several participants even exhibiting creativity in processing their tempeh into more advanced tempeh products, such as tempeh noodles, tempeh pudding, and tempeh steak. In addition, their positive perception of tempeh as a healthy food item increased after attending the training.
Genotypic Characterization of Rhizopus Spp. Tempeh and Usar: Traditional Inoculum of Tempeh in Indonesia tati barus; Jason Wiranata Sanjaya; Anastasia Tatik Hartanti; Adi Yulandi; Vivitri Dewi Prasasty; David Tandjung
Microbiology Indonesia Vol. 14 No. 3 (2020): September 2020
Publisher : Indonesian Society for microbiology

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1214.939 KB) | DOI: 10.5454/mi.14.3.3

Abstract

Abstract. Soybeans tempeh (tempeh) is processed by fermentation using Rhizopus spp. Tempeh is an important source of protein in Indonesia. The traditional inoculum in fermentation locally is known as Usar which is made from the leaves of Hibiscus tiliaceus. However, Rhizopus information from Usar is still limited. Therefore, this study aims to identify and investigate the genetic diversity of Rhizopus species from Usar and tempeh based on the Internal Transcribed Spacer (ITS) sequence and the Random Amplified Polymorphic DNA (RAPD) markers. Twenty-three Rhizopus strains were isolated from Usar and ten Rhizopus strains were isolated from tempeh. Based on ITS sequences, the isolates were similar to R Rhizopus microsporus (30 isolates) and Rhizopus delemar (3 isolates) with 98-99% similarity. The genetics of R. microsporus and R. delemar are varied and different from the genetics of R. microsporus from tempeh. The growth temperature of R. microsporus varies from 33 to 48°C and R. delemar can grow to a maximum at 33°C. The role of R. microsporus and R. delemar from Usar in determining the quality of tempeh is still limited. Therefore, it needs to be investigated further.
Interaction Studies Between Cyclic Peptide ADT-C3 (Ac-CADTPC-NH2) with E-Cadherin Protein using the Molecular Docking Method Simulated on 120ns Parsaoran Siahaan; Vivitri Dewi Prasasty; Atiatul Manna; Dwi Hudiyanti
Jurnal Kimia Sains dan Aplikasi Vol 21, No 2 (2018): Volume 21 Issue 2 Year 2018
Publisher : Chemistry Department, Faculty of Sciences and Mathematics, Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (744.917 KB) | DOI: 10.14710/jksa.21.2.85-91

Abstract

The treatment of diseases that attack the brain is very difficult, because the delivery of drug molecules to the brain is often hindered by the blood-brain barrier (BBB). So that the drug delivery is not right on the target cell. Thus, was developed a method in modulation of intercellular junctions using ADTC3 cadherin peptide, Where the cadherin peptide is derived from the cadherin sequence itself. The method used in this research is molecular dynamics (DM) and molecular docking. In this study have been evaluated some peptide conformation in modulating intercellular junction. The results show that cyclic peptide ADT-C3 (Ac-CADTPC-NH2) was conducted DM for 120 ns (120000 ps), which has considerable activity in modulating intercellular junctions with binding energies of -33.10 kJ.mol-1 and Ki of 1.58 μM at the 79187 ps conformation. The binding site on residues Asp1, Trp2, Ile4, Lys25, Ser26, Asn27, Met92 in the adhesion arm-acceptor pocket region.
Pemanfaatan Media Sosial Instagram Untuk Promosi Kampung Pancasila Vivitri Endah Andriani; Mira Adita Widianti; Muhammad Iqbal Aulia
Jurnal Informasi Pengabdian Masyarakat Vol. 2 No. 2 (2024): Mei : Jurnal Informasi Pengabdian Masyarakat
Publisher : Institut Nalanda

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.47861/jipm-nalanda.v2i2.952

Abstract

The limited knowledge of the village community regarding social media Instagram as a medium for promoting Pancasila Village, Cikadu Village means that they are less able to introduce Pancasila Village optimally. Through Community Service activities, it is hoped that we can contribute to the use of Instagram social media to the local community. The aim of this activity is to provide education to the public on how to use Instagram social media to introduce and promote Pancasila Village and the potential that exists in Cikadu Village, so that it is hoped that the wider community can become more familiar and aware of the existence of Pancasila Village and its various potentials in Cikadu Village. Apart from that, this activity is expected to provide education regarding digital media literacy.
Uji Aktivitas Enzim Selulase Baglog Jamur Pleurotus cystidiosus, Pleurotus ostreatus dan Auricularia auricula dengan Pelarut Berbeda Zulfa, Astri; Qonitah, Tsabitah Athifah; Ragamustari, Safendrri K; Prasasty, Vivitri Dewi
Jurnal Pro-Life Vol. 11 No. 2 (2024): Juli
Publisher : Program Studi Pendidikan Biologi Fakultas Keguruan dan Ilmu Pendidikan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33541/jpvol6Iss2pp102

Abstract

Cellulase enzyme activity is essential for the breakdown of cellulose, a major component of plant cell walls. This enzyme is produced by a variety of microorganisms, including fungi such as mushrooms. This study aimed to evaluate the cellulase enzyme activity extracted from the baglogs of three different mushrooms: Pleurotus cystidiosus (brown oyster mushroom), Pleurotus ostreatus (white oyster mushroom), and Auricularia auricula (wood ear mushroom). The extraction was conducted using three different solvents: aquadest (distilled water), saline solution, and citrate buffer at pH 4. The cellulase activity was assessed under optimal conditions of 60 °C incubation temperature and 60 minutes incubation time. The results indicated that the lowest cellulase activity was found in the baglogs of Pleurotus cystidiosus extracted with aquadest, measuring at 0.0253 IU/mL. Conversely, the highest cellulase activity was observed in the baglogs of Pleurotus ostreatus extracted with aquadest, with an activity level of 0.0728 IU/mL. The glucose concentration, which serves as an indicator of the enzymatic hydrolysis of carboxymethyl cellulose (CMC), was highest in Pleurotus ostreatus extracted with aquadest at 393.043 ppm. These findings suggest that Pleurotus ostreatus is the most effective species for cellulase production among the tested mushrooms when extracted with aquadest. The optimal extraction and assay conditions determined in this study can guide future research and industrial applications in enhancing cellulase enzyme production from mushroom baglogs, particularly in bioconversion processes and bioethanol production.
Co-Authors A.A. Ketut Agung Cahyawan W ADI YULANDI Albert Deniel Sitorus Alfonsus Samuel Satya Pradipta Anam, M. Khairul Anastasia Tatik Hartanti Atiatul Manna Aziz, Husna Abdul Berliana, Ester Bryant Adelar Bungaran David Simanjuntak Camin, Yeremiah Rubin David Tandjung Desak Putu Oki Lestari Dinar Kadarsih DR Sunarto Dwi Hudiyanti Enade Perdana Istyastono Enade Perdana Istyastono Ernawati Sinaga Fatmawaty Fatmawaty Febriani, Amadhea Zahra Firyal Nailah Khansa Gian Primahana Gracia Halim Hapsari Dwiningtyas Hildayani, Suci Jason Wiranata Sanjaya Jeremy Oktavian Kartika Sari Khairul Anam Linar Zalinar Udin Linar Zalinar Udin, Linar Zalinar Lumbantoruan, Lamtiur M Bayu Widagdo Mario Gunadi Marthin, Jeffrey Meda Canti Mira Adita Widianti Muhammad Hanafi Muhammad Hanafi Muhammad Iqbal Aulia Noverita Novitasari Novitasari Nur’aida, Tasya Parsaoran Siahaan Pradhana, Yudha Primahana, Gian Qonitah, Tsabitah Athifah Ragamustari, Safendrri K Ramadhan, Muhammad Alfahrezi Baihaqi Rianita Pramitasari Roihandro, Mohammad Daffa Rory Anthony Hutagalung Rosmalena Rosmalena Rosmalena Rosmalena Rosmalena, Rosmalena Septi Panca Sakti Simanjuntak, Bungaran David Simanjuntak, Kristina Siti Nurbaya Soewono, Arka Dwinanda Suci Hildayani Tati Barus Vinella Winata Vinvin Vinvin Wicaksono, Wisnu Adi Widianti, Mira Adita Widyah Widyah Widyah, Widyah Wisnu Adi Wicaksono Yudhi Nugraha Zulfa, Astri