diskusi santuyy covid-19...apa itu sars-cov-2/covid-19 ? • severe acute respiratory syndrome...
TRANSCRIPT
Divisi Biologi Molekuler dan Genetika, Generasi Biologi Indonesia Foundation
Jl. Swadaya Barat No. 4, Semampir, Cerme, Gresik, Jawa Timur
Viol Dhea Kharisma, S.Si., AMRSB
DISKUSI SANTUYY COVID-19 “Peranan Pendekatan Komputasi dalam Proses Penelitian Obat dan Vaksin“
Apa Itu SARS-CoV-2/COVID-19 ?
• Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from International Committee on Taxonomy of Viruses (ICTV) & Coronavirus Disease (COVID-19) from World Health Organization (WHO)
• SARS-CoV-2 belongs to the broad family of viruses known as coronaviruses
• It is a positive-sense single-stranded RNA (+ssRNA) virus
• Each SARS-CoV-2 virion is approximately 50–200 nanometres in diameter
Illustration of a SARS-CoV-2 virion
(https://phil.cdc.gov/details.aspx?pid=23312) • The WHO considers bats the most likely natural
reservoir of SARS-CoV-2
Kok Bisa Coronavirus Mengenai Manusia ?
Sumber : Epomedicine
ADAPTASI SEL INANG
VIRUS TIPE BARU
Rekombinasi Genetik Mutasi
COVID-19 vs Virus Influenza
Source Image: Horsetalk NZ
Virus Influenza Source Image: Science Friday
Virus Influenza
Struktur Virus
Image Source: (https://www.assaygenie.com/)
• Like other coronaviruses, SARS-CoV-2 has four structural proteins, known as the S (spike), E (envelope), M (membrane glycoprotein, and N (nucleocapsid protein)
• N protein holds the RNA genome
• S, E, and M proteins together create the viral envelope
• The spike protein is the protein responsible for allowing the virus to attach to the membrane of a host cell
• SARS-CoV-2 has sufficient affinity to the angiotensin converting enzyme 2 (ACE2) receptors of human cells to use them as a mechanism of cell entry.
Molecular Simulation of Complex SARS-CoV-2 Glycoprotein-ACE2 (these manuscript is under review by publisher)
Contoh Simulasi Komputasi
• Spike glycoprotein S1 attaches the virion to the cell membrane by interacting with host receptor, initiating the infection.
• Binding to human ACE2
• Internalization of the virus into the endosomes of the host cell induces conformational changes in the S glycoprotein
Bagaimana caranya agar kita dapat menentukan strategi yang tepat untuk mendesain obat maupun vaksin dari COVID-19 melalui komputasi ?
Proses Perbanyakan COVID-19
Vaksin Obat
Problematika Waktu Penelitian
Image Source: Researchgate
Mengenal Bioinformatika
Mengenal Bioinformatika
Alat Penelitian Komputasi
Database
Webserver
Software
https://www.ncbi.nlm.nih.gov/
https://pubchem.ncbi.nlm.nih.gov/ >seq COVID MFVFLLLSVPRDVVLTGRVLVYIRGFNCG
https://swissmodel.expasy.org/
https://pyrx.sourceforge.io/ https://pymol.org/2/
Contoh Data Penelitian COVID-19 >MN908947.3_NCBI MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT
Kode Genetik Protein Spike COVID-19
Model Struktur 3D Spike COVID-19
©Arif Nur Muhammad Ansori & Viol Dhea Kharisma
Contoh Data Penelitian COVID-19
Pemetaan Epitop Sel B Pada Spike COVID-19 Peptida Kandidat Vaksin COVID-19 Berikatan Pada
Reseptor Sel B
©Arif Nur Muhammad Ansori & Viol Dhea Kharisma
Contoh Hasil Riset Komputasi Desain Obat
Simulasi Pengikatan Senyawa Kandidat Obat Berbasis Bahan Alam Pada Protein
Fungsional HIV-1
Referensi: Kharisma, V. D., Septiadi, L., & Syafrudin, S. (2019). Prediction of Novel Bioactive Compound from Zingiber officinale as Non-nucleoside Reverse Transcriptase Inhibitors (NNRTIs) of HIV-1 through Computational Study. Bioinformatics and Biomedical Research Journal, 1(2), 49-55.
Sumplemen Referensi
SARS-CoV-2
Bioinformatics
Ji, W., W. Wang W, X. Zhao, J. Zai, & X. Li. 2020. Cross-species transmission of the newly identified coronavirus 2019-nCoV. J. Med. Virol. 92(4):433-440. doi: 10.1002/jmv.25682.
Guo, Y. R., Cao, Q. D., Hong, Z. S., Tan, Y. Y., Chen, S. D., Jin, H. J., Tan, K. S., Wang, D. Y., & Yan, Y. (2020). The origin, transmission and clinical therapies on coronavirus disease 2019 (COVID-19) outbreak - an update on the status. Military Medical Research, 7(1), 11. https://doi.org/10.1186/s40779-020-00240-0
https://www.nytimes.com/interactive/2020/03/11/science/how-coronavirus-hijacks-your-cells.html
Cao, Y., Li, L., Feng, Z. et al. Comparative genetic analysis of the novel coronavirus (2019-nCoV/SARS-CoV-2) receptor ACE2 in different populations. Cell Discov 6, 11 (2020). https://doi.org/10.1038/s41421-020-0147-1
Ansori, A.N.M., & V.D. Kharisma. 2020. Characterization of Newcastle Disease Virus in Southeast Asia and East Asia: Fusion Protein Gene. EKSAKTA: Jurnal Ilmu-ilmu MIPA. 20(1): 20-28. doi: 10.20885/eksakta.vol1.iss1.art3
Adianingsih, O.R., & V.D. Kharisma. 2019 Study of B cell epitope conserved region of the Zika virus envelope glycoprotein to develop multi-strain vaccine. J. Appl. Pharm. Sci. 9(01):098–103.
Syafrudin, S., Septiadi, L., Alfaruqi, N., Wahyudi, D. and Kharisma, V. (2018) “The In Silico Analysis and Identification of Possible Inhibitor of H5N1 Virus”, Bioinformatics and Biomedical Research Journal, 1(2), pp. 33-39.