Drug/Vaccine Design and Delivery

Viral infection is a very serious threat to humanity. It causes malicious diseases, such as HIV/AIDS, dengue, and Avian Influenza, therefore, novel method in virology to combat the viral infection is necessary. Bioinformatics provides outstanding tools for developing vaccines, PCR primers, mutation detection and drugs based design on genetic engineering principles. Those tools are mostly freeware. Algorithm from the computer science has made major contribution to them. Bioinformatics experiment greatly reduces the cost and time in wet laboratory experiment. Our labs has successfully designed PCR primers, vaccines, drugs, and mutations prediction. The future of medicine will greatly be shaped by advancement in bioinformatics.

I'm collaborating on this project with Prof Usman Sumo Tambunan's Bioinfomatics labs in Bioinformatics Research Group, Department of Chemistry, University of Indonesia. Here is the list of our collaborators:

• Dr. Ridla Bakri from Department of Chemistry FMIPA UI
• Dr Syarifuddin Idrus from Indonesian Ministry of Industrial affair,
• Prof. Djati Kerami from Department of Mathematics FMIPA UI,
• Fitri Amelia.,MSi from Department of Chemistry, State University of Padang,
• Hilyatuz Zahroh.,MSi from Department of Chemistry, State Islamic University of Syarif Hidayatullah Jakarta

Here is my publications:

1. A.A. Parikesit, Introductory Chapter: The Contribution of Bioinformatics as Blueprint Lead for Drug Design, in: Ivana Glavic (Ed.), Mol. Insight Drug Des., IntechOpen, London, 2018: p. 7. doi:10.5772/INTECHOPEN.79664. [link available here]
2. A.A.P. Parikesit, U.S.F. Tambunan, COMPUTATIONAL PROTEIN DESIGN IN GREEN CHEMISTRY, Rasayan J. Chem. 11 (2018) 1133–1138. doi:10.31788/RJC.2018.1133038. [link available here]
3. A.A. Parikesit, R. Nurdiansyah, D. Agustriawan, TELAAH SISTEMATIS TERHADAP BASIS DATA BAHAN ALAM UNTUK PENGEMBANGAN PRODUK SUPLEMEN HERBAL, Pros. SEMNASTAN. 0 (2018) 62–68. https://jurnal.umj.ac.id/index.php/semnastan/article/view/2259/1874 (accessed January 28, 2018). [link available here]
4. F. Amelia, Iryani, P.Y. Sari, A.A. Parikesit, R. Bakri, E.P. Toepak, U.S.F. Tambunan, Assessment of Drug Binding Potential of Pockets in the NS2B/NS3 Dengue Virus Protein, IOP Conf. Ser. Mater. Sci. Eng. 349 (2018) 012021. doi:10.1088/1757-899X/349/1/012021.[link available here]
5. U.S.F. Tambunan, A.A. Parikesit, M.A.F. Nasution, A. Hapsari, D. Kerami, Exposing the Molecular Screening Method of Indonesian Natural Products Derivate as Drug Candidates for Cervical Cancer (Summer 2017), Iran. J. Pharm. Res. 16 (2017) 1113–1127. [link available here] .
6. U. Sumo, F. Tambunan, A.A. Parikesit, V.C. Adam, M. Arfin, F. Nasution, R.D. Puspitasari, D. Kerami, VIRTUAL SCREENING OF COMMERCIAL CYCLIC PEPTIDES AS β - OG POCKET BINDER INHIBITOR IN DENGUE VIRUS SEROTYPE 2, Int. J. Spec. Issue Sci. Eng. Environ. 12 (2017) 60–68. doi:10.21660/2017.37.2780. [link available here]
7. U. Tambunan, M. Nasution, F. Azhima, A. Parikesit, E. Toepak, S. Idrus, D. Kerami, Modification of -Adenosyl--Homocysteine as Inhibitor of Nonstructural Protein 5 Methyltransferase Dengue Virus Through Molecular Docking and Molecular Dynamics Simulation, Drug Target Insights. 11 (2017). doi:10.1177/1177392817701726.[link available here]
8. U.S.F. Tambunan, A.H. Alkaff, M.A.F. Nasution, A.A. Parikesit, D. Kerami, Screening of commercial cyclic peptide conjugated to HIV-1 Tat peptide as inhibitor of N-terminal heptad repeat glycoprotein-2 ectodomain Ebola virus through in silico analysis, J. Mol. Graph. Model. 74 (2017) 366–378. doi:10.1016/j.jmgm.2017.04.001.[link available here]
9. U.S.F. Tambunan, A.A. Parikesit, F. Wardani, M.A.. Nasution, D. Kerami, IN SILICO STUDY OF GUANOSINE TRIPHOSPHATE (GTP) AND RIBAVIRIN DERIVATIVES AS THE INHIBITOR FOR NS5 METHYLTRANSFERASE OF DENGUE VIRUS, Rasayan J. Chem. 10 (2017) 910–921. doi:10.7324/RJC.2017.1031613. [link available here]
10. U.S.F. Tambunan, M.A.F. Nasution, A.A. Parikesit, H. Noviardi, D. Kerami, Designing of Disulfide Cyclic Peptide for Inhibiting Polymerase A and B1 (PAC-PB1N) in H1N1 Virus using Molecular Simulation Approach, Online J. Biol. Sci. 16 (2016) 122–129. doi:10.3844/ojbsci.2016.122.129. [link available here]
11. Friend Tambunan, Usman Sumo, William Chua, Arli Aditya Parikesit, and Djati Kerami. Designing Disulfide Cyclic Peptide as Fusion Inhibitor That Targets Denv Envelope Protein. Jurnal Teknologi 78, no. 4–3 (April 18, 2016). doi:10.11113/jt.v78.8259. [available online]
12. Tambunan, Usman, Feimmy Sipahutar, Arli Parikesit, and Djati Kerami. Vaccine Design for H5N1 Based on B- and T-Cell Epitope Predictions. Bioinformatics and Biology Insights 2016, no. 10 (April 28, 2016): 27. doi:10.4137/BBI.S38378. [available online]
13. Tambunan, U.S.F, R Bakri, A.A. Parikesit, T. Ariyani, R.D. Puspitasari, and D. Kerami. In Silico Modification of Zn 2+ Binding Group of Suberoylanilide Hydroxamic Acid (SAHA) by Organoselenium Compounds as Homo Sapiens Class II HDAC Inhibitor of Cervical Cancer. IOP Conference Series: Materials Science and Engineering 107, no. 1 (February 5, 2016): 012054. . [available online]
14. Parikesit, A A, B Ardiansah, D M Handayani, U S F Tambunan, and D Kerami. Virtual Screening of Indonesian Flavonoid as Neuraminidase Inhibitor of Influenza a Subtype H5N1. IOP Conference Series: Materials Science and Engineering 107, no. 1 (February 5, 2016): 012053. [available online].
15. Tambunan, U.S.F., Zahroh, H., Parikesit, A.P., Idrus, S., Kerami, D. 2015. Screening analogs of β-OG pocket binder as fusion inhibitor of dengue virus 2. Drug Target Insight/Libertas Academica [available online]
16. Tambunan, U.S.F., Parikesit,A.P., Abi S. Ghifari., Cipta Prio Satriyanto . In silico identification of 2-oxo-1,3-thiazolidine derivatives as novel inhibitors candidate of class II histone deacetylase (HDAC) in cervical cancer treatment. Arabian Journal of Chemistry. Elsevier [in press, pre-print available online]
17. Tambunan, U.S.F., Chua, W., Parikesit,A.P., Kerami, D. 2015. Designing Disulfide Cyclic Peptide as Fusion Inhibitor That Targets DENV Envelope Protein. ICCSS 2015 Conference Proceeding [in press]
18. Tambunan, U.S.F., Parikesit,A.P., Gunadi, Y., Kerami, D. 2015. Designing cyclopentapeptide inhibitor of neuraminidase H5N1 virus through molecular and pharmacology simulations. IEEE Journal of Tsinghua Science and Technology [available online]
19. Tambunan, U.S.F., Rachmania, R., Parikesit,A.P. 2015. In silico modification of oseltamivir as neuraminidase inhibitor of influenza A virus subtype H1N1. Journal of Biomedical Research/Journal of Nanjing Medical University 9(2):150-159 [available online]
20. Bakri, R.,Parikesit, A.P.,Satriyanto, C.P.,Kerami, D.,Tambunan, U.S.F. 2014. The in silico Molecular Interaction of Organoboron Compounds as Curative Measure toward Cervical Cancer. Conference Proceeding of 9th Joint Conference on Chemistry, Diponegoro University, Semarang [available online]
21. Parikesit, A.P.,Noviardi, H.,Tambunan, U.S.F., Kerami, D. 2014. The Complexity of Molecular Interactions and Bindings between Cyclic Peptide and inhibit Polymerase A and B1 (PAC-PB1N) H1N1. Conference Proceeding of 9th Joint Conference on Chemistry, Diponegoro University, Semarang [available online]
22. Bakri, R.,Parikesit, A.P.,Satriyanto, C.P.,Kerami, D.,Tambunan, U.S.F. 2014. Utilization of boron compounds for the modification of suberoyl anilide hydroxamic acid (SAHA) as inhibitor of histone deacetylase (HDAC) class II Homo sapiens. Advances in Bioinformatics. 7. Hindawi Press [available online]
23. Bakri, R.,Parikesit, A.P.,Satriyanto, C.P.,Kerami, D.,Tambunan, U.S.F. 2014. Utilization of boron compounds for the modification of suberoyl anilide hydroxamic acid (SAHA) as inhibitor of histone deacetylase (HDAC) class II Homo sapiens. Advances in Bioinformatics. 7. Hindawi Press [available online]
24. Tambunan, U.S.F.,Zahroh, H.,Bimmo B.U., Parikesit, A.A. 2014. Screening of Commercial Cyclic Peptide as Inhibitor NS5 Methyltransferase of Dengue Virus through Molecular Docking and Molecular Dynamics Simulation .Bioinformation, 10(1) [available online]
25. Tambunan, U.S.F., Parikesit, A.A., Dephinto, Y., Sipahutar, F.R.P. 2014. Computational design of drug candidates for influenza A virus subtype H1N1 by inhibiting the viral neuraminidase-1 enzyme. Acta Pharmaceutica, 2/14 (Indexed in Web of Science) [available online]
26. Zahroh, H., Parikesit, A.A., Prio Satriyanto, C.,Tambunan, U.S.F. 2013. The In silico binding interaction of Oseltamivir Derivatives with H7N9 Haemagglutinin and Neuraminidase . ISTB-ITB 2013 Conference Proceeding [in press]
27. Tambunan, U.S.F.,Parikesit, A.A., Prasetia, T., Kerami, D. 2013. In Silico Molecular Interaction Studies of Suberoylanilide Hydroxamic Acid and Its Modified Compounds with Histones Deacetylase Class II Homo sapiens as Curative Measure towards Cervical Cancer. ICBBE 2013 Engineering Conference Proceeding. Engineering 5 (10B), 203-206. [available online]
28. Parikesit, A.A., Zahroh, H., Nugroho, A., Hapsari, A.,Tambunan, U.S.F. 2013. The Computation of Cyclic Peptide with Prolin-Prolin Bond as Fusion Inhibitor of DENV Envelope Protein through Molecular Docking and Molecular Dynamics Simulation. ICBS-UGM 2013 Conference Proceeding [available online]
29. Tambunan, U.S.F., Limans, I.K., Parikesit, A.A. 2013. Molecular dynamic simulation of complex NS2B-NS3 DENV2 protease with potential inhibitors of cyclic tripeptide. African Journal of Biotechnology. 12(28): 4419-4431 [available online]
30. Tambunan, U.S.F., Bakri, R., Prasetia, T.,Parikesit, A.A.,Kerami, D. 2013. Molecular dynamics simulation of complex Histones Deacetylase (HDAC) Class II Homo Sapiens with suberoylanilide hydroxamic acid (SAHA) and its derivatives as inhibitors of cervical cancer. Bioinformation. 9(13): 696-700 [available online]
31. Tambunan, U.S.F., Parikesit, A.A. 2013. In silico approach towards H5N1 virus protein and transcriptomics-based medication. African Journal of Biotechnology. 12(21): 3110-3114 [available online]
32. Tambunan, U.S.F., Pratomo, H., Parikesit, A.A. 2013. Modification of Kampmann A5 as Potential Fusion Inhibitor of Dengue Virus using Molecular Docking and Molecular Dynamics Approach. Journal of Medical Sciences. [available online]
33. Parikesit,A.A.,Kinanty., Tambunan, U.S.F, 2013. Screening of Commercial Cyclic Peptides as Inhibitor Envelope Protein Dengue Virus (DENV) Through Molecular Docking and Molecular Dynamics. Pakistan Journal of Biological Science. [available online]
34. Tambunan, U.S.F., Mochamad Reza Rachdiansyah and A.A. Parikesit , 2013. In Silico Design of the M2 Proton Channel Inhibitors of H1N1 Virus. OnLine Journal of Biological Sciences 03/2013; 13(1):1-12. [available online]
35. Tambunan, U.S.F., Noval Amri and A.A. Parikesit , 2012. In silico design of cyclic peptides as influenza virus, a subtype H1N1 neuraminidase inhibitor. African Journal of Biotechnology. Vol. 11(52), pp. 11474-11491. [available online]
36. Tambunan, U.S.F., Danang Febrianto and A.A. Parikesit , 2012. In silico Genetic Variation Pathogenicity Analysis of Hemagglutinin, Matrix 1, and Non Structural 1 Protein of Human H5N1 Indonesian Strain. IIOABJ. Vol.3 (3):5-14. [available online]
37. Tambunan, U.S.F., R.Harganingtyas and A.A. Parikesit , 2012. In silico Modification of (1R, 2R, 3R, 5S)-(-)- Isopinocampheylamine as Inhibitors of M2 Proton Channel in Influenza A Virus Subtype H1N1, using the Molecular Docking Approach. Trends in Bioinformatics . [available online]
38. Usman Sumo Friend Tambunan and Arli Aditya Parikesit (2012). HPV Bioinformatics: In Silico Detection, Drug Design and Prevention Agent Development, Topics on Cervical Cancer With an Advocacy for Prevention, Rajamanickam Rajkumar (Ed.), ISBN: 978-953-51-0183-3, InTech [available online]
39. Tambunan, U.S.F., N Bramantya and A.A. Parikesit , 2011. In silico modification of suberoylanilide hydroxamic acid (SAHA) as potential inhibitor for class II histone deacetylase (HDAC). BMC Bioinformatics.12(Suppl 13):S23 (Indexed in Web of Science) [available online]
40. Usman Sumo Friend Tambunan, Nissia Apriyanti, Arli Aditya Parikesit , William Chua and Katarina Wuryani. 2011. Computational design of disulfide cyclic peptide as potential inhibitor of complex NS2B-NS3 dengue virus protease. African Journal of Biotechnology Vol. 10 (57), pp. 12281-12290,ISSN 1684-5315 . Academic Journals .(Indexed in Web of Science) [available online]
41. Tambunan, U.S.F., R.S. Noors, A.A. Parikesit , Elyana and W. Ronggo, 2011. Molecular dynamics simulation of DENV RNA-dependent RNA-polymerase with potential inhibitor of disulfide cyclic peptide. OnLine J. Biol. Sci., 11: 48-62.DOI: 10.3844/ojbsci.2011.48.62 [available online]
42. Tambunan, U.S.F., Fadilah and A.A. Parikesit , 2010. Bioactive compounds screening from zingiberaceae family as influenza a/swine flu virus neuraminidase inhibitor through docking approach. OnLine J. Biol. Sci., 10: 151-156. [available online]
43. Usman Sumo Friend Tambunan, and Arli Aditya Parikesit :Cracking The Genetic Code of Human Virus by using Open Source Bioinformatics tools. Journal of Fundamental Sciences Vol 6, No 1 (2010). 42-50 . [available online]
44. Usman Sumo Friend Tambunan, Agus Limanto and Arli Aditya Parikesit : In Silico Analysis of Hemagglutinin, Neuraminidase, and Matrix2 of H5N1 Virus Indonesian Strain Related to Its High Pathogenicity. IIOABJ, 2010; Vol.1 (3): 17-24. [available online]
45. Tambunan, Usman Sumo., Parikesit, Arli Aditya . 2010. In silico Design of Drugs and Vaccines for Dengue Disease. Trends in Bioinformatics. Vol 3. [available online]
46. Tambunan, Usman Sumo., Sugito, Sylvia., Parikesit, Arli Aditya . 2010. Design and Evaluation of Three Pair Primers for Exon 1 Amplification of Hyaluroglucosaminidase-1 Gene. OnLine Journal of Biological Science. 10(2):66-72 [available online]
47. Tambunan, Usman Sumo., Parikesit, Arli Aditya., Hendra., Ichsan Taufik, Rizky., Amelia, Fitri,. Syamsudin., 2009. In Silico Analysis of E DENV-2 and E DENV-3 Protein as the Backbone of Dengue Virus Tetravalent Vaccine by Using Homology Modeling Method. OnLine Journal of Biological Science. 9(1):6-16 [available online]
48. Tambunan, Usman Sumo., Parikesit, Arli Aditya . Tochary, Theo., Sugiono, Dedy. 2007. Computational Study of Post Translation Modification in Chimeric Virus Like Particles Vaccine of Human Papilloma Virus with Virion Capsid L1. Makara journal of Science. University of Indonesia. Vol.11(2):56-62. [available online]