The Bioinformatics Research Groups

Group Leader: Prof. Dr. Usman Sumo Friend Tambunan

Group Members:

Research Fellows:

Ratih Dyah Puspitasari, M.Si

Linggih Saputro (University of South Florida, FL, USA)

Erwin Prasetya Toepak, M.Si

Beny Ernawan, M.Si

Gana L. Dewanto

Notable Alumni

Ahmad Husein Alkaff, M.Si

Atika Marnolia, M.Si

Syafrida Siregar, M.Si

Ade Hanna Natalia, S.Pd, M.Si

Mutiara Saragih, M.Si

Satya Anindita, S.T.P, M.Si

Eka Gunarti Ningsih, S.Pd

Yulianti, S.Si, M.Si

Agustinus C. B. Kantale, S.Pd, M.Si

Elsafira Ariavianti, S.Si, M.Si

Muhammad Chandra Haikal, S.Si

Ina Nur Istiqomah, S.Si

Mega Maulina Ekawati, S.Si

Anjas Randy Bagastama, S.Si

Andrei Bernadette, S.Si

Vincent Jonathan Fleming, S.Si

Muhammad Fauzi Hidayat, S.Si

Hersal Hermana Putra, S.Si

Mochammad Faisal, S.Si

PhD student(s):

Filia Stephanie, S.Si, M.Si

Master student(s):

Wisi Wilanda Syamsi, S.T

Muhammad Reza, S.Si

Sabrina, S.Si

M. Irmawan, S.Si

Shabrina N. Imana, S.T.P

Bachelor student(s):

Zevano C. Sibarani

Ikhsan Muttaqin

Sabar Mulia Sitio

Herland Satriawan

Ig. Satrio Wicaksono

M. Ihsan Muttaqin

M. Irmawan

Saskhia L. T. Putri

Yovita Yudith C.

Zevano C. Sibarani

Della Nurmalasari

Puja Andana

Manaman

National Collaborators:

  1. Dr. Syarifuddin Idrus (Indonesian Ministry of Industrial Affair)
  2. Prof. Dr. Ridla Bakri (Inorganic Chemistry laboratory, Department of Chemistry, Faculty of Mathematics and Science, University of Indonesia)
  3. Hilyatuz Zahroh, M.Sc (YARSI University, Jakarta)
  4. Fitri Amelia, M.Sc (Biochemistry laboratory, Department of Chemistry, Faculty of Science, State University of Padang)
  5. Dr. Arry Yanuar (Faculty of Pharmacy, University of Indonesia)
  6. Taufiq Wirahman, M.Sc (Research Center for Informatics, Indonesian Institute of Sciences)

International Collaborators:

  1. Prof. Dr. Mamoru Suzuki, Laboratorium of Supramolecular Crystallography, Institute of Protein Research, Osaka University, Japan.

More on our research group, kindly click this video profile here.

Bioinformatics is the newly developed field of study that combines computer science and molecular biology. The starting point of this field is the overflowing of information that derives from the Human Genome Project. After its completion, the scientific community realized that there are still many things to do for annotating the genome-based data. The annotation process, as the information arrangement pipeline, is undergoing unfinished works, as the data generation from the wet labs is progressing as well.

The bioinformatics research group is using the groundbreaking softwares, such as MOE, GROMACS, Autodock, and others. As an indispensable part of Chemistry department, we are currently focusing ourselves as users of those softwares.

This group, as a member of Biochemistry Peer Group of Department Chemistry, is focusing its works on the applied biomedics and especially on the drugs, vaccines, and primer design discoveries. However, we had been working as well for the industrial application of bioinformatics, such as the improvement of enzyme stability. Our research is funded by Hibah Dikti/UI. For PhD (doctorate) research, we are surely open to suggestion on how to create the novel pipeline for the data annotation process. To this date, we have secured access to the Indonesian Institute of Sciences (LIPI) cluster computing that provide us sufficient power to conduct complicated calculations.

Current Research Activities:

1. Drugs and Vaccines design of Dengue Virus

Dengue virus is a tropical disease that is surely life threatening. We already developed special pipelines for annotating biomedical related information that beneficial for the development of Drugs and Vaccines for this virus. The protein of NS2B-NS3 dengue virus protease, NS5 methyltransferase (Figure 1), DENV RNA-dependent RNA-polymerase, E DENV-2 and E DENV-3 are the targets of our research. Dengue virus diagnostics, therapeutics and preventive agents development are the focal point for our research roadmap.

 

NS5 methyltransferase

Figure 1: We designed novel drugs for Dengue, targeting NS5 methyltransferase (PDB ID: 3P8Z). The figure shows NS5 methyltransferase binds with 36A ligand (IUPAC Name: (S)-2-amino-4-(((2S,3S,4R,5R)-5-(6-(3-chlorobenzylamino)- 9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran- 2-yl)methylthio)butanoic acid). In our current research, we are trying to find a novel drugs for NS5 methyltransferase by screening the anti-viral database compound and further validate it with computational ADMET test and molecular dynamics simulation.

 

2. Drugs and Vaccines design of Influenza Virus

Influenza Virus are a threatening disease for humanity, as the spread of Avian (H5N1) and Swine (H1N1) influenza are becoming global threat. We already developed special pipelines for annotating biomedical related information that beneficial for the development of Drugs and Vaccines for this virus. For drugs, we are targeting several proteins as our targets, such as neuraminidase, Hemagglutinin, Matrix 1, M2 Proton Channel, and Nonstructural 1. Several inhibitors for those proteins have been developed (Figure 2).

 

Figure 2: The molecular interaction and visualization between neuraminidase-1 (PDB ID: 3CKZ) and Kaempferol 3-rhamnosil-(1-3)-rhamnosyl-(1-6)-glucoside (Parikesit et al., 2016).

 

3. Drugs and Vaccines design of Human Papillomavirus

Human Papilloma Virus (HPV) is the cause of Cervical Cancer that could be life-threatening for women. We already developed special pipelines for annotating biomedical related information that beneficial for the development of Drugs and Vaccines for this virus. Mostly some of our research targeting Histone Deacetylase (HDAC) class II as our approach to combating the HPV, but we also have a research to targeting HDAC class I, Hedgehog and Wnt signaling pathway in order to cure this type of cancer.

 

Figure 3: We designed novel drugs for HPV, one of them is targeting Sonic Hedgehog (Shh) protein. The figure shows the interaction of Sd32 ligand and Shh protein (PDB ID: 3H05).

 

4. Bioinorganic chemistry studies of Enzyme-ligand interaction

We have successfully demonstrated that our computational procedure could detect significant role of organoboron compounds in the enzyme lead compound interaction. The ‘closo’boron based compounds were proven to interact with the amino acid residues, as proven in molecular dynamics simulation (Figure 4 and 5). We constructed this studies based upon the efficacy of organoboron compound as drugs in clinical trial.

orgbrn

Figure 4: The Modification of SAHA with organoboron-based functional group (Bakri et al, 2014)

MD

Figure 5: The molecular dynamics results of organoboron-HDAC interaction (Bakri et al, 2014)

 

5. Drug Design and Development of Ebola Virus (EBOV)

Ebola virus disease (EVD), or simply known as Ebola, remains as one of the most dangerous diseases around the world. According to the World Health Organization (WHO), this disease has caused 11,310 death from 28,616 cases in three countries (Guinea, Sierra Leone, and Liberia) on the recent outbreak in 2014. Moreover, this disease proves to be lethal with 50% average fatality rate, varied from 25% to 90% in the past outbreaks. The most common symptoms of Ebola is fever, headache, vomiting, weakness, loss of appetite, hiccups, conjunctivitis, and diarrhea. Although unexplained hemorrhage (such as bruising and bleeding), kidney and liver dysfunction, cardiovascular distress and hypovolemic shock may occur as well in more serious cases. Although several compounds have been proposed to treat this pathogenic disease, neither approved antiviral drugs nor vaccines are available in the market right now, and most of the drugs that are already given for the Ebola patients only meant to reduce the current symptoms, not directly targeting the virus. Moreover, the extortionate cost of the newly-developed, non-FDA-approved drugs makes the Ebola treatment, especially in poverty areas such as Africa, render ineffective. Thus, the development of new effective, yet inexpensive Ebola drug candidates is necessary and needed at this time. As for today, our studies has created a general pipeline for finding a new drugs for Ebola using our current, latest research pipeline.

 

ebov-gp

Figure 6: The 3D Visualization of EBOV GP in complex with variable Fab domains of IgGs c2G4 and c13C6 (PDB ID: 5KEL)

Previous Research Activities:

 

1. Primer Design for Hyaluroglucosaminidase-1 (HYAL1) Gene

The mutation study of HYAL1 gene was carried out by many researchers, but until now, mutation study of HYAL1 still in progress and limited due to the lack of primer used in amplification of selected DNA sequence of HYAL1 gene and maximum length limitation imposed by DNA sequencer. Online Primer3 program was used to design three pairs of primers. The selected pairs of primer had been subjected to BLASTn operation for selectivity examination while onlineNetPrimer operation was carried out for examination of secondary structures.The results from both operations and trial to real samples using these primers indicated that three pairs of primer were satisfactory for use. The three pairs of primers could be used to amplify specified segments of HYAL1 gene.

 

2. Isolation, Purification, and Characterization of Hyaluronidase from Local Bull Testis

The activity test of Hyaluronidase enzyme is useful for gathering data, before progressing into the molecular biology and bioinformatics study.

3. The enhancement of Enzyme Activity for industrial application

Riboflavin synthase catalyzes conversion of two molecules of 6,7-dimethyl-8-ribityllumazine into one of riboflavin. An In silico simulation of riboflavin synthase of Eremothecium gossypii to convert 6,7-dimethyl-8-ribityllumazine to riboflavin is described. Only one enzyme active site (N-terminal domain) catalyzed riboflavin formation. His108 was an active site from the N-terminal domain, which acted at an early stage of the riboflavin catalysis reaction. These engineering efforts are expected to increase the stability of the enzyme.

 

Selected Publications:

 

Tambunan, U.S.F., Bakri,R., Parikesit,A.A., Ariyani,T., Puspitasari,R.D., & Kerami, D. (2016). In Silico Modification of Zn2+ binding group of suberoylanilide hydroxamic acid (SAHA) by organoselenium compounds as Homo Sapiens class II HDAC inhibitor of cervical cancer. IOP Conference Series:Material Science and Engineering, Volume 107. [ Published manuscript available here]

Parikesit, A.A., Ardiansah B., Handayani, D.M., Tambunan, U.S.F., & Kerami, D. (2016). Virtual Screening of Indonesian flavonoid as neuraminidase inhibitor of influenza A subtype H5N1. IOP Conference Series:Material Science and Engineering, Volume 107. [ Published manuscript available here]

Tambunan, U.S.F., Zahroh, H., Parikesit, A.A., Idrus,S., & Kerami,D. (2015). Screening Analogs of β-OG Pocket Binder as Fusion Inhibitor of Dengue Virus 2. Libertas Academica: Drug Target Insights 2015:9 33–49 doi:10.4137/DTI.s31566. [ Published manuscript available here]

Tambunan USF, Parikesit AA, Ghifari AS, Satriyanto CP. In silico identification of 2-oxo-1,3-thiazolidine derivatives as novel inhibitors candidate of class II histone deacetylase (HDAC) in cervical cancer treatment. Arab. J. Chem. [Internet]. King Saud University; 2015; [Published manuscript avaiable here]

Tambunan, U.S.F., Parikesit, A.A., Unadi, Y.C., & Kerami, D. (2015). Designing Cyclopentapeptide Inhibitor of Neuraminidase H5N1 Virus Through Molecular and Pharmacology Simulations. Tsinghua Science and Technology: ISSN 1007-0214 01/10 pp431-440 volume 20, Number 5, October 2015.  [Published manuscript available here]

Tambunan, U. S. F., Rachmania, R. A., & Parikesit, A. A. (2015). In silico modification of oseltamivir as neuraminidase inhibitor of influenza A virus subtype H1N1. Journal of Biomedical Research, 29(2), 150–159. doi:10.7555/JBR.29.20130024. [Published manuscript available here]

Bakri, R., Parikesit, A.A., Satriyanto, C.P., Kerami, D., & Tambunan, U.S.F. (2014). Utilization of Boron Compounds for the Modification of Suberoyl Anilide Hydroxamic Acid as Inhibitor of Histone Deacetylase Class II Homo sapiens. Advances in Bioinformatics 7(3): p.1–10. [Published manuscript available here]

Tambunan, U.S.F., Randy, A., Parikesit, A.A., 2014. Design of Candida antarctica Lipase B Thermostability Improvement by Introducing Extra Disulfide Bond Into the Enzyme. Online Journal of Biological Science. 14, 108. [Published manuscript available here]

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 (Zagreb, Croatia), 64(2), 157–72. doi:10.2478/acph-2014-0015 [Published manuscript available here]

Tambunan, U. S. F., Zahroh, H., Utomo, B. B., & Parikesit, arli aditya. (2014). Screening of commercial cyclic peptide as inhibitor NS5 methyltransferase of Dengue virus through Molecular Docking and Molecular Dynamics Simulation. Bioinformation, 10(1), 23–27. [Published manuscript available here]

Prasasty, V. D., Krause, M. E., Tambunan, U. S. F., Anbanandam, A., Laurence, J. S., & Siahaan, T. J. (2014). (1)H, (13)C and (15)N backbone assignment of the EC-1 domain of human E-cadherin. Biomolecular NMR Assignments. doi:10.1007/s12104-013-9539-6.  [Published manuscript available here]

Prasasty, V. D., Tambunan, U. S. F., & Siahaan, T. J. (2014). Homology Modeling and Molecular Dynamics Studies of EC1 Domain of VE-Cadherin to Elucidate Docking Interaction with Cadherin-Derived Peptide. OnLine Journal of Biological Sciences, 14(2), 155. doi:10.3844/ojbsci.2014.155.162. [Published manuscript available here]

Tambunan, U. S., M. R. Rahdiansyah, and A. A. Parikesit. (2013). In Silico Design of the M2 Proton Channel Inhibitors of H1N1 Virus. OnLine Journal of Biological Sciences 13:1–12. doi: 10.3844/ojbsci.2013.1.12. [Published manuscript available here]

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. 9 696–700. [Published manuscript available here]

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. [Published manuscript available here]

Tambunan, U.S.F., Amri, N and Parikesit, A.A, (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. [Published manuscript available here]

Tambunan, U.S.F., Febrianto, D., and Parikesit, A.A ,(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. [Published manuscript available here]

Idrus, S., and Tambunan, U.S.F, (2012). Simulation of riboflavin synthase in Eremothecium gossypii  conversion of 6,7-dimethyl-8-ribityllumazine to riboflavin.  Online Journal of Bioinformatics. Volume 13 (1):41-49.

Tambunan, U.S.F., Bramantya, N and Parikesit , A.A, (2011). In silico modification of suberoylanilide hydroxamic acid (SAHA) as potential inhibitor for class II histone deacetylase (HDAC). BMC Bioinformatics.12(Suppl 13):S23 . [Published manuscript available here]

Tambunan, U.S.F,. Apriyanti, N., Parikesit , A.A,. Chua, W and Wuryani, K. (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. [Published manuscript available here]

Tambunan, U.S.F., Sugito, S., Parikesit, A.A. (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. [Published manuscript available here]

 

Teaching:

 

Bachelor/S1 Students that interested in bioinformatics research group are encouraged to take advance biochemistry subject as elective courses. In addition, solid knowledge on biochemistry, molecular biology, especially in enzyme and proteins will be beneficial for the completion of the research. The graduate and post-graduate students/S2-S3 should be enrolled into the biotechnology field of study/sub-major, as a primary requirement to work on our research. However, students with special interest with computer science will be accommodated as well.

 

 

Links:

NCBI: http://www.ncbi.nlm.nih.gov/

EMBL-EBI: http://www.ebi.ac.uk/

DDBJ: http://www.ddbj.nig.ac.jp/

PROTEIN DATA BANK: http://www.rcsb.org/pdb/home/home.do

PUBMED: http://www.ncbi.nlm.nih.gov/pubmed

SWISSMODEL: http://swissmodel.expasy.org/

GENO3D: http://geno3d-pbil.ibcp.fr/

ACDLab: http://www.acdlabs.com/home/

ToxTree: http://toxtree.sourceforge.net/

MOE Corporation: http://www.chemcomp.com/MOE-Molecular_Operating_Environment.htm

PFAM: http://pfam.sanger.ac.uk/

SUPERFAMILY: http://supfam.cs.bris.ac.uk/SUPERFAMILY/

GENSCAN: http://genes.mit.edu/GENSCAN.html

AUGUSTUS: http://bioinf.uni-greifswald.de/augustus/

 

 

  1 comment for “The Bioinformatics Research Groups

  1. Dr. Titik Taufikurohmah,M.Si
    January 28, 2015 at 4:17 pm

    I interested this program to develop my knowledge. My research related with cosmetics material and the developing in the future with nano material. I am glad to join your research because it is a new topics for me. I am glad to have new friend and new experience.
    Thank You

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