careers@pes.edu +91-8055524555
Biotechnology
RingRoadCampus
prashanthakarunakar@pes.edu
+91-80-26721983 Extn 344

Dr. Prashantha Karunakar

Assistant Professor
Bio
Teaching
Responsibilities
Research
Publications

Dr. Prashantha Karunakar obtained his Masters in Bioinformatics from Kuvempu University and Ph.D degree from PES Institute of Technology (Affiliated to Kuvempu University, Shankarghatta). He worked on the Ph.D research topic titled "Crystal structure and molecular docking analysis of furan derivatives having pharmaceutical significance and determination of assembly of chains in protein targets". Prior to joining PESIT, he worked as Research Associate at Indgen Life Technologies, Bangalore and Research Assistant at Vittal Mallya Scientific Research Foundation, Bangalore where he contributed by performing target identification, validation and docking studies of different ligands for their pharmaceutical significance. He worked at two famous international synchrotron facilities like DESY, Hamburg, Germany and ESRF, Grenoble, France where he contributed on automating the number of monomers in the asymmetric unit of protein crystal and analysis of X-ray data and resulting structure from UV induced radiation damage phasing. He has published more than 20 articles in National and International Journals. Solved two protein crystal structures of Histidine kinases during the stay at Hamburg, Germany. He is the recipient of the prestigious EMBO Practical Course on Computational Structural Biology 07-11 April 2014, at the European Bioinformatics Institute, Hinxton, UK with complete travel support. He has completed a course on Symmetry in the Solid State conducted by Prof. T. N. Guru Row at Solid State Structural Chemistry Unit, Indian Institute of Science (IISc), Bangalore, India. He is also the Editor-in-chief for International Journal of Computational Biology and Bioinformatics, Strings Publications and Scientific Advisor for DNAskew Analytics Pvt Ltd.

Education

  • Ph.D, Kuvempu University 2014

Experience

  • Project Trainee, European Molecular Biology Laboratory (EMBL), Hamburg, Germany, 2009- 2010
  • Research Assistant, Vittal Mallya Scientific Research Foundation, Bangalore, India, 2008-2009
  • Research Associate, Indgen Life Technologies, Bangalore, India, 2007-2008
  • Assistant Professor, PES University, 11/12/2011
  • Visiting Scientist, European Synchrotron Radiation Facility (ESRF) / European Molecular Biology Laboratory (EMBL), Grenoble, France, 2011 -2011

Achivements

  • EMBO fellowship to participate in training course on Computational Structural Biology - From Data to Structure to Function, EMBL-EBI, Hinxton, UK (07/04/2014-11/04/2014)
  • Best oral presentation award at the National Conference on Challenges and Opportunities for Chemical Sciences in 21st Century [COCS21C-2012], Bangalore, India (01/2013)
  • Best poster presentation award at the National Conference on Biotechnology and Clinical Research, IISc, Bangalore, India (03/2008)
  • Advanced Bioinformatics
  • Chemoinformatics
  • Proteomics, Biomolecular Modeling & Simulation
  • Bioinformatics
  • In silico drug design
  • Molecular Modelling and simulation
  • Next Generation Sequencing
  • Computational Medicinal Chemistry
  • Departmental IQAC Coordinator
  • Board of Examiners, DSCE, Bangalore, BMSCE, RVCE, SIT, Tumkur, JSS, Mysore
  • Serve and support functional activities of departmental committees
  • Consultant - Bioinformatics related projects
  • Mentor students in research projects

Research Interest

  • Crystallography, Chemoinformatics, Bioinformatics

Research Projects (Current)

  • Inhibition of Pebrine by targeting SPN106 and SWP26: An In silico approach
  • Identification of potential agonist or/and antagonist of Human & Mouse FFAR3 by homology modelling and molecular docking approach
  • Docking of dyes to the crystal structure of cellulose
  • Quantum mechanics-Molecular mechanics studies of heterocyclic organic compounds

Conferences

  • 1st International Conference on Life, Chemical and Health Sciences (ICLCHS-2019) Organized by Department of Life Sciences Ramaiah College of Arts, Science & Commerce, Bangalore: In silico modeling and virtual screening for identification of inhibitors for Spore Wall Protein-5 in Nosema bombycis. Prashantha Karunakar, Saarika P B, V Krishnamurthy., October, 2019
  • National Conference on Challenges and Opportunities for Chemical Sciences in 21st Century [COCS21C-2012], Karnataka State Higher Education Council (KSHEC) in Association with Tumkur University at KSHEC, Bangalore, India: In silico docking analysis of difurfurylidene succinic acid with cyclooxygenases. Karunakar, P., Girija, C.R., Krishnamurthy, V., Krishna, V., Jan 2013
  • National Conference on Biotechnology and Society-NCBS2012, Kuvempu University, Shankarghatta, India: Determining empirically the number of molecules in the asymmetric unit of a protein. Karunakar, P., Krishnamurthy, V., Girija, C.R., Krishna, V., Panjikar, S., Tucker, P.A., Makam, R., Apr 2012
  • National Conference on Recent Advances in Health, Agriculture and Environmental Biotechnology (HAEB - 2012), M. S. Ramaiah Institute of Technology, Bangalore, India: In silico docking analysis of piperine with cyclooxygenases. Karunakar, P., Krishnamurthy, V., Girija, C.R., Krishna, V., Vasundara, D.E., Begum, N.S., Syed, A.A., Apr 2012
  • 40th National Seminar on Crystallography, Department of Physics, Osmania University, Hyderabad, India: Determining Empirically the Number of Molecules in the Asymmetric Unit of a Protein. Karunakar, P., Krishnamurthy, V., Girija, C.R., Krishna, V., Panjikar, S., Tucker, P.A., Makam, R., Nov 2011

Journals

  • Divya Joseph Pereira, B. S. Mahanash Kumar, Prashantha Karunakar, and Seema Tharannum (2021) Anticancer, Anticollagenase and in Silico Docking Studies of Anethum sowa L. Herb Oil against HCT 116 Human Colorectal Cancer Cell Line, Journal of Pharmaceutical Research International 33(30A): 1-13
  • Sridevi S.P, Girija C.R, C.D Satish, Prashantha Karunakar (2021) Synthesis, Characterization and Antimicrobial Studies of 3-Methoxy-4-Hydroxy Benzaldehyde & O-Phenylene Diamine Schiff Base Ligand and Its Mixed Ligand Metal Complex Synthesized by Microwave Assisted Method, International Journal of Innovative Research in Technology, Volume 7 Issue 11, 347-354 (ISSN: 2349-6002)
  • Pavan Heggadadevanakote Kendaganna, Govindaraju Shruthi, Prashantha Karunakar, Sharanagouda Patil, Shiva Prasad Kollur, Chandrashekar Srinivasa, Chandan Shivamallu (2020) In Silico Study of Ceftazidime and Piperacillin Against Penicillin-Binding Protein 2, Beta-Lactamase (OXA-1 and SHV-28) of Klebsiella pneumoniae U25, International Journal of Green Pharmacy 14 (4), 403 - 411
  • Vandana C D, Shanti K N, Prashantha Karunakar, Vivek Chandramohan. (2020) In silico studies of bioactive phytocompounds with anticancer activity from in vivo and in vitro extracts of Justicia wynaadensis (Nees) T.Anderson, International Journal of Computational Biology and Drug Design Vol.13 No.5/6, pp.582 - 601
  • H Prabhavathi, KR Dasegowda, KH Renukananda, Prashantha Karunakar, K Lingaraju, H Raja Naika (2020) Molecular docking and dynamic simulation to identify potential phytocompound inhibitors for EGFR and HER2 as anti-breast cancer agents, Journal of Biomolecular Structure and Dynamics (ISSN: 1538-0254)
  • Prashantha Karunakar, Saarika P. B. & Krishnamurthy V (2020) In silico modelling and virtual screening for identification of inhibitors for spore wall protein-5 in Nosema bombycis, Journal of Biomolecular Structure and Dynamics (ISSN: 1538-0254)
  • T. Pooventhiran, Utsab Bhattacharyya, D. Jagadeeswara Rao, Vivek Chandramohan, Prashantha Karunakar, Ahmad Irfan, Y. Sheena Mary & Renjth Thomas (2020) Detailed spectra, electronic properties, qualitative non-covalent interaction analysis, solvatochromism, docking and molecular dynamics simulations in different solvent atmosphere of cenobamate., Structural Chemistry https://doi.org/10.1007/s11224-020-01607-8
  • Mangala K Jayadevappa, Pooja R Karkera, Ravikumar Y Siddappa, Sandeep Telkar, Prashantha Karunakar Investigation of plant flavonoids as potential dengue protease inhibitors Journal of Herbmed Pharmacology 2020; 9(4): 366-373
  • Mishra, S.P.; Karunakar, P.; Taraphder, S.; Yadav, H. (2020) "Free Fatty Acid Receptors 2 and 3 as Microbial Metabolite Sensors to Shape Host Health: Pharmacophysiological View". Biomedicines, 8, 154
  • UM, Shravan, Prashantha Karunakar, and V. Krishnamurthy. (2019) "Homology modeling, virtual screening and dynamics study of proteins involved in Pebrine-Serine Protease Inhibitor 106 and Spore Wall Protein 26." Journal of Biomolecular Structure and Dynamics 1-11.
  • Veerabhadraswamy Maruthyunjaya, Bhimashankar B Molkere, Prashantha Karunakar. (2019) Synthesis and Evaluation of Insecticidal Activity of Bis-Semicarbazones and Bis-(5-Aryl substituted-1, 3, 4-Oxadiazole), Indian Journal of Pharmaceutical Education and Research., 53(3s), s423-s432
  • H P Prashanth Kumar, Prachurjya Panda, Prashantha Karunakar, Shiksha K Venkat, Laxmi Singh, Nijalingappa Ramesh, Talambedu Usha, Sushil Kumar Middha. (2019) Cyclooxygenase (COX2) enzyme inhibitors from Myrica nagi by In-situ click chemistry, Pharmacognosy Magazine, 15(64) 280-287
  • Rajamma DB, Iyer GCR, Madar IH, Karunakar P. (2019) Identification of (1E, 3E)-1, 3-bis [(2-hydroxy-1-naphthyl) methylene] Urea as Mutated MAP Kinase P38 Inhibitor through Reverse Pharmacophore Mapping Approach: Green Synthesis, Characterisation and In silico Docking analysis. Indian Journal of Pharmaceutical Education and Research, 53(2):276-285
  • Padmini Arunkumar, Kumar Sankaran, Shivangi Naik and Prashantha Karunakar (2018) Predicting Pathogenic Missense Mutations in the Human c-MET Oncogene Using a Nucleotide Scoring Function - An approach using mammalian nucleotide sequences, International Journal of Fundamental and Applied Sciences, 7(4):6-9
  • Bhimashankar B. Molkere, M. Veerabhadraswamy, Prashantha Karunakar (2017) Synthesis and Evaluation of Biological Activities of Triazoles. Journal of Pharmaceutical, Chemical and Biological Sciences; 4(4): 512- 521
  • Vivek, M., Karunakar, P. (2016) Evaluation of plants extracts for acetylcholinesterase inhibitory activity and GSK-3. International Journal of Advanced Scientific Research and Publications, 2(3): 29-34
  • Manjegowda, D.S., Karunakar, P., Ramachandra, N.B. (2015) Effect of structural changes in proteins derived from GATA4 nonsynonymous single nucleotide polymorphisms in congenital heart disease. Indian Journal of Pharmaceutical Sciences, 77(6): 735-741
  • Kiran, K.S., Kokila, M.K., Guruprasad, R., Karunakar, P., Pasha, M.A., Lokanath, N., Naveen, S. (2015) Crystal and molecular docking studies of 3-[Bis-(2-hydroxy-4,4-dimethyl-6-oxo-cyclohex-1-enyl)-methyl]benzonitrile with focal adhesion kinase inhibitors. Der Pharma Chemica, 7(9): 268-273
  • Rajesh, K., Vasavan, J., Karunakar, P., Verma, R.J. (2015) Mechanism of protective effect of phyllanthin against carbon tetrachloride-induced hepatotoxicity and experimental liver fibrosis in mice. Toxicology Mechanisms and Methods, 25(9): 708-717
  • Shivakumar, K.V., Karunakar, P., Chatterjee, J. (2014) Inhibition of NarL of Mycobacterium tuberculosis: An in silico approach. Interdisciplinary Sciences: Computational Life Sciences, 6(4): 292-299
  • Karunakar, P., Girija, C.R., Krishnamurthy, V., Krishna, V., Shivakumar, K.V. (2014) In Silico Antitubercular Activity Analysis of Benzofuran and Naphthofuran Derivatives. Tuberculosis Research and Treatment, Volume 2014, Article ID 697532, 10 pages
  • Karunakar, P., Krishnamurthy, V., Girija, C.R., Krishna, V. (2013) Crystal Structure and Molecular Docking Analysis of Difurfurylidene Succinic Acid With Cyclooxygenases. International Journal of Pharma and Bio Sciences, 4(3): (B) 912-921
  • Yamuna, A.J., Karunakar, P., Girija, C.R., Vaidya, V.P., Krishnamurthy, V. (2013) Ethyl 3-amino-5-bromo-1-benzofuran-2-carboxylate. Acta Crystallographica Section E, 69(Pt 5): o775
  • Bhattacharjee, B., Simon, R.M., Gangadharaiah, C., Karunakar, P. (2013) Chemogenomics profiling of drug targets of peptidoglycan biosynthesis pathway in Leptospira interrogans by virtual screening approaches. Journal of Microbiology and Biotechnology, 23(6): 779-784
  • Karunakar, P., Krishnamurthy, V., Girija, C.R., Krishna, V., Vaidya, V.P., Yamuna, A.J. (2013) Ethyl 5-bromo-3-ethoxycarbonylamino-1-benzofuran-2-carboxylate. Acta Crystallographica Section E, 69(Pt 3): o342
  • Girija, C.R., Shalini, S., Jotani, M.M., Karunakar, P., Venugopala, K.N., Venkatesha, T.V. (2013) Semi-empirical Quantum Chemical calculations and Hirshfeld Surface Analysis in 2,6-Bis(2-Furanyl methylidene) cyclohexanone. Conference proceedings of National Conference on 'Challenges and Opportunities for Chemical Sciences in 21st Century', 7-14
  • Shalini, S., Girija, C.R., Karunakar, P., Jotani, M.M., Venugopala, K.N., Venkatesh, T.V. (2013) Synthesis, characterisation, docking analysis and biological evaluation of a,a'-bis(p-dimethylamino-benzylidene)-γ-methylcyclohexanone. Indian Journal of Chemistry, 52B: 282-288
  • Karunakar, P., Krishnamurthy, V., Girija, C.R., Krishna, V., Vasundhara, D.E., Begum, N.S., Syed, A.A. (2012) In silico docking analysis of piperine with cyclooxygenases. Journal of Biochemical Technology, 3(5): S122-127
  • Bhattacharjee, B., Vijayasarathy, S., Karunakar, P., Chattejee, J. (2012) Comparative reverse screening approach to identify potential anti-neoplastic targets of saffron functional components and binding mode. Asian Pacific Journal of Cancer Prevention, 13(11): 5605-5611
  • Preu, J., Panjikar, S., Morth, P., Jaswal, R., Karunakar, P., Tucker, P.A. (2012) The sensor region of the ubiquitous cytosolic sensor kinase, PdtaS, contains PAS and GAF domain sensing modules. Journal of Structural Biology, 177(2): 498-505
  • Karunakar, P., Krishnamurthy, V., Girija, C.R., Krishna, V., Vasundhara, D.E., Begum, N.S., Syed, A.A. (2011) Molecular interaction of fenvalarate with actin. Bioinformation, 7(5): 234-238
  • Dinesh, S.M., Karunakar, P., Amruthavalli, C., Ramachandra, N.B. (2010) Analysis and Homology Modeling of Proteins Derived from NKX2.5 Non-synonymous Single Nucleotide Polymorphisms Involved in Congenital Heart Disease. Nature and Science, 8(9): 27-38
  • Girija, C.R., Karunakar, P., Poojari, C.S., Begum, N.S., Syed, A.A. (2010) Molecular Docking Studies of Curcumin Derivatives with Multiple Protein Targets for Procarcinogen Activating Enzyme Inhibition. Journal of Proteomics & Bioinformatics, (3): 200-203

Others

  • National Bureau of Agriculturally Important Insect (NBAII), Bangalore, India: "Protein structure prediction (Secondary and tertiary) and Protein Docking", Nov 2012
  • Department of Biotechnology, Garden City College, Bangalore, India: "Protein crystallography and hands on Proteomics tools", May 2014
  • Department of Biotechnology, New Horizon College of Engineering, Bangalore, India: "Protein-Ligand Docking", Apr 2013, Oct 2017
  • Department of Biochemistry, Central College, Bangalore "Protein secondary and tertiary structure prediction", Dec 2018
  • Department of Molecular Biology, Bangalore University, Bangalore "Bioinformatics Unit" Mar-2019
  • POSTER PRESENTATION - Abstracts of the EMBO Practical Course on Computational Structural Biology - From Data to Structure to Function, EMBL-EBI, Hinxton, UK: Towards automated determination of the number of molecules in the asymmetric unit of a protein crystal. Karunakar, P., Krishnamurthy, V., Girija, C.R., Krishna, V., Panjikar, S., Tucker, P.A., Makam, R., Apr 2014
  • Razazan A, Karunakar P, Mishra SP, Sharma S, Miller B, Jain S and Yadav H (2021) Activation of Microbiota Sensing ? Free Fatty Acid Receptor 2 Signaling Ameliorates Amyloid-β Induced Neurotoxicity by Modulating Proteolysis-Senescence Axis. Front. Aging Neurosci. 13:735933
  • Pavan Heggadadevanakote Kendaganna, Chandan Shivamallu, Govindaraju Shruthi, Mekhala Nagabushan Chitagudigi, Sushma Pradeep, Prashantha Karunakar, Amachawadi G. Raghavendra, Sharanagouda S. Patil, Asad Syed, Abdallah M. Elgorban, Ali H. Bahkali, Ravindra Veerapur, Shiva Prasad Kollur (2021) In silico screening and validation of KPHS_00890 protein of Klebsiella pneumoniae proteome: An application to bacterial resistance and pathogenesis, Journal of King Saud University - Science 33 (6) 101537 (ISSN 1018-3647)
  • Pavan Heggadadevanakote Kendaganna, Chandan Shivamallu, Govindaraju Shruthi, Mekhala Nagabushan Chitagudigi, Sushma Pradeep, Prashantha Karunakar, Amachawadi G. Raghavendra, Sharanagouda S. Patil, Asad Syed, Abdallah M. Elgorban, Ali H. Bahkali, Ravindra Veerapur, Shiva Prasad Kollur (2021) In silico screening and validation of KPHS_00890 protein of Klebsiella pneumoniae proteome: An application to bacterial resistance and pathogenesis, Journal of King Saud University - Science 33 (6) 101537 (ISSN 1018-3647)
  • Razazan A, Karunakar P, Mishra SP, Sharma S, Miller B, Jain S and Yadav H (2021) Activation of Microbiota Sensing ? Free Fatty Acid Receptor 2 Signaling Ameliorates Amyloid-β Induced Neurotoxicity by Modulating Proteolysis-Senescence Axis. Front. Aging Neurosci. 13:735933
  • GY Nagesh, Mohammad Javeed, Jeelan N Basha, K Prashantha, R Nithin, PR Thanushree, S Vivekananda, Siri S Gowda, HB Punarva, SM Basavarajaiah (2022) Design, Spectral analysis, DFT calculations, antimicrobial, anti-TB, antioxidant activity and molecular docking studies of novel bis-benzoxazines with cytochrome c peroxidase, Journal of Molecular Structure, Volume 1262, 132977