IIITDM Jabalpur

Profile

Assistant Professor in the field of Physics

Dr. Nihar Ranjan Jena received his PhD degree from Banaras Hindu University (BHU), India in 2006. Subsequently, he did his Postdoctoral from the Hebrew University of Jerusalem, Jerusalem, Israel, and National Taiwan Normal University, Taipei, Taiwan. He has also worked as a Guest Scientist in the German Cancer Research Center (DKFZ), Heidelberg, Germany, and a research scientist in the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India. He is also a recipient of the Indo-Australia visiting fellowship (2013-2014) from the Indian National Science Academy, which was availed in the University of Queensland, Australia. Currently, he is working as an Assistant Professor in Physics at the PDPM-Indian Institute of Information Technology Design and Manufacturing Jabalpur, India.

Interest

Artificial DNA, Biosensors, Drug design, DNA-Protein interactions, Enzymatic catalysis.

Qualifications

PhD
Banaras Hindu University

Professional Experience

- Research Scientist
Molecular Biophysics Unit, Indian Institute of Science, Bangalore
- Visiting Academic
University of Queensland, Australia
- Research scientist
Indian Institute of Science, Bangalore, India
- Lecturer
Ravenshaw University, Cuttack, Odisha
- Postdoc
National Taiwan Normal University, Taiwan
- Guest scientist
DKFZ (German Cancer Research Centre), Germany
- Postdoc
Hebrew University of Jerusalem, Israel

Administrative Positions

- Member of the IWD Tender Committee
- Member of Central Purchase Committee
- Warden, Hall-III

Honors & Awards

Senior Research Fellowship Award from the Council of Scientific and Industrial Research
International Travel Award from DST
Late Shri Harbansh Singh Memorial Best Young Scientist Award by Laser & Spectroscopy Society of India
Young Scientist Award from Indian Science Congress
Visiting Academic at the University of Queensland, Australia
2013-2014

School of Chemistry and Molecular Biosciences, University of Queensland, Australia

My courses

Current & Previous

Current

Course Code	Course name	Category	Department
Phys-601	Nanobiotechnology	PG/PhD	Natural Sciences
NS-531	Advanced Quantum Mechanics	PG/PhD	Natural Sciences
NS-205(g)	Modern Physics		Natural Sciences
NS-104	Electrodynamics and Optics	UG/	Natural Sciences
NS-102	Engineering Mechanics	UG/	Natural Sciences

Course Code	Course name	Category	Institute

Research

Areas or Specialisation / Project Activities / Publications / Books

Areas / Specialization

Molecular Biophysics

Project Activities

Understanding of DNA Damage and Repair by Enzyme Residues.
DST-sponsored project. Funds Approved: ~ Rs 14,00000 Tenure: 2009-2012
Computational Design of Functional Nucleotides for Artificial Life.
SERB-sponsored project. Funds approved: Rs 50,00160 Tenure: 2017-2020
Mechanisms of Activation of Type I Cytokine Receptors.
Indian National Science Academy (as a part of Indo-Australia S&T programme), Funds approved: ~Rs 20,00000
Mutational properties of DNA base Lesions.
IIITDM Jabalpur, Funds approved: ~10,00000
Discovery of Therapeutic Candidates for the Treatment of Zika Viral Infection by using Advanced Computational Techniques
CSIR-sponsored project. Funds approved: Rs 17,84000 Tenure: 2022-2025
Design and Development of Biosensors for the Early Diagnosis of Cancer and Other Diseases
DIC-sponsored project. Funds approved: Rs 13,00000 Project surrendered

Books/Book chapter

N.R. Jena, Neha Agnihotri, P.C. Mishra (2014) Formation of DNA Lesions, Its Prevention and Repair. Book Title: Computational Techniques in Pharmacy and Medicine, Springer, 59-94.

Publications

A Few Selected Journal Publications :

N.R. Jena* and P.K. Shukla (2023) Structure and Stability of Different Triplets Involving Artificial Nucleobases: Clues for the Formation of Semisynthetic Triple Helical DNA. Scientific Reports, 13, 19246.

S. Pant and N.R. Jena* (2023) Mechanisms of NTP binding to the NS5 RdRp of the ZIKA Virus to Block the RNA Replication State. Current Medicinal Chemistry (Accepted).

S. Pant and N.R. Jena* (2023) Repurposing of Anti-parasitic Drugs Against the NS2B-NS3 Polymerase of the ZIKA Virus. J. Biomol. Struct. Dyn. https://doi: 10.1080/07391102.2023.2255648.

N.R. Jena*, and S. Pant (2023) Peptide Inhibitors Derived from nsp7 and nsp8 Cofactors of nsp12 Targeting Different Substrate Binding Sites of nsp12 of the SARS-CoV-2. J. Biomol. Struct. Dyn. https://doi.org/10.1080/07391102.2023.2235012.

N. R. Jena* and P. Das (2023): Hybrid nucleobases as new and efficient unnatural genetic letters, J. Biomol. Struct. Dyn., 41, 1, 366-376.

N.R. Jena*, P. Das, and P.K. Shukla (2023) Complementary Base Pairing Interactions between Different Rare Tautomers of the Second-generation Artificial Genetic Alphabets J. Mol. Model. 29, 125.

P.K. Shah, N.R. Jena, and P.K. Shukla, (2023) A theoretical characterization of mechanisms of action of osmium(III)-based drug Os-KP418: Hydrolysis and its binding with guanine, Structural Chemistry, 34:995-1003.

P.K. Shah, N.R. Jena, and P.K. Shukla, (2022) Reactions of Ru(III)-drugs KP1019 and KP418 with Guanine, 2'-Deoxyguanosine and Guanosine: A DFT Study, (under review).

S. Pant, and N.R. Jena* (2022) C-terminal Extended Hexapeptides as Potent Inhibitors of the NS2B-NS3 Protease of the ZIKA Virus, Frontiers in Medicine, 1904.

S. Pant, G. Bhattacharya, and N.R. Jena* (2022) Structures and Dynamics of Peptide and Peptidomimetic Inhibitors Bound to the NS2B-NS3 Protease of the ZIKA Virus. J. Biomol. Struct. Dyn. DOI: 10.1080/07391102.2022.2045223

N.R. Jena* (2022) Rare Tautomers of Artificially Expanded Genetic Letters and Their Effects on the Base Pair Stabilities. ChemPhysChem, 23, e202100908

N. R. Jena* and P. Das (2021): Hybrid Nucleobases as New and Efficient Unnatural Genetic Letters, J. Biomol. Struct. Dyn., DOI: 10.1080/07391102.2021.2003863.

Suyash Pant and N.R. Jena*, (2021) Inhibition of the RNA-dependent RNA Polymerase of SARS-CoV-2 by Short Peptides, Eur. J. Pharm. Sci. 167, 106012.

N.R. Jena*, (2021) Drug Targets and Therapeutics against SARS-CoV-2, Chemical Physics Impact 2, 100011.

N.R. Jena*, Suyash Pant, and Hemant Kumar Srivastava, (2021) Artificially Expanded Genetic Information Systems as Potent Inhibitors of the RNA-dependent RNA polymerase of SARS-CoV-2. J. Biomol. Struct. Dyn. 1-17, doi: 10.1080/07391102.2021.1883112.

N.R. Jena*, (2020) Role of Different Tautomers on the Base-Pairing Abilities of Some of the Vital Antiviral Drugs used Against COVID-19. Phys. Chem. Chem. Phys., 22, 28115-28122.

N.R. Jena* (2020) Identification of Potent Drugs and Antiviral Agents for the Treatment of the SARS-CoV-2 Infection. ChemRxiv. Preprint. https://doi.org/10.26434/chemrxiv.12330599.v1

N.R. Jena*, (2020) Electron and Hole Interactions with P, Z, and P:Z and the Formations of Mutagenic Products by Proton Transfer Reactions, Phys. Chem. Chem. Phys. 22, 919-931.

B. Behera, P. Das, and N.R. Jena* (2019) Accurate Base Pair Energies of Artificial Genetic Alphabets: Clues for Their Mutagenic Characteristics. J. Phys. Chem. B 123, 31, 6728-6739.

N.R. Jena*, (2019) Manganese Coordinated Tyrosine Bio Materials for the Sensing of Reactive Oxygen Species. ChemistrySelect 4, 6945-6953.

N.R. Jena*, C. Patel, S.C. Sahoo, and P.C. Mishra (2018), Cysteine-metal Porous Frameworks as Biosensing Elements for the Adsorption of Reactive Oxygen Species., ChemistrySelect 3, 7732-7740.

N.R. Jena*, P. Das, B. Behera, and P.C. Mishra, (2018) Analogues of P and Z as Efficient Artificially Expanded Genetic Information System., J. Phys. Chem. B., 34, 8134-8145.

M.K. Tiwari, N.R. Jena, and P.C. Mishra (2018), Mechanisms of Scavenging Superoxide, Hydroxyl, Nitrogen Dioxide and Methoxy Radicals by Allicin: Catalytic Role of Superoxide Dismutase in Scavenging Superoxide Radical. J. Chem. Sci., 130, 105.

N.R. Jena* and P.C. Mishra (2016) Normal and Reverse Base Pairs of Iz and Oz Lesions in DNA: Structural Implications for Mutagenesis, RSC Advances, 6, 64019-64027.

N.R. Jena*, Manju Bansal, and P.C. Mishra (2016) Conformational Stabilities of Iminoallantoin and its Base Pairs in DNA: Implications for Mutagenicity, Physical Chemistry Chemical Physics, 18, 12774-12783.

N.R. Jena*, V. Gaur, and P.C. Mishra (2015) The R-and S-diastereoisomeric Effects on the Guanidinohydantoin-induced Mutations in DNA, Phys. Chem. Chem. Phys. 17, 8111-18120.

N.R. Jena*, A.E. Mark, and P.C. Mishra (2014) Does Tautomerization of FapyG Influence its Mutagenicity? ChemPhysChem, 15, 1779-1784.

N.R. Jena* and P.C. Mishra (2013) Is FapyG Mutagenic? Evidence from the DFT Study. ChemPhysChem 14, 3263-3270.

N.R. Jena* (2012) DNA Damage by Reactive Species: Mechanisms, Mutation and Repair. J. Biosci. 37, 503-517.

N.R. Jena*, and P.C. Mishra (2012) Formation of Ring-opened and Rearranged Products of Guanine: Mechanisms and Biological Significance. Free Radic. Biol. Med. 53, 81-94.

N.R. Jena* (2012) Binding of Bis Like and Other Ligands with the GSK-3? Kinase: A Combined Docking and Molecular Dynamics Study. J. Mol. Model. 18, 631-644.

N.R. Jena* and Manju Bansal (2011) Mutagenicity Associated with O6-Methylguanine DNA Damage and Mechanism of Nucleotide Flipping by AGT During Repair. Phys. Biol. 8, 046007.

P.K. Shukla, N.R. Jena, and P.C. Mishra (2011) Quantum Theoretical Study of Molecular Mechanisms of Mutation and Cancer: A review. Proc. Natl. Acad. Sc. A (India), 81A, 79-98.

N.R. Jena*, P.S. Shukla, H.S. Jena, P.C. Mishra, and S. Suhai (2009) O6-Methylguanine Repair by O6-Alkylguanine Alkyl Transferase. J. Phys. Chem. B, 113, 16285-16290.

W.-H. Wang, N.R. Jena, and Y.-C. Wang, Y.-C. Sun (2009) A 3D-QSAR study of Celebrex-based PDK1 Inhibitors Using CoMFA Method. J. Chin. Chem. Soc. 56, 59-64.

N.R. Jena*, P.C. Mishra, and S. Suhai (2009) Protection against Radiation-Induced DNA Damage by Amino Acids: A DFT Study. J. Phys. Chem. B 113, 5633-5644.

N.R. Jena and P.C. Mishra (2009) Interactions of Guanine, Its Anions and Radicals with Lysine in Different Charge States. J. Phys. Chem. B 11, 5418-5424.

N.R. Jena, P.S. Kushwaha, and P.C. Mishra (2008) Reaction of Hypochlorous Acid with Imidazole: Formation of 2-Chloro and 2-Oxoimidazoles. J. Comput. Chem. 29, 98-107.

N.R. Jena and P.C. Mishra (2007) Formation of 8-Nitroguanine and 8-Oxoguanine Due to Reactions of Peroxynitrite with Guanine. J. Comput. Chem. 28, 1321-1335.

N.R. Jena and P.C. Mishra (2007) A Theoretical Study of Some New Analogues of the Anti-Cancer Drug Camptothecine. J. Mol. Model. 13, 267-274.

N.R. Jena and P.C. Mishra (2006) Addition and Hydrogen Abstraction reactions of an OH Radical with 8-oxoguanine. Chem. Phys. Letts. 422, 417-423.

N.R. Jena and P.C. Mishra (2005) Mechanisms of Formation of 8-oxoguanine Due to Reactions of One and Two OH Radicals and the H2O2 Molecule with Guanine: A Quantum Computational Study. J. Phys. Chem. B 109, 14205-14218.

N.R. Jena and P.C. Mishra (2005) An ab-initio and Density Functional Study of Microsolvation of Carbon Dioxide in Water Clusters and Formation of Carbonic Acid. Theor. Chem. Accts. 114, 189-199.

N.R. Jena and P.C. Mishra (2005) Study of Relationship of Atomic Orbital Hybridization with Bonding Using Hybridization Displacement Charge: Optimal Hybridization Principle. J. Mol. Struct. (Theochem) 719, 75-84.

N.R. Jena, Neha Agnihotri, and P.C. Mishra (2014) Formation of DNA Lesions, Its Prevention and Repair. Book Title: Computational Techniques in Pharmacy and Medicine, Springer, 59-94, edited by Leonid Gorb, Victor Kuz'min, Eugene Muratov, ISBN: 978-94-017-9257-8.

As Conference/Workshop Abstracts or Proceedings: (International)

N.R. Jena (2022) RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 as an attractive drug target to contain COVID-19, Chem. Phys. Impact. (Elsevier) DOI: 10.52843/cassyni.zpj4nt, (Jun 9, 2022).

N.R. Jena (2021), Peptide and Non-peptide Therapeutics for the Inhibition of the Replication of SARS-CoV-2, Drug Discovery Webinar, Scholars International Webinar (Aug 25-26, 2021).

N.R. Jena (2019) Computational Design of Unnatural Nucleotides for Artificial Life, ACS Spring 2019 National Meeting, Orlando, USA (March 31-April 4).

N.R. Jena (2017) Electrocatalytic Effects of Biomaterials for Sensing Applications, SUNCAT Summer Institute 2017: Fundamentals and Applications of Heterogeneous Catalysis, Stanford University, USA.

N.R. Jena (2013) Design of New Potent Inhibitors for The GSK3-beta kinase, 245th ACS Meeting, New Orleans, LA, USA.

N.R. Jena (2011) DNA Damage by Reactive Species: Mechanisms, Mutation and Repair, International Conference on “Disorders in Nucleic Acids and Disease”, IIT Delhi, India.

N.R. Jena (2011) How Does AGT Find and Repair its Target on DNA. 20th Conference on current trends in computational chemistry, Jackson, MS, USA.

N.R. Jena (2011) GSK-3 as Potential Therapeutic Target, International Conference on “Medichem”, Beijing, China.

N.R. Jena (2010) DNA Damage, Its Consequences and Repair. International Conference on “Frontiers in Biological Sciences”, NIT Rourkela, India.

N.R. Jena (2010) DNA Repair by Enzymes: Current Progress and Future Challenges. International Conference on “Recent Advances in Bioinformatics”, KIIT, Bhubaneswar, India.

N.R. Jena (2009) Substrate Hydroxylation by the P450s: Is There any Consensus Mechanism? 238th ACS Meeting, Washington DC, USA.

N.R. Jena (2007) DNA-Protein Interaction: The Good and Bad. Lise-Meitner Minerva Center for Quantum Chemistry, Israel.

N.R. Jena (2005) Peroxynitrite Mediated Formation of Two Highly Mutagenic Agents: A Quantum Computational Study. Humboldt Kolleg, BHU, Varanasi, India.

As Conference/Workshop Abstracts or Proceedings: (national)

N.R. Jena (2021) “Uses of QM, Docking, and MD Methods in Drug Design, Invited Talk in “Tools and techniques to perform molecular modeling and computer-aided drug design” (MMTT-2021, 11-17 Jan) at NIPER Guwahati.

N.R. Jena (2019) Design of Novel Biosensor Materials for the Detection of Carcinogenic Reactive Species, National Conference on Frontiers in Advanced Materials, BSSU Burla, (July 27-28, 20219).

N.R. Jena (2017) Computational Design of Sensor Materials Inspired from Biology, National Conference on Chemical Physics, Assam University, Silchar, India (March 20-21).

N.R. Jena (2012) Mechanisms of Lesion Recognition and Repair by AGT., National Conference on “Advances in Lasers and Spectroscopy”, ISM, Dhanbad, India.

N.R. Jena (2010) Can Theory Guide Experiment: Substrate Hydroxylation by P450 as an Example. National Symposium on “Recent Trends in Biophysics, BHU, Varanasi, India.

N.R. Jena (2007) Effects of DNA Modification on Protein Structures. National Conference organized by Lase and Spectroscopy Society of India, Varanasi, India.

N.R. Jena (2007) Quantum Computation and Drug Design. National conference organized by Indian Science Congress Association, India.

N.R. Jena (2006) Molecular Mechanisms of Cancer: Formation of 8-oxoguanine. National Conference Organized by Indian Science Congress Association, India.

N.R. Jena (2004) A Quantum Mechanical and Density functional Study of Structures and Properties of Some Water Clusters”. National symposium on “Atomic, Molecular structures, interactions and Laser Spectroscopy” BHU, Varanasi, India.

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