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Structures (PDB) deposited to RCSB:


Crystal Structure of SUVH5 SRA bound to fully hydroxymethylated CG DNA: PDB ID: 4YGI

Crystal structure of UHRF1 SRA complexed with fully-mCHG DNA: PDB ID: 6M2V

Crystal structure of VIM1 PHD finger: PDB ID: 7DUF

Crystal structure of thiomorpholine-carboxylate dehydrogenase from Candida parapsilosis:PDB ID: 8H8P


From IIT Hyderabad

#: Corresponding author

  1. Nitin K and Rajakumara E#.  Proxy-approach in understanding the bisubstrate activity of strictosidine synthases (Under revision).

  2. Gupta Raj G, Reddy MR, Nitin K, Satyanarayana G# and Rajakumara E#. Computational and in vitro binding studies of the redesigned Pentoxifylline analogue against phosphodiesterases function in sperm (Under revision).

  3. Hanuman DS, Singh Neeharika S and Rajakumara E#. G-quadruplex recognition by the human PARP2 stimulates the PARylation activity of PARP2 (Under review).

  4. Gupta Raj V, Abhishek S, Nitin K, Dey S, Rajakumara E#. Computational, in vitro binding and competition binding studies of theophylline against phosphodiesterases functioning in sperm (Under review).

  5. Mahesh MVNU, Abhishek S, Faidh MA, Rajakumara E#, and Chadhaa A#. Structure and Mechanism of an Ornithine Cyclodeaminase/µ-Crystallin homolog from the yeast Candida parapsilosis ATCC 7330 (Under review).

  6. Abhishek S#, Deeksha W, Nethravathi KR, Davari MD#, Rajakumara E#. Allosteric crosstalk in modular proteins: function fine-tuning and drug design. Comput Struct Biotechnol J. 2023 Oct 10;21:5003-5015.

  7. Deeksha W, Rajakumara E#. Regulatory apoptotic fragment of PARP1 complements catalytic fragment for PAR and DNA-dependent activity but inhibits PARP2 activity. DNA Repair (Amst). 2023. Nov 15;133:103593. doi: 10.1016/j.dnarep.2023.103593.

  8. Hasan U, Rajakumara E, Giri J. Reversal of multidrug resistance by the synergistic effect of reversan and hyperthermia to potentiate the chemotherapeutic response of doxorubicin in glioblastoma and glioblastoma stem cells. ACS Appl Bio Mater. 2023. Nov 17. doi: 10.1021/acsabm.3c00644. 

  9. Reddy MR, Rajakumara E and Satyanarayana G. Transition Metal Free and Temperature Dependent One-Pot Access to Phenanthrene Fused Heterocycles via Condensation, Intramolecular 1,3-Dipolar Cycloaddition, and Aromatization Sequence. Chem Commun (Camb) 2023. Nov 16;59(92):13755-13758.

  10. Deeksha W, Abhishek S, Rajakumara E#. PAR recognition by multiple reader domains of PARP1 allosterically regulates the DNA-dependent activities and independently stimulates the catalytic activity of PARP1. FEBS J. doi: 10.1111/febs.16907.). (2023). (Journal Cover-page; Editor-in-Chief choice article; Used to promote the new issue on our Twitter feed and LinkedIn).

  11. Deeksha W, Abhishek S, Giri J, Rajakumara E#. Regulation of PARP1 and its apoptotic variant activity by single-stranded DNA. FEBS J. doi: 10.1111/febs.16875.  (2023).

  12. Dey S, Rathod S, Gumphalwad K, Yadav N, Choudhari P, Rajakumara E, Dhavale R, Mahuli D. Exploring α, β-unsaturated carbonyl compounds against bacterial efflux pumps via computational approach. J Biomol Struct Dyn Aug 11:1-14. doi: 10.1080/07391102.2023.2246568. (2023)

  13. Rathod S, Dey S, Pawar S, Dhavale R, Choudhari P, Rajakumara E, Mahuli D, Bhagwat D, Tamboli Y, Sankpal P, Mali S, More H.J. Identification of potential biogenic chalcones against antibiotic resistant efflux pump (AcrB) via computational study. J. Biomol Struct Dyn.  doi: 10.1080/07391102.2023.2225099. (2023).

  14. Abhishek S, Deeksha W, Rajakumara E#. Mechanistic insights into allosteric regulation of methylated DNA and histone H3 recognition by SRA and SET domains of SUVH5 and the basis for di-methylation of lysine residue. FEBS J. 290(4):1060-1077 (2023).

  15. Dey S, Pratibha M, Rajakumara E#. Characterization of Host Receptor Interaction with Envelop Protein of Kyasanur Forest Disease Virus and Predicting Suitable Epitopes for Vaccine Candidate. J Biomol Struct Dyn Jun 1-11. doi: 10.1080/07391102.2023.2218924. (2023)

  16. Dagur HS, Behmard E, Rajakumara E#, Barzegari E#. Identifying potent inhibitory phytocompounds from Lagerstroemia speciosa against SARS-Coronavirus-2: Structure-based virtual screening. J Biomol Struct Dyn. doi: 10.1080/07391102.2023.2205942.  (2023).

  17. Nitin K, Rajakumara E#. Binding order and apparent binding affinity in the bisubstrate activity of strictosidine synthase. J Biomol Struct Dyn doi: 10.1080/07391102.2023.2193643 (2023).

  18. Rajakumara E#, Saniya D, Bajaj P, Rajeshwari R, Giri J, Davari MD. Hijacking Chemical Reactions of P450 Enzymes for Altered Chemical Reactions and Asymmetric Synthesis. Int. J. Mol. Sci.  24(1), 214 (2022).

  19. Pratibha M, Abhishek S, Rajakumara E#. Designing ferritin nanocage based vaccine candidates for SARS-CoV-2 by in silico engineering of its MHC I and MHC II epitope peptides. J Biomol Struct Dyn. Jul 27:1-13 (2022).

  20. Satish M, Kumari S, Nitin K, Ninjoor YK, Babu A, Adiga SK, Kalthur G#, Rajakumara E#.  Computational, biochemical and ex vivo evaluation of xanthine derivatives against phosphodiesterases to enhance the sperm motility. J Biomol Struct Dyn. Jun 13:1-11 (2022).

  21. Singh R, Roopmani P, Chauhan M, Basu, S. M., Deeksha, W., Kazem, MD, Hazra S, Rajakumara E & Giri J#. Silver sulfadiazine loaded core-shell airbrushed nanofibers for burn wound healing application. Int. J. Pharm. 613, 121358 (2022).

  22. Rajakumara E#, Abhishek, S., Nitin, K., Saniya, D., Bajaj, P., Schwaneberg, U. & Davari, M. D#. Structure and Cooperativity in Substrate–Enzyme Interactions: Perspectives on Enzyme Engineering and Inhibitor Design. ACS Chem. Biol. doi:10.1021/acschembio.1c00500. (2022).

  23. Mehta G#, Sanyal K, Abhishek S, Rajakumara E & Ghosh SK#.Minichromosome maintenance proteins in eukaryotic chromosome segregation. BioEssays 44, 2100218 (2022).

  24. Satish M, Kumari S, Deeksha W, Abhishek S, Nitin K, Adiga SK, Hegde P, Dasappa JP, Kalthur G#, Rajakumara E#. Structure-based redesigning of pentoxifylline analogs against selective phosphodiesterases to modulate sperm functional competence for assisted reproductive technologies, Nature Scientific Reports 11(1):12293 (2021).  ‘mPTX-IVF- News-Coverage’

  25. Abhishek S, Deeksha W, Rajakumara E#. Helical and β-Turn Conformations in the Peptide Recognition Regions of the VIM1 PHD Finger Abrogate H3K4 Peptide Recognition. Biochemistry. 60(35):2652-2662 (2021). (Journal Cover-page).

  26. Abhishek S, Nakarakanti NK, Deeksha W, Rajakumara E#. Mechanistic insights into recognition of symmetric methylated cytosines in CpG and non-CpG DNA by UHRF1 SRA. Int J Biol Macromol. 170:514-522 (2021).

  27. Pullaguri N, Grover P, Abhishek S, Rajakumara E, Bhargava Y, Bhargava A#. Triclosan affects motor function in zebrafish larva by inhibiting ache and syn2a genes. Chemosphere. 266:128930 (2021). 

  28. Rajakumara E#, Satish M, Abhishek S. In vitro studies on non-canonical DNA binding specificities of KAP6 and HMO1 and mechanistic insights into DNA bound and unbinding dynamics of KAP6. Int J Biol Macromol. 160: 925-933 (2020).  

  29. Akila M, Rajakumara E, Qureshi A#. Ambient concentration of airborne microbes and endotoxins in rural households of southern India. Building and Environment, 179, 106970 (2020).

  30. Girdharv A, Bharathi V, Tiwari VR, Abhishek S Mahawar US, Raju G, Singh SK, Prabusankar G, Rajakumara E and Patel BK#. Computational insights into mechanism of AIM4-mediated inhibition of aggregation of TDP-43 protein implicated in ALS and evidence for in vitro inhibition of liquid-liquid phase separation (LLPS) of TDP-432C-A315T by AIM4. Int J Biol Macromol.147:117-130 (2020).

  31. Abhishek S, Sivadas S, Satish M, Deeksha W, Rajakumara E#. Dynamic Basis for Auranofin Drug Recognition by Thiol-Reductases of Human Pathogens and Intermediate Coordinated Adduct Formation with Catalytic Cysteine Residues. ACS Omega, 4, 9593-9602. (2019)

  32. Abhishek S, Nivya MA, Nakarakanti NK, Deeksha W, Khosla S#, Rajakumara E#. Biochemical and dynamic basis for combinatorial recognition of H3R2K9me2 by dual domains of UHRF1. Biochimie, 149, 105-1142018 (2018).

  33. Satish M, Nivya MA, Abhishek S, Nakarakanti NK, Shivani DM, Vani V, Rajakumara E#. Computational characterization of substrate and product specificities, and functionality of SAM binding pocket in histone lysine methyltransferases from Arabidopsis, rice and maize. Proteins: Structure, Function, and Bioinformatics. 86(1):21-34 (2018).

  34. Rajakumara E#, Nakarakanti NK, Nivya MA and Satish, M. Mechanistic insights into the recognition of 5-methylcytosine oxidation derivatives by the SUVH5 SRA domain. Scientific Reports. 6: 2016 (2016).

  35. Devi S, Rajakumara E, Ahmed N#. Induction of Mincle by Helicobacter pylori and consequent anti-inflammatory signaling denote a bacterial survival strategy. Scientific Reports. 5:15049 (2015).

Before Joining IITH (*: First or Co-First author)

  1. Gonzalez-Huici V, Szakal B, Urulangodi M., Psakhye I, Castellucci F, Menolfi D, Rajakumara E, Fumasoni M, Bermejo R, Jentsch S, Branzei D. DNA bending facilitates the error-free DNA damage tolerance pathway and upholds genome integrity. EMBO J. 33(4): 327-40 (2014).

  2. Rajakumara E*, Wang Z*, Ma H, Hu L, Chen H, Lin Y, Guo R, Wu F, Li H, Lan F, Shi YG, Xu Y, Patel DJ, Shi Y. PHD finger recognition of unmodified histone H3R2 links UHRF1 to regulation of euchromatic gene expression. Molecular Cell 43: 275–284 (2011). (Selected article in ‘Epigenetics and chromatin’ field by Molecular Cell).

  3. Rajakumara E*, Law JA*, Simanshu DK, Voigt P, Johnson LM, Reinberg D, Patel DJ, Jacobsen SE. A dual flip-out mechanism for 5mC recognition by the Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo. Genes and Dev. 25(2):137-52 (2011). (Journal Cover Page; Evaluated by Faculty of 1000 Biology and Medicine).

  4. Arora P*, Goyal A*, Natarajan VT*, Rajakumara E, Verma P, Gupta R, Yousuf M, Trivedi OA, Mohanty D, Tyagi A, Sankaranarayanan R, Gokhale RS. Nat Chem Biol. 5(3):166-73 (2009). (IF: 16.1).

  5. Rajakumara E*, Acharya P*, Ahmad S, Sankaranaryanan R and Rao NM. Biochim Biophys Acta. 1784(2):302-11 (2008).

  6. Goyal A, Yousuf M, Rajakumara E, Arora P, Gokhale RS, Sankaranarayanan R. Crystallization and preliminary X-ray crystallographic studies of the N-terminal domain of FadD28, a fatty-acyl AMP ligase from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun. 62(Pt 4):350-2 (2006).

  7. Rajakumar E*, Aggarwal R, Singh B. Acta Phytopathologica et Entomologica Hungarica, 40 (1-2), 35-42 (2005).

  8. Madhurantakam C*, Rajakumara, E*, Mazumdar PA, Saha B, Mitra D, Wiker HD, Sankaranarayanan R, Das AK. J. Bacteriol. 187(6); 2175-81 (2005).

  9. Acharya P*, Rajakumara E*, Sankaranarayanan R, Rao NM. J Mol Biol, 341(5); 1271-81 (2004).

  10. Rajakumara E*, Acharya P, Ahmad S, Shanmugam VM, Rao NM. and Sankaranarayanan, R. Acta crystallogr. D60; 160-162 (2004).

Patents (Provisional) Filed

Application No. 202341028077

Title: Enzymatic synthesis of a novel anionic polymer: Poly(Cytidine diphosphate ribose)

Inventors (all from IITH) : Dr. Rajakumara Eerappa, Ms. Deeksha Waghela

Application No. 202341028076

Title: Synthesis and evaluation of inhibitor against phosphodiesterases PDE4A, PDE4D, and PDE10

Inventors (all from IITH): Dr. Rajakumara Eerappa, Prof. G. Satyanarayana, Mr. Raj Virendra Gupta, Mr. M. Ramachandra Reddy

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