Recent Publications

79. G-quadruplex-Mediated Specific Recognition, Stabilization and Transcriptional Repression of bcl-2 by Small Molecule, Archives of Biochemistry and Biophysics, 2022

N. Pandya, M. Singh, R. Rani, V. Kumar, Amit Kumar*

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78. DNA Aptamer Targets Mycobacterium tuberculosis DevR/DosR Response Regulator Function by Inhibiting Its Dimerization and DNA Binding Activity, ACS Infectious Diseases, 2022

P. Chauhan, I Datta, A. Dhiman, U Shankar, Amit Kumar, A Vashist , T. K. Sharma, J. S. Tyagi,

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77. Structural and Functional Characterization of a Small-Molecule Inhibitor Targeting HutC Protein Rv0792c in Mycobacterium tuberculosis, Microbiology Spectrum, 2022

N. K. Chauhan, A. Anand, A. Sharma, K. Dhiman, T.P. Gosain, P. Singh, P. Singh, E. Khan, G. Chattopadyay Amit Kumar, D. Sharma , Ashish, T. K. Sharma, Ramandeep Singh

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76. Discovery of potent Guanidine derivative that selectively binds and stabilizes the human BCL-2 G-quadruplex DNA and downregulates the transcription, Gene, 2022

N. Pandya, R. Rani, V. Kumar, Amit Kumar*,

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75. Identification of Substrates of MBL Associated Serine Protease-1 (MASP-1) from Human Plasma using N-terminomics Strategy, Molecular Immunology, 2022

SR Bhagwat, K. Choudhary, N. Pandya, S. Sharma, RD Makde, S. Srivastava, Amit Kumar, K. Hajela.

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74. Development and Challenges of Diclofenac-Based Novel Therapeutics: Targeting Cancer and Complex Diseases, Cancers, 2022

A. Amanullah, A. Upadhyay, R. Dhiman, S. Singh, Amit Kumar, D. K. Ahirwar , R. K. Gutti, A. Mishra,

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73. A multi-epitope vaccine candidate developed from unique immunogenic epitopes against Cryptosporidium hominis by utilizing immunoinformatics-driven approach, Journal of Biomolecular Structure & Dynamics, 2022

N. Pandya* and Amit Kumar *,

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72. Ni+2 permease system of Helicobacter pylori contains a highly conserved G-Quadruplex motif as a potential drug target, Infection, Genetics and Evolution, 2022

U. Shankar, S.K. Mishra, N. Jain, A. Tawani, P. Yadav, Amit Kumar*

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71. Identification of novel Efflux pump inhibitors for Neisseria gonorrhoeae via multiple ligand-based pharmacophores, e-pharmacophore, molecular docking, density functional theory, and Molecular dynamics approaches, Computational Biology and Chemistry, 2022

N. Jain*, Md. Fulbabu, Amit Mishra, Parimal Kar and Amit Kumar*

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70. Conserved G-quadruplex motifs regulate gene expression in Neisseria meningitidis, ACS Infectious Diseases, 2022

N. Jain, U. Shankar, Amit Kumar *

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69. Immunoinformatics analysis for design of multi-epitope subunit vaccine by using Heat shock proteins against Schistosoma mansoni. Journal of Biomolecular Structure & Dynamics, 2022

N. Pandya* and Amit Kumar *,

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68. Novel benzoic thiazolidin-4-one derivatives targeting DevR dormancy regulator of Mycobacterium tuberculosis: Novel thiazolidin-4-one targeting dormant mycobacteria, Journal of Molecular Structure, 2022

D. Sharma, S. Sharma, N. Sinha, N. Jain, Amit Kumar, A. Sarkar, J. S. Tyagi, R. K. Gupta

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67. Biophysical characterization of the homodimers of HomA and HomB, outer membrane proteins of Helicobacter pylori. Scientific Reports, 2021.

A. Tamrakar, R. Singh. Amit Kumar, R. D. Makde, Ashish, P. Kodgire

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66. Piperine-Loaded PLGA Nanoparticles as Cancer Drug Carriers Carriers, ACS Applied Nano Materials. 2021

J. Kaur, R. Singh, E. Khan, Amit Kumar, A. Joshi.

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65.Small molecules screening discover compounds that reduce FMRpolyG protein aggregates and splicing defect toxicity in Fragile X-associated tremor/ataxia syndrome Molecular Neurobiology, 2021

A.K. Verma, E. Khan, S.K. Mishra, Amit Kumar *

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64. G-quadruplex-Mediated Specific Recognition, Stabilization and Transcriptional Repression of bcl-2 by Small Molecule, RSC Medicinal Chemistry, 2021(submitted)

N. Pandya, M. Singh, R. Rani, V. Kumar, Amit Kumar *

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63. Piperine analogs arrest G-quadruplex motif in human promoter region of c-myc gene leading to downregulation of transcription for targeting Cancer, Scientific Reports, 2021

N. Pandya, Amit Kumar *

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62. Biochemical strategies of E3 ubiquitin ligases target viruses in critical diseases, Journal of Cellular Biochemistry

A.R. Dubey, Y.A. Jagtap, P. Kumar, S.M. Patwa, S. Kinger, S. Singh, Amit Kumar A. Prasad, N.R. Jana, Amit Mishra

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61.Regulatory role of Non-canonical DNA Polymorphisms in human genome and their relevance in cancer BBA Reviews on Cancer, 2021

Pandya, N., Bhagwat, S.R., Amit Kumar*.

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60.Complex target SELEX-based identification of DNA aptamers against Bungarus caeruleus venom for the detection of envenomation using a paper-based device Biosensors and Bioelectronics. 2021

A. Anand, B. Chateerjee, A. Dhiman, R. Goel, E. Khan, A. Malhotra, V. Santra, N. Salvi, M. V. Khadilkar, Amit Kumar, A. Asthana, T. K. Sharma*.

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59.A novel G-quadruplex aptamer-based spike trimeric antigen test for the detection of SARS-CoV-2. Molecular Therapy-Nucleic Acids. 2021.

A. Gupta, A. Anand, N. Jain, S.Goswami, A. Ananthraj, S. Patil, R. Singh, Amit Kumar, T. Shrivastava, S. Bhatnagar, T.K. Sharma*.

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58.Proteome Linked Biochemical Targets: Can Repair Defective Cellular Physiological Mechanisms? Cell Physiol Biochem. 2021

A.R. Dubey, A. Prasad, K.M. Poluri, Amit Kumar, A Mishra.

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57. Interaction analysis of anti-cancer drug Methotrexate with bcl-2 promoter stabilization and its transcription regulation. Gene Reports 2021

N Pandya, N Jain, Amit Kumar*

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56.G-Quadruplex Structures in Bacteria - Biological Relevance and Potential as Antimicrobial Target. Journal of Bacteriology, 2021

P. Yadav, N. Kim, M. Kumari, S. Verma, T. K. Sharma, V. Yadav and Amit Kumar

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55.Inhibition of Zika Virus Replication by G-Quadruplex Binding Ligands. Molecular Therapy nucleic acid, 2020

P. Majee, A. Pattnaik, B. R. Sahoo, U. Shankar, A. K. Pattnaik*, Amit Kumar* and D. Nayak*

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54.Scrutinizing the SARS-CoV-2 protein information for designing an effective vaccine encompassing both the T-cell and B-cell epitopes. Infection, Genetics and Evolution, 2020

N. Jain, U. Shankar, P. Majee, and Amit Kumar*

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53. Mining of Ebola virus genome for the construction of multi-epitope vaccine to combat its infection. Journal of Biomolecular Structure & Dynamics, 2020

Shankar, U., Jain, N., Mishra, S.K., Sk, M. F., Kar, P. and Amit Kumar*

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52.Curcumin analogs exhibit anti-cancer activity by selectively targeting G-quadruplex forming c-myc promoter sequence Biochimie, 2020

N. Pandya; E. Khan; N. Jain; S. Lakshminarayana; R. Singh; A. Mishra; R. D. Makde and Amit Kumar*

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51. An Aptamer Linked Immobilized Sorbent Assay (ALISA) to detect circulatory IFN-α, an inflammatory protein among Tuberculosis patients. ACS Combinatorial Science, 2020

Taneja, V.; Goel, M.; Shankar, U.; Amit Kumar; Khilnani, G.; Prasad, H.; Prasad, GBKS.; Gupta, U.; and T. K. Sharma*.

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50. GOLD SELEX: A novel SELEX approach for the development of high-affinity aptamers against small molecules sans residual activity. Microchimica Acta, 2020

B. Chatterjee, N. Kalyani, A. Anand, E. Khan, S. Das, V. Bansal, Amit Kumar and T. K. Sharma*.

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49. G-quadruplex stabilization in the ions and maltose transporters inhibit Salmonella enterica growth and virulence, Genomics, 2020

N. Jain, S. K. Mishra, U. Shankar, A. Jaiswal, T. K. Sharma, P. Kodgire and Amit Kumar*

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48. Exploring computational and biophysical tools to study the presence of G-quadruplex structures: a promising therapeutic solution for drug-resistant Vibrio cholerae. Frontiers in Genetics, 2020

U. Shankar, N. Jain, P. Majee, P. Kodgire, T. K. Sharma, and Amit Kumar*

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47.Conserved G-quadruplex motifs in the gene promoter region reveal a novel therapeutics approach to target multidrug resistance Klebsiella pneumoniae. Frontiers in Microbiology, 2020

U. Shankar, N. Jain, S. K. Mishra, T. K. Sharma, and Amit Kumar*

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46.Discovery of New Hydroxyethylamine Analogs Against 3CLpro Protein Target of SARS-CoV-2: Molecular Docking, Molecular Dynamics Simulation and Structure-Activity Relationship Studies.Journal of Chemical Information and Modeling (ACS) , 2020

Kumar, S; Sharma, P; Shankar, Uma; Kumar, D; Joshi, S ; Pena, L; Durvasula, R; Amit Kumar, Kempaiah, P; Poonam, *; Rathi, B.

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45.Genome-wide analysis reveals a regulatory role for G-quadruplexes during Adenovirus multiplication. Virus Research, 2020

P. Majee, U. Shankar, S. Pasadi, K. Muniyappa, D. Nayak, and Amit Kumar*

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44.Ultrasonic atomizer driven development of doxorubicin-chitosan nanoparticles as anticancer therapeutics: Evaluation of anionic cross-linkers Journal of Drug Delivery Science and Technology. 2020

B. Joshi, J. Kaur, E. Khan, Amit Kumar and A.Joshi*

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43. Curcumin regulates the r(CGG)exp RNA hairpin structure and ameliorates defects in fragile X-associated tremor ataxia syndrome. Frontiers in Neuroscience. 2020

A. K. Verma, E. Khan, S. K. Mishra, A. Mishra, N. Charlet-Berguerand and Amit Kumar*

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42. Designing of a multi-epitope vaccine candidate against Nipah virus by in silico approach: A putative prophylactic solution for the deadly virus, Journal of Biomolecular Structure and Dynamics. 2020

Prativa Majee, Neha Jain, and Amit Kumar*

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41. Identification and characterization of two conserved G-quadruplex forming motifs in the Nipah virus genome and their interaction with G-quadruplex specific ligands Scientific Reports, 2020

Prativa Majee, Subodh Kumar Mishra, Nirali Pandya, Uma Shankar, Sanjeev Pasadi, K Muniyappa, Debasis Nayak, and Amit Kumar*

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40. Structural basis for the unusual substrate specificity of unique two-domain M1 metallopeptidase.International Journal of Biological Macromolecules. 2020

R. Agrawal, V. Durani Goyal, A. Kumar, N. K Gaur, S. N Jamdar, Ravindra D. Makde*, Amit Kumar*

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39. Identification of Unexplored Substrates of the Serine Protease, Thrombin, using N- Terminomics Strategy. International Journal of Biological Macromolecules. 2020

S.R. Bhagwat, K. Hajela, S. Bhutada, K. Choudhary, M. Saxena, Amit Kumar

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38.Exploring the potential of small molecules based therapeutic approaches for targeting Trinucleotide repeats Disorders, Molecular Neurobiology, 2020

A. K. Verma, E. Khan, S. Bhagwat, and Amit Kumar*

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37. Discovery of a potent small molecule inhibiting Huntington’s disease pathogenesis via targeting CAG repeat RNA and Poly Q protein Scientific Reports, 2019

E. Khan, S. K. Mishra, R. Mishra, A. Mishra, and Amit Kumar*

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36. Theranostic application of a novel G-Quadruplex forming DNA aptamer targeting glyoxylate cycle enzyme malate synthase of Mycobacterium tuberculosis. 2019, Molecular Therapy- Nucleic Acids

A. Dhiman, C. Kumar, S. K. Mishra, K. Sikri, I. Datta, P. Sharma, T. Singh, S. Haldar, N. Sharma, A. Bansal, Y. Ahmad, Amit Kumar, T. K. Sharma, and J.S. Tyagi

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35. Piperine modulates RNA and protein gain of function toxicity in FXTAS through interacting with expanded r(CGG)exp repeat RNA. 2019, ACS Chemical Neuroscience

A. K. Verma, E. Khan, S. K. Mishra, N. Jain and Amit Kumar*

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34.Two-domain aminopeptidase of M1 family: Structural features for substrate binding and gating in absence of C-terminal domain. 2019, Journal of Structural Biology

R. Agrawal, V. D. Goyal, A. Kumar, N. K. Gaur, S. N. Jamdar, Amit Kumar and Ravindra D. Makde

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33.Rationally designed small molecules targeting toxic CAG repeat RNA that causes Huntington's Disease (HD) and Spinocerebellar ataxia (SCAs), Biochimie, 2019

E. Khan, S. Biswas, S. K. Mishra, R. Verma, S. Samanta, A. Mishra, Amit Kumar*

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32.Characterization of G-quadruplex motifs in espB, espK and cyp51 genes of Mycobacterium tuberculosis as a potential drug targets Molecular Therapy- Nucleic Acids, 2019

S. K. Mishra, U. Shankar, N. Jain, K. Sikri, J. S. Tyagi, T. K. Sharma, J.-L. Mergny, Amit Kumar*

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31. Polyphenolic Flavonoid (Myricetin) Upregulated Proteasomal Degradation Mechanisms: Eliminates Neurodegenerative Proteins Aggregations, Journal of Cellular Physiology 2019

V. Joshi, R. Mishra, A. Upadhyay, A. Amanullah, Amit Kumar, A. Mishra

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30. Characterization of highly conserved G-quadruplex motifs as potential drug targets in Streptococcus pneumoniae, Scientific Reports, 2019

S. K. Mishra, U. Shankar, N. Jain, T. K. Sharma, Amit Kumar*

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29. Restoration of miRNA-149 expression by TmPyP4 induced unfolding of quadruplex within its precursor. ACS Biochemistry,2019

Ghosh A, Ekka MK, Tawani A, Amit Kumar, Chakraborty D, Maiti S.

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28. Analytical techniques for characterization of biological molecules, Bioanalysis, 2019

H. Kaur, S. Bhagwat, T. K. Sharma, and Amit Kumar

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27.Crystal structures of pyrrolidone-carboxylate peptidase I from Deinococcus radiodurans reveal the mechanism of L-pyroglutamate recognition, Acta Crystallographica Section D Structural Biology, 2019

R. Agrawal, R. Singh, A. Kumar, Amit Kumar and Ravindra D. Makde.

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26.Targeting G-quadruplex structures in virus genome and its associated host factors could hold potential for antiviral drug discovery, 2018 (Submitted)

P. Majee, Amit Kumar* and D. Nayak*.

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25. Rational truncation of aptamer for cross-species application to detect kraitenvenomation, Scientific Reports, 2018

Dhiman, A., Anand, A., Malhotra,A., Khan, E., Santra, V., Kumar, A., Sharma, T.K.

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24.Structural switching electrochemical DNA aptasensor for the rapid diagnosis of tuberculous meningitis, International Journal of Nanomedicine, 2019

Das, R.; Dhiman, A.; Mishra, S. K.; Haldar S.; Sharma, N.; Bansal, A.; Ahmad., Y.; Amit Kumar; Sharma, T. K; Tyagi J. S.

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23.G-quadruplex forming DNA aptamers inhibit DNA-binding function of HupB (Rv2986c) and Mycobacterium tuberculosis entry into host cells, Molecular Therapy Nucleic Acids, 2018.

Kalra, P, Mishra S K.; Kaur S.; Prasad, H, P.; Amit Kumar ; Sharma, T. K; Tyagi J. S.

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22. Generation and application of DNA aptamers against HspX for accurate diagnosis of Tuberculous meningitis, Tuberculosis, 2018

A. Dhiman, K. Tripathi, S. Haldar, S. K. Mishra, N. Sharma, A. Bansal, A. S. Ethayathulla, Y. Ahmad, Amit Kumar , T. K. Sharma, J. S. Tyagi

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21.Aptamers in the therapeutics and diagnostics pipelines, Theranostics, 2018

H. Kaur, J.G. Bruno, Amit Kumar, T.K. Sharma

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20. Proteolysis to Identify Protease Substrates: Cleave to Decipher, Proteomics, 2018.

S.R. Bhagwat, K. Hajela Amit Kumar

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19.Multifunctional Inosine Monophosphate Coordinated Metal-Organic Hydrogel: Multi-stimuli Responsiveness, Self-healing Properties and Separation of Water from Organic Solvents, ACS Sustainable Chemistry & Engineering, 2018.

N. Thakur, B. Sharma, S. Bishnoi, S.K. Mishra, D. Nayak, Amit Kumar, T.K. Sarma

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18. SMMDB: Database for small molecule modulators as therapeutics in neurological diseases, Database, 2018.

S. K. Mishra, N. Jain, U. Shankar, A. Tawani, A. Mishra , Amit Kumar*

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17. Myricetin targeting CAG repeat RNA ameliorates pathophysiology of Huntington’s disease (HD) and Spino Cerebellar Ataxias (SCAs), ACS Chemical Biology, 2018.

Khan E.#; Tawani, A.#; Mishra, K. S.#; Verma, A.; Upadhyay, A.; Kumar, M.; Sandhir, R.; Mishra, A.; Kumar, Amit*

# Equal contribution

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16. Gp78 E3 Ubiquitin Ligase: Essential Functions and Contributions In Proteostasis, Frontiers in Cellular Neuroscience, 2017.

V. Joshi, A. Upadhyay, Amit Kumar and A. Mishra

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15. Structural insight for the recognition of G-quadruplex structure at human c-myc promoter sequence by flavonoid Quercetin, Scientific Reports, 2017.

A. Tawani, S. K. Mishra, Amit Kumar*

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14. Emerging Methods for Structural Analysis of Protein Aggregation, Protein and Peptide Letters, 2017.

E. Khan, S. K. Mishra, Amit Kumar*

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13. Lanosterol Suppresses The Aggregation And Cytotoxicity of Misfolded Proteins Linked with Neurodegenerative Diseases, Molecular Neurobiology, 2017. - Cover Page Story

A. Upadhyay, A. Amanullah, R. Mishra, Amit Kumar , A. Mishra

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12. Evidences for Piperine inhibiting cancer by targeting human G-quadruplex DNA sequences, Scientific Reports, 2016.

Arpita Tawani, Ayeman Amanullah, Amit Mishra and Amit Kumar*

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11. G4IPDB: A database for G-quadruplex structure forming nucleic acid interacting proteins, Scientific Reports, 2016.

Subodh Kumar Mishra, Arpita Tawani, Amit Mishra and Amit Kumar*

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10. A Decade of boon or burden: what has the CHIP ever done for cellular protein quality control mechanism implicated in Neurodegeneration and Aging?, Frontiers in Molecular Neurosciences, 2016.

Vibhuti Joshi, Ayeman Amanullah, Arun Upadhyay, Ribhav Mishra, Amit Kumar and Amit Mishra

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9. NALDB: Nucleic Acid Ligand Database for small molecules targeting nucleic acid, Oxford Database, 2016.

Subodh Kumar Mishra, Amit Kumar*

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8. Structural Insight into the interaction of Flavonoids with Human Telomeric Sequence, Scientific Reports, 2016.

Arpita Tawani, Amit Kumar*

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7. Structural Insights Reveal the Dynamics of the Repeating r(CAG) Transcript Found in Huntington's Disease (HD) and Spinocerebellar Ataxias (SCAs), PLOS One, 2015.

Arpita Tawani, Amit Kumar*

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6. Lomofungin and dilomofungin: inhibitors of MBNL1-CUG RNA binding with distinct cellular effects, Nucleic Acid Research, 2013.

Hoskins JW, Ofori L,Chen CZ, Amit Kumar ,Sobczak K,Nakamori M,Southall N,Patnaik S,Marugan J, Zheng W, Austin CP, Disney MD, Miller BL, and Thornton CA.

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5. Design of a Bioactive Small Molecule That Targets the Myotonic Dystrophy Type 1 RNA via an RNA Motif-Ligand Database and Chemical Similarity Searching, Journal of American Chemical Society, 2012.

Parkesh R, Childs-Disney JL, Nakamori M, Amit Kumar , Wang E, Wang T, Hoskins J, Tran T, Housman D, Thornton CA, and Disney MD.

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4. Chemical correction of pre-mRNA splicing defects associated with sequestration of muscleblind-like 1 protein by expanded r(CAG)-containing transcripts, ACS Chemical Biology, 2012.

Amit Kumar , Parkesh R, Sznajder LJ, Childs-Disney JL, Sobczak K, Disney MD.

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3. A Crystal Structure of a Model of the Repeating r(CGG) Transcript Found in Fragile X Syndrome, ChemBioChem, 2011.

Amit Kumar , Fang P, Park H, Guo M, Nettles KW, Disney MD.

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2. Assessment of Genetic Diversity in Valeriana jatamansi Jones. Germplasm Using RAPD Markers, National Academy Science Letters, 2011.

Amit Kumar* , Shirkot P, Thakur AK, Raina R

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1. Myotonic dystrophy type 1 RNA crystal structures reveal heterogeneous 1X1 nucleotide UU internal loop conformations, Biochemistry, 2011.

Amit Kumar , Park H, Fang P, Parkesh R, Guo M, Nettles KW, Disney MD.

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Professor Amit Kumar,
702, BSBE, SILICON
INDIAN INSTITUTE OF TECHNOLOGY INDORE
SIMROL CAMPUS, Khandwa road, INDORE,
Madhya Pradesh 453 552 INDIA

Telephone: +91-731-660-3347

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