Publication List

108. Yadav, B.; Gaikwad, S. S.; Kumar, A.; Gupta, G. D.; Kumar, A.; Makde, R. D. Crystal Structure and Nucleic Acid Binding Activity of the Conserved UPF0235 Family Protein PF1765 from Pyrococcus Furiosus. Biochemical and Biophysical Research Communications 2025, 782, 152568. https://doi.org/10.1016/j.bbrc.2025.152568.

107. Yadav, B.; Gaikwad, S. S.; Kumar, A.; Gupta, G. D.; Kumar, A.; Makde, R. D. Crystal Structure and Nucleic Acid Binding Activity of the Conserved UPF0235 Family Protein PF1765 from Pyrococcus Furiosus. Biochemical and Biophysical Research Communications 2025, 782, 152568. https://doi.org/10.1016/j.bbrc.2025.152568.

106. Singh, K.; Shukla, S.; Kumari, A. P.; Kumar, A*. Lacosamide Interaction with Expanded CGG Repeats RNA and Its Role in Modulating Poly-Glycine Protein-Mediated Toxicity in Fragile-X Tremor/Ataxia Syndrome. ACS Pharmacol. Transl. Sci. 2025, acsptsci.5c00198. https://doi.org/10.1021/acsptsci.5c00198.

105. Chetia, P.; Kumar, A*. From Unearthing to an Intriguing Cancer-Fighting Target: The Human BCL-2 Promoter G-Quadruplex and i-Motif. Biochimica et Biophysica Acta (BBA) – Reviews on Cancer 2025, 1880 (5), 189391. https://doi.org/10.1016/j.bbcan.2025.189391.

104. Chandravanshi, K.; Jamdar, S. N.; Singh, R.; Kumar, A.; Mahato, A.; Agrawal, R.; Kumar, S. A.; Kumar, A.; Makde, R. D. Structural and Functional Investigation of Putative Peptidase from Mycolicibacterium Phlei : An Exclusive Endopeptidase among S9C Subfamily. Biochemistry 2025, 64 (12), 2596–2610. https://doi.org/10.1021/acs.biochem.5c00047.

103. Choudhury, S. D.; Ghosh, S.; Kumar, P.; Bhardwaj, A.; Singh, K.; Singh, A.; Kumar, A.; Basu, B.; Giri, R.; Choudhury, D. Attenuation of C-Myc Expression in Breast Cancer by Hesperidin-Mediated Stabilization of Its Promoter Proximal G Quadruplex Region. International Journal of Biological Macromolecules 2025, 309, 143000. https://doi.org/10.1016/j.ijbiomac.2025.143000.

102. Chakraborty, A.; Kumar, A. Computational Screening for Natural Compounds as Potential Immune Checkpoint Inhibitors against TIGIT, a New Avenue in Cancer Immunotherapy. Mol Divers 2025. https://doi.org/10.1007/s11030-025-11172-z.

101. Singh, K.; Shukla, S.; Ghosh, T.; Das, A. K.; Kumar, A. Tyrosine Peptides Alleviates Multifaceted Toxicity Linked to Expanded CGG Repeats in Fragile X-Associated Tremor/Ataxia Syndrome. ACS Pharmacol. Transl. Sci. 2025. https://doi.org/10.1021/acsptsci.4c00647.

  1. Choudhury, S. D.; Ghosh, S.; Kumar, P.; Bhardwaj, A.; Singh, K.; Singh, A.; Kumar, A.; Basu, B.; Giri, R.; Choudhury, D. Attenuation of C-Myc Expression in Breast Cancer by Hesperidin-Mediated Stabilization of Its Promoter Proximal G Quadruplex Region. International Journal of Biological Macromolecules 2025, 309, 143000. https://doi.org/10.1016/j.ijbiomac.2025.143000.
  2. Chakraborty, A.; Kumar, A. Computational Screening for Natural Compounds as Potential Immune Checkpoint Inhibitors against TIGIT, a New Avenue in Cancer Immunotherapy. Mol Divers 2025. https://doi.org/10.1007/s11030-025-11172-z.
  3. Singh, K.; Shukla, S.; Ghosh, T.; Das, A. K.; Kumar, A. Tyrosine Peptides Alleviates Multifaceted Toxicity Linked to Expanded CGG Repeats in Fragile X-Associated Tremor/Ataxia Syndrome. ACS Pharmacol. Transl. Sci. 2025. https://doi.org/10.1021/acsptsci.4c00647.
  4. Singh, K.; Gupta, K.; Shukla, S.; Kumari, A. P.; Kumar, A. Repurposing Oseltamivir Against CAG Repeat Mediated Toxicity in Huntington’s Disease and Spinocerebellar Ataxia Using Cellular and Drosophila Model. ACS Omega 2025, 10 (15), 14980–14993. https://doi.org/10.1021/acsomega.4c10338.
  5. Alam, M. S.; Dhiman, A.; Bhardwaj, T.; Chatterjee, S.; Lakra, V.; Tripathi, M.; Lohani, K.; Sharma, Y. D.; Mirdha, B. R.; Kumar, A.; Sharma, T. K.; Rathore, S. Aptamer-Based Diagnosis for Plasmodium vivax Specific Malaria. ACS Infectious Diseases 2025, 11(3), 762–772. https://doi.org/10.1021/acsinfecdis.4c01047.
  6. Kumari, M.; Jaiswal, S.; Shankar, U.; Gupta, S.; Pradeepkumar, P. I.; Kumar, A.; Nayak, D.; Yadav, V.; Yadav, P. Characterization of G‐quadruplexes in the Helicobacter pylori genome and assessment of therapeutic potential of G4 ligands. Biotechnology and Applied Biochemistry 2025, 72(1), 29–42. https://doi.org/10.1002/bab.2644.
  7. Shukla, S.; Gupta, K.; Singh, K.; Mishra, A.; Kumar, A. An Updated Canvas of the RFC1-mediated CANVAS (Cerebellar Ataxia, Neuropathy and Vestibular Areflexia Syndrome). Molecular Neurobiology 2025, 62(1), 693–707. https://doi.org/10.1007/s12035-024-04307-0.
  8. Kumar, P.; Kinger, S.; Dubey, A. R.; Jagtap, Y. A.; Choudhary, A.; Karmakar, S.; Lal, G.; Kumar, A.; Bhattacharyya, S.; Poluri, K. M.; Mishra, A. Ketorolac disturbs proteasome functions and induces mitochondrial abnormality‐associated apoptosis. IUBMB Life 2025, 77(1), e2937. https://doi.org/10.1002/iub.2937.
  9. Joshi, A.; Kaushik, A.; Taneja, N. K.; Chauhan, K.; Kumar, A.; Sharma, T. K. Development of novel DNA aptamers and colorimetric nanozyme aptasensor for targeting multi-drug-resistant, invasive Salmonella typhimurium strain SMC25. Biosensors and Bioelectronics: X 2024, 21, 100555. https://doi.org/10.1016/j.biosx.2024.100555.
  10. Chandravanshi, K.; Singh, R.; Kumar, A.; Bhange, G. N.; Kumar, A.; Makde, R. D. Structural adaptations for carboxypeptidase activity in putative S9 acylaminoacyl peptidase from Bacillus subtilis. International Journal of Biological Macromolecules 2024, 282, 136734. https://doi.org/10.1016/j.ijbiomac.2024.136734.
  11. Singh, K.; Shukla, S.; Shankar, U.; Jain, N.; Nag, R.; Pramod, K. A.; Kumar, A. Elucidating the pathobiology of Cerebellar Ataxia with Neuropathy and Vestibular Areflexia Syndrome (CANVAS) with its expanded RNA structure formation and proteinopathy. Scientific Reports 2024, 14(1), 28054. https://doi.org/10.1038/s41598-024-78947-6.
  12. Singh, A.; Majee, P.; Mishra, L.; Prajapat, S. K.; Sharma, T. K.; Kalia, M.; Kumar, A. Role of RNA G-Quadruplexes in the Japanese Encephalitis Virus Genome and Their Recognition as Prospective Antiviral Targets. ACS Infectious Diseases 2024, acsinfecdis.4c00507. https://doi.org/10.1021/acsinfecdis.4c00507.
  13. Jagtap, Y. A.; Kumar, P.; Dubey, A. R.; Kinger, S.; Choudhary, A.; Karmakar, S.; Lal, G.; Kumar, A.; Kumar, A.; Prasad, A.; Mishra, A. Acetaminophen induces mitochondrial apoptosis through proteasome dysfunctions. Life Sciences 2024, 349, 122732. https://doi.org/10.1016/j.lfs.2024.122732.
  14. Singh, A.; Jain, N.; Shankar, U.; Sharma, T. K.; Kumar, A. Characterization of G-quadruplex structures in genes involved in survival and pathogenesis of Acinetobacter baumannii as a potential drug target. International Journal of Biological Macromolecules 2024, 269, 131806. https://doi.org/10.1016/j.ijbiomac.2024.131806.
  15. Chandravanshi, K.; Singh, R.; Bhange, G. N.; Kumar, A.; Yadav, P.; Kumar, A.; Makde, R. D. Crystal structure and solution scattering of Geobacillus stearothermophilus S9 peptidase reveal structural adaptations for carboxypeptidase activity. FEBS Letters 2024, 598(6), 684–701. https://doi.org/10.1002/1873-3468.14834.
  16. Zhao, Y.; Kumar, A.; Yang, Y. Unveiling practical considerations for reliable and standardized SERS measurements: Lessons from a comprehensive review of oblique angle deposition-fabricated silver nanorod array substrates. Chemical Society Reviews 2024, 53(2), 1004–1057. https://doi.org/10.1039/D3CS00540B.
  17. Gupta, A.; Mathew, R.; Anand, A.; Bhardwaj, T.; Singh, A.; Singh, K.; Kumar, A.; Mishra, P. R.; Sharma, T. K. A DNA aptamer-based assay for the detection of soluble ST2, a prognostic biomarker for monitoring heart failure. International Journal of Biological Macromolecules 2024, 256, 128295. https://doi.org/10.1016/j.ijbiomac.2023.128295.
  18. Pandya, N.; Kumar, A. An immunoinformatics analysis: Design of a multi-epitope vaccine against Cryptosporidium hominis by employing heat shock protein triggers the innate and adaptive immune responses. Journal of Biomolecular Structure and Dynamics 2023, 41(23), 13563–13579. https://doi.org/10.1080/07391102.2023.2175373.
  19. Jain, N.; Shankar, U.; Singh, A.; Sharma, T. K.; Kumar, A. G-quadruplex motifs in Neisseria gonorrhoeae as anti-gonococcal targets. Applied Microbiology and Biotechnology 2023, 107(16), 5145–5159. https://doi.org/10.1007/s00253-023-12646-6.
  20. Pandya, N.; Kumar, A. A multi-epitope vaccine candidate developed from unique immunogenic epitopes against Cryptosporidium hominis by utilizing an immunoinformatics-driven approach. Journal of Biomolecular Structure and Dynamics 2023, 41(10), 4614–4631. https://doi.org/10.1080/07391102.2022.2070284.
  21. Kinger, S.; Dubey, A. R.; Kumar, P.; Jagtap, Y. A.; Choudhary, A.; Kumar, A.; Prajapati, V. K.; Dhiman, R.; Mishra, A. Molecular Chaperones’ Potential against Defective Proteostasis of Amyotrophic Lateral Sclerosis. Cells 2023, 12(9), 1302. https://doi.org/10.3390/cells12091302.
  22. Joshi, B.; Shankar, U.; Vishwakarma, S.; Kumar, A.; Kumar, A.; Joshi, D.; Joshi, A. Multifunctional Ultrasmall Theranostic Nanohybrids Developed by Ultrasonic Atomizer for Drug Delivery and Magnetic Resonance Imaging. ACS Applied Bio Materials 2023, 6(5), 1943–1952. https://doi.org/10.1021/acsabm.3c00151.
  23. Pandya, N.; Kumar, A. Discovery of a potent Guanidine derivative that selectively binds and stabilizes the human BCL-2 G-quadruplex DNA and downregulates the transcription. Gene 2023, 851, 146975. https://doi.org/10.1016/j.gene.2022.146975.
  24. Pandya, N.; Singh, M.; Rani, R.; Kumar, V.; Kumar, A. G-quadruplex-mediated specific recognition, stabilization and transcriptional repression of bcl-2 by small molecule. Archives of Biochemistry and Biophysics 2023, 734, 109483. https://doi.org/10.1016/j.abb.2022.109483.
  25. Chauhan, N. K.; Anand, A.; Sharma, A.; Dhiman, K.; Gosain, T. P.; Singh, P.; Singh, P.; Khan, E.; Chattopadhyay, G.; Kumar, A.; Sharma, D.; Ashish; Sharma, T. K.; Singh, R. Structural and Functional Characterization of Rv0792c from Mycobacterium tuberculosis: Identifying Small Molecule Inhibitor against HutC Protein. Microbiology Spectrum 2023, 11(1), e01973-22. https://doi.org/10.1128/spectrum.01973-22.
  26. Chauhan, P.; Datta, I.; Dhiman, A.; Shankar, U.; Kumar, A.; Vashist, A.; Sharma, T. K.; Tyagi, J. S. DNA Aptamer Targets Mycobacterium tuberculosis DevR/DosR Response Regulator Function by Inhibiting Its Dimerization and DNA Binding Activity. ACS Infectious Diseases 2022, 8(12), 2540–2551. https://doi.org/10.1021/acsinfecdis.2c00414.
  27. Bhagwat, S. R.; Choudhary, K.; Pandya, N.; Sharma, S.; Srivastava, S.; Kumar, A.; Hajela, K. Identification of substrates of MBL Associated Serine Protease-1 (MASP-1) from human plasma using N-terminomics strategy. Molecular Immunology 2022, 151, 114–125. https://doi.org/10.1016/j.molimm.2022.09.001.
  28. Amanullah, A.; Upadhyay, A.; Dhiman, R.; Singh, S.; Kumar, A.; Ahirwar, D. K.; Gutti, R. K.; Mishra, A. Development and Challenges of Diclofenac-Based Novel Therapeutics: Targeting Cancer and Complex Diseases. Cancers 2022, 14(18), 4385. https://doi.org/10.3390/cancers14184385.
  29. Shankar, U.; Mishra, S. K.; Jain, N.; Tawani, A.; Yadav, P.; Kumar, A. Ni+2 permease system of Helicobacter pylori contains highly conserved G-quadruplex motifs. Infection, Genetics and Evolution 2022, 101, 105298. https://doi.org/10.1016/j.meegid.2022.105298.
  30. Shankar, U.; Jain, N.; Mishra, S. K.; Sk, M. F.; Kar, P.; Kumar, A. Mining of Ebola virus genome for the construction of multi-epitope vaccine to combat its infection. Journal of Biomolecular Structure and Dynamics 2022, 40(11), 4815–4831. https://doi.org/10.1080/07391102.2021.1874529.
  31. Jain, N.; Sk, M. F.; Mishra, A.; Kar, P.; Kumar, A. 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, 98, 107682. https://doi.org/10.1016/j.compbiolchem.2022.107682.
  32. Sharma, D.; Sharma, S.; Sinha, N.; Jain, N.; Kumar, A.; Sarkar, A.; Tyagi, J. S.; Gupta, R. K. Novel benzoic thiazolidin-4-one derivatives targeting DevR/DosR dormancy regulator of Mycobacterium tuberculosis. Journal of Molecular Structure 2022, 1254, 132278. https://doi.org/10.1016/j.molstruc.2021.132278.
  33. Jain, N.; Shankar, U.; Kumar, A. Conserved G-Quadruplex Motifs Regulate Gene Expression in Neisseria meningitidis. ACS Infectious Diseases 2022, 8(4), 728–743. https://doi.org/10.1021/acsinfecdis.1c00383.
  34. Verma, A. K.; Khan, E.; Mishra, S. K.; Kumar, A. Small Molecule Screening Discovers Compounds that Reduce FMRpolyG Protein Aggregates and Splicing Defect Toxicity in Fragile X-Associated Tremor/Ataxia Syndrome. Molecular Neurobiology 2022, 59(3), 1992–2007. https://doi.org/10.1007/s12035-021-02697-z.
  35. Dubey, A. R.; Jagtap, Y. A.; Kumar, P.; Patwa, S. M.; Kinger, S.; Kumar, A.; Singh, S.; Prasad, A.; Jana, N. R.; Mishra, A. Biochemical strategies of E3 ubiquitin ligases target viruses in critical diseases. Journal of Cellular Biochemistry 2022, 123(2), 161–182. https://doi.org/10.1002/jcb.30143.
  36. Tamrakar, A.; Singh, R.; Kumar, A.; Makde, R. D.; Ashish; Kodgire, P. Biophysical characterization of the homodimers of HomA and HomB, outer membrane proteins of Helicobacter pylori. Scientific Reports 2021, 11(1), 24471. https://doi.org/10.1038/s41598-021-04039-4.
  37. Gupta, A.; Anand, A.; Jain, N.; Goswami, S.; Anantharaj, A.; Patil, S.; Singh, R.; Kumar, A.; Shrivastava, T.; Bhatnagar, S.; Medigeshi, G. R.; Sharma, T. K. A novel G-quadruplex aptamer-based spike trimeric antigen test for the detection of SARS-CoV-2. Molecular Therapy - Nucleic Acids 2021, 26, 321–332. https://doi.org/10.1016/j.omtn.2021.06.014.
  38. Anand, A.; Chatterjee, B.; Dhiman, A.; Goel, R.; Khan, E.; Malhotra, A.; Santra, V.; Salvi, N.; Khadilkar, M. V.; Bhatnagar, I.; Kumar, A.; Asthana, A.; Sharma, T. K. 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, 193, 113523. https://doi.org/10.1016/j.bios.2021.113523.
  39. Pandya, N.; Bhagwat, S. R.; Kumar, A. Regulatory role of Non-canonical DNA Polymorphisms in human genome and their relevance in Cancer. Biochimica et Biophysica Acta (BBA) - Reviews on Cancer 2021, 1876(2), 188594. https://doi.org/10.1016/j.bbcan.2021.188594.
  40. Kaur, J.; Singh, R. R.; Khan, E.; Kumar, A.; Joshi, A. Piperine-Loaded PLGA Nanoparticles as Cancer Drug Carriers. ACS Applied Nano Materials 2021, 4(12), 14197–14207. https://doi.org/10.1021/acsanm.1c03664.
  41. Pandya, N.; Kumar, A. Piperine analogs arrest c-myc gene leading to downregulation of transcription for targeting cancer. Scientific Reports 2021, 11(1), 22909. https://doi.org/10.1038/s41598-021-01529-3.
  42. Yadav, P.; Kim, N.; Kumari, M.; Verma, S.; Sharma, T. K.; Yadav, V.; Kumar, A. G-Quadruplex Structures in Bacteria: Biological Relevance and Potential as an Antimicrobial Target. Journal of Bacteriology 2021, 203(13). https://doi.org/10.1128/JB.00577-20.
  43. Pandya, N.; Jain, N.; Kumar, A. Interaction analysis of anti-cancer drug Methotrexate with bcl-2 promoter stabilization and its transcription regulation. Gene Reports 2021, 23, 101155. https://doi.org/10.1016/j.genrep.2021.101155.
  44. Majee, P.; Jain, N.; Kumar, A. 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 2021, 39(4), 1461–1480. https://doi.org/10.1080/07391102.2020.1734088.
  45. Dubey, A. R.; Prasad, A.; Poluri, K. M.; Kumar, A.; Kumar, A.; Mishra, A. Proteome Linked Biochemical Targets: Can Repair Defective Cellular Physiological Mechanisms? Cellular Physiology and Biochemistry 2021, 55(S2), 49–70. https://doi.org/10.33594/000000350.
  46. Majee, P.; Pattnaik, A.; Sahoo, B. R.; Shankar, U.; Pattnaik, A. K.; Kumar, A.; Nayak, D. Inhibition of Zika virus replication by G-quadruplex-binding ligands. Molecular Therapy - Nucleic Acids 2021, 23, 691–701. https://doi.org/10.1016/j.omtn.2020.12.030.
  47. Pandya, N.; Khan, E.; Jain, N.; Satham, L.; Singh, R.; Makde, R. D.; Mishra, A.; Kumar, A. Curcumin analogs exhibit anti-cancer activity by selectively targeting G-quadruplex forming c-myc promoter sequence. Biochimie 2021, 180, 205–221. https://doi.org/10.1016/j.biochi.2020.11.006.
  48. Jain, N.; Shankar, U.; Kumar, A. 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 2021, 87, 104648. https://doi.org/10.1016/j.meegid.2020.104648.
  49. Chatterjee, B.; Kalyani, N.; Anand, A.; Khan, E.; Das, S.; Bansal, V.; Kumar, A.; Sharma, T. K. GOLD SELEX: A novel SELEX approach for the development of high-affinity aptamers against small molecules without residual activity. Microchimica Acta 2020, 187(11), 618. https://doi.org/10.1007/s00604-020-04577-0.
  50. Jain, N.; Mishra, S. K.; Shankar, U.; Jaiswal, A.; Sharma, T. K.; Kodgire, P.; Kumar, A. G-quadruplex stabilization in the ions and maltose transporters gene inhibit Salmonella enterica growth and virulence. Genomics 2020, 112(6), 4863–4874. https://doi.org/10.1016/j.ygeno.2020.09.010.
  51. Taneja, V.; Goel, M.; Shankar, U.; Kumar, A.; Khilnani, G. C.; Prasad, H. K.; Prasad, G. B. K. S.; Gupta, U. D.; Sharma, T. K. An Aptamer Linked Immobilized Sorbent Assay (ALISA) to Detect Circulatory IFN-α, an Inflammatory Protein among Tuberculosis Patients. ACS Combinatorial Science 2020, 22(11), 656–666. https://doi.org/10.1021/acscombsci.0c00108.
  52. Shankar, U.; Jain, N.; Majee, P.; Kodgire, P.; Sharma, T. K.; Kumar, A. 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, 11, 935. https://doi.org/10.3389/fgene.2020.00935.
  53. Majee, P.; Shankar, U.; Pasadi, S.; Muniyappa, K.; Nayak, D.; Kumar, A. Genome-wide analysis reveals a regulatory role for G-quadruplexes during Adenovirus multiplication. Virus Research 2020, 283, 197960. https://doi.org/10.1016/j.virusres.2020.197960.
  54. Shankar, U.; Jain, N.; Mishra, S. K.; Sharma, T. K.; Kumar, A. Conserved G-Quadruplex Motifs in Gene Promoter Region Reveals a Novel Therapeutic Approach to Target Multi-Drug Resistance Klebsiella pneumoniae. Frontiers in Microbiology 2020, 11, 1269. https://doi.org/10.3389/fmicb.2020.01269.
  55. Kumar, S.; Sharma, P. P.; Shankar, U.; Kumar, D.; Joshi, S. K.; Pena, L.; Durvasula, R.; Kumar, A.; Kempaiah, P.; Poonam; Rathi, B. 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 2020, 60(12), 5754–5770. https://doi.org/10.1021/acs.jcim.0c00326.
  56. Joshi, B.; Kaur, J.; Khan, E.; Kumar, A.; Joshi, A. Ultrasonic atomizer driven development of doxorubicin-chitosan nanoparticles as anticancer therapeutics: Evaluation of anionic cross-linkers. Journal of Drug Delivery Science and Technology 2020, 57, 101618. https://doi.org/10.1016/j.jddst.2020.101618.
  57. Shankar, U.; Jain, N.; Majee, P.; Mishra, S. K.; Rathi, B.; Kumar, A. Potential Drugs Targeting Nsp16 Protein May Corroborates a Promising Approach to Combat SARSCoV-2 Virus. https://doi.org/10.26434/chemrxiv.12279671.v1.
  58. Verma, A. K.; Khan, E.; Mishra, S. K.; Mishra, A.; Charlet-Berguerand, N.; Kumar, A. Curcumin Regulates the r(CGG)exp RNA Hairpin Structure and Ameliorate Defects in Fragile X-Associated Tremor Ataxia Syndrome. Frontiers in Neuroscience 2020, 14, 295. https://doi.org/10.3389/fnins.2020.00295.
  59. Agrawal, R.; Goyal, V. D.; Singh, R.; Kumar, A.; Jamdar, S. N.; Kumar, A.; Makde, R. D. Structural basis for the unusual substrate specificity of unique two-domain M1 metallopeptidase. International Journal of Biological Macromolecules 2020, 147, 304–313. https://doi.org/10.1016/j.ijbiomac.2019.12.239.
  60. Bhagwat, S. R.; Hajela, K.; Bhutada, S.; Choudhary, K.; Saxena, M.; Sharma, S.; Kumar, A. Identification of unexplored substrates of the serine protease, thrombin, using N-terminomics strategy. International Journal of Biological Macromolecules 2020, 144, 449–459. https://doi.org/10.1016/j.ijbiomac.2019.12.137.
  61. Majee, P.; Kumar Mishra, S.; Pandya, N.; Shankar, U.; Pasadi, S.; Muniyappa, K.; Nayak, D.; Kumar, A. 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, 10(1), 1477. https://doi.org/10.1038/s41598-020-58406-8.
  62. Verma, A. K.; Khan, E.; Bhagwat, S. R.; Kumar, A. Exploring the Potential of Small Molecule-Based Therapeutic Approaches for Targeting Trinucleotide Repeat Disorders. Molecular Neurobiology 2020, 57(1), 566–584. https://doi.org/10.1007/s12035-019-01724-4.
  63. Dhiman, A.; Kumar, C.; Mishra, S. K.; Sikri, K.; Datta, I.; Sharma, P.; Singh, T. P.; Haldar, S.; Sharma, N.; Bansal, A.; Ahmad, Y.; Kumar, A.; Sharma, T. K.; Tyagi, J. S. Theranostic Application of a Novel G-Quadruplex-Forming DNA Aptamer Targeting Malate Synthase of Mycobacterium tuberculosis. Molecular Therapy - Nucleic Acids 2019, 18, 661–672. https://doi.org/10.1016/j.omtn.2019.09.026.
  64. Sharma, P.; Kumar, A.; Singh, D. Dietary Flavonoids Interaction with CREB-BDNF Pathway: An Unconventional Approach for Comprehensive Management of Epilepsy. Current Neuropharmacology 2019, 17(12), 1158–1175. https://doi.org/10.2174/1570159X17666190809165549.
  65. Khan, E.; Mishra, S. K.; Mishra, R.; Mishra, A.; Kumar, A. Discovery of a potent small molecule inhibiting Huntington’s disease (HD) pathogenesis via targeting CAG repeats RNA and Poly Q protein. Scientific Reports 2019, 9(1), 16872. https://doi.org/10.1038/s41598-019-53410-z.
  66. Agrawal, R.; Goyal, V. D.; Kumar, A.; Gaur, N. K.; Jamdar, S. N.; Kumar, A.; Makde, R. D. Two-domain aminopeptidase of M1 family: Structural features for substrate binding and gating in absence of C-terminal domain. Journal of Structural Biology 2019, 208(1), 51–60. https://doi.org/10.1016/j.jsb.2019.07.010.
  67. Verma, A. K.; Khan, E.; Mishra, S. K.; Jain, N.; Kumar, A. Piperine Modulates Protein Mediated Toxicity in Fragile X-Associated Tremor/Ataxia Syndrome through Interacting Expanded CGG Repeat (r(CGG)exp ) RNA. ACS Chemical Neuroscience 2019, 10(8), 3778–3788. https://doi.org/10.1021/acschemneuro.9b00282.
  68. Khan, E.; Biswas, S.; Mishra, S. K.; Mishra, R.; Samanta, S.; Mishra, A.; Tawani, A.; Kumar, A. Rationally designed small molecules targeting toxic CAG repeat RNA that causes Huntington’s disease (HD) and spinocerebellar ataxia (SCAs). Biochimie 2019, 163, 21–32. https://doi.org/10.1016/j.biochi.2019.05.001.
  69. Mishra, S. K.; Shankar, U.; Jain, N.; Sikri, K.; Tyagi, J. S.; Sharma, T. K.; Mergny, J.-L.; Kumar, A. Characterization of G-Quadruplex Motifs in espB, espK, and cyp51 Genes of Mycobacterium tuberculosis as Potential Drug Targets. Molecular Therapy - Nucleic Acids 2019, 16, 698–706. https://doi.org/10.1016/j.omtn.2019.04.022.
  70. Agrawal, R.; Singh, R.; Kumar, A.; Kumar, A.; Makde, R. D. Crystal structures of pyrrolidone-carboxylate peptidase I from Deinococcus radiodurans reveal the mechanism of L -pyroglutamate recognition. Acta Crystallographica Section D Structural Biology 2019, 75(3), 308–316. https://doi.org/10.1107/S2059798319000676.
  71. Ghosh, A.; Ekka, M. K.; Tawani, A.; Kumar, A.; Chakraborty, D.; Maiti, S. Restoration of miRNA-149 Expression by TmPyP4 Induced Unfolding of Quadruplex within Its Precursor. Biochemistry 2019, 58(6), 514–525. https://doi.org/10.1021/acs.biochem.8b00880.
  72. Mishra, S. K.; Jain, N.; Shankar, U.; Tawani, A.; Sharma, T. K.; Kumar, A. Characterization of highly conserved G-quadruplex motifs as potential drug targets in Streptococcus pneumoniae. Scientific Reports 2019, 9(1), 1791. https://doi.org/10.1038/s41598-018-38400-x.
  73. Joshi, V.; Mishra, R.; Upadhyay, A.; Amanullah, A.; Poluri, K. M.; Singh, S.; Kumar, A.; Mishra, A. Polyphenolic flavonoid (Myricetin) upregulated proteasomal degradation mechanisms: Eliminates neurodegenerative proteins aggregation. Journal of Cellular Physiology 2019, 234(11), 20900–20914. https://doi.org/10.1002/jcp.28695.
  74. Kaur, H.; Bhagwat, S. R.; Sharma, T. K.; Kumar, A. Analytical Techniques for Characterization of Biological Molecules – Proteins and Aptamers/Oligonucleotides. Bioanalysis 2019, 11(2), 103–117. https://doi.org/10.4155/bio-2018-0225.
  75. Das, R.; Dhiman, A.; Mishra, S. K.; Haldar, S.; Sharma, N.; Bansal, A.; Ahmad, Y.; Kumar, A.; Tyagi, J. S.; Sharma, T. K. Structural switching electrochemical DNA aptasensor for the rapid diagnosis of tuberculous meningitis. International Journal of Nanomedicine 2019, Volume 14, 2103–2113. https://doi.org/10.2147/IJN.S189127.
  76. Dhiman, A.; Anand, A.; Malhotra, A.; Khan, E.; Santra, V.; Kumar, A.; Sharma, T. K. Rational truncation of aptamer for cross-species application to detect krait envenomation. Scientific Reports 2018, 8(1), 17795. https://doi.org/10.1038/s41598-018-35985-1.
  77. Kalra, P.; Mishra, S. K.; Kaur, S.; Kumar, A.; Prasad, H. K.; Sharma, T. K.; Tyagi, J. S. G-Quadruplex-Forming DNA Aptamers Inhibit the DNA-Binding Function of HupB and Mycobacterium tuberculosis Entry into Host Cells. Molecular Therapy - Nucleic Acids 2018, 13, 99–109. https://doi.org/10.1016/j.omtn.2018.08.011.
  78. Dhiman, A.; Haldar, S.; Mishra, S. K.; Sharma, N.; Bansal, A.; Ahmad, Y.; Kumar, A.; Sharma, T. K.; Tyagi, J. S. Generation and application of DNA aptamers against HspX for accurate diagnosis of tuberculous meningitis. Tuberculosis 2018, 112, 27–36. https://doi.org/10.1016/j.tube.2018.07.004.
  79. Kumar, A.; Datta, M.; Nema, A. K.; Singh, R. K.; Gurjar, B. R. Improved Rating System for Hazard Assessment Related to Subsurface Migration of Landfill Gas from Municipal Solid Waste Landfills and Dumps. Journal of Hazardous, Toxic, and Radioactive Waste 2018, 22(3), 04018003. https://doi.org/10.1061/(ASCE)HZ.2153-5515.0000393.
  80. Bhagwat, S. R.; Hajela, K.; Kumar, A. Proteolysis to Identify Protease Substrates: Cleave to Decipher. PROTEOMICS 2018, 18(13), 1800011. https://doi.org/10.1002/pmic.201800011.
  81. Kaur, H.; Bruno, J. G.; Kumar, A.; Sharma, T. K. Aptamers in the Therapeutics and Diagnostics Pipelines. Theranostics 2018, 8(15), 4016–4032. https://doi.org/10.7150/thno.25958.
  82. Jain, N.; Mishra, S. K.; Shankar, U.; Jaiswal, A.; Sharma, T. K.; Kodgire, P.; Kumar, A. G-quadruplex stabilization in the ions and maltose transporters gene inhibit Salmonella enterica growth and virulence. Genomics 2020, 112(6), 4863–4874. https://doi.org/10.1016/j.ygeno.2020.09.010.
  83. Thakur, N.; Sharma, B.; Bishnoi, S.; Mishra, S. K.; Nayak, D.; Kumar, A.; Sarma, T. K. Multifunctional Inosine Monophosphate Coordinated Metal–Organic Hydrogel: Multistimuli Responsiveness, Self-Healing Properties, and Separation of Water from Organic Solvents. ACS Sustainable Chemistry & Engineering 2018, 6(7), 8659–8671. https://doi.org/10.1021/acssuschemeng.8b00963.
  84. Upadhyay, A.; Amanullah, A.; Mishra, R.; Kumar, A.; Mishra, A. Lanosterol Suppresses the Aggregation and Cytotoxicity of Misfolded Proteins Linked with Neurodegenerative Diseases. Molecular Neurobiology 2018, 55(2), 1169–1182. https://doi.org/10.1007/s12035-016-0377-2.
  85. Khan, E.; Tawani, A.; Mishra, S. K.; Verma, A. K.; Upadhyay, A.; Kumar, M.; Sandhir, R.; Mishra, A.; Kumar, A. Myricetin Reduces Toxic Level of CAG Repeats RNA in Huntington’s Disease (HD) and Spino Cerebellar Ataxia (SCAs). ACS Chemical Biology 2018, 13(1), 180–188. https://doi.org/10.1021/acschembio.7b00699.
  86. Kumar, A.; Datta, M.; Nema, A. K.; Singh, R. K.; Gurjar, B. R. Closure of municipal solid waste dumps. Site rating for odor impact. Environment Protection Engineering 2018, 44(2). https://doi.org/10.37190/epe180203.
  87. Mishra, S. K.; Jain, N.; Shankar, U.; Tawani, A.; Mishra, A.; Kumar, A. SMMDB: A web-accessible database for small molecule modulators and their targets involved in neurological diseases. Database 2018. https://doi.org/10.1093/database/bay082.
  88. Tawani, A.; Mishra, S. K.; Kumar, A. Structural insight for the recognition of G-quadruplex structure at human c-myc promoter sequence by flavonoid Quercetin. Scientific Reports 2017, 7(1), 3600. https://doi.org/10.1038/s41598-017-03906-3.
  89. Kumar, A.; Mishra, S.; Khan, E. Emerging Methods for Structural Analysis of Protein Aggregation. Protein & Peptide Letters 2017, 24(4), 331–339. https://doi.org/10.2174/0929866524666170206123150.
  90. Joshi, V.; Upadhyay, A.; Kumar, A.; Mishra, A. Gp78 E3 Ubiquitin Ligase: Essential Functions and Contributions in Proteostasis. Frontiers in Cellular Neuroscience 2017, 11, 259. https://doi.org/10.3389/fncel.2017.00259.
  91. Tawani, A.; Amanullah, A.; Mishra, A.; Kumar, A. Evidences for Piperine inhibiting cancer by targeting human G-quadruplex DNA sequences. Scientific Reports 2016, 6(1), 39239. https://doi.org/10.1038/srep39239.
  92. Mishra, S. K.; Tawani, A.; Mishra, A.; Kumar, A. G4IPDB: A database for G-quadruplex structure forming nucleic acid interacting proteins. Scientific Reports 2016, 6(1), 38144. https://doi.org/10.1038/srep38144.
  93. Joshi, V.; Amanullah, A.; Upadhyay, A.; Mishra, R.; Kumar, A.; Mishra, A. 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 Neuroscience 2016, 9. https://doi.org/10.3389/fnmol.2016.00093.
  94. Kumar Mishra, S.; Kumar, A. NALDB: Nucleic acid ligand database for small molecules targeting nucleic acid. Database 2016, baw002. https://doi.org/10.1093/database/baw002.
  95. Tawani, A.; Kumar, A. Structural Insight into the interaction of Flavonoids with Human Telomeric Sequence. Scientific Reports 2015, 5(1), 17574. https://doi.org/10.1038/srep17574.
  96. Tawani, A.; Kumar, A. Structural Insights Reveal the Dynamics of the Repeating r(CAG) Transcript Found in Huntington’s Disease (HD) and Spinocerebellar Ataxias (SCAs). PLOS ONE 2015, 10(7), e0131788. https://doi.org/10.1371/journal.pone.0131788.
  97. Hoskins, J. W.; Ofori, L. O.; Chen, C. Z.; Kumar, A.; Sobczak, K.; Nakamori, M.; Southall, N.; Patnaik, S.; Marugan, J. J.; Zheng, W.; Austin, C. P.; Disney, M. D.; Miller, B. L.; Thornton, C. A. Lomofungin and dilomofungin: Inhibitors of MBNL1-CUG RNA binding with distinct cellular effects. Nucleic Acids Research 2014, 42(10), 6591–6602. https://doi.org/10.1093/nar/gku275.
  98. Sharma, A.; Kumar, A. HD III, and DW Jacobs. Generalized multiview analysis: A discriminative latent space. In IEEE Conference on Computer Vision and Pattern Recognition (CVPR) 2012, June.
  99. Kumar, A.; Parkesh, R.; Sznajder, L. J.; Childs-Disney, J. L.; Sobczak, K.; Disney, M. D. 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, 7(3), 496–505. https://doi.org/10.1021/cb200413a.
  100. Parkesh, R.; Childs-Disney, J. L.; Nakamori, M.; Kumar, A.; Wang, E.; Wang, T.; Hoskins, J.; Tran, T.; Housman, D.; Thornton, C. A.; Disney, M. D. 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 the American Chemical Society 2012, 134(10), 4731–4742. https://doi.org/10.1021/ja210088v.
  101. Kumar, A.; Park, H.; Fang, P.; Parkesh, R.; Guo, M.; Nettles, K. W.; Disney, M. D. Myotonic Dystrophy Type 1 RNA Crystal Structures Reveal Heterogeneous 1 × 1 Nucleotide UU Internal Loop Conformations. Biochemistry 2011, 50(45), 9928–9935. https://doi.org/10.1021/bi2013068.
  102. Kumar, A.; Fang, P.; Park, H.; Guo, M.; Nettles, K. W.; Disney, M. D. A Crystal Structure of a Model of the Repeating r(CGG) Transcript Found in Fragile X Syndrome. ChemBioChem 2011, 12(14), 2140–2142. https://doi.org/10.1002/cbic.201100337.