My research interests revolve around (i) Molecular mechanisms underlying cell signaling events particularly cross-regulation of post-translational modifications and (ii) Structure-guided inhibitor development.
| Mishra B, Basu A, Shehadeh F, Felix L, Kollala SS, Chhonker YS, Naik MT, Dellis C, Zhang L, Ganesan N, Murry DJ, Gu J, Sherman MB, Ausubel FM, Sotiriadis PP, Mylonakis E. "Antimicrobial Peptide Developed with Machine Learning Sequence Optimization Targets Drug Resistant Staphylococcus aureus in Mice." Journal of Clinical Investigation, 2025. |
| Huie EZ, Yang X, Rioult-Pedotti MS, Tran K, Monsen ER, Hansen K, Erickson MA, Naik M, Yotova AY, Banks WA, Huang YA, Silverman JL, Marshall J. "Peptidomimetic inhibitors targeting TrkB/PSD-95 signaling improves cognition and seizure outcomes in an Angelman Syndrome mouse model." Neuropsychopharmacology, vol. 50, no. 5, 2025, pp. 772-782. |
| Li S, Lund-Andersen P, Wang SH, Ytreberg FM, Naik MT, Patel JS, Rowley PA. "The identification of a novel interaction site for the human immunodeficiency virus capsid on nucleoporin 153." The Journal of general virology, vol. 106, no. 5, 2025. |
| Li S, Lund-Andersen P, Wang SH, Ytreberg FM, Naik MT, Patel JS, Rowley PA. "The identification of a novel interaction site for the human immunodeficiency virus capsid on nucleoporin 153." The Journal of general virology, vol. 106, no. 5, 2025. |
| Naik MT, Naik N, Kung CC, Huang TH. "NMR residual dipolar couplings investigation in the topology of house dust mite Group V allergens." Journal of Structural Biology, 2024, pp. 108138. |
| Ke S, Dang F, Wang L, Chen JY, Naik MT, Li W, Thavamani A, Kim N, Naik NM, Sui H, Tang W, Qiu C, Koikawa K, Batalini F, Stern Gatof E, Isaza DA, Patel JM, Wang X, Clohessy JG, Heng YJ, Lahav G, Liu Y, Gray NS, Zhou XZ, Wei W, Wulf GM, Lu KP. "Reciprocal antagonism of PIN1-APC/C(CDH1) governs mitotic protein stability and cell cycle entry." Nature Communications, vol. 15, no. 1, 2024, pp. 3220. |
| Li KR, Huan MJ, Yao J, Li JJ, Cao Y, Wang S, Naik MT, Fang Y, Marshall J, Lan CG, Cao C. "Syn3, a newly developed cyclic peptide and BDNF signaling enhancer, ameliorates retinal ganglion cell degeneration in diabetic retinopathy." Protein & cell, 2024. |
| Shi X, Zhou XZ, Chen G, Luo WF, Zhou C, He TJ, Naik MT, Jiang Q, Marshall J, Cao C. "Targeting the postsynaptic scaffolding protein PSD-95 enhances BDNF signaling to mitigate depression-like behaviors in mice." Science Signaling, vol. 17, no. 834, 2024, pp. eadn4556. |
| Qiu C, Arora P, Malik I, Laperuta AJ, Pavlovic EM, Ugochukwu S, Naik M, Kaplan CD. "Thiolutin has complex effects in vivo but is a direct inhibitor of RNA polymerase II in vitro." Nucleic acids research, 2024. |
| Clark NE, Katolik A, Gallant P, Welch A, Murphy E, Buerer L, Schorl C, Naik N, Naik MT, Holloway SP, Cano K, Weintraub ST, Howard KM, Hart PJ, Jogl G, Damha M, Fairbrother WG. "Activation of human RNA lariat debranching enzyme Dbr1 by binding protein TTDN1 occurs though an intrinsically disordered C-terminal domain." Journal of Biological Chemistry, 2023, pp. 105100. |
| Naik MT, Naik N, Hu T, Wang SH, Marshall J. "Structure-based design of peptidomimetic inhibitors of PSD-95 with improved affinity for the PDZ3 domain." FEBS Letters, vol. 598, no. 2, 2023, pp. 233-241. |
| Li, Qiang, Hu, Cheng, Li, Mengjie, Truong, Phuc, Li, Jinghao, Lin, Hao-Sheng, Naik, Mandar T., Xiang, Sisi, Jackson, Brian E., Kuo, Winson, Wu, Wenhao, Pu, Yunqiao, Ragauskas, Arthur J., Yuan, Joshua S. "Enhancing the multi-functional properties of renewable lignin carbon fibers via defining the structure–property relationship using different biomass feedstocks." Green Chemistry, 2021. |
| Newton JC, Naik MT, Li GY, Murphy EL, Fawzi NL, Sedivy JM, Jogl G. "Phase separation of the LINE-1 ORF1 protein is mediated by the N-terminus and coiled-coil domain." Biophysical Journal, vol. 120, no. 11, 2021, pp. 2181-2191. |
| Ryan, Veronica H, Perdikari, Theodora M, Naik, Mandar T, Saueressig, Camillo F, Lins, Jeremy, Dignon, Gregory L, Mittal, Jeetain, Hart, Anne C, Fawzi, Nicolas L. "Tyrosine phosphorylation regulates hnRNPA2 granule protein partitioning and reduces neurodegeneration." The EMBO Journal, vol. 40, no. 3, 2021, pp. e105001. |
| Li Q, Hu C, Li M, Truong P, Naik MT, Prabhu D, Hoffmann L Jr, Rooney WL, Yuan JS. "Discovering Biomass Structural Determinants Defining the Properties of Plant-Derived Renewable Carbon Fiber." iScience, vol. 23, no. 8, 2020, pp. 101405. |
| Zhou, Lanlan, Huntington, Kelsey, Zhang, Shengliang, Carlsen, Lindsey, So, Eui-Young, Parker, Cassandra, Sahin, Ilyas, Safran, Howard, Kamle, Suchitra, Lee, Chang-Min, Geun Lee, Chun, A. Elias, Jack, S. Campbell, Kerry, T. Naik, Mandar, J. Atwood, Walter, Youssef, Emile, A. Pachter, Jonathan, Navaraj, Arunasalam, A. Seyhan, Attila, Liang, Olin, S. El-Deiry, Wafik. "MEK inhibitors reduce cellular expression of ACE2, pERK, pRb while stimulating NK-mediated cytotoxicity and attenuating inflammatory cytokines relevant to SARS-CoV-2 infection." Oncotarget, vol. 11, no. 46, 2020, pp. 4201-4223. |
| Yang J, Naik N, Patel JS, Wylie CS, Gu W, Huang J, Ytreberg FM, Naik MT, Weinreich DM, Rubenstein BM. "Predicting the viability of beta-lactamase: How folding and binding free energies correlate with beta-lactamase fitness." PLOS ONE, vol. 15, no. 5, 2020, pp. e0233509. |
| Perdikari, Theodora Myrto, Murthy, Anastasia C, Ryan, Veronica H, Watters, Scott, Naik, Mandar T, Fawzi, Nicolas L. "SARS‐CoV‐2 nucleocapsid protein phase‐separates with RNA and with human hnRNPs." The EMBO Journal, vol. 39, no. 24, 2020, pp. e106478. |
| Ryan VH, Watters S, Amaya J, Khatiwada B, Venditti V, Naik MT, Fawzi NL. "Weak binding to the A2RE RNA rigidifies hnRNPA2 RRMs and reduces liquid-liquid phase separation and aggregation." Nucleic acids research, vol. 48, no. 18, 2020, pp. 10542-10554. |
| Tharmalingam N, Ribeiro NQ, da Silva DL, Naik MT, Cruz LI, Kim W, Shen S, Dos Santos JD, Ezikovich K, D'Agata EM, Mylonakis E, Fuchs BB. "Auranofin is an effective agent against clinical isolates of Staphylococcus aureus." Future Medicinal Chemistry, vol. 11, no. 12, 2019, pp. 1417-1425. |
| Soma S, Morgada MN, Naik MT, Boulet A, Roesler AA, Dziuba N, Ghosh A, Yu Q, Lindahl PA, Ames JB, Leary SC, Vila AJ, Gohil VM. "COA6 Is Structurally Tuned to Function as a Thiol-Disulfide Oxidoreductase in Copper Delivery to Mitochondrial Cytochrome c Oxidase." Cell Reports, vol. 29, no. 12, 2019, pp. 4114-4126.e5. |
| Clark H, Knapik LO, Zhang Z, Wu X, Naik MT, Oulhen N, Wessel GM, Brayboy LM. "Dysfunctional MDR-1 disrupts mitochondrial homeostasis in the oocyte and ovary." Scientific reports, vol. 9, no. 1, 2019, pp. 9616. |
| Whitaker AM, Naik MT, Mosser RE, Reinhart GD. "Propagation of the Allosteric Signal in Phosphofructokinase from <i>Bacillus stearothermophilus</i> Examined by Methyl-Transverse Relaxation-Optimized Spectroscopy Nuclear Magnetic Resonance." Biochemistry, 2019. |
| Wang A, Conicella AE, Schmidt HB, Martin EW, Rhoads SN, Reeb AN, Nourse A, Ramirez Montero D, Ryan VH, Rohatgi R, Shewmaker F, Naik MT, Mittag T, Ayala YM, Fawzi NL. "A single N-terminal phosphomimic disrupts TDP-43 polymerization, phase separation, and RNA splicing." EMBO J, vol. 37, no. 5, 2018. |
| Li, Qiang, Naik, Mandar T., Lin, Hao-Sheng, Hu, Cheng, Serem, Wilson K., Liu, Li, Karki, Pravat, Zhou, Fujie, Yuan, Joshua S. "Tuning hydroxyl groups for quality carbon fiber of lignin." Carbon, 2018. |
| Tatli M, Naik MT, Okada S, Dangott LJ, Devarenne TP. "Isolation and Characterization of Cyclic C33 Botryococcenes and a Trimethylsqualene Isomer from Botryococcus braunii Race B." Journal of natural products, vol. 80, no. 4, 2017, pp. 953-958. |
| Naik MT, Kang M, Ho CC, Liao PH, Hsieh YL, Naik N, Wang SH, Chang I, Shih HM, Huang TH. "Molecular mechanism of K65 acetylation-induced attenuation of Ubc9 and the NDSM interaction." Scientific Reports, vol. 7, no. 1, 2017, pp. 17391. |
| Li, Qiang, Serem, Wilson K., Dai, Wei, Yue, Yuan, Naik, Mandar T., Xie, Shangxian, Karki, Pravat, Liu, Li, Sue, Hung-Jue, Liang, Hong, Zhou, Fujie, Yuan, Joshua S. "Molecular weight and uniformity define the mechanical performance of lignin-based carbon fiber." J. Mater. Chem. A, vol. 5, no. 25, 2017, pp. 12740-12746. |
| Li, Qiang, Xie, Shangxian, Serem, Wilson K., Naik, Mandar T., Liu, Li, Yuan, Joshua S. "Quality carbon fibers from fractionated lignin." Green Chem., vol. 19, no. 7, 2017, pp. 1628-1634. |
| Thapa HR, Naik MT, Okada S, Takada K, Molnár I, Xu Y, Devarenne TP. "A squalene synthase-like enzyme initiates production of tetraterpenoid hydrocarbons in Botryococcus braunii Race L." Nature Communications, vol. 7, 2016, pp. 11198. |
| Huang SY, Chang CF, Fang PJ, Naik MT, Güntert P, Shih HM, Huang TH. "The RING domain of human promyelocytic leukemia protein (PML)." Journal of biomolecular NMR, vol. 61, no. 2, 2015, pp. 173-80. |
| Kung CC, Naik MT, Wang SH, Shih HM, Chang CC, Lin LY, Chen CL, Ma C, Chang CF, Huang TH. "Structural analysis of poly-SUMO chain recognition by the RNF4-SIMs domain." Biochem. J., vol. 462, no. 1, 2014, pp. 53-65. |
| Huang SY, Naik MT, Chang CF, Fang PJ, Wang YH, Shih HM, Huang TH. "The B-box 1 dimer of human promyelocytic leukemia protein." Journal of biomolecular NMR, vol. 60, no. 4, 2014, pp. 275-81. |
| Hsieh YL, Kuo HY, Chang CC, Naik MT, Liao PH, Ho CC, Huang TC, Jeng JC, Hsu PH, Tsai MD, Huang TH, Shih HM. "Ubc9 acetylation modulates distinct SUMO target modification and hypoxia response." EMBO J, vol. 32, no. 6, 2013, pp. 791-804. |
| Naik MT, Chang CC, Naik NM, Kung CC, Shih HM, Huang TH. "NMR chemical shift assignments of a complex between SUMO-1 and SIM peptide derived from the C-terminus of Daxx." Biomolecular NMR assignments, vol. 5, no. 1, 2011, pp. 75-7. |
| Chang CC, Naik MT, Huang YS, Jeng JC, Liao PH, Kuo HY, Ho CC, Hsieh YL, Lin CH, Huang NJ, Naik NM, Kung CC, Lin SY, Chen RH, Chang KS, Huang TH, Shih HM. "Structural and functional roles of Daxx SIM phosphorylation in SUMO paralog-selective binding and apoptosis modulation." Molecular Cell, vol. 42, no. 1, 2011, pp. 62-74. |
| Brautigam CA, Wynn RM, Chuang JL, Naik MT, Young BB, Huang TH, Chuang DT. "Structural and thermodynamic basis for weak interactions between dihydrolipoamide dehydrogenase and subunit-binding domain of the branched-chain alpha-ketoacid dehydrogenase complex." Journal of Biological Chemistry, vol. 286, no. 26, 2011, pp. 23476-88. |
| Naik MT, Chang CF, Kuo IC, Kung CC, Yi FC, Chua KY, Huang TH. "Roles of structure and structural dynamics in the antibody recognition of the allergen proteins: an NMR study on Blomia tropicalis major allergen." Structure (London, England : 1993), vol. 16, no. 1, 2008, pp. 125-36. |
| Naik MT, Chang CF, Kuo IC, Yu T, Fang PJ, Chua KY, Huang TH. "Complete 1H, 13C and 15N resonance assignments of Blo t 5, a major mite allergen from Blomia tropicalis." Journal of biomolecular NMR, vol. 38, no. 2, 2007, pp. 189. |
| Naik MT, Suree N, Ilangovan U, Liew CK, Thieu W, Campbell DO, Clemens JJ, Jung ME, Clubb RT. "Staphylococcus aureus Sortase A transpeptidase. Calcium promotes sorting signal binding by altering the mobility and structure of an active site loop." Journal of Biological Chemistry, vol. 281, no. 3, 2006, pp. 1817-26. |
| Naik MT, Lee H, Bracken C, Breslow E. "NMR investigation of main-chain dynamics of the H80E mutant of bovine neurophysin-I: demonstration of dimerization-induced changes at the hormone-binding site." Biochemistry, vol. 44, no. 35, 2005, pp. 11766-76. |
| Naik MT, Huang TH. "Conformational stability and thermodynamic characterization of the lipoic acid bearing domain of human mitochondrial branched chain alpha-ketoacid dehydrogenase." Protein Sci., vol. 13, no. 9, 2004, pp. 2483-92. |
| Naik MT, Chang YC, Huang TH. "Folding kinetics of the lipoic acid-bearing domain of human mitochondrial branched chain alpha-ketoacid dehydrogenase complex." FEBS Letters, vol. 530, no. 1-3, 2002, pp. 133-8. |
R21 grant from the National Institute of Allergy and Infectious Diseases.
Pilot project from COBRE Center for Antimicrobial Resistance and Therapeutic Discovery.
| Year | Degree | Institution |
|---|---|---|
| 2000 | PhD | University of Mumbai |
| 1996 | MS | University of Mumbai |
| 1994 | BS | University of Mumbai |
| Postdoctoral Associate | Rutgers University | 2008- | |
| Postdoctoral Fellow | University of California at Los Angeles | 2004- | |
| Postdoctoral Fellow | Weill Cornell Medical College | 2002- | |
| Postdoctoral Fellow | Academia Sinica | 2000- |
2013 Ramalingaswami Fellowship (award declined)
| Name | Title |
|---|---|
| Atwood, Walter | Viatris Professor of Biology and Medicine, Chair of Molecular Biology, Cell Biology and Biochemistry, Professor of Neurology |
| Fawzi, Nicolas | Professor of Medical Science |
| Kurtis, Jonathan | Stanley M. Aronson Professor of Pathology and Laboratory Medicine, Chair of Pathology and Laboratory Medicine, Executive Director of the MD-PhD Program |
| Marshall, John | Professor of Medical Science |
| Weinreich, Daniel | Professor of Ecology, Evolution, and Organismal Biology, Chair of Ecology, Evolution, and Organismal Biology |
Member, American Chemical Society
Member, American Society for Biochemistry and Molecular biology
Member, Taiwan Biophysical Society
| Associate Research Scientist. Texas A & M University, 2014-2016 |
| Special Technical Personnel. Academia Sinica, 2008-2014 |
