​A Paroimiae Company

PUBLICATIONS

This page contains selected publications of our work
​

• Tomalika R. Ullah, Matt D. Johansen, Katherine R. Balka, Rebecca L. Ambrose, Linden J. Gearing, James Roest, Julian P. Vivian, Sunil Sapkota, W. Samantha N. Jayasekara, Daniel S. Wenholz, Vina R. Aldilla, Jun Zeng, Stefan Miemczyk, Duc H. Nguyen, Nicole G. Hansbro, Rajan Venkatraman, Jung Hee Kang, Ee Shan Pang, Belinda J. Thomas, Arwaf S. Alharbi, Refaya Rezwan, Meredith O’Keeffe, William A. Donald, Julia I. Ellyard, Wilson Wong, Naresh Kumar, Benjamin T. Kile, Carola G. Vinuesa, Graham E. Kelly, Olivier F. Laczka, Philip M. Hansbro, Dominic De Nardo & Michael P. Gantier. (2023) Pharmacological inhibition of TBK1/IKKε blunts immunopathology in a murine model of SARS-CoV-2 infection.  Nature Communication. 14:5666. doi: 10.1038/s41467-023-41381-9
• Hong He, Chelsea Dumesny, Ching-Seng Ang, Li Dong, Yi Ma, Jun Zeng, Mehrdad Nikfarjam. (2022) A novel PAK4 inhibitor suppresses pancreatic cancer growth and ehances the inhibitory effect of gemcitabine.  Transl Oncol. Feb;16:101329. doi: 10.1016/j.tranon.2021.101329. Epub 2021 Dec 29
• Evison BJ, Palmer JT, Lambert G, Treutlein H, Zeng J, Nativel B, Chemello K, Zhu Q, Wang J, Teng Y, Tang W, Xu Y, Rathi AK, Kumar S, Suchowerska AK, Parmar J, Dixon I, Kelly GE, Bonnar J. (2020) A Small Molecule Inhibitor of PCSK9 that Antagonizes LDL Receptor Binding via Interaction with a Cryptic PCSK9 Binding Groove. Bioorg Med Chem. 28:115344
• Zeng X, Legge FS, Huang C, Zhang X, Jiao Y, Treutlein HR, Zeng J (2019) Computational Prediction of the Epitopes of HA1 Protein of Influenza Viruses to its Neutralizing Antibodies, antibodies, 8:2:
• Shi MS, Xu DG, Zeng J (2018) GPU accelerated quantum virtual screening: application for the natural inhibitors of New Dehli Metalloprotein (NDM-1), Frontiers in Chemistry, 6:564.
• Tan X, Liu N, Legge, SF, Yang MH, Zeng J (2018) Computational identification of antibody epitopes of human papillomavirus 16 (HPV16) L1 proteins, Journal of Theoretical and Computational Chemistry, 17:1850017
• Chagan J, Chan JY, Bryce NS, Lucas CA, Zeng J, Hook J, Treutlein H, Laybutt DR, Stehn JR, Gunning PW, Kee AJ (2018) On-target action of anti-tropomyosin drugs regulates glucose metabolism. Sci Rep. 8:4604. doi: 10.1038/s41598-018-22946-x.
• Tan X, Liu N, Yang M, Duan M, Zeng J (2017) Design of Peptide Inhibitors of Human Papillomavirus 16 (HPV16) Transcriptional Regulator E1-E2 Formation, Journal of Theoretical and Computational Chemistry, 16(3)
• Currier MA, Stehn JR, Swain A, Chen D, Hook J, Eiffe E, Heaton A, Brown D, Nartker B, Eaves DW, Kloss N, Treutlein H, Zeng J, Alieva IB, Dugina VB, Hardeman EC, Gunning PW, Cripe TP (2017). Identification of Cancer-Targeted Tropomyosin Inhibitors and Their Synergy With Microtubule Drugs. Mol Cancer There, doi: 10.1158/1535-7163
• Jones ML, Legge FS, Lebani K, Mahler SM, Young PR, Watterson D, Treutlein HR, Zeng J (2017). Computational Identification of Antibody Epitopes on the Dengue Virus NS1 Protein. Molecules. 22(4). pii: E607. doi: 10.3390/molecules22040607
• Jiao Y, Legge FS, Zeng X, Treutlein HR, Zeng J (2014). Antibody Recognition of Shiga Toxins (Stxs): Computational Identification of the Epitopes of Stx2 Subunit A to the Antibodies 11E10 and S2C4. PLoS ONE, 9(2), e88191. doi:10.1371/journal.pone.0088191.s001
• Zhang W, Zeng X, Zhang L, Peng H, Jiao Y, Zeng J, Treutlein HR. Computational Identification of Epitopes in the Glycoproteins of Novel Bunyavirus (SFTS Virus) Recognized by a Human Monoclonal Antibody (MAb 4-5), J Comput Aided Mol Des, vol. 27, no. 6, pp. 539–550, Jun. 2013. doi:10.1007/s10822-013-9661-7 
• Stehn J, Haass NK, Bonello T, Desouza N, Kottyan G, Treutlein HR, Zeng J, Nascimento PRBB, Sequeira VB, Tanya L. Butler TL, Allanson M, Fath T, Hill  TA, McCluskey A, Schevzov G, Palmer SJ, Hardeman EC, Winlaw D, Reeve VE, Dixon I, Weninger W, Cripe TP, Gunning PW. A novel class of anti cancer compounds which target the actin cytoskeleton of tumor cells, Cancer Research, vol. 73, no. 16, pp. 5169–5182, Aug. 2013.
• Zeng J; Zhang RQ; Treutlein HR (Eds.), Quantum Simulations of Materials and Biological Systems, Springer Netherlands: Dordrecht, 2012, http://dx.doi.org/10.1007/978-94-007-4948-1.
• Burns CJ, Bourke DG, Andrau L, Xianyong Bu, Charman SA, Donohue AC, Fantino E, Farrugia M, Feutrill JT,  Joffe M, Kling MR, Kurek M, Nero TL, Nguyen T, Palmer JT, Phillips I, Shackleford DM, Sikanyika H, Styles M, Su S, Treutlein HR, Zeng J, Wilks AF, Phenylaminopyrimidines as inhibitors of Janus kinases (JAKs). Bioorganic & Medicinal Chemistry Letters, 2009. 
• Burns CB, Harte MF, Xianyong Bu, Fantino E, Giarrusso M, Joffe M, Kurek M, Legge FS, Razzino P, Su S, Treutlein HR, Wan SS, Zeng J, Wilks AF, Bioorganic & Medicinal Chemistry Letters, 19 (2009) 1206, Discovery of 2-(a-methylbenzylamino) pyrazines as potent Type II inhibitors of FMS.
• Yan W, Xie D, Zeng J, Phys. Chem. Chem. Phys. 11 (2009) 6042.  The 559 to 600 nm shift observed in red fluorescent protein eqFP611 is attributed to cis-trans isomerization of the chromophore in an anionic protein pocket.
• Treutlein HR, Styles M, Zeng J. Successful computational prediction of the structure-activity relationship of a potent JAK2 inhibitor. Conference paper, PRIB 2008 October 15-17, 2008, http://arrow.monash.edu.au/hdl/1959.1/63727 , 2008,  http://en.scientificcommons.org/51705355 (2008).
• Xie D, Zeng J, J. Computational Chemistry, 26 (2005) 1487, “Electronic excitations of green fluorescent proteins: protonation states of chromophore model compound in solutions”
• Tran TT, Zeng J, Treutlein HR, Antony W. Burgess, J. Am. Chem. Soc. 124 (2002) 5222, “Effects of thioamide substitutions on the conformation and stability of α- and 310-Helices” 
• Tan Trung Tran, Antony W. Burgess, Herbert Treutlein, Jun Zeng, J. Mol. Graph Model. 20 (2001) 245 “Conformational analysis of thiopeptides: free energy calculations on the effects of thio-substitutions on the conformational distributions of the alanine dipeptides”
• Zeng J, Treutlein HR, George B. Rudy, J. Computer-Aided Mol. Des., 15 (2001) 573, “Predicting sequences and structures of MHC-binding peptides: a computational combinatorial approach” 
• Zeng J, Thao Vuong-Nhen, Anna Zorzet, Bruno Catimel, Ed. Nice, Antony W. Burgess, Treutlein HR, Protein Engineering 14 (2001) 39, “Computational combinatorial design of short peptides that interfere with Ras-Raf association in vitro”.
• Zeng J, Comb. Chem. High Throughput Screen. 3 (2000) 355, “Mini-review: computational design of inhibitors that target protein surfaces” 
• Zeng J, Fridman M, Maruta H, Treutlein HR, Simonson T, "Protein-protein recognition: an experimental and computational study of the R89K mutation in Raf and its effect on Ras binding", Protein Science 8, 50, 1999.
• Zeng J., Treutlein HR, A method for computational combinatorial peptide design of inhibitors of Ras. Protein Engineering 12, 457-468, 1999. 

Selective works on Material Sciences

• ​​Fan Wenjie, Zeng J., Zhang Ruiqin, "Quantum Mechanical Quantification of Weakly Interacting Complexes of Peptides with Single-Walled Carbon Nanotubes",  J. Chem. Theory Comput., 2009, 5 (10), pp 2879–2885

Selective works on Quantum Chemistry and Spectroscopy

• Zeng J, Hush NS, Reimers JR, J. Am. Chem. Soc., 118 (1996) 2059, "Solvent effects on molecular and ionic spectra: 7, Modelling the absorption and electroabsorption spectra of pentaamino-ruthenium(II)-pyrazine and its conjugate acid in water" 
• Zeng J, Hush NS, Reimers JR. J. Chem. Phys., 99 (1993) 1508, "Solvent effects on molecular and ionic spectra: III, absorption to and emission from the lowest singlet (n,π*) state of dilute pyridimine in water"