Publications

  1. Modukuri, R. K., Yu, Z., Tan, Z., Ta, H. M., Ucisik, M. N., Jin, Z., Anglin, J. L., Sharma, K. L., Nyshadham, P., Li, F., Riehle, K., Faver, J. C., Duong, K., Nagarajan, S., Simmons, N., Palmer, S. S., Teng, M., Young, D. W., Yi, J. S., Kim, C., and Matzuk, M. M. (2022) Discovery of potent BET bromodomain 1 stereoselective inhibitors using DNA-encoded chemical library selections. Proc. Natl. Acad. Sci. 119, e2122506119. DOI: 10.1073/pnas.2122506119
  2. Chamakuri, S., Lu, S., Ucisik, M. N., Bohren, K. M., Chen, Y.-C., Du, H.-C., Faver, J. C., Jimmidi, R., Li, F., Li, J.-Y., Nyshadham, P., Palmer, S. S., Pollet, J., Qin, X., Ronca, S. E., Sankaran, B., Sharma, K. L., Tan, Z., Versteeg, L., Yu, Z., Matzuk, M. M., Palzkill, T., and Young, D. W. (2021) DNA-encoded chemistry technology yields expedient access to SARS-CoV-2 Mpro inhibitors. Proc. Natl. Acad. Sci. 118, e2111172118. DOI: 10.1073/pnas.2111172118
  3. Yu, Z., Ku, A. F., Anglin, J. L., Sharma, R., Ucisik, M. N., Faver, J. C., Li, F., Nyshadham, P., Simmons, N., Sharma, K. L., Nagarajan, S., Riehle, K., Kaur, G., Sankaran, B., Storl-Desmond, M., Palmer, S. S., Young, D. W., Kim, C., and Matzuk, M. M. (2021) Discovery and characterization of bromodomain 2-specific inhibitors of BRDT. Proc. Natl. Acad. Sci. 118, e2021102118. DOI: 10.1073/pnas.2021102118
  4. Dawadi, S., Simmons, N., Miklossy, G., Bohren, K. M., Faver, J. C., Ucisik, M. N., Nyshadham, P., Yu, Z., and Matzuk, M. M. (2020) Discovery of potent thrombin inhibitors from a protease-focused DNA-encoded chemical library. Proc. Natl. Acad. Sci. U. S. A. 117, 16782–16789. DOI: 10.1073/pnas.2005447117
  5. Taylor, D. M., Anglin, J., Park, S., Ucisik, M. N., Faver, J. C., Simmons, N., Jin, Z., Palaniappan, M., Nyshadham, P., Li, F., Campbell, J., Hu, L., Sankaran, B., Prasad, B. V. V., Huang, H., Matzuk, M. M., and Palzkill, T. (2020) Identifying Oxacillinase-48 Carbapenemase Inhibitors Using DNA-Encoded Chemical Libraries. ACS Infect. Dis., 6, 1214-1217. DOI: 10.1021/acsinfecdis.0c00015
  6. Chen, Y.-C., Faver, J. C., Ku, A. F., Miklossy, G., Riehle, K., Bohren, K. M., Ucisik, M. N., Matzuk, M. M., Yu, Z., and Simmons, N. (2020) C–N Coupling of DNA-Conjugated (Hetero)aryl Bromides and Chlorides for DNA-Encoded Chemical Library Synthesis. Bioconjug. Chem. 31, 770-780. DOI: 10.1021/acs.bioconjchem.9b00863
  7. Chacón, K. N., Perkins, J., Mathe, Z., Alwan, K., Ho, E. N., Ucisik, M. N., Merz, K. M., and Blackburn, N. J. (2018) Trapping intermediates in metal transfer reactions of the CusCBAF export pump of escherichia coli, Commun. Biol. 1, 192. DOI: 10.1038/s42003-018-0181-9
  8. Ucisik, M. N., and Hammes-Schiffer, S. (2017) Effects of active site mutations on specificity of nucleobase binding in human DNA polymerase eta, J. Phys. Chem. B 121, 3667-3675. DOI: 10.1021/acs.jpcb.6b09973
  9. Ucisik, M. N., Bevilacqua, P. C., and Hammes-Schiffer, S. (2016) Molecular dynamics study of twister ribozyme: Role of Mg2+ ions and hydrogen-bonding network in active site, Biochemistry 55, 3834–3846. DOI: 10.1021/acs.biochem.1026b00203.
  10. Ucisik, M. N., and Hammes-Schiffer, S. (2015) Comparative Molecular Dynamics Studies of Human DNA Polymerase η, J. Chem. Inf. Model. 55, 2672–2681​. DOI: 10.1021/acs.jcim.5b00606
  11. Ucisik, M. N., and Hammes-Schiffer, S. (2015) Relative Binding Free Energies for Adenine and Guanine to Damaged and Undamaged DNA in Human DNA Polymerase η: Clues for Fidelity and Overall Efficiency, J. Am. Chem. Soc. 137, 13240-13243. DOI: 10.1021/jacs.5b08451
  12. Ucisik, M. N., Chakravorty, D. K., and Merz, K. M. (2015) Models for the Metal Transfer Complex of the N-terminal Region of CusB and CusF, Biochemistry, 54, 4226-4235. DOI: 10.1021/acs.biochem.5b00195 
  13.  Ucisik, M. N., and Merz, K. M. (2015) N‑Terminal Domain of the Cu(I)Binding Protein CusB, In Encyclopedia of Inorganic and Bioinorganic Chemistry, John Wiley & Sons, Ltd., West Sussex, United Kingdom.
  14. Minkara, S.M., Ucisik, M. N., Weaver, M. N., Merz, K. M. (2014) Molecular dynamics study of Helicobacter pylori urease, J. Chem. Theory Comput.​ 10, 1852-1862.  DOI: 10.1021/ct5000023
  15. Ucisik, M. N., Zheng, Z., Faver, J. C., Merz, K. M. (2014) Bringing clarity to the prediction of protein-ligand binding free energies via “blurring”. J. Chem. Theory Comput., 10, 1314–1325. DOI: 10.1021/ct400995c
  16. Zheng, Z., Ucisik, M. N., Merz, K.M. (2013) The movable type method applied to protein-ligand binding, J. Chem. Theory Comput. 9, 5526–5538. DOI: 10.1021/ct4005992
  17.  Ucisik, M. N., Chakravorty, D. K., Merz, K. M. (2013) Structure and dynamics of the N-terminal domain of the Cu(I) binding protein CusB, Biochemistry 52, 6911-6923. DOI: 10.1021/bi400606b
  18. Faver, J. C., Ucisik, M. N., Yang, W., Merz, K. M. (2013) Computer-aided drug design: using numbers to your advantage, ACS Med. Chem. Lett. 4, 812-814. DOI: 10.1021/ml4002634
  19. Yang, Y., Wang, B., Ucisik, M. N., Cui, G. L., Fierke, C. A., and Merz, K. M. (2012) Insights into the mechanistic dichotomy of the protein farnesyltransferase peptide substrates CVIM and CVLS, J Am Chem Soc 134, 820-823. DOI: 10.1021/ja209650h
  20. Benson, M. L., Faver, J. C., Ucisik, M. N., Dashti, D. S., Zheng, Z., and Merz, K. M. (2012) Prediction of trypsin/molecular fragment binding affinities by free energy decomposition and empirical scores, J. Comput.-Aided Mol. Des. 26, 647-659. DOI: 10.1007/s10822-012-9567-9
  21. Chakravorty, D. K., Wang, B., Ucisik, M. N., and Merz, K. M. (2011) Insight into the cation-pi interaction at the metal binding site of the copper metallochaperone CusF, J Am Chem Soc 133, 19330-19333. DOI: 10.1021/ja208662z
  22. Ucisik, M. N., Dashti, D. S., Faver, J. C., and Merz, K. M. (2011) Pairwise additivity of energy components in protein-ligand binding: the HIV II protease-Indinavir case, J Chem Phys 135, 085101. DOI: :10.1063/1.3624750
  23. Agopcan, S., Celebi-Olcum, N., Ucisik, M. N., Sanyal, A., and Aviyente, V. (2011) Origins of the diastereoselectivity in hydrogen bonding directed Diels-Alder reactions of chiral dienes with achiral dienophiles: a computational study, Org Biomol Chem 9, 8079-8088. DOI: 10.1039/C1OB06285A