Publications
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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.
- 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
- 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
- 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
- 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.
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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