Audie Lab
SHU Drug Design Center
Department of Chemistry and Physics, Sacred Heart University, Fairfield, CT
SHU Drug Design Center
Department of Chemistry and Physics, Sacred Heart University, Fairfield, CT
The Audie lab develops and applies physics-based and data-driven computational methods to enable rational peptide drug design. Research projects and activities are typically done under the auspices of the SHU Drug Design Center and in collaboration with SHU faculty or external academic or industry partners. Current Projects include:
1) Design of beta-lactamase inhibitors in collaboration with Prof. Todd Sullivan of SHU
2) Design of peptide drug candidates for an undisclosed target in collaboration with Prof. Stephen Ansell of the Mayo Clinic
3) Design of peptide drug candidates for an undisclosed target in collaboration with L2 Diagnostics
4) Design of peptide drug inhibitors of CDK5 in collaboration with Cogentis Therapeutics
Selected Publications:
1: Audie J, Swanson J. Recent work in the development and application of
protein-peptide docking. Future Med Chem. 2012 Aug;4(12):1619-44. doi:
10.4155/fmc.12.99. PMID: 22917249.
2: Diller DJ, Swanson J, Bayden AS, Jarosinski M, Audie J. Rational, computer-
enabled peptide drug design: principles, methods, applications and future
directions. Future Med Chem. 2015;7(16):2173-93. doi: 10.4155/fmc.15.142. Epub
2015 Oct 29. PMID: 26510691.
3: Audie J, Swanson J. Advances in the prediction of protein-peptide binding
affinities: implications for peptide-based drug discovery. Chem Biol Drug Des.
2013 Jan;81(1):50-60. doi: 10.1111/cbdd.12076. PMID: 23066895.
4: Audie J, Boyd C. The synergistic use of computation, chemistry and biology to
discover novel peptide-based drugs: the time is right. Curr Pharm Des.
2010;16(5):567-82. doi: 10.2174/138161210790361425. PMID: 19929848.
5: Diller DJ, Swanson J, Bayden AS, Brown CJ, Thean D, Lane DP, Partridge AW,
Sawyer TK, Audie J. Rigorous Computational and Experimental Investigations on
MDM2/MDMX-Targeted Linear and Macrocyclic Peptides. Molecules. 2019 Dec
14;24(24):4586. doi: 10.3390/molecules24244586. PMID: 31847417; PMCID:
PMC6943714.
6: Price-Troska T, Yang ZZ, Diller D, Bayden A, Jarosinski M, Audie J, Ansell
SM. Inhibiting IL-2 signaling and the regulatory T-cell pathway using
computationally designed peptides. Invest New Drugs. 2019 Feb;37(1):9-16. doi:
10.1007/s10637-018-0606-9. Epub 2018 Apr 26. PMID: 29696509.
7: Considine KL, Stefanidis L, Grozinger KG, Audie J, Alper BJ. Efficient
synthesis of α-fluoromethylhistidine di-hydrochloride and demonstration of its
efficacy as a glutathione S-transferase inhibitor. Bioorg Med Chem Lett. 2017
Mar 15;27(6):1335-1340. doi: 10.1016/j.bmcl.2017.02.024. Epub 2017 Feb 14. PMID:
28228363.
8: Ponomarev SY, Audie J. Computational prediction and analysis of the DR6-NAPP
interaction. Proteins. 2011 May;79(5):1376-95. doi: 10.1002/prot.22962. Epub
2011 Feb 18. PMID: 21337622.
9: Diller KI, Bayden AS, Audie J, Diller DJ. PeptideNavigator: An interactive
tool for exploring large and complex data sets generated during peptide-based
drug design projects. Comput Biol Med. 2018 Jan 1;92:176-187. doi:
10.1016/j.compbiomed.2017.11.016. Epub 2017 Nov 24. PMID: 29207334.
10: Bayden AS, Gomez EF, Audie J, Chakravorty DK, Diller DJ. A combined
cheminformatic and bioinformatic approach to address the proteolytic stability
challenge in peptide-based drug discovery. Biopolymers. 2015 Nov;104(6):775-89.
doi: 10.1002/bip.22711. PMID: 26270398.
11: Audie J, Scarlata S. A novel empirical free energy function that explains
and predicts protein-protein binding affinities. Biophys Chem. 2007
Sep;129(2-3):198-211. doi: 10.1016/j.bpc.2007.05.021. Epub 2007 Jun 7. PMID:
17600612.
12: Swanson J, Audie J. An unexpected way forward: towards a more accurate and
rigorous protein-protein binding affinity scoring function by eliminating terms
from an already simple scoring function. J Biomol Struct Dyn. 2018
Jan;36(1):83-97. doi: 10.1080/07391102.2016.1268974. Epub 2017 Jan 16. PMID:
27989231.
13: Audie J. Development and validation of an empirical free energy function for
calculating protein-protein binding free energy surfaces. Biophys Chem. 2009
Feb;139(2-3):84-91. doi: 10.1016/j.bpc.2008.10.007. Epub 2008 Nov 8. PMID:
19041170.
14: Audie J. Continued development of an empirical function for predicting and
rationalizing protein-protein binding affinities. Biophys Chem. 2009
Aug;143(3):139-44. doi: 10.1016/j.bpc.2009.05.003. Epub 2009 May 14. PMID:
19487068.