Audie Lab

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.