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Werner HM, Cabalteja CC, Horne WS. Peptide Backbone Composition and Protease Susceptibility: Impact of Modification Type, Position, and Tandem Substitution. Chembiochem 2015. [PMID: 26205791 DOI: 10.1002/cbic.201500312] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The clinical utility of peptides is limited by their rapid degradation by endogenous proteases. Modification of the peptide backbone can generate functional analogues with enhanced proteolytic stability. Existing principles for the design of such oligomers have focused primarily on effective structural mimicry. A more robust strategy would incorporate a rational approach for engineering maximal proteolytic stability with minimal unnatural residue content. We report here the systematic comparison of the proteolytic resistance imparted by four backbone modifications commonly employed in the design of protease-stable analogues of peptides with complex folding patterns. The degree of protection was quantified as a function of modification type, position, and tandem substitution in the context of a long, unstructured host sequence and a canonical serine protease. These results promise to inform ongoing work to develop biostable mimics of increasingly complex peptides and proteins.
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Affiliation(s)
- Halina M Werner
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15213, USA
| | - Chino C Cabalteja
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15213, USA
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15213, USA.
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Lin Z, Oostenbrink C, van Gunsteren WF. On the use of one-step perturbation to investigate the dependence of NOE-derived atom–atom distance bound violations of peptides upon a variation of force-field parameters. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2014; 43:113-9. [DOI: 10.1007/s00249-014-0943-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 01/13/2014] [Accepted: 01/17/2014] [Indexed: 11/28/2022]
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Eichenberger AP, Allison JR, Dolenc J, Geerke DP, Horta BAC, Meier K, Oostenbrink C, Schmid N, Steiner D, Wang D, van Gunsteren WF. GROMOS++ Software for the Analysis of Biomolecular Simulation Trajectories. J Chem Theory Comput 2011; 7:3379-90. [DOI: 10.1021/ct2003622] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andreas P. Eichenberger
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, Zürich, Switzerland
| | - Jane R. Allison
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, Zürich, Switzerland
| | - Jožica Dolenc
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, Zürich, Switzerland
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Daan P. Geerke
- Division of Molecular and Computational Toxicology, Free University Amsterdam, Amsterdam, The Netherlands
| | - Bruno A. C. Horta
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, Zürich, Switzerland
| | - Katharina Meier
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, Zürich, Switzerland
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Nathan Schmid
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, Zürich, Switzerland
| | - Denise Steiner
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, Zürich, Switzerland
| | - Dongqi Wang
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, Zürich, Switzerland
| | - Wilfred F. van Gunsteren
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, Zürich, Switzerland
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