Studies towards a hydrophobic serine protease model

Recently, the synthesis of a molecule has been reported that belongs to a Lysine based, branched cyclic peptide class. This work explores the ability of such molecules to preserve the 3D geometry of the Trypsin's Active Site (TAS) by applying an integrated framework of automated computer procedures. The following four factors a) D/L chirality, b) different amino acids at different positions of the molecular scaffold's cyclic part, c) the application of AMBER and CHARMM force fields and d) different implicit solvation models were evaluated against TAS similarity. It was found that a number of molecules exhibit satisfactory geometric affinity to the TAS during extended Molecular Dynamics runs. We estimated that more than 2000 molecules (belonging to this class) could retain good similarity to the TAS arrangement.

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“…f) The use of non peptides as molecular scaffolds for enacting proper 3D topology of the active site [29,30].…”

Section: Accepted M Manuscriptmentioning

confidence: 99%

Molecular Dynamics as a pattern recognition tool: An automated process detects peptides that preserve the 3D arrangement of Trypsin's Active Site

Tatsis¹,

Stavrakoudis²,

Demetropoulos³

2008

Biophysical Chemistry

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Solid‐Supported Synthesis of Highly Functionalized Tripodal Peptides with Flexible but Preorganized Geometry: Towards Potential Serine Protease Mimics

et al. 2006

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Tripodal scaffold 1 has been used in the synthesis of a representative member of a library of serine protease mimics, possessing three independent functionalized peptide chains on a central core. Each peptide chain contains one residue of the classical catalytic triad (serine, histidine and aspartate) found in the active site of the serine protease α-chymotrypsin. A particular feature of the novel tripodal design is its essentially flexible yet preorganized structure as deduced from molecular modeling studies. The choice of suitable scaf-

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Studies towards a hydrophobic serine protease model

Cited by 2 publications

References 7 publications

Molecular Dynamics as a pattern recognition tool: An automated process detects peptides that preserve the 3D arrangement of Trypsin's Active Site

Molecular Dynamics as a pattern recognition tool: An automated process detects peptides that preserve the 3D arrangement of Trypsin's Active Site

Solid‐Supported Synthesis of Highly Functionalized Tripodal Peptides with Flexible but Preorganized Geometry: Towards Potential Serine Protease Mimics

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