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Synthesis of Bioactive Peptides for Pharmaceutical Applications
Published in Peter Grunwald, Pharmaceutical Biocatalysis, 2019
Jaison Jeevanandam, Ashish Kumar Solanki, Shailza Sharma, Prabir Kumar Kulabhusan, Sapna Pahil, Michael K. Danquah
The endoproteases enzymes possess the ability to catalyze and cleave terminal or penultimate peptide bond. They are further classified into amino and carboxypeptidases based on the cleavage of enzymes at amino or carboxy terminus. On the other hand, endoproteases are the enzymes that cleave the internal peptide bond. They are further classified based on the amino acids involved in catalytic mechanism which includes serine proteases, threonine proteases, cysteine proteases, metalloproteases, and aspartic proteases.
Comparative study of the nucleophilic attack step in the proteases catalytic activity: A theoretical study
Published in Molecular Physics, 2020
Sebastián A. Cuesta, José R. Mora, Cesar H. Zambrano, F. Javier Torres, Luis Rincón
Five experimental protease models were built based on crystallographic structures found in the Protein Data Bank and prepared using Pymol [40] and Gaussview 05 [41] according to Schemes 1 and 2. Model preparation consisted on the analysis of the three-dimensional structures, identification of the active site, and elimination of all the amino acids and atoms not directly involved in the nucleophilic attack. Then, the positions of the amino acids involved in the catalytic centre were fixed and the Gly–Gly substrate was relaxed using quantum mechanical methods until the corresponding minima in each case was found. For the Cysteine protease, the model was built based on the X-ray diffraction crystal structure of Trypanosoma cruzís Cruzain Cysteine Protease (PDB: 1AIM) [33,42]; for the serine protease, the 2.4 A resolution X-ray crystalografic structure of Hepatitis C Virus NS3/NS4A Serine Protease (PDB: 1DXP) model was used [43]. Aspartyl protease model was built based on the Crystal structure of human BACE2 in complex with a hydroxyethylenamine (PDB: 2EWY) [44,45]; while Zn-protease was based on the 2.5 A resolution Crystal structure of human matrix metalloproteinase MMP9 (PDB:1L6J) [46,47]; Finally, threonine protease model was built based on the Cryo-Electron Microscopy structure of Human 26S proteasome (PDB: 6MSB) [48].