In silico structure-activity-relationship (SAR) models from machine learning: a review

2010 ◽  
Vol 72 (2) ◽  
pp. 138-146 ◽  
Author(s):  
Xia Ning ◽  
George Karypis
Keyword(s):  
Machine Learning ◽  
In Silico ◽  
Structure Activity Relationship ◽  
Activity Relationship ◽  
Structure Activity

scholarly journals In Silico and In Vitro Structure–Activity Relationship of Mastoparan and Its Analogs

Molecules ◽  
2022 ◽  
Vol 27 (2) ◽  
pp. 561
Author(s):  
Prapenpuksiri Rungsa ◽  
Steve Peigneur ◽  
Nisachon Jangpromma ◽  
Sompong Klaynongsruang ◽  
Jan Tytgat ◽  
...  
Keyword(s):  
Antibacterial Activity ◽  
Biological Activity ◽  
Hemolytic Activity ◽  
In Silico ◽  
Structure Activity Relationship ◽  
Activity Relationship ◽  
Helical Conformation ◽  
Structure Activity ◽  
Wide Range ◽  
Α Helix

Antimicrobial peptides are an important class of therapeutic agent used against a wide range of pathogens such as Gram-negative and Gram-positive bacteria, fungi, and viruses. Mastoparan (MpVT) is an α-helix and amphipathic tetradecapeptide obtained from Vespa tropica venom. This peptide exhibits antibacterial activity. In this work, we investigate the effect of amino acid substitutions and deletion of the first three C-terminal residues on the structure–activity relationship. In this in silico study, the predicted structure of MpVT and its analog have characteristic features of linear cationic peptides rich in hydrophobic and basic amino acids without disulfide bonds. The secondary structure and the biological activity of six designed analogs are studied. The biological activity assays show that the substitution of phenylalanine (MpVT1) results in a higher antibacterial activity than that of MpVT without increasing toxicity. The analogs with the first three deleted C-terminal residues showed decreased antibacterial and hemolytic activity. The CD (circular dichroism) spectra of these peptides show a high content α-helical conformation in the presence of 40% 2,2,2- trifluoroethanol (TFE). In conclusion, the first three C-terminal deletions reduced the length of the α-helix, explaining the decreased biological activity. MpVTs show that the hemolytic activity of mastoparan is correlated to mean hydrophobicity and mean hydrophobic moment. The position and spatial arrangement of specific hydrophobic residues on the non-polar face of α-helical AMPs may be crucial for the interaction of AMPs with cell membranes.

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