New Milk Protein-Derived Peptides with Potential Antimicrobial Activity: An Approach Based on Bioinformatic Studies

Abstract

New peptides with potential antimicrobial activity, encrypted in milk protein sequences, were searched for with the use of bioinformatic tools. The major milk proteins were hydrolyzed in silico by 28 enzymes. The obtained peptides were characterized by the following parameters: molecular weight, isoelectric point, composition and number of amino acid residues, net charge at pH 7.0, aliphatic index, instability index, Boman index, and GRAVY index, and compared with those calculated for known 416 antimicrobial peptides including 59 antimicrobial peptides (AMPs) from milk proteins listed in the BIOPEP database. A simple analysis of physico-chemical properties and the values of biological activity indicators were insufficient to select potentially antimicrobial peptides released in silico from milk proteins by proteolytic enzymes. The final selection was made based on the results of multidimensional statistical analysis such as support vector machines (SVM), random forest (RF), artificial neural networks (ANN) and discriminant analysis (DA) available in the Collection of Anti-Microbial Peptides (CAMP database). Eleven new peptides with potential antimicrobial activity were selected from all peptides released during in silico proteolysis of milk proteins.

Antimicrobial Protein Candidates from the Thermophilic Geobacillus sp. Strain ZGt-1: Production, Proteomics, and Bioinformatics Analysis

“…The Boman index values, reflecting the potential of a peptide/protein to interact with other proteins [38], for 6_35, 23_543, and 4_4 are 1.12, 1.57, and 1.19, respectively (Table 2), which also fit within the range of 1–2 for AMPs in the BIOPEP database [32]. …”

“…The proteins 6_35, 23_543, and 4_4 scored 80.08, 110.33, and 96.76 on the aliphatic index, respectively (Table 2), again within the predominant range of 40–120 for AMPs in the BIOPEP database [32]. …”

Discovery of Anti-Hypertensive Oligopeptides from Adlay Based on In Silico Proteolysis and Virtual Screening

“…Compared to in vivo proteolysis, the accuracy of in silico proteolysis has been validated by multiple approaches, including liquid chromatograph-mass spectrometer (LC-MS) [10,12,13,14]. In silico proteolysis is widely used to analyze natural proteins and generate bioactive peptides from food and halobios, such as milk, meat, tilapia, sea cucumber and so on [15,16,17,18]. A biological assay indicated the reliability of in silico proteolysis, which could be further used for other types of natural products or TCM.…”

Strategies for the discovery, identification and validation of milk protein-derived bioactive peptides

“…Chemometric approaches such as quantitative structure activity relationship 180 (QSAR), artificial neural networks (ANN) and virtual screening have recently been reviewed 181 (Iwaniak et al, 2015). ANNs, which are based on machine learning algorithms, have been used 182 in certain instances to aid in the discovery of novel milk BAPs such as antimicrobial peptides 183 (AMPs) (Dziuba & Dziuba, 2014). Other in silico methods such as molecular docking and 184 QSAR will be described in the following paragraphs.…”

“…Milk protein sequences can be accessed 145 from online databases such as UniProtKB/Swiss-Prot (http://www.uniprot.org/uniprot/). In silico 146 (software-based) methods may be used to elucidate milk protein-derived peptide candidates for 147 further in vitro testing (Dziuba & Dziuba, 2014). While a specific protein substrate may be 148 indicated as a rich source of BAPs, it is necessary to subsequently identify enzymatic hydrolysis 149 strategies to optimally release these peptides (Dziuba, Dziuba, & Iwaniak, 2009).…”