Recent trends in antimicrobial peptide prediction using machine learning techniques

Abstract

The importance to develop effective alternatives to known antibiotics due to increased microbial resistance is gaining momentum in recent years. Therefore, it is of interest to predict, design and computationally model Antimicrobial Peptides (AMPs). AMPs are oligopeptides with varying size (from 5 to over100 residues) having key role in innate immunity. Thus, the potential exploitation of AMPs as novel therapeutic agents is evident. They act by causing cell death either by disrupting the microbial membrane by inhibiting extracellular polymer synthesis or by altering intra cellular polymer functions. AMPs have broad spectrum activity and act as first line of defense against all types of microorganisms including viruses, bacteria, parasites, fungi and as well as cancer (uncontrolled celldivision) progression. Large-scale identification and extraction of AMPs is often non-trivial, expensive and time consuming. Hence, there is a need to develop models to predict AMPs as therapeutics. We document recent trends and advancement in the prediction of AMP.

Expression of Hybrid Peptide EF-1 in Pichia pastoris, Its Purification, and Antimicrobial Characterization

“…In recent years, novel peptides have been designed by hybridizing different AMPs to improve their individual properties [ 32 ]. The replacement of conserved amino acid residues does not affect their activity, and several suitable sequences can enhance the efficiency of hybrid peptides [ 3 ]. PlnEF, a cationic bacteriocin, has been demonstrated to counteract Gram-positive bacteria through disrupting bacterial membrane.…”

“…Antimicrobial peptides (AMPs) are considered a good starting point to develop of future antibiotics [ 1 ]. AMPs are typically naturally distributed amphipathic, cationic, small polypeptides [ 2 ] which secreted by various organisms such as vertebrates, plants, fungi, and bacteria [ 3 ]. They exhibit a great number of acting ways, for example, they can disrupt cell membrane through “barrel-stave” [ 4 ], “toroidal-pore” [ 5 ], and “carpet” [ 6 ] models and inhibit cell wall biosynthesis and cell division [ 7 , 8 ].…”

A Hybrid Peptide DEFB-TP5 Expressed in Methylotrophic Yeast Neutralizes LPS With Potent Anti-inflammatory Activities

“…However, the specific part of the amino acid sequence of the peptide has an inordinate influence on the antibacterial and anti-inflammatory activities. The appropriate replacement of the conserved sequence doesn't affect its activity but some suitable substitutions enhance the efficiency of hybrid peptides (Shah et al, 2017). Hybridization of various parental peptides and alterations in physicochemical properties (net charge, a-helix structure, and hydrophobicity) by reducing the size are the common practices for the development of potent hybrid peptides (Brown et al, 2008).To date, there are different systems for the manufacturing of peptides such as extraction from natural sources, chemical, synthesis, and DNA recombinant technology (Van Harten et al, 2018).…”

“…Recently, about 500 antipathogenic natural peptides have been revealed to show potential actions against microbes. Segregation of these peptides has been done from an extensive variety of organisms such as vertebrates, invertebrates, bacteria, plants and fungi (Hancock and Chapple, 1999;Shah et al, 2017). Antimicrobial peptides (AMPs) were reflected in one of the exceptional preferences to use as a substitute or in combination with conventional therapeutics.…”

In vitro Impact of Yeast Expressed Hybrid Peptide CATH-2TP5 as a Prophylactic Measure Toward Sepsis and Inflammation

“…TP5 shows likewise organic action as thymopoietin in-charge of phenotypic separation of T-cells and the regulation of the immune system (Singh et al, 1998). It has been perceived as an immune modulator for the treatment of essential immune deficiency diseases such as AIDS (Sundal and Bertelletti, 1994), rheumatoid arthritis (Shah et al, 2017), and immune system infections.…”