De Novo Design and In Vitro Testing of Antimicrobial Peptides against Gram-Negative Bacteria

Abstract

Antimicrobial peptides (AMPs) have been identified as a potentially new class of antibiotics to combat bacterial resistance to conventional drugs. The design of de novo AMPs with high therapeutic indexes, low cost of synthesis, high resistance to proteases and high bioavailability remains a challenge. Such design requires computational modeling of antimicrobial properties. Currently, most computational methods cannot accurately calculate antimicrobial potency against particular strains of bacterial pathogens. We developed a tool for AMP prediction (Special Prediction (SP) tool) and made it available on our Web site (https://dbaasp.org/prediction). Based on this tool, a simple algorithm for the design of de novo AMPs (DSP) was created. We used DSP to design short peptides with high therapeutic indexes against gram-negative bacteria. The predicted peptides have been synthesized and tested in vitro against a panel of gram-negative bacteria, including drug resistant ones. Predicted activity against Escherichia coli ATCC 25922 was experimentally confirmed for 14 out of 15 peptides. Further improvements for designed peptides included the synthesis of D-enantiomers, which are traditionally used to increase resistance against proteases. One synthetic D-peptide (SP15D) possesses one of the lowest values of minimum inhibitory concentration (MIC) among all DBAASP database short peptides at the time of the submission of this article, while being highly stable against proteases and having a high therapeutic index. The mode of anti-bacterial action, assessed by fluorescence microscopy, shows that SP15D acts similarly to cell penetrating peptides. SP15D can be considered a promising candidate for the development of peptide antibiotics. We plan further exploratory studies with the SP tool, aiming at finding peptides which are active against other pathogenic organisms.

Increases in Hydrophilicity and Charge on the Polar Face of Alyteserin 1c Helix Change its Selectivity towards Gram-Positive Bacteria

“…The search for new antibiotics is currently intensifying due to the increase of cases of bacterial resistance, which represents a major threat to public health worldwide [22]. Among the strategies being used, the design of antimicrobial peptides (AMPs) from sequences already reported has been pursued, with the purpose of enhancing antimicrobial activity while reducing protease sensitivity and toxicity [23]. Here, we used Alyteserin 1c as a template peptide due to its reduced cationic charge and the presence of hydrophobic residues on the polar face of its helix.…”

Computer-Aided Design of Antimicrobial Peptides: Are We Generating Effective Drug Candidates?

“…DSP has been used to computationally design short AMP candidates with high therapeutic indexes and promising effects on Gram-negative bacteria. Based on that, Vishnepolsky et al (2019) reported that, among the 15 DSP designed AMPs, 14 had their antibacterial efficacy confirmed experimentally against E. coli. In addition, these peptides demonstrated high antimicrobial activity against P. aeruginosa and Acinetobacter baumannii pathogens (Vishnepolsky et al, 2019).…”

“…Based on that, Vishnepolsky et al (2019) reported that, among the 15 DSP designed AMPs, 14 had their antibacterial efficacy confirmed experimentally against E. coli. In addition, these peptides demonstrated high antimicrobial activity against P. aeruginosa and Acinetobacter baumannii pathogens (Vishnepolsky et al, 2019). Considering the obstacle imposed by AMP degradation when administrated in animal models, D-enantiomer analogs were also generated in that study and one synthetic D-peptide (SP15D) revealed the highest antibacterial effects toward E. coli, with MIC values ranging from 0.2 to 0.9 µM (0.39 to 1.56 µg.mL −1 ).…”

Anti-Acne Action of Peptides Isolated from Burdock Root—Preliminary Studies and Pilot Testing

“…Another Georgian-American team of scientists working on de novo AMP synthesis pointed out that the design of AMPs with high therapeutic indexes, low cost of synthesis, high resistance to proteases, and high bioavailability remains a challenge. Authors have developed a digital tool to predict AMP algorithms for the design of de novo AMPs, and short peptides with high therapeutic indexes against Gram-negative bacteria have been designed [43].…”