Computer-Aided Design of Antimicrobial Peptides http://crdd.osdd.net/raghava/antibp2/ ClassAMP Uses RF and SVM to predict the propensity of a protein sequence to have antibacterial, antifungal, or antiviral activity http://www.bicnirrh.res.in/classamp/ AMPA Web tool for assessing the antimicrobial domains of proteins, with a focus on the design on new antimicrobial drugs http://tcoffee.crg.cat/apps/ampa/do DBAASP Provides users with information on detailed structure (chemical, 3D) and activity for those peptides, for which antimicrobial activity against particular target species have been evaluated experimentally https://dbaasp.org/home Joker An algorithm to design antimicrobial peptides using their language https://github.com/williamfp7/Joker
Computer-aided
screening of antimicrobial peptides (AMPs) is a
promising approach for discovering novel therapies against multidrug-resistant
bacterial infections. Here, we functionally and structurally characterized
an Escherichia coli-derived AMP (EcDBS1R5) previously
designed through pattern identification [α-helical set (KK[ILV](3)[AILV])], followed by sequence optimization. EcDBS1R5 inhibited
the growth of Gram-negative and Gram-positive, susceptible and resistant
bacterial strains at low doses (2–32 μM), with no cytotoxicity
observed against non-cancerous and cancerous cell lines in the concentration
range analyzed (<100 μM). Furthermore, EcDBS1R5 (16 μM)
acted on Pseudomonas aeruginosa pre-formed biofilms
by compromising the viability of biofilm-constituting cells. The in vivo antibacterial potential of EcDBS1R5 was confirmed
as the peptide reduced bacterial counts by two-logs 2 days post-infection
using a skin scarification mouse model. Structurally, circular dichroism
analysis revealed that EcDBS1R5 is unstructured in hydrophilic environments,
but has strong helicity in 2,2,2-trifluoroethanol (TFE)/water mixtures
(v/v) and sodium dodecyl sulfate (SDS) micelles. The TFE-induced nuclear
magnetic resonance structure of EcDBS1R5 was determined and showed
an amphipathic helical segment with flexible termini. Moreover, we
observed that the amide protons for residues Met2-Ala8, Arg10, Ala13-Ala16,
and Trp19 in EcDBS1R5 are protected from the solvent, as their temperature
coefficients values are more positive than −4.6 ppb·K–1. In summary, this study reports a novel dual-antibacterial/antibiofilm
α-helical peptide with therapeutic potential in vitro and in vivo against clinically relevant bacterial
strains.
Antimicrobial peptides (AMPs) are pinpointed as promising molecules against antibiotic-resistant bacterial infections. Nevertheless, there is a discrepancy between the AMP sequences generated and the tangible outcomes in clinical trials. AMPs’...
An unusual N-capping asparagine-lysine-proline (5NKP7) motif yields a coil/N-cap/α-helix multifunctional scaffold in a computer-made peptide selective for anionic surfaces and with anticancer, antibacterial, antibiofilm, anti-infective (in vivo), and immunomodulatory potential.
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