Table 2.
Hybrid penetratin-like peptides with predicted DNA binding, CPP, antimicrobial, anticancer, antiviral, antifungal, anti-inflammatory, hemolytic, and toxic activity.
| No. | Peptide/Gene/Origin * | Extended TriPaxB or Reverse Penetratin/Sequence Number * | DNA- Bind. ** |
CPP $ | Anti- Microbial ‡ |
Anti- Cancer $$ |
Anti- Viral & |
Anti- Fungal ⁋ |
Anti-Inflamm. Activity § | Hemo- lytic ¥ |
Toxicity/Score † |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | P02833/D. melanogaster penetratin/E |
RQIKIWFQNRRMKWKK /339–254/pAntp |
+ | 0.998/H | 0.97/0.42 | 0.812/0.985 | 1.0/0.70/0.77 | 0.28/0.95 | 0.57/0.68 | 0.94/+ | −0.66 |
| 2 | Rev. VV-pen. [136]/E | KKWKMRRNQFWVKVQR | + | 0.956/H | 0.96/0.53 | 0.649/0.981 | 0.10/0.44/0.28 | 0.15/0.68 | 0.52/0.66 | 0.19/− | −0.81 |
| 3 | TriPaxB penetratin | RVVQVWFQNQRAKLKK | + | 0.807/L | 0.74/0.42 | 0.036/0.971 | 0.00/0.40/0.01 | 0.22/0.21 | 0.52/0.61 | 0.02/− | −1.42 |
| 4 | A0A7M5V8Y3/N/A /Clytia hemisphaerica |
GLSVRVVQVWFQNQRAKLKKIQKK/227–250 | + | 0.642/L | 0.96/0.32 | 0.189/0.980 | 0.44/0.47/0.82 | 0.56/0.59 | 0.65/0.62 | 0.03/− | −1.45 |
| 5 | T2M9B9/UP &&/Hydra vulgaris | GLSVRVVQVWFQNQRAKLKKLHRK/227–250 and 108–131 | + | 0.761/L | 0.93/0.37 | 0.065/0.983 | 0.66/0.46/0.97 | 0.58/0.45 | 0.66/0.61 | 0.03/− | −1.16 |
| 6 | A0A1S0TPC1/UP &&/ Loa loa |
NLSVRVVQVWFQNQRAKLKKIQRK/118–141 | + | 0.715/L | 0.91/0.29 | 0.049/0.769 | 0.21/0.57/1.0 | 0.28/0.59 | 0.67/0.63 | 0.04/− | −1.47 |
| 7 | PexNC-TriPaxB-I/DJ | GIGK-RVVQVWFQNQRAKLKK-ILKK | + | 0.731/L | 0.99/0.67 | 0.968/0.980 | 0.93/0.75/1.0 | 0.97/0.59 | 0.61/0.58 | 0.09/− | −1.51 |
| 8 | PexShort-TriPaxB-II (PexT)/DJ | GIGKLKKAKKFGKKILKK-G- RVVQVWFQNQRAKLKK |
+ | 0.792/L | 1.0/0.98 | 0.995/0.951 | 0.98/0.76/0.52 | 1.0/0.61 | 0.64/0.58 | 0.13/− | −1.17 |
| 9 | PexNC-rev. VV-pen./DJ | GIGK-G-KKWKMRRNQFWVKVQR-ILKK | + | 0.849/H | 1.0/0.58 | 0.919/0.982 | 1.0/0.65/0.95 | 0.94/0.93 | 0.55/0.67 | 0.26/− | −1.17 |
| 10 | TriPaxB–antifungal BP16 [144]/DJ |
RVVQVWFQNQRAKLKK-G- KKLFKKILKKL |
+ | 0.816/L | 0.98/0.95 | 0.992/0.981 | 1.0/0.70/0.93 | 0.98/0.54 | 0.54/0.64 | 0.62/+ | −1.46 |
| 11 | Anti-cancer-I-Rev. VV-pen. [136]/E | PPLSQETFS- KKWKMRRNQFWVKVQRG |
+ | 0.503/H | 0.41/0.53 | NACP/NACP | 0.40/0.90/1.0 | 0.15/0.05 | 0.62/0.62 | 0.13/− | −1.09 |
| 12 | pAntp-TPR [145]/E |
RQIKIWFQNRRMKWKK- KAYARIGNSYFK |
+ | 0.834/H | 0.91/0.50 | 0.923/0.939 | 1.0/0.80/0.54 | 0.83/0.65 | 0.59/0.62 | 0.91/+ | −1.09 |
| 13 | Rev.-VV-pen. [136]-TPR/DJ |
KKWKMRRNQFWVKVQR-G- KAYARIGNSYFK |
+ | 0.766/H | 0.83/0.48 | 0.766/0.952 | 1.0/0.79/1.0 | 0.87/0.40 | 0.60/0.63 | 0.59/+ | −1.13 |
| 14 | Rev. amoeba (Filasterea) pen. with added N-term-Arg/DJ | RRQKARRNQFWIRIVRR | + | 0.958/H | 1.0/0.46 | 0.110/0.984 | 0.01/0.27/0.73 | 0.44/0.71 | 0.59/0.62 | 0.07/− | −0.58 |
| 15 | Rev. R-am.pen.-tLyP-1 [146]/DJ |
RRQKARRNQFWIRIVRR- CGIKRTK |
+ | 0.962/H | 0.98/0.51 | 0.259/0.984 | 0.78/0.91/0.93 | 0.88/0.43 | 0.68/0.62 | 0.02/− | −0.88 |
| 16 | Optimal penetratin (o-pen P14 [56]/E | RKKRWFRRRRPKWKK | + | 0.992/H | 1.0/1.0 | 0.767/0.978 | 0.97/0.57/1.0 | 0.32/1.0 | 0.47/0.56 | 0.02/− | −0.89 |
| 17 | Rev. opt. penetratin (r-o-p)/DJ | KKWKPRRRRFWRKKR | + | 0.992/H | 1.0/0.99 | 0.767/0.980 | 1.0/0.92/1.0 | 0.32/1.0 | 0.48/0.49 | 0.01/− | −1.11 |
| 18 | Rev.opt.pen. (r-o-p)-tLyP-1 [146]/DJ |
KKWKPRRRRFWRKKR- CGIKRTK |
+ | 0.987/H | 0.94/1.0 | 0.854/0.979 | 1.0/0.82/0.59 | 0.71/0.96 | 0.65/0.68 | 0.006/− | −1.30 |
| 19 | Fusion peptide 46 [139]/E | GSRAHSSHLKSKKGQSTSRH- KKWKMRRNQFWVKVQRG |
+ | 0.741/L | 0.76/0.87 | 0.61/0.65 | 0.98/0.48/0.15 | 0.81/0.44 | 0.67/0.59 | ND | −0.89 |
| 20 | Rev.opt.pen. (r-o-p A8I15)-tLyP-1 [146]-analog1/DJ |
KKWKPRRARFWRKKI- CGIKRTK |
+ | 0.987/H | 0.96/0.993 | 0.972/0.98 | 1.0/0.8183/0.77 | 0.89/0.922 |
0.6674/0.647/
1.397 |
0.007/− | −1.39 |
| 21 | Rev.opt.pen. A8I15— tLyPA3-1-analog2/DJ |
KKWKPRRARFWRKKI- CGAKRTK |
+ | 0.985/H | 0.97/0.99 | 0.943/0.981 | 1.0/0.78/0.27 | 0.86/0.96 | 0.66/0.66/ 1.56083 |
0.006/− | −1.22 |
| 22 | Rev. optimized penetratin analog/DJ | GKRIGKKWKPRRRRFWRK | + | 0.991/H | 1.0/1.0 | 0.944/0.979 | 1.0/0.96/0.95 | 0.59/1.0 | 0.61/0.61 | 0.003/− | −1.26 |
* Highlighted peptides (bold name) with underlined activity scores are our selection for the designed peptides with the best overall score (see Table 6). All peptides are assumed to be amidated at their C-terminal. Letter ‘E’ after peptide name means that the sequence has been synthesized and tested in experiments. DJ abbreviation means that according to our knowledge, we were the first to find or design that peptide. Bold sequence segments have predicted or verified CPP activity. Underlined residues are optimal substitutions for increasing anti-inflammatory activity or decreasing peptide toxicity. ** The results of DP-Bind server http://lcg.rit.albany.edu/dp-bind/ (accessed on 7 August 2022) by Hwang et al. [36] for sequence-based prediction of DNA-binding residues in DNA-binding proteins. The “+” sign means that the server found several DNA-binding residues. $ The probability that the peptide is cell-penetrating peptide (CPP) or non-CPP (NCPP) with the MLCPP server http://www.thegleelab.org/MLCPP/ [22]. Predicted high and low uptake efficiency is denoted with, respectively, letters ‘H’ and ‘L’. ‡ Antimicrobial peptide probabilities with CAMPR3 Support Vector Machine algorithm of the server http://www.camp.bicnirrh.res.in/predict (accessed on 7 August 2022) [24] and with AmpGram (http://biongram.biotech.uni.wroc.pl/AmpGram/ [25]. $$ The ACPred server (http://codes.bio/acpred/ [26] is used to classify peptides as anticancer (ACP) or non-anticancer (NACP) with a given probability. The mACPred server (http://thegleelab.org/mACPpred/ [27] results for the probability of anticancer activity are added after the ‘/’ symbol. & Results of peptide antiviral prediction with servers ENNAVIA (https://research.timmons.eu/ennavia [28], sequence length restricted between 7 and 40 residues)/FIRM-AVP (https://msc-viz.emsl.pnnl.gov/AVPR/ (accessed on 7 August 2022) [29]/Meta-iAVP (http://codes.bio/meta-iavp/ (accessed on 7 August 2022) [30]. ⁋ Results of iAMPpred peptide antifungal prediction by Meher et al. [31] (http://cabgrid.res.in:8080/amppred/server.php, (accessed on 7 August 2022)) and Zhang et al. [32] (https://www.chemoinfolab.com/antifungal/, (accessed on 7 August 2022)). § Results for the prediction of anti-inflammatory activity (Anti-inf.) by the AIPpred (first number; http://www.thegleelab.org/AIPpred/ (accessed on 7 August 2022) [33], PreAIP (second number; http://kurata14.bio.kyutech.ac.jp/PreAIP/ (accessed on) [34] server, and the score output of the AntiInflam server (http://metagenomics.iiserb.ac.in/antiinflam/ (accessed on 7 August 2022) [35] server when it predicts the anti-inflammatory activity. ¥ The probability that the peptide has hemolytic activity by the HAPPENN server [40] https://research.timmons.eu/happenn (accessed on 7 ugust 2022). After the peptide name, we introduced the |lcl|cTer term to obtain the prediction for the amidated C-terminal. Symbols ‘+’ and ‘−’ are used for peptide classification as hemolytic or not. † Toxicity prediction by the ToxinPred server https://webs.iiitd.edu.in/raghava/toxinpred/ (accessed on 7 August 2022) [37,38,39]. We used batch submission for peptides [37]. The design module of that server was used when we wished to optimize the peptide for decreased toxicity after several amino acid substitutions. && UP = Uncharacterized protein.