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. 2022 Sep 3;11(9):1196. doi: 10.3390/antibiotics11091196

Table 6.

Ranking of predictions for the best multifunctional peptide constructs with the reward for a predicted negative mean of hemolytic and toxic activity.

Length-Amph-AMP * Table-
Peptide # 		CPP Anti-
Microbial & 		Anti-
Cancer & 		Anti-
Viral & 		Anti-
Fung & 		Anti-
Inflamm. $ 		Sum/6 Rank † Hemol. Probab. Tox. Score Reward Low tox. Total Score § Overall
Rank		 CPP
Part
25-αd-temp V1R9 T3-37 0.97/H 0.955 0.965 1.00 0.975 0.997 0.9869 1 0.130 −1.27 0.570 0.92734 1st WFS6R7
31-αtαd-temp R9R14 T4-39 0.92/H 0.983 0.9445 0.972 0.949 1.0412 0.9682 6 0.010 −1.25 0.620 0.91846 2nd WFA5R7
25-αd-temp R9 T3-36 0.96/H 0.955 0.97 1.00 0.98 0.927 0.9670 7 0.180 −1.30 0.560 0.90886 3rd WFS6R7
31-αtαd-temp R9R14 T4-38 0.94/H 0.993 0.9495 0.985 0.952 0.9368 0.9594 10 0.028 −1.20 0.586 0.90606 4th WFR8
22-αd-temp T4-30 0.95/H 0.99 0.99 0.927 0.96 0.996 0.9688 5 0.070 −1.12 0.525 0.90540 5th KW
22-αd-r-o-p A8I15 T2-20 0.987/H 0.977 0.976 0.863 0.906 0.9038 0.9353 0.007 −1.39 0.692 0.90047 6th tLyP-1
29-βαd-PexS T5-35 0.90/H 0.995 0.985 0.83 0.995 0.9435 0.9414 21 0.054 −1.34 0.643 0.89877 7th MFC
25-αd-temp T3-9 0.97/H 0.99 0.975 1.00 0.985 0.757 0.9461 19 0.170 −1.35 0.590 0.89523 8th WFR8
31-αtαd-temp R9R14 T4-37 0.95/H 0.9985 0.961 0.927 0.98 0.8538 0.9450 20 0.032 −1.18 0.574 0.89200 9th WFR8
22-αtαd-temp T5-48 0.959/H 1.00 0.7156 0.986 0.825 1.1563 0.9472 18 0.190 −1.30 0.555 0.89119 10th rP9a
31-αtαd-mapegin-a2 T3-50 0.881/L 0.756 0.8295 0.967 0.983 0.9556 0.8953 0.077 −1.81 0.867 0.89118 11th TATa
25-αd-BMAP T4-33 0.905/H 0.991 0.9715 0.993 0.905 0.9868 0.9567 12 0.080 −1.05 0.485 0.88931 12th KW
35-βtαd- PR-35a T5-45 0.821/L 0.994 0.6675 0.982 0.910 1.134 0.9180 0.012 −1.44 0.714 0.88886 13th whole
25-αd- temp L9V14 T3-35 0.96/H 0.999 0.97 1.00 0.98 0.978 0.9738 4 0.760 −1.47 0.355 0.88540 14th WFR8
28-αd-T2R1-L7S17-a2 T4-32 0.93/H 0.914 0.974 0.997 0.785 0.9557 0.9260 0.050 −1.30 0.625 0.88300 15th KT2W
25-αd-BMAP-18 T4-25 0.90/H 1.00 0.98 1.00 0.930 0.875 0.9475 17 0.090 −1.01 0.460 0.87787 16th KW
27-αtβ d -temp V1R9 T5-52 0.940/H 0.992 0.974 0.963 0.960 0.888 0.9528 14 0.098 −0.94 0.421 0.87684 17th Sub 5
25-βαd-BMAP-a2 T4-36 0.849/H 0.987 0.9665 0.990 0.912 1.0828 0.9646 8 0.399 −1.09 0.346 0.87616 18th KW
33-αd-adepantin-1A T4-18 0.86/L 1.00 0.955 1.00 0.98 0.8668 0.9436 0.630 −1.56 0.465 0.87525 19th WFR8
25-αtβd-novispirin-a1 T4-50 0.903/H 0.959 0.9885 0.920 0.975 0.5942 0.8899 0.195 −1.63 0.7175 0.87307 20th KW
33-αd adepantin-1A-L15 T4-51 0.878/L 0.9995 0.9358 0.965 0.972 0.954 0.9506 16 0.826 −1.63 0.402 0.87225 21 WFR8
22-r-o-pA8I15 T2-21 0.985/H 0.98 0.962 0.683 0.91 0.960 0.9134 0.006 −1.22 0.607 0.86963 22 tLyPA3-1
20-αβ BP100 T4-34 0.927/H 0.9975 0.9735 0.987 0.935 1.0426 0.9772 3 0.894 −1.32 0.213 0.86803 23 KW
19-αβ BP33 T4-9 0.93/H 1.00 0.985 1.00 0.96 1.001 0.9793 2 0.820 −1.19 0.185 0.86583 25 KW
28-αtα-novispirin-a1 T3-38 0.94/H 1.00 0.8745 0.995 0.978 0.9305 0.9526 15 0.551 −1.17 0.310 0.86073 26 WFL5R7
35-α adep1a T4-17 0.80/L 0.995 0.965 1.00 0.99 0.8552 0.9342 0.660 −1.46 0.400 0.85789 29 WFR8
31-αtα mapegin-a1 T3-49 0.958/H 0.990 0.798 0.868 0.97 1.1887 0.9621 9 0.717 −1.09 0.187 0.85127 30 TAT
18-αtα r-o-p-analog T2-22 0.991/H 1.00 0.962 0.97 0.795 0.61 0.8879 0.003 −1.26 0.629 0.85091 31 whole
25-α-BMAP2-18 T4-52 0.961/H 0.9995 0.988 0.948 0.955 0.6315 0.9139 0.176 −1.09 0.457 0.84862 32 KW
34-αtα-Zyk1a T4-35 0.833/L 0.9985 0.9815 0.983 0.987 0.9377 0.9534 13 0.938 −1.33 0.196 0.84520 33 WFR8

* The amphiphilic character of the peptide was assessed by the SPLIT 3.5 server (http://split.djpept.com/split/ accessed on 7 August 2022 [42]). Bold or normal font α, β, and t symbols are stronger or weaker predicted profiles of hydrophobic moments for helix, beta-strand, and turn secondary structure. The “d” symbol is for predominantly disordered structure when indicated by the flDPnn server [191] for the first 20 peptides. The same server predicts DNA and RNA binding sites for all 20 best peptides from 41% to 100% of their residues. Peptide’s abbreviations are in Table 2, Table 3, Table 4 and Table 5. For instance, the temp abbreviation stands for the L-K6V1 temporin 1CEb with the sequence IKKIVSKIKKLLK [112]. The a1 or a2 abbreviation is for analog1 or analog2. The single code letter with the subscript for the residue sequence position is used for substituted amino acids. In the asparagutin case (WFR8), R7 or R8 means the total number of arginines. # The peptide code number is “Tn-m” for “n” = 2,3,4,5, referring to the corresponding Table, and “m” for the peptide number in Table n. & Mean values of predicted probabilities for antimicrobial, anticancer, antiviral, and antifungal activity. See Table 2 for server addresses and corresponding references. We used the gray background to highlight cases among 20 best peptides when the probability for anticancer and antiviral activity is close to 1.0 (>0.95). $ Mean value of predicted scores by AIPpred, PreAIP, and AntiInflam servers. See Table 2 for server addresses and corresponding references. The AntiInflam server was included in the calculated mean for the cases when three or fewer amino acid substitutions were enough to raise the predicted score above 1.0 (except for the PR-35 analog with seven substitutions). † Peptides are first ranked (yellow background) regardless of their predicted hemolytic activity and toxicity. § Total score is calculated as: (CPP probability + mean antimicrobial probability + mean anti-cancer probability + mean antiviral probability + mean antifungal probability + mean anti-inflammatory score)/6 − (hemolytic activity probability + toxicity score)/2. The subtracted number is a positive reward for low toxicity. We used the blue and green background to rank the 20 best peptides according to their total score.