A Uniform In Vitro Efficacy Dataset to Guide Antimicrobial Peptide Design
Abstract
:1. Introduction
- Individual studies report MIC values obtained using varying protocols, which produce different results.
- Different groups use different type cultures of the same organism for MIC estimation.
- Negative data (MIC results for ineffective peptides) is seldom published.
2. Data Description
2.1. Minimum Inhibitory Concentration (MIC) Data
2.2. Circular Dichroism (CD) Data
3. Preliminary Analyses
3.1. Identifying Effective Peptides Based on MIC Data
- X: a matrix of MIC values,
- M: rows containing MIC values for a given organism,
- N: columns containing MIC values for a given peptide,
- ,
- Multiple minimum MIC values can occur along a given row.
3.2. MIC Experiments Suggest a Common Mechanism of Action for Both Gram-Positive and Gram-Negative Organisms
- For an organism, susceptibility to one effective peptide indicates greater susceptibility to all effective peptides.
- For an effective peptide, efficacy for one organism indicates greater efficacy for all organisms.
3.3. Positively Charged Residues Are Associated with Increased Peptide Activity
3.4. Apolar Residues Are Associated with Increased Peptide Activity
3.5. Helicity Is Not Essential for Peptide Activity
4. Discussion
- Our previous work [10] reported prominent blebbing observed on the S. haemolyticus cell membrane, and large-scale membrane damage observed on E. coli, upon treatment with peptides NN2_0018 and NN2_0050. These disruptions cannot be explained through the formation of nanometer-scale pores alone. Previously, the carpet model had successfully explained similar blebbing on the P. aeruginosa cell membrane [9].
5. Materials and Methods
5.1. Computational Design and Selection of Antimicrobial Peptides
5.2. Peptide Synthesis
5.3. Antimicrobial Susceptibility Assays
5.4. Circular Dichroism Experiments
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Peptide | Sequence |
---|---|
NN2_0000 | EVAKKLLASALKLALAI |
NN2_0001 | EDWNHLGAAVHTLKHVYK |
NN2_0002 | AIVEQLRKRC |
NN2_0003 | KLSASLKHVAHRARHLS |
NN2_0004 | ESRAGKLAAKAAFKAAKR |
NN2_0005 | EWAAARQVIIHATRKY |
NN2_0006 | EILSKALSALSPLAN |
NN2_0007 | EKAILSALKLLRLAL |
NN2_0008 | ETAKGVAKHLPPAIA |
NN2_0009 | KVYARLHAVIKRLHRRLH |
NN2_0018 | YLARAIRRTLARLLL |
NN2_0022 | EWRVARRAVQRLRHLARRYH |
NN2_0024 | ALKKMLRLAKRLS |
NN2_0027 | VLSAFHKVIKIIHHISHF |
NN2_0029 | RKFRKILHRARKWI |
NN2_0035 | RRWGRWHRMRRRGR |
NN2_0039 | FWKGLVKAAFKIVHAGS |
NN2_0046 | GWKAIHKAAKGIHTYVN |
NN2_0050 | SWKKFFKKARSLPKLF |
NN2_0055 | YKRWKKWRSKAKKIL |
Organism | Culture ID | NN2_ | NN2_ | NN2_ | NN2_ | NN2_ | NN2_ | NN2_ | NN2_ | NN2_ | NN2_ | NN2_ | NN2_ | NN2_ | NN2_ | NN2_ | NN2_ | NN2_ | NN2_ | NN2_ | NN2_ |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0000 | 0001 | 0002 | 0003 | 0004 | 0005 | 0006 | 0007 | 0008 | 0009 | 0018 | 0022 | 0024 | 0027 | 0029 | 0035 | 0039 | 0046 | 0050 | 0055 | ||
E. coli | K12 MG1655 | 16 | 32 | 16 | 64 | 32 | 8 | 64 | 4 | 4 | |||||||||||
A. baumanii | MTCC 9829 | 128 | 32 | 16 | 16 | 128 | 16 | 8 | 16 | 4 | 16 | ||||||||||
S. boydii | MTCC 11947 | 128 | 128 | 8 | 32 | 8 | 64 | 16 | 1 | 64 | 2 | 8 | |||||||||
S. flexnerii | MTCC 1457 | 128 | 128 | 4 | 8 | 1 | 32 | 8 | 4 | 64 | 4 | 8 | |||||||||
S. typhimurium | ATCC 14028 | 32 | 32 | 16 | 16 | 8 | 32 | ||||||||||||||
S. enterica | MTCC 9844 | 128 | 32 | 16 | 16 | 32 | 32 | 16 | 8 | 16 | |||||||||||
K. pneumoniae | MTCC 7407 | 32 | 128 | 64 | 32 | 128 | |||||||||||||||
K. oxytoca | MTCC 2275 | 128 | 8 | 16 | 8 | 128 | 32 | 64 | 64 | 16 | 32 | ||||||||||
P. aeruginosa | MTCC 3542 | 128 | 16 | 32 | 128 | ||||||||||||||||
P. vulgaris | MTCC 1771 | 128 | 128 | 64 | 16 | 64 | |||||||||||||||
P. mirabilis | MTCC 3158 | ||||||||||||||||||||
C. koserii | MTCC 1657 | 128 | 128 | 32 | 16 | 16 | 64 | 16 | 64 | 16 | 64 | 8 | 16 | ||||||||
C. freundii | MTCC 1658 | 32 | 16 | 64 | 32 | 32 | 128 | ||||||||||||||
N. mucosa * | MTCC 1772 | 128 | 128 | 32 | 16 | 32 | 128 | 32 | 32 | 64 | 128 | 16 | 64 | ||||||||
V. cholerae | MTCC 3904 | 128 | 64 | 128 | 128 | 128 | 64 | 128 | |||||||||||||
E. gergoviae | MTCC 3826 | 128 | 128 | 128 | 64 | ||||||||||||||||
H. influenzae | MTCC 621 | 64 | 128 | 128 | 16 | 4 | 8 | 8 | 64 | 8 | 8 | 128 | 64 | 2 | 32 | ||||||
A. fecalis | MTCC 1937 | 32 | 128 | 128 | 64 | ||||||||||||||||
B. bronchiseptica | MTCC 6837 | 16 | 64 | 4 | 4 | 2 | 8 | 4 | 1 | 8 | 128 | 1 | 8 | ||||||||
E. aerogenes | MTCC 111 | 32 | 16 | 128 | |||||||||||||||||
S. maltophilia | MTCC 1890 | 128 | 16 | 64 | 128 | 128 | 16 | 128 | |||||||||||||
M. luteus * | MTCC 425 | 32 | 128 | 32 | 32 | 32 | 0.5 | 2 | 2 | 2 | 8 | 1 | 0.25 | 0.25 | 2 | 64 | 2 | 0.5 | |||
S. aureus | MTCC 3160 | 16 | 128 | 128 | |||||||||||||||||
S. hemolyticus | MTCC 3383 | 128 | 4 | 16 | 16 | 128 | 32 | 8 | 4 | 16 | 8 | 4 | |||||||||
E. faecalis | MTCC 439 | 64 | 128 | ||||||||||||||||||
C. glutamicum | MTCC 2679 | 32 | 64 | 32 | 2 | 4 | 1 | 16 | 4 | 2 | 4 | 2 | 64 | 2 | 2 | ||||||
C. pseudoTB * | MTCC 3158 | 128 | |||||||||||||||||||
B. alcalophilis | MTCC 860 | 64 | 32 | 16 | 16 | 32 | 64 | 32 | 16 | 32 | 64 | ||||||||||
M. smegmatis * | MC2155 | 128 | 32 | 64 | 16 | 64 | 32 | 16 | 16 | 128 | 64 | 32 | |||||||||
C. albicans * | MTCC 425 | 32 | 128 | 64 | 128 | 64 | 64 | 64 | 64 | ||||||||||||
net charge | 3 | 2 | 3 | 4 | 6 | 3 | 1 | 3 | 2 | 6 | 4 | 7 | 5 | 2 | 7 | 8 | 3 | 3 | 6 | 8 | |
peptide score | 3 | 10 | 5 | 6 | 3 | 1 | 14 | 2 |
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Nagarajan, D.; Nagarajan, T.; Nanajkar, N.; Chandra, N. A Uniform In Vitro Efficacy Dataset to Guide Antimicrobial Peptide Design. Data 2019, 4, 27. https://doi.org/10.3390/data4010027
Nagarajan D, Nagarajan T, Nanajkar N, Chandra N. A Uniform In Vitro Efficacy Dataset to Guide Antimicrobial Peptide Design. Data. 2019; 4(1):27. https://doi.org/10.3390/data4010027
Chicago/Turabian StyleNagarajan, Deepesh, Tushar Nagarajan, Neha Nanajkar, and Nagasuma Chandra. 2019. "A Uniform In Vitro Efficacy Dataset to Guide Antimicrobial Peptide Design" Data 4, no. 1: 27. https://doi.org/10.3390/data4010027