SAPD - SYNTHETIC ANTIBIOTIC PEPTIDES DATABASE

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					                                                                      Protein and Peptide Letters, Vol. 9, No. 1, pp. 53-57, 2002
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                           SYNTHETIC ANTIBIOTIC PEPTIDES DATABASE
                                        David Wade1* and Jukka Englund2
                                    1
                                    Peptide Laboratory, Haartman Institute, and
                       2
                        Research and Development Unit, National Library of Health Sciences,
                                     FIN-00014 Helsinki University, Finland



          A computerized database for synthetic antibiotic peptides, the SAPD, has been created and is available on
the Internet at web address, http://oma.terkko.helsinki.fi:8080/~SAPD. The SAPD is modelled on two pre-existing
computer databases for naturally occurring peptide antibiotics, the Antimicrobial Sequences Database and the
Peptaibol Database, and it will contain both chemical and biological information on all published synthetic antibiotic
peptides.

KEYWORDS: peptide antibiotics, synthetic peptides, computer database, world wide web, internet


INTRODUCTION
         During the past two decades, there has developed a serious public health problem caused by antibiotic
resistant microorganisms, and this has necessitated a need for the development of new antibiotics. Fortuitously,
during the same period, an entirely new category of antibiotics was discovered, the gene-encoded, peptide
antibiotics of the animal, plant, and bacterial kingdoms [1]. These new peptide antibiotics are thought to represent a
previously unrecognised form of innate immunity, and there is extensive interest in them as a potential partial
solution to the need for new antibiotics. The numbers of new peptide antibiotics being discovered, and scientific
articles about them, has been growing almost exponentially (Figure 1). This has created a need for a centralized
catalog, or database, of information about these new compounds. One such database has been created for naturally
occurring peptide antibiotics, the Antimicrobial Sequences Database (AMSDb), and it is available on the Internet
(http://www.bbcm.univ.trieste.it/~tossi/pag1.htm) [2]. At the time of this writing, the AMSDb contains over 600
peptide structures for gene-encoded peptides from animal and plant sources; bacterial sources have been excluded.
Hopefully, databases will eventually be developed for the new antibiotic peptides from bacterial sources, or the
AMSDb will be expanded to include these other antibiotic peptides. The AMSDb contains both chemical and
biological information about each peptide, plus a list of literature references. There is also another related database
available on the Internet, the Peptaibol Database (http://www.cryst.bbk.ac.uk/peptaibol/welcome.html) and it
currently contains about 242 peptaibol structures [3]. The combined number of naturally occurring antibiotics in
these two databases is quite substantial. Due to the availability of solid phase synthesis and combinatorial chemistry
technologies, the number of possible synthetic variations of the naturally occurring peptide antibiotic
structures is in the millions. Thousands of new peptides have already been synthesized based on the
naturally occurring structures, and some of these peptides have shown therapeutic potential and are currently

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in clinical trials. Figure 1 gives only a rough indication of the scope of this new field because many of the articles
about new synthetic antibiotic peptides contain information on several peptides. For example, a recent paper about
synthetic derivatives of a cecropin-melittin hybrid peptide antibiotic, CA(1-7)M(2-9)NH2, contained information on
100 derivative peptides [4]. The discovery of new peptide antibiotics appears to be limited only by the speed with
which these new synthetic peptides can be tested for biological activities. The rapid pace of this research activity has
created a need for a centralized catalog of chemical and biological information about the new synthetic peptides, and
it was in response to this need that the Synthetic Antibiotic Peptides Database (SAPD) was created. It is expected
that the information available on the SAPD, the AMSDb, and Peptaibol databases will help to accelerate the pace of
antibiotics research by preventing the duplication of research efforts and stimulating new research ideas.




                                         100
                                          90
                                          80
                    Number of articles




                                          70
                                          60
                                          50
                                          40
                                          30
                                          20
                                          10
                                           0
                                            1968 1972 1976 1980 1984 1988 1992 1996 2000
                                                               Year

Figure 1. Increase in the number of articles published on antibiotic peptides during the past two decades. Data was
obtained by doing a search of Medline from 1966 to 2000 using the search terms, “antibacterial-, antibiotic-, or
antimicrobial peptide”. There were no articles containing the search terms in 1966-67.




METHODS
      The data on new synthetic antibiotic peptides is available in the literature in two forms, in printed journals
and in journals available in electronic format. Most of the data that is in electronic journals is available only for
recent years (e.g., since 1997 for many of the more than 1,500 electronic journals available
                                                                                                                        55



through Finland’s National Library of Health Sciences). As can be seen from Figure 1, many of the articles on
antibiotic peptides in the medical literature were published after 1980. Therefore, much of the collection of data on
antibiotic peptides for the SAPD is being done through the use of printed journals.
       Searching for articles on antibiotic peptides is done through electronic databases, such as Medline, Current
Contents, and Chemical Abstracts. Some of these databases are more complete in the range of journals that they
cover (e.g., Chemical Abstracts is more complete than Medline and Current Contents for the chemical literature),
and since the field of synthetic antibiotic peptides includes both chemical and biological specialities, all of these
literature databases are being utilized in developing the SAPD.
       The SAPD currently consists of a series of files, one for each peptide antibiotic, that were created as Netscape
hypertext documents using the Composer function within Netscape Communicator 4.7 [5]. The SAPD website
consists of commercially available software, and data files are added to the SAPD by simply posting them on the
website. When a user wants to access the SAPD, they must register and create a user identification name and
password. This is less convenient than the AMSDb or Peptaibol Database, but it enables the SAPD manager to
determine statistics on usage of the database. Once logged onto the database, a user selects the file for the desired
peptide, and is then presented with a text document. The SAPD also includes a function for searching text
throughout the entire database. Due to the enormous task involved in developing the SAPD, it includes a feature for
acknowledging data contributions by users who are not primarily involved in SAPD development. Every
contribution of a substantial amount of verifiable data (e.g., all of the chemical, biological, and literature reference
data for one peptide antibiotic) is acknowledged in a highly visible location in the beginning of the contributed file.
This feature is not available in the AMSDb or Peptaibol Database, and its purpose is to encourage users of the SAPD
to make data contributions themselves. One feature of the AMSDb that is not currently available in the SAPD, but
may be included at some future date, is that most of the AMSDb entries are correlated to entries found in the
SWISS-PROT protein sequences database (http://www.expasy.ch/sprot/), and it includes the SWISS-PROT ID code.
The reason for this omission in the SAPD is due to the fact that unlike the proteins in the SWISS-PROT database,
relatively few of the peptide sequences listed in the SAPD occur in nature. Additional features that will be included
as the size of the database increases are links both within the database and to other relevant sites on the Internet.



RESULTS
       The SAPD currently contains information for about 200 synthetic antibiotic peptides. The format for one
representative entry from the SAPD, that of Temporin A (TA), is shown in Table 1. For comparison purposes, the
AMSDb entry for the naturally occurring form of TA is shown in Table 2, with font styles and sizes modified to
conform to journal requirements.
56



Table 1. Typical format for one entry from the synthetic antibiotic peptides database (SAPD).
1. Temporin A (TA)
2. Literature references:
       a. Simmaco, M., Mignogna, G., et al. Rana temporaria. Eur. J. Biochem. (1996) 242: 788.
       b. Harjunpää, I., Kuusela, P., et al., FEBS Letts. (1999) 449: 187.
       c. Mangoni, M.L., Rinaldi, A.C., et al.. Eur. J. Biochem. (2000) 267: 1447.
       d. Wade, D., Silberring, J., et al., FEBS Letts. (2000) 479: 6.
3. Contributor of information to database:
       a. D. Wade, Haartman Institute, Helsinki University, Finland.
       b. Dates of contribution, verification, entry into database, and updating: June 9, 2001.
4. Structural information:
     a. The peptide is found in the skin secretions of the European red frog, Rana temporaria.
     b. AA sequence: FLPLIGRVLSGIL-NH2; amidated carboxyl terminus.
     c. Both all-L and all-D variants of TA have been synthesized (Refs. a, b, d).
     d. Secondary structure, methods of determination, and comments:
          1) α-Helices present when peptide is in an aqueous solution of trifluoroethanol (TFE).
          2) Structure determined by circular dichroism:
            a) Helical in water plus TFE; max. helicity in 30% (Ref. c) or 80% TFE (Ref. d)
            b) Antibacterial activity of temporins correlated to increased helix formation. (Ref. a)
5. Bioactivity of peptide:
     a. Antibacterial activities [LC, lethal concentration (Ref. a) or MIC*, minimal inhibitory concentration
           (Refs. b and d) values (µM)]:
          1) Aerobic bacteria:
             a) Gram-positive (MRSA, methicillin resistant Staph. aureus; VRE, vancomycin resistant
                 Enterococcus):
                 (1) all-L TA:      Bacillus megaterium Bm11: 1.2;
                                    Staphylococcus aureus: Cowan I, 2.3; Newman, 6.8*; K35 (MRSA), 2.6-13.7*;
                                                                   K52, 5.2-13.7*; ATCC 25923, 2.6*
                                    Enterococcus faecium (VRE): 18578, 10.5-27.3*; 18172, 10.5-54.6*
                                    Enterococcus faecalis ATCC 29212: 20.9*
                                    Streptococcus pyogenes (β hem. group A): 2
                                    Acinetobacter junii (Rt-4): 7.7; (Bo-2): 24.0
                 (2) all-D TA:      Staphylococcus aureus: K35 (MRSA), 3.1*; K52, 3.1*; ATCC 25923, 2.6*
                                    Enterococcus faecium (VRE): 18578, 12.5*; 18172, 12.5*
                                    Enterococcus faecalis ATCC 29212: 10.5*
             b) Gram-negative (all-L TA):          Yersinia pseudotuberculosis: 2
                                                   Esherichia coli (D21): 11.9
                                                   Pseudomonas aeruginosa ATCC15692: >360
                                                   Klebsiella pneumoniae (Rt-1): 9.6
                                                   Proteus vulgaris (Rt-3): >340
                                                   Aeromonas hydrophila (Bo-3): >360; (Bo-4): >20
                                                   Enterobacter agglomerans (Bo-1): >50
          2) Anaerobic bacteria: Not tested.
     b. Other cell types or organisms: Eukaryotic cells [Refs. a and c; LC values (µM)]:
       1) Fungus: Candida albicans: 3.4
       2) Human red blood cells (hemolysis): >120 (agarose method); 50% hemol. at 42 µM (saline method)
6. Physicochemical properties of peptide:
       a. MW: 1397 (Calc. from ExPASy Molecular Biology server,
                    http://www.expasy.ch/tools/pi_tool.html)
       b. Electromagnetic radiation absorption characteristics: UV (210, 260 nm)
       c. Solubility: Soluble in water (≥ 2.5 mg/ml)
                                                                                                            57



    Table 2. Representative entry from the Antimicrobial Sequences Database (AMSDb) for Temporin A [2].

TMPA_RANTE
ID TMPA_RANTE LOCAL          PRT; 13 AA.
AC
DE TEMPORIN A
OS RANA TEMPORARIA (RED FROG/RANA SPECIES /AMPHIBIAN).
RN [1]
RP SEQUENCE
RC TISSUE=SKIN
RA SIMMACO M., MIGNOGNA G., CANOFEI S., MIELE R., MANGONI M., BARRA D.
RL EUR. J. BIOCHEM. 242:788-792(1996).
RN [2]
RP SPECTRUM OF ACTIVITY
RA MANGONI M., RINALDI A.C., DI GIULIO A., MIGNOGNA G.,BOZZI A., BARRA D.,   SIMMACO
M.,
RL EUR. J. BIOCHEM. 267:1447-1454 (2000)
CY LINEAR PEPTIDE
TY (?)
FY TEMPORINS
AY ANTIBACT.: G+ (B. MEGATERIUM, S. AUREUS, S. PYOGENES, MIC 1-2 MICROMOLAR)
AY ANTIBACTERIAL: G- LESS ACTIVE (E. COLI MIC = 12 MICROMOLAR)
AY ANTIFUNGAL: (C. ALBICANS MIC 3.4 MICROMOLAR
AY HEMOLYTIC (E50 = 10 MICROM)
CC -!- FUNCTION: SHOWS ANTIBACTERIAL ACTIVITY AGAINST REPRESENTATIVE
CC         GRAM-POSITIVE BACTERIAL SPECIES. POORLY ACTIVE AGAINST G- SPECIES.
CC         SHOWS ANTIFUNGAL ACTIVITY AGAINST C. ALBICANS.
CC -!- SIMILARITY: TO PEPTIDES OF THE TEN-MEMBERED FAMILY OF TEMPORINS
CC     THE RELATED PEPTIDES TEMPORINS F AND G MAY HAVE A SIMILAR ACTIVITY.
CC -!- TISSUE SPECIFICITY: SKIN.
CC -!- SUBCELLULAR LOCATION: SECRETED (?).
FT MOD_RES 13       13 AMIDATION
FT ANALOG      7   7 ARG -> LYS IN TEMPORIN F
KW AMPHIBIAN SKIN; ANTIBIOTIC; HEMOLYSIS.
MW MATURE PEPTIDE: 1397;
SQ SEQUENCE 13 AA; TMPA_RANTE flpligrvlsgil*

ACKNOWLEDGEMENTS
D.W. thanks Dr. Alessandro Tossi, of the University of Trieste, for encouragement and helpful discussions during
the early stages of the creation of the synthetic antibiotic peptides database. D.W. also thanks the Academy of
Finland for providing visiting scientist fellowship support during 1998, 1999, and 2001, and the Wade Research
Foundation for supplemental support during these periods.

REFERENCES
[1] Boman, H.G. (1998) Scand. J. Immunol., 48, 15.
[2] Tossi, A., University of Trieste, Dept. of Biochemistry, Biophysics, and Macromolecular Chemistry,
    Trieste, Italy.
[3] Whitmore, L., Chugh, J., Snook, C. F., and Wallace B. A. (2000) The Peptaibol Database. Birkbeck
    College, Crystallography Dept., London, U.K.
[4] Mee, R.P., Anton, T.R. and Morgan, P.J. (1997) J. Peptide Res., 49, 89-102.
[5] Netscape Comunicator 4.76, Netscape Communications Corporation. Netscape and the Netscape N and
    Ship's Wheel logos are registered trademarks of Netscape Communications Corporation in the U.S. and other
    countries.

				
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