DBAASPv2.13 Database of antimicrobial activity and structure of peptides

The Database of Antimicrobial Activity and Structure of Peptides (DBAASP) has been created to provide users with information on detailed chemical structure and activity for those peptides which antimicrobial activity against particular targets have been evaluated experimentally. The database is manually curated and contains information on ribosomal, nonribosomal and synthetic peptides that show antimicrobial activity as Monomers, Dimers and Multi-Peptides.

In DBAASP:

 

Ribosomal peptides are peptides which amino acid sequence is genetically encoded and naturally produced despite its termini modification and intrachain bond.  

 

Nonribosomal peptides are a class of peptide secondary metabolites, usually produced by microorganisms like bacteria and fungi. They are not synthesized by ribosomes.

 

Monomer - consists of one polypeptide chain.  

 

Dimer - consists of two polypeptide chains with interchain covalent bond(s).  

 

Multi-Peptide - consists of two or more different polypeptide chains in equimolar concentrations without interchain covalent bond.

 

Utilities of database are:   Search , , , PropertyCalculation, API  

 

In Statistics are presented three kinds of data: General Data, Compositional Data, Physicochemical Data

General Data consists of data on: a) compositions according to type of synthesis, complexity, target groups etc.;  b) distribution of lengths.

Compositional Data consists of data on:  a) amino acid compositions b) Statistics of occurrence of sequential pairs of residues.

Physicochemical Data consists of data on distributions of values of different phyico-chemical parameters such as hydriphobicity, amphipathicity, isoelectical point etc.

 

By means of “Property calculation” various physico-chemical characteristics of peptides are calculated, such as hydrophobicity, hydrophobic moment, charge, isoelectric point, etc.

 

API describes how the database can be accessed with programs. All resources (individual entries as well as sets of entries retrieved by queries) are accessible using simple URLs.

 

Prediction predicts antimicrobial and hemolytic/cytotoxic activity of a peptide.

 

Users are provided with information on synonyms (based on the NCBI Taxonomy Database). Information about existence of synonyms of particular target species can be obtained by search tool.

For detailed information see links below:

Search

Page Search includes several options: 


ID(s)

Peptides can be found using one (77), several (77, 99) or interval (77-99) of ID.  


Name

In this field either full or part of peptide name should be written. 


Sequence

Search by sequence can be performed using two options: 1) Full Sequence and 2) Part of Sequence (peptide can be found by fragment of amino acid chain).  


Sequence Length 

Finds peptides according to the length interval.  


N Terminus, C Terminus 

Peptides can be found by their termini modification. Modification types are presented in dropdown menu. Description of each type is given below in Abbreviations.  


Complexity 

The peptides are divided into three types by complexity - Monomers, Dimers and Multi-Peptides. Complexity type should be selected from dropdown menu. 


Unusual Amino Acid 

This field gives possibility to find peptides containing unusual, posttranslationally modified or artificial amino acids. Such amino acids are presented in dropdown menu (see abbreviations).


Bond 

Finds monomers with intrachain covalent bonds. Bond type should be selected from dropdown menu (see abbreviations).


Synthesis Type 

Finds peptides according to synthesis type (ribosomal, nonribosomal and synthetic). Synthesis type should be selected from dropdown menu.  


Kingdom 

This field gives possibility to select peptides according to the kingdom level of taxonomy of source organism. Kingdom can be selected from dropdown menu.  


Source 

This field gives possibility to select peptides according to the name of the source organism. Latin name (or part of name) of the peptide source organism should be written.  


Target Group 

Selects peptides according to the groups of target species. To select the group move mouse pointer over name of a group and click left key of mouse. To select more than one group keep Ctrl key pressed and select the groups by mouse clicking.  


Target Object of Cell 

Target Object of Cell is the subcellular structure or molecule that peptide interacts with. Selection can be done as described in Target Group.  


Target Species 

Selects peptides according to the target species (bacteria, fungus, virus, cancer).  Name or part of name of the target species can be used for searching.  


Nonstandard Experimental Conditions 

Selects peptides which activities are measured in nonstandard salt or pH conditions. 


Hemolytic and Cytotoxic activities 

Selects peptides with hemolytic and/or cytotoxic activity. 


UniProt ID

Selects peptides according to UniProt ID. We distinguish three types of Peptide UniProt IDs and they are named as Peptide ID, Precursor ID, Probable Precursor ID.

1) UniProt ID is defined as “Peptide ID” if amino acid sequence coincides to sequence in UniProt entry.

2) UniProt ID is defined as “Precursor ID” if amino acid sequence corresponds to the part of UniProt entry which is defined as precursor. 

3) UniProt ID is defined as “Probable Precursor ID” if amino acid sequence corresponds to the part of UniProt entry which can be considered as precursor. 

    

3D Structure

Selects peptides that contain link to PDB database and/or information about MD model.

 

Search result

Each row of the table corresponds to particular peptide. Each row contains information on peptide ID, name, N terminus modification, sequence, C terminus modification. Lowercase letter indicates D amino acid. Posttranslationally modified, unusual or artificial amino acids are depicted by X or x. (Exception is disulfide bond of cysteine where cysteines are depicted by C or c). In order to get full information on peptide one should click on View at the right edge of row.

Ranking Search 


Ranking Search gives information about peptides and activities for given target species/cell and activity/lysis measure ranked by activity value. Target species/cell and activity measure/lysis can be selected from dropdown menu. Search by target species/cell and activity/lysis measure can be combined with other search options: Sequence Length, N Terminus, C Terminus, Complexity, Unusual Amino Acid, Bond, Synthesis Type, Kingdom, Source, Medium, CFU. For ranking search some activity measures are systematized.


Hemolytic/cytotoxic measures of  activity


In literature several measures are used for cytotoxicity and hemolysis. ECn (n=25, 50), HCn (n=10, 50, 100), HDn (n=50), HLn (n=50), LCn (n=50), LDn (n=50) are used as measures of hemolysis. All of them are defined as peptide concentration at which n% erythrocyte lysis occurs. In addition MHC is defined as minimal peptide concentration at which no detectable hemolytic activity is observed. Some authors define MHC as a peptide concentration at which n% hemolysis occurs (n=0–10). Thus, for “Ranking search” it is reasonable to do standardization of the measures and the common term – “n% Hemolysis“ is used instead of various denotations.

EC50 and LC50 are used for cytotoxic measure. They present peptide concentration inducing a 50% cell death. Instead of these two measurements we use 50% Cell death. 


Antiviral activity measurements


AMP antiviral activity should be distinguished from antibacterial activity. Bacteria is fully self-sufficient objects and able to grow without host cells. Therefore, bacteria growth inhibition or killing is measured directly. Virus is not self-sufficient object and cannot be reproduced without host cell. Consequently, inhibition of the different processes connected with virus multiplication in the host cell are: activities of integrase; reverse transcriptase; protease; replication; Vif-Vif binding; cell fusion/entry, plaque formation, etc. In literature characteristic measures of these processes are IC50 and EC50.  Consequently, systematized is needed.

For ranking search activity measures for integrase activity; reverse transcriptase activity; protease activity and virus replication are systematized as following:

1) Integrase 3' end processing and strand transfer measurements are depicted by IC50 IN 3’EP ad IC50 IN ST, respectively.

2) Retroviral reverse transcriptase has three activities: RNA-dependent DNA polymerase, DNA-dependent DNA polymerase and ribonuclease H. For these activities we use IC50 RT RDDP, IC50 RT DDDP and IC50 RT RH, correspondingly.

3) Activity measures for protease activity, replication and plaque formation are denoted by IC50 PR, IC50 REP and IC50 P, respectively.

Measures of Vif-Vif binding; cell fusion/entry etc. cannot be systematized. Therefore, corresponding activities do not take part in ranking search.


Medium


As antimicrobial activities were found to differ under various conditions, information on Medium and CFU is given in the Peptide Card.

“Ranking search” provides available information of the antimicrobial activities of the definite target species in the definite medium and with definite CFU. 

Prediction section predicts antimicrobial activity of peptides. Web site contains two types of prediction tools: General Prediction and Special Prediction.


General Prediction is a tool of prediction of only Linear peptides which are active against someone bacterial strain. It based on the machine learning algorithm. Initially the following physico-chemical characteristics of peptides and hydrophobic scales were used: physico-chemical characteristics: Normalized Hydrophobic moment, Normalized Hydrophobicity, Charge Density, Isoelectric Point, Penetration Depth, Orientation of Peptides relative to the surface of membrane (Tilt angle), Propensity to Disordering, Linear Moment, in vitro aggregation (Tango) and  in vivo aggregation (Aggrascan); hydrophobic scales: MF - Moon and Fleming scale [1], KD - Kyte and Doolittle scale [2], WW - Wimley and White scale [3], EW - Eisenberg and Weiss scale [4], UH - Unified Hydrophobicity scale [5], HW - Hessa and White scale [6]. 


Finally, MF hydrophobic scale and the following characteristics were selected: Hydrophobic moment, Charge density and depth-dependent potential (for the detail see [7]). Peptide should consist of 20 canonical amino acids and sequence be in FASTA format.


Special Prediction is a tool of prediction of Linear AMPs, which are active against particular strains. 


Active peptide implies MIC<25 µg/ml. Non-Active peptide implies MIC>100 µg/ml. The strain can be selected from drop-down menu. The number of stains will be permanently risen. Length of the peptide should not exceed 30 amino acids. The results are presented as positive or negative predictive values (PPV and NPV).


A semi-supervised machine-learning approach relying on density-based clustering algorithm DBSCAN was developed to optimize the predictive model. Moon and Fleming hydrophobic scale and the following characteristics are used in the QSAR study: Normalized Hydrophobic moment, Normalized Hydrophobicity, Charge, Isoelectric Point, Penetration Depth, Orientation of Peptides relative to the surface of membrane (Tilt angle), Propensity to Disordering, Linear Moment and In vitro aggregation [8].


References

1.       Moon C. P., Fleming K. G. Proc. Natl. Acad. Sci. U. S. A. 2011, 108 (25), 10174-10177.

2.       Kyte J., Doolittle R. F. J. Mol. Biol. 1982, 157, 105-132.

3.       Wimley W. C., White S. H. Nat. Struct. Biol. 1996, 3, 842-848.

4.       Eisenberg D., et al. Proc. Natl. Acad. Sci. U. S. A. 1984, 81, 140-144.

5.       Koehler J., et al. Proteins 2009, 76, 13-29.

6.       Hessa T., et al. Nature 2005, 433, 377-381.

7.       Vishnepolsky B., Pirtskhalava M. J. Chem. Inf. Model. 2014, 54, 1512−1523.

8.     Vishnepolsky B., et al. J. Chem. Inf. Model. 2018, 58, 1141-1151.

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NCBI Taxonomy database synonyms
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