dPABBs: A webserver for Designing of Peptides Against Bacterial Biofilms
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Welcome to dPABBs

Research into the biofilm phenotype, spanning over almost three decades, has presented us with overwhelming evidence of its clinical relevance. Still, no approved drugs specifically targeting bacterial biofilms exist, and susceptibility testing against biofilms is conspicuously missing from antibiotic discovery pipelines. AMPs with activity against biofilms offer a promising avenue for the development of new standalone therapeutics or adjuvants acting synergistically with pre-existing antibiotics.
The dPABBs webserver is an attempt to develop a prediction strategy for the identification and optimisation of such anti-biofilm peptides, offering a comprehensive platform that allows the user to check both peptides and protein fragments for potential anti-biofilm activity and provides features like simultaneous multi-model predictions and mutant generation.
Schematic representation of the biofilm ultrastructure: The bacterial cells are present in matrix-enclosed "towers" or microcolonies, which behave like the structural units of a biofilm. In natural as well as human pathogenic systems, biofilms are predominantly polymicrobial (microcolonies 'A' and 'B', constructed by the green species 'A' and orange species 'B', respectively). The synergy with multiple bacterial species within a single community confers a competitive advantage to the residents of a biofilm. The microcolonies are interspersed with a network of open water channels that distribute nutrients and oxygen to different locations in the biofilm, allowing it to grow in both complexity and thickness. However, a decreasing gradient of nutrient and oxygen availability still exists between the surface and the deeper layers of the biofilm (depicted as a gradient of the colour yellow) leading to a varied population of cells in differential states of growth (depicted in shades of green and orange for the respective species). More metabolically active cells (dark green/orange) are found in the outer layers and the slow-growing, 'persister' cells (lighter green/orange) are present in the oxygen and nutrient-deprived inner layers, hence phenotypic variations arise as a result of individual cells responding to their respective microenvironments.
Bacteria use a sophisticated system of intercellular communication known as quorum sensing (QS) that involves the production, detection and response to signalling molecules called autoinducers (AI). There are specific autoinducing molecules for intra-species signalling (depicted as violet diamonds in species 'A' and as red triangles in species 'B') and a "universal language" (depicted by blue circles) for inter-species communication.
The biofilm lifecycle and its stages targeted by anti-biofilm peptides: A schematic representation of the major stages constituting the biofilm lifecycle. In the BaAMPs database, the ABPs were reported to prevent the adhesion of planktonic bacteria to a substratum, inhibit formation and destroy pre-existing biofilms. Corresponding stages are marked with a red "X".

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Citation: If you are using this server, please cite:

Gupta, P. et al. dPABBs: A Novel in silico Approach for Predicting and Designing Anti-biofilm Peptides. Sci. Rep. 6, 21839; doi: 10.1038/srep21839 (2016).



Developed by: OSDD Unit, CSIR- HQ, New Delhi- 110001