Antimicrobial Peptide Biophysics – construction, synthesis and characterisation

• prof.dr.sc. Alessandro Tossi, Department for Life Sciences, University of Trieste, Italy
• dr.sc. Goran Gajski
• dr.sc. Yogesh Sonavane

Research description:

The research connects three interdisciplinary and complementary segments Peptide design, Experimental testing and Molecular simulations.
Using numerical methods, based on the specific amino acid properties molecular descriptors are constructed. Those descriptors are then used to connect mentioned properties with biological activity, which provides the basis on which we design new peptides (“QSAR” approach). Signal sequences of the peptides, that are evolutionary well preserved, can be used for EST and SRA database survey that also defines new peptide sequences.
Sequences with the best biophysical characteristics are synthesised that is followed with biophysical, microbiological and molecular biology characterisation. The conformation of peptides is determined, their microbiological activity and toxicity to host cells is measured to distinguish if the new antimicrobial peptide is also potential antibiotic. Mechanism of action of peptides is measured with permeability tests on flow cytometry and with atomic force microscopy. Using molecular dynamic simulations of peptides in various solutions as well as in interaction with model membranes structural and dynamical properties of peptides are examined as well as mechanisms of action.

CONTACTS WITH ACADEMIC AND OTHER INSTITUTIONS:

1. Odjel za životne znanosti, Sveučilište u Trstu, Italija
2. Medicinski fakultet u Splitu
3. Klinički bolnički centar Split
4. Mediteranski Institut za istraživanje života, Split, MedILS
5. Institut za medicinska istraživanja i medicinu rada, Zagreb, IMI
6. Institut Ruđer Bošković, Zagreb, IRB
7. Građevinski fakultet, Zagreb
8. Građevinski fakultet, Split
9. Odjel za kemiju, Sveučilište u Melbourne, Australija
10. Institut za imunobiologiju, St. Gallen, Švicarska

Description of the current cooperation:

Sa svim navedenim ustanovama imamo ostvarenu uspješnu suradnju bilo u vidu laboratorijskog rada ili razvoja teorema & molekulskih deskriptora. Posebno treba istaknuti suradnju s Odjelom za životne znanosti Sveučilišta u Trstu kao i voditelja grupe na istoj instituciji, prof. Alessandra Tossi-ja s kojim smo do sada objavili nekoliko znanstvenih radova. Članovi naše grupe su nekoliko puta boravili na Odjelu za životne znanosti u svrhu usavršavanja, a pod uskim vodstvom prof. Tossi-ja nekoliko studenta je izradilo i uspješno obranilo svoje diplomske/doktorske radove.

Plans for future research:

Future plans are a further molecular descriptor and algorithm development for new antimicrobial peptide (AMP) construction and continuing to work on transcriptomic, genomic and proteomic databases. Interesting results can be achieved with the targeted sequencing of genes in combination with available data from previously mentioned databases, so in the near future, we also plan to put emphasis on that aspect of the problem for finding new suitable sequences. The mechanism of action of AMPs will be investigated throughout biological and biophysical measurements on a model and bacterial membranes (flow cytometry, atomic force microscopy…) that will be combined with the results of the molecular dynamics simulations of the peptide-membrane systems with the goal of developing a strong and functional hypothesis.

LIST OF SELECTED RESEARCH PAPERS:

• Juretić, D., Vukicević, D., Ilić, N., Antcheva, N., & Tossi, A. (2009). Computational design of highly selective antimicrobial peptides. Journal of Chemical Information and Modeling, 49(12), 2873–2882. https://doi.org/10.1021/ci900327a
• Juretić, D., Vukičević, D., Petrov, D., Novković, M., Bojović, V., Lučić, B., … Tossi, A. (2011). Knowledge-based computational methods for identifying or designing novel, non-homologous antimicrobial peptides. European Biophysics Journal: EBJ, 40(4), 371–385. https://doi.org/10.1007/s00249-011-0674-7
• Tessera, V., Guida, F., Juretić, D., & Tossi, A. (2012). Identification of antimicrobial peptides from teleosts and anurans in expressed sequence tag databases using conserved signal sequences. The FEBS Journal, 279(5), 724–736. https://doi.org/10.1111/j.1742-4658.2011.08463.x
• Kamech, N., Vukičević, D., Ladram, A., Piesse, C., Vasseur, J., Bojović, V., … Juretić, D. (2012). Improving the selectivity of antimicrobial peptides from anuran skin. Journal of Chemical Information and Modeling, 52(12), 3341–3351. https://doi.org/10.1021/ci300328y
• Novković, M., Simunić, J., Bojović, V., Tossi, A., & Juretić, D. (2012). DADP: the database of anuran defense peptides. Bioinformatics (Oxford, England), 28(10), 1406–1407. https://doi.org/10.1093/bioinformatics/bts141
• Ilić, N., Novković, M., Guida, F., Xhindoli, D., Benincasa, M., Tossi, A., & Juretić, D. (2013). Selective antimicrobial activity and mode of action of adepantins, glycine-rich peptide antibiotics based on anuran antimicrobial peptide sequences. Biochimica Et Biophysica Acta, 1828(3), 1004–1012. https://doi.org/10.1016/j.bbamem.2012.11.017
• Simunić, J., Petrov, D., Bouceba, T., Kamech, N., Benincasa, M., & Juretić, D. (2014). Trichoplaxin – a new membrane-active antimicrobial peptide from placozoan cDNA. Biochimica Et Biophysica Acta, 1838(5), 1430–1438. https://doi.org/10.1016/j.bbamem.2014.02.003
• Kozić, M., Vukičević, D., Simunić, J., Rončević, T., Antcheva, N., Tossi, A., & Juretić, D. (2015). Predicting the Minimal Inhibitory Concentration for Antimicrobial Peptides with Rana-Box Domain. Journal of Chemical Information and Modeling, 55(10), 2275–2287. https://doi.org/10.1021/acs.jcim.5b00161
• Rončević, T., Gajski, G., Ilić, N., Goić-Barišić, I., Tonkić, M., Zoranić, L., … Juretić, D. (2017). PGLa-H tandem-repeat peptides active against multidrug resistant clinical bacterial isolates. Biochimica Et Biophysica Acta, 1859(2), 228–237. https://doi.org/10.1016/j.bbamem.2016.11.011