finDr: A web server for in silico D-peptide ligand identification

Helena Engel; Felix Guischard; Fabian Krause; Janina Nandy; Paulina Kaas; Nico Höfflin; Maja Köhn; Normann Kilb; Karsten Voigt; Steffen Wolf; Tahira Aslan; Fabian Baezner; Salomé Hahne; Carolin Ruckes; Joshua Weygant; Alisa Zinina; Emir Bora Akmeriç; Enoch B Antwi; Dennis Dombrovskij; Philipp Franke; Klara L Lesch; Niklas Vesper; Daniel Weis; Nicole Gensch; Barbara Di Ventura; Mehmet Ali Öztürk

doi:10.1016/j.synbio.2021.11.004

finDr: A web server for in silico D-peptide ligand identification

Synth Syst Biotechnol. 2021 Nov 23;6(4):402-413. doi: 10.1016/j.synbio.2021.11.004. eCollection 2021 Dec.

Authors

Helena Engel¹, Felix Guischard¹, Fabian Krause¹, Janina Nandy¹, Paulina Kaas¹, Nico Höfflin^{1

2}, Maja Köhn^{1

2}, Normann Kilb^{3

4}, Karsten Voigt², Steffen Wolf⁵, Tahira Aslan¹, Fabian Baezner¹, Salomé Hahne¹, Carolin Ruckes¹, Joshua Weygant¹, Alisa Zinina¹, Emir Bora Akmeriç¹, Enoch B Antwi¹, Dennis Dombrovskij¹, Philipp Franke⁶, Klara L Lesch^{1

3

7

8}, Niklas Vesper¹, Daniel Weis¹, Nicole Gensch⁹, Barbara Di Ventura^{1

3}, Mehmet Ali Öztürk^{1

3}

Affiliations

¹ Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany.
² Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany.
³ Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany.
⁴ AG Roth-Lab for MicroarrayCopying, ZBSA-Centre for Biological Systems Analysis, University of Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany.
⁵ Biomolecular Dynamics, Institute of Physics, University of Freiburg, Hermann-Herder-Strasse 3a, 79104, Freiburg, Germany.
⁶ Institute for Biochemistry, University of Freiburg, Albertstr. 21, 79104, Freiburg, Germany.
⁷ Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstraße 19A, 79104, Freiburg, Germany.
⁸ Internal Medicine IV, Department of Medicine, Medical Center, University of Freiburg, Hugstetter Straße 55, 79106, Freiburg, Germany.
⁹ Core Facility Signalling Factory, Centre for Biological Signaling Studies (BIOSS), University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany.

Abstract

In the rapidly expanding field of peptide therapeutics, the short in vivo half-life of peptides represents a considerable limitation for drug action. D-peptides, consisting entirely of the dextrorotatory enantiomers of naturally occurring levorotatory amino acids (AAs), do not suffer from these shortcomings as they are intrinsically resistant to proteolytic degradation, resulting in a favourable pharmacokinetic profile. To experimentally identify D-peptide binders to interesting therapeutic targets, so-called mirror-image phage display is typically performed, whereby the target is synthesized in D-form and L-peptide binders are screened as in conventional phage display. This technique is extremely powerful, but it requires the synthesis of the target in D-form, which is challenging for large proteins. Here we present finDr, a novel web server for the computational identification and optimization of D-peptide ligands to any protein structure (https://findr.biologie.uni-freiburg.de/). finDr performs molecular docking to virtually screen a library of helical 12-mer peptides extracted from the RCSB Protein Data Bank (PDB) for their ability to bind to the target. In a separate, heuristic approach to search the chemical space of 12-mer peptides, finDr executes a customizable evolutionary algorithm (EA) for the de novo identification or optimization of D-peptide ligands. As a proof of principle, we demonstrate the validity of our approach to predict optimal binders to the pharmacologically relevant target phenol soluble modulin alpha 3 (PSMα3), a toxin of methicillin-resistant Staphylococcus aureus (MRSA). We validate the predictions using in vitro binding assays, supporting the success of this approach. Compared to conventional methods, finDr provides a low cost and easy-to-use alternative for the identification of D-peptide ligands against protein targets of choice without size limitation. We believe finDr will facilitate D-peptide discovery with implications in biotechnology and biomedicine.

Keywords: D-AA, dextrorotatory amino acid; D-peptide; EA, evolutionary algorithm; Evolutionary algorithm; L-AA, levorotatory amino acid; MD, molecular dynamics; MIEA, mirror-image evolutionary algorithm; MIPD, mirror-image phage display; MIVS, mirror-image virtual screening; MRSA, methicillin-resistant Staphylococcus aureus; Mirror-image phage display; Molecular docking; NCL, native chemical ligation; PD-1, receptor programmed death 1; PPI, protein-protein interaction; PSMα3, phenol soluble modulin alpha 3; Peptide design; SPPS, solid phase peptide synthesis; Web server.