Supplemental Material for Klim et al., 2018

p { margin-bottom: 0.21cm; direction: ltr; color: rgb(0, 0, 10); line-height: 115%; text-align: left; }p.western { font-family: "Calibri", serif; font-size: 11pt; }p.cjk { font-family: "Calibri"; font-size: 11pt; }p.ctl { font-family: "Arial"; font-size: 11pt; }a:link { color: rgb(0, 0, 255); text-decoration: none; } <p><b>Additional file 1.</b> Final alignments (files with .aln.fasta extension) and phylogenetic trees (files with fastree.newick extension) for all the protein families analyzed in the study. Additionally, in case of three protein families: AIF, OMI and caspase/metacaspase the subfolders were created, containing the key subtrees (files in nexml format generated with Dendroscope).</p> <p><br> </p> <p><b>Additional file 2</b><b>.</b> Additional BLASTP results and taxonomy reports conducted to confirm the key results in case of the three protein families: AIF, caspase/metacaspase and htra. BLASTP results and taxonomy reports were obtained with NCBI WWW with two strategies: by selecting only a few eukaryotic proteomes (for the species from Table S2 in Supplementary Methods) as a search database (see file eukaryotic_strategy.pdf) and by extending selected proteomes from the first search strategy with all bacterial and archeal proteomes (see file extended_strategy.pdf). Please see README.md for more details regarding information for given specific file. </p> <p><br> </p> <p><b>Additional file 3. </b>Mega sessions for consensus phylogenetic trees calculated for arbitrarily chosen metacaspases and caspases, OMI/HTRA proteases and AIFs. Separate sessions files are available for calculations based on MLE (maximum likelihood estimation), NJ (neighbor-joining) and ME (minimal evolution).</p> <p><br> </p> <p><b>Additional Figure S1.</b> Competition assay between <i>ndi1</i><i>Δ </i>and wild-type Saccharomyces cerevisiae BY4741 strains under anaerobic conditions.</p> <p><br> </p> <p><b>Additional Figure S2.</b> Growth curves for all tested in this study yeast strains cultivated in prolonged cultures in aerobic (A) or anaerobic (B) conditions. The values of mean and standard deviation from duplicate experiments are shown for each time point.</p> <p><br> </p> <p><b>Additional Figure S3. </b>Yeast strains used in the experimental evolution are unable to grow on medium supplemented with non-fermentable carbon source. Cells grown on glucose-containing (A) and glycerol-containing (B) solid medium. Single colonies were streaked on the appropriate plate and incubated at 28⁰C for 3 days. Wild-type strain shows robust growth on both media, whereas mutant strains grow only on glucose-containing plate.<br> <br> </p

DataSheet1_Improvement of native structure-based peptides as efficient inhibitors of protein-protein interactions of SARS-CoV-2 spike protein and human ACE2.PDF

New pathogens responsible for novel human disease outbreaks in the last two decades are mainly the respiratory system viruses. Not different was the last pandemic episode, caused by infection of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). One of the extensively explored targets, in the recent scientific literature, as a possible way for rapid development of COVID-19 specific drug(s) is the interaction between the receptor-binding domain of the virus’ spike (S) glycoprotein and human receptor angiotensin-converting enzyme 2 (hACE2). This protein-protein recognition process is involved in the early stages of the SARS-CoV-2 life cycle leading to the host cell membrane penetration. Thus, disrupting this interaction may block or significantly reduce the infection caused by the novel pathogen. Previously we have designed (by in silico structure-based analysis) three very short peptides having sequences inspirited by hACE2 native fragments, which effectively bind to the SARS-CoV-2 S protein and block its interaction with the human receptor. In continuation of the above mentioned studies, here we presented an application of molecular modeling approach resulting in improved binding affinity of the previously proposed ligand and its enhanced ability to inhibit meaningful host-virus protein-protein interaction. The new optimized hexapeptide binds to the virus protein with affinity one magnitude higher than the initial ligand and, as a very short peptide, has also great potential for further drug development. The peptide-based strategy is rapid and cost-effective for developing and optimizing efficient protein-protein interactions disruptors and may be successfully applied to discover antiviral candidates against other future emerging human viral infections.</p