Projekt “SKUPNOSTNA ZNANOST IN BOJ PROTI KORONA VIRUSU” je odprt projekt skupnosti dobromislečih raziskovalcev in prostovoljcev, ki želijo s svojim delom, znanjem in izkušnjami, prispevati kamenček v mozaiku poznavanja novega korona virusa in bolezni COVID-19, ki jo ta virus povzroča. Skupino vodita strokovnjaka dr. Črtomir Podlipnik in dr. Marko Jukić, z dolgoletnimi izkušnjami s področja računalniško podprtega načrtovanja molekul, farmacevtske kemije in kemo/bioinformatike.
S somišljeniki ter prostovoljci so v zelo kratkem času razvili lastno tehnologijo, ki omogoča porazdeljeno računanje molekulskega sidranja. Tehnologija je osnovana na programčku, ki omogoča povezavo uporabnikovega računalnika s strežnikom, ki porazdeli del knjižnice molekul pripravljenih za molekulsko sidranje (trenutno 10 000 000 spojin). Po končanem sidranju (s programom RxDock), programček pošlje izračunane podatke nazaj na zbirno mesto na strežniku. Po analizi sidranih spojin je končni rezultat seznam molekul s potencialno vezavo na terapevtsko tarčo (v našem primeru so to virusni proteini). Nato lahko preverimo ali so te spojine dobavljive in organiziramo biološko testiranje v sodelovanju z ostalimi raziskovalnimi skupinami. Podatke o nedobavljivih spojinah lahko v nasprotnem primeru posredujemo raziskovalnim skupinam za izvedbo sinteze. V optimalnem scenariju bi lahko identificirali spojine zanimive za farmacevtsko industrijo. Rešitev, ki temelji na porazdeljenem računanju je osnovana na odprtokodnih rešitvah.In our project, we are looking for ligands – small molecules that can successfully bind to protein targets and modulate a specific process that is crucial for the virus biochemistry. Together we have developed software that can be easily installed on your computer to help participants help find the cure for today’s invisible enemy. Based on molecular docking, the ideal ligand should be complementary in shape and properties to the binding site of the target biomolecule. Although the complementarity of small molecules is only one prerequisite for the use of a molecule as a drug. The search for the right molecule is best illustrated by finding a small needle in a huge haystack. It is a much more difficult problem because of the number of possible molecular structures. The amount of all possible molecular structures is also called the chemical universe – the size of this abstract space can be estimated to be 10 to the power of 80. There are many galaxies in this chemical universe, and one of the galaxies is a galaxy with potentially pharmacologically active molecules. The method for this purpose is called virtual screening. In principle, the larger the part of the chemical universe that we study, the higher the likelihood of finding a potential cure for the coronavirus
