Month: August 2020

Calculating the change in Gibbs free energy (ddGbind) of an improved alpha-ketoamide inhibitor binding associated with genetic variations of SARS-CoV-2 main protease – post18

Posted onAuthorSetayesh YazdaniLeave a comment

Since we posted our analysis of genetic variation of SARS-CoV-2 main protease (MPro) with inhibitor N3 (PDB: 7bqy), there have been other inhibitors co-crystallized with the MPro (PDB: 6lze, PDB: 6m0k, and PDB: 6y2f). In my last post, I talked about the two inhibitors, 11a and 11b (PDB: 6lze, PDB: 6m0k) and in today’s post, Read More …

Brachyury (TBXT) ligands for chordoma: 1. Fragment optimization strategy 2. fragment F9000505, B-site, PDB 5QRU

Posted onAuthorDavid DrewryLeave a comment

Introduction In this blog post I will share details on the new molecules we have designed and synthesized or purchased based on one of our original hits from the x-ray crystallography fragment screen. The compound is called F9000505 and it is bound to pocket B. The crystal structure was deposited in the Protein Data Bank Read More …

Electroporation: a second look

Posted onAuthorElizabeth BrownLeave a comment

It’s never too late to take another look at your data. The incredibly knowledgeable Sally Cowley suggested that I shouldn’t just think about how many cells contain any AlexFluor488 antibody after electroporation, but how bright each cell is (i.e. the amplitude of fluorescence). Looking at this instead will give me an idea of how much Read More …

Structure and X-ray Fragment screening of SARS-Cov-2 helicase (Nsp13)

Posted onAuthorJoseph NewmanLeave a comment

My name is Joseph Newman and I have been working in Lab of Opher Gileadi at SGC Oxford since 2013 mainly on targeting DNA repair factors as synthetic lethal targets for early stage development of new cancer therapeutics. Like many scientists my normal laboratory based research activities were disrupted by the lockdown, and when Opher Read More …

Back to SARS-CoV-2 Main Protease: Calculating the change in Gibbs free energy (ddGbind) of two peptidomimetic aldehyde Inhibitors binding associated with genetic variations of SARS-CoV-2 main protease – post17

Posted onAuthorSetayesh YazdaniLeave a comment

Since we posted our analysis of genetic variation of SARS-CoV-2 main protease (MPro) with inhibitor N3 (PDB: 7bqy), there have been other inhibitors co-crystallized with the MPro (PDB: 6lze and PDB: 6m0k). MPro acts like a scissor by cutting SARS-CoV-2 polyproteins into functional pieces, making it a critical target for antiviral therapies against SARS-CoV-2. In Read More …