Instruct-ERIC webinar series: structure meets function
Meeting
Date: 18-Aug-2020
Instruct
Instruct-ERIC will be running a series of scientific webinars via Zoom. The first one will take place on Tuesday, 18th August and will be hosted by Instruct-Centre, Israel
Date: 18th August
Time: 10:00-11.30 BST and 11:00-12:30 CEST
Talk 1: Crowdsourcing for SARS-CoV-2 Mpro inhibitor - a global effort driven by structural biology
Speaker: Dr Nir London
COVID-19, caused by SARS-CoV-2, lacks effective therapeutics. Additionally, no antiviral drugs or vaccines were developed against the closely related coronavirus, SARS-CoV-1 or MERS-CoV, despite previous zoonotic outbreaks. To identify starting points for such therapeutics, we performed a large-scale screen of electrophile and non-covalent fragments through a combined mass spectrometry and X-ray approach against the SARS-CoV-2 main protease. The results with more than 71 co-crystal structures that span the entire active site, were released to the public and we implemented a crowd-sourcing platform to solicit next generation design ideas. Thousands of suggestions were submitted, of which we made and tested hundreds, through a global consortium including academic labs, chemical vendors, pharma advisors and more. This effort resulted in sub-uM inhibitors with crystallographic confirmation that are now being further developed and assessed by live virus assays. We hope this initiative can serve as a template for an alternative drug discovery pipeline for areas that are unappealing to traditional pharma such as pandemic preparedness and antibiotic development.
Talk 2: Line-FRAP, a method to measure diffusion rates of a large range of molecules in vitro and in vivo
Speaker: Prof Gideon Schreiber
Many methods exist to measure diffusion, including of proteins. These include methods based on fluorescence recovery after photobleaching (FRAP). However, despite the many years the method is in use, the evaluation of diffusion constants for fast diffusing molecules in cells was shown to be problematic. A main reason for this is the slow acquisition time of FRAP. Here, we altered the data acquisition method, increasing acquisition time from 20-50 Hz to 1000 Hz. This provides fundamental advantages both in the time of the first data point and in the number of data points along the measurement. As FRAP half-life for standard proteins is 50-200 ms, conventional FRAP will have ~5 significant data points before most of the recovery has happened. Moreover, the first data point, which will be taken after 30-50 ms after bleach will already include strong blurring due to diffusion happening during this time. As a result, the important parameter of radius of bleach will be wrong. As the bleach radius is squared in the data analysis, while the rate is not, errors in bleach radius have a large effect on the calculated diffusion rate. In the Line-FRAP method presented here, acquisition starts 1 ms after bleach, avoiding this problem. In the first part of the talk I will introduce our method in detail and compare it to conventional FRAP. In the second part of the talk I will show a wide range of interesting biological examples of using the method. These include measuring diffusion constants of different proteins in buffer, in the presence of increased crowding, within eukaryotic cells and within prokaryotic cells. Finally, I will show how diffusion of drug-like molecules is surprisingly slow, which may have major effects of their efficacy.
