From 19th-22nd February I was fortunate enough to participate in the joint Keystone Symposium on Next-Generation Antibody Therapeutics and Multispecific Immune Cell Engagers, held in Banff, Canada. Now in their 51st year, the Keystone Symposia are a comprehensive programme of scientific conferences spanning the full range of topics relating to human health, from studies on fundamental bodily processes through to drug discovery.
Continue readingCategory Archives: Protein Engineering
3 Key Questions to Think About When Designing Proteins Computationally
We have reached the era of design, not just ‘hunting’. Particularly exciting to me is the de novo design of proteins, which have a wide and ever increasing range of applications from therapeutics to consumer products, biomanufacturing to biomaterials. Protein design has been a) enabled by decades of research that contributed to our understanding of protein sequence, structure & function and b) accelerated by computational advances – capturing the information we have learned from proteins and representing it for computers and machine learning algorithms.
In this blog post, I will discuss three key methodological considerations for computational protein design:
- Sequence- vs structure-based design
- ML- vs physics-based design
- Target-agnostic vs target-aware design
A quantitative way to measure targeted protein degradation
Whenever we order consumables in the Chemistry department, the whole lab gets an email notification once they arrive. So I can understand why I got some puzzled reactions from my colleagues when one such email arrived saying that my ‘artichoke’ was ready to collect from stores. Had I been sneakily doing my grocery shopping on a university research budget?
Artichoke is, in fact, the name of a plasmid designed by the Ebert lab (https://www.addgene.org/73320/), which I have been using in some of my research on targeted protein degradation. The premise is simple enough: genes for two different fluorescent proteins, one of which is fused to a protein-of-interest.
Continue readingWhat is a plantibody?
Plants can be genetically engineered to express non-native proteins, for example, crops can be engineered to produce insect toxins in order to improve disease-resistance. However, I was not aware of their ability to express antibodies until, inspired by my expanding collection of house plants, I googled ‘plant immune systems’.
Plants don’t naturally produce antibodies – they do not possess an adaptive immune system or any circulating immune defence cells. Despite this, plants can be made to express and assemble full length antibody heavy chains and light chains. This was first published back in 1989, when Hiatt et al. [1] successfully introduced mouse immunoglobulin genes to tobacco plants and produced functional antibodies with reasonable efficiency. The excellent term ‘plantibody‘ was coined soon after, to refer to antibodies and fragments of antibodies produced by plants transformed with antibody-coding genes.
Continue readingAntibody Engineering and Therapeutics Conference
I was invited to speak at the Antibody Engineering and Therapeutics Conference (presenting mine and Matt’s recently published epitope profiling paper), in San Diego (December 12th – 16th). Unfortunately, the pandemic had other ideas so I decided not to travel but luckily the conference was hybrid.
The conference included 1 day of pre-conference workshops and 4 days of presentations from academic and industry, with livestreaming of the initial keynotes (including one from Charlotte). Remaining talks were recorded and made available after the conference. I’ve highlighted a few of my favourite talks and conference themes, with links to papers where available.
Naturally, a lot of the presented research related to covid-19. I was speaking in the ‘Antibody Repertoires and Covid-19’ session, where there were interesting presentations from Professor Eline Luning Prak from the University of Pennsylvania and Elaine Chen from Vanderbilt University analysing antibody responses in covid-recovered individuals, and comparing vaccine responses in covid-recovered vs covid-naiive individuals. Other talks around SARS-CoV-2 vaccines included Dr Laura Walker from Adimab/Adagio Therapeutics comparing BCR repertoire responses to different types of vaccinations, and the effect of using different booster types.
Continue readingHighlights from the European Antibody Congress 2021
Last month, I was fortunate enough to be able to attend (in person!) and present at the Festival of Biologics European Antibody Congress (9-11 November, 2021) in Basel, Switzerland. The Festival of Biologics is an annual conference, which brings together researchers from industry and academia. It was an excellent opportunity to learn about exciting research and meet people working in the antibody development field.
Here are some of my highlights from the European Antibody Congress, with a focus on antibody design and engineering:
Continue readingTargeted protein degradation phenotypic studies using HaloTag CRISPR/Cas9 endogenous target tagging and HaloPROTAC
Biologists currently have several options in their arsenal when it comes to gene silencing. if you want to completely vanquish the gene in question, you can use CRISPR to knock the gene out completely. This is a great way to completely eliminate the gene, and hence compare cell phenotypes with and without the gene, but it’s less good if the gene is essential and the cells won’t grow without it in the first place.
Otherwise you can use RNA interference, where small pieces of RNA that complement the mRNA for that gene are introduced to the cell, with the overall effect of blocking transcription of that gene’s mRNA, hence silencing it. However, this method suffers from side effects and varying levels of gene knockdown efficiency. Moreover, it does not vanquish existing protein, it just stops more from being produced.
Continue readingA to Z of Alternative Antibody Formats: Next-Generation Therapeutics
Do you know your diabodies from your zybodies?
Antibodies are a highly important class of therapeutics used to treat a range of diseases. Given their success as therapeutics, a wide variety of alternative antibody formats have been developed – these are driving the next generation of antibody therapeutics.
To note, this is not an exhaustive list but rather intended to demonstrate the range of existing antibody formats.
Inspired by this article in The Guardian: “Rachel Roddy’s A-Z of pasta“
Many of these figures were adapted from Spiess et al., 2015. Additionally, some of these formats have multiple variations or further possible forms (e.g., trispecific antibodies) – in these cases, one example is given here.
A – Antibodies
Antibodies – a fitting place to start this post. Antibodies are proteins produced by our immune systems to detect and protect against foreign pathogens. The ability of antibodies to bind molecules strongly and specifically – properties essential to their role in our immune defence – also make them valuable candidates for therapeutics. Antibody therapies have been developed for the treatment of various diseases, including cancers and viruses, and form a market estimated at over $100 billion1.
Continue readingHow fast can a protein fold?
A protein’s folding time is the time required for it to reach its unique folded state starting from its unfolded ensemble. Globular, cytosolic proteins can only attain their intended biological function once they have folded. This means that protein folding times, which typically exceed the timescales of enzymatic reactions that proteins carry out by several orders of magnitude, are critical to determining when proteins become functional. Many scientists have worked tirelessly over the years to measure protein folding times, determine their theoretical bounds, and understand how they fit into biology. Here, I focus on one of the more interesting questions to fall out of this field over the years: how fast can a protein fold? Note that this is a very different question than asking “how fast do proteins fold?”
Continue readingThe Coronavirus Antibody Database: 10 months on, 10x the data!
Back in May 2020, we released the Coronavirus Antibody Database (‘CoV-AbDab’) to capture molecular information on existing coronavirus-binding antibodies, and to track what we anticipated would be a boon of data on antibodies able to bind SARS-CoV-2. At the time, we had found around 300 relevant antibody sequences and a handful of solved crystal structures, most of which were characterised shortly after the SARS-CoV epidemic of 2003. We had no idea just how many SARS-CoV-2 binding antibody sequences would come to be released into the public domain…
10 months later (2nd March 2021), we now have tracked 2,673 coronavirus-binding antibodies, ~95% with full Fv sequence information and ~5% with solved structures. These datapoints originate from 100s of independent studies reported in either the academic literature or patent filings.
