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The Chemistry Nobels, 2018

The 2018 Nobel Prize in Chemistry has gone to Frances Arnold (for directed evolution of enzymes) and to George Smith and Gregory Winter for phage display. These are worthy discoveries, techniques that have gone on to be used for a huge variety of work ranging from blue-sky research to marketed drugs, and the Nobel committee is definitely correct when they refer to them as having “harnessed the power of evolution”.

The proteins we have around us in living systems have, of course, been shaped by evolutionary forces. In fact, there’s really no better place to see the idea at work. On those occasions when I’ve encountered someone skeptical of the whole idea of evolution, I’ve wanted (and in some cases tried to) bring them up to speed on protein sequences and what they tell us. In short, that’s a history of random mutations, each of them put to the test in every organism. Fitness to reproduce asks several questions, very insistently, of any new mutation: does your current form help to pass on this new sequence? Do you at least not hurt the current chances of doing so? By chance, would you happen to be useful for anything else? Looking over related organisms at the protein-sequence and DNA-sequence level shows you a lurching, staggering mutational history as various residues get changed easily (to apparently not much effect), while others are strongly conserved (can’t touch ’em without trouble) and others lead to the new protein wandering into completely new roles over time.

Frances Arnold tried to harness this sort of thing deliberately. Here’s the 1993 paper on those efforts, which showed how a well-known enzyme (subtilisin) could be modified, by rounds of mutation and selection, to produce a variation that could still function in a decidedly non-natural environment (60% dimethylformamide/water, a brew that would stop most native proteins in their tracks). The abstract of the paper finished up by saying “Great variability is exhibited among naturally occurring sequences that code for similar three-dimensional structures–it is possible to make use of this sequence flexibility to engineer enzymes to exhibit features not previously developed (or required) for function in vivo“, and that about sums it up. We don’t have to play the hand we’re dealt; we can shuffle the cards and try for something else, then keep the ones we like and draw to those to improve. (It has just occurred to me that draw poker is an excellent metaphor for the whole process!) There are a *lot* of protein features that we might want to engineer in, and this paper and its follow-ups have led to a whole new field that spends its time doing just that.

I wrote about Arnold’s most recent work just earlier this year, and over the years I’ve also written about enzymes engineered to fluorinate compounds, to do metal-catalyzed transformations, and to produce pharmaceutical intermediates to order. There’s still a great deal of chance and luck involved in these studies, but that’s not a complaint: chance and luck are what got us the proteins that are keeping us alive right now. The molecular machinery of biology lets you industrialize that sort of thing, running through huge numbers of variations and selecting out the interesting ones, in ways that regular organic chemistry is just not equipped to do. This area of research has come a long way in 25 years, but the horizon is still nowhere in sight.

The second half of today’s prize is for phage display, a technique that’s closely related to directed evolution of proteins. Bacteriophages are viruses that infect bacteria, and they display various peptides on their surfaces. George Smith’s breakthrough was to engineer one of these (PIII, previously not exactly a star player) to express new sequences. The idea was that these would show up on the phage’s surface, and that after it had had a chance to reproduce itself in some unlucky bacteria, you could take the resulting solution and flow it across some sort of affinity purification. That’s a basic and powerful technique in chemical and molecular biology: you have some sort of solid support (a column of resin, say) that has on it a known binding partner for your species of interest. You pour some sort of gemisch across this, and the species in it that stick the tightest to the resin binding partner stay there while you wash everything else off. You then switch to more vigorous solvent/buffer conditions to get the strong-binding things to wash off, and voila: you have purified out the best binders.

Smith did that with the phages in the mid-to-late 1980s – after all, they have proteins on their surface – and showed that such a protein-displaying phage would indeed be captured by affinity purification. As the technique was refined, he and his lab demonstrated that they could enhance the concentration of some particular phage by huge amounts in affinity purification (hundred-million-fold!) and this led to the next stage of things: setting up the phages so that they didn’t just display one particular protein that you stuck in there, but a whole range of variations, all produced randomly at the same time (those tools of molecular biology again). That had immediate applications in antibody work, since the whole thing about antibodies is that they recognize peptide sequences/surfaces with high affinity. Phage display suddenly made it possible to determine just exactly what sequences bound with the most affinity, and to produce comprehensive maps of what any particular antibody liked the most.

On the flip side, it also let you optimize synthetic antibody sequences to a given protein as well, and that was where Gregory Winter’s lab came in, showing that functional antibody sequences could be expressed on the phage surface. You can let this rip with millions upon millions of possibilities simultaneously, picking out the best binders from the whole collection. Then you can use the sequence that you found to design another round of more focused variations and send it back around again, etc. All this started getting reduced to practice (in both directions) in the early 1990s, and the worth of these techniques was utterly, obviously apparent at the very start. As were the sorts of variations you would want to try (different regions of the antibody protein, longer stretches of them, different gene-shuffling techniques to make variation libraries, optimizing antibodies against things that you couldn’t get by classic immunization techniques, and on and very much on).

These advances are what has led to the modern antibody industry. That ranges from sheer-research lab reagents, through diagnostic kits, all the way to multibillion dollar marketed therapies. Being able to run through gigantic piles of possibilities and enrich the best ones by factors of ten-to-the-whatever with every round of selection really opened up the field, as well it should have. There have been many advances over the last 25 years in making human-type antibodies directly, in different sorts of phages (and in using things for protein display beyond phage as well, such as yeast cells and whole bacteria), new affinity-selection techniques. . .a person could go on for quite a while, and I have to make a living (although, to be fair, these topics are directly relevant to how I make that living!) I can recommend the Nobel committee’s scientific background paper for more details and for leading references. If you’d like to see one way that all the topics of today’s award intersect, here’s a blog I wrote about a technique to use phage display to try to make new evolved enzymes – you can mix and match this stuff forever.

Or at least for a very long time. And that’s what’s going on now – the possibilities are very far from being exhausted, and the rewards are still huge. Protein engineering in general is going to be with us for a very long time to come, and I wouldn’t even want to guess what forms it might take. Congratulations to today’s winners! (And I can’t resist linking to Arnold’s Twitter account from a few days ago!)

Update: for those who have asked, I have some broader thoughts on the Chemistry Nobels and the Nobel prize awards in general, but those will have to wait until tomorrow. . .

27 comments on “The Chemistry Nobels, 2018”

  1. a says:

    Bummer that pip stemmer – the inventor of gene shuffling – didn’t survive to get recognized at this level.

    1. Andre says:

      PIM Stemmer. Otherwise, I agree!

      1. Yup says:

        I would have gone with Stemmer, Arnold, and Smith.

        Or without Pim, just Arnold and Smith.

        Winter is an obvious next step–not fundamental, not evolution, not inventive. Just commercial.

  2. anon says:

    I understand the groundbreaking and conceptual significance of Arnold’s work but if you evaluate from a non-hype, real-world application standard of the use of directed evolution of enzymes in chemical production processes or everyday research, how does it hold up? (Not read much in this area, so have no idea)

    1. tt says:

      It holds up a lot…see some of the links in Derek’s post. As a process chemist, directed evolution and substrate walking technology has had a huge impact in evolving new activities to enable green and efficient drug manufacture as well as enabling fast scale-ups to the clinic by doing quick ketone reductions and aminations, to the point where it has largely displaced transition metal catalysis (not to mention resolutions, ene-reductions, etc…). In short, we are no longer stuck with mother nature’s toolbox of diverse enzymes, we can evolve our own to suit our needs and that ability has completely transformed biocatalysis and process chemistry..

      1. Nick K says:

        Your post is most interesting to me (I have been out of Process Research several for several years now). Do you have a reference to a review?

        Thanks

    2. Hugo says:

      In addition to tt’s remarks:

      The worldwide market for enzymes is several billion dollars and all of the big players (Novozymes, BASF, Dupont, DSM) have large protein engineering labs where they perform directed evolution.

      Not every enzyme you see is adapted, but it’s highly likely the lipase or protease in your laundry detergent has a non-natural sequence.

      1. Chrispy says:

        The number of subtilisin variations in patents is astonishing! It must be a popular additive in detergents.

  3. A former Arnold lab postdoc says:

    @anon: Last I checked, directed evolution had been used in developing production pipelines by several companies. Sometimes to get the enzymes to work in the non-natural environments that are used in industrial scale synthesis, sometimes for other things. It’s definitely become a practical tool. My own postdoc in the Arnold lab was funded by Procter and Gamble evolving enzymes for laundry detergents.

    Congratulations Frances! Well deserved.

  4. BK says:

    I’m sure these folks are deserving, but I will never not continue to question why Goodenough has not won the Nobel prize yet.

    1. road says:

      I guess he’s not Good Enough!!!

      …I’ll show myself out…

  5. Imaging guy says:

    I doubt page display is widely used for making therapeutic antibodies or even binding antibodies used in ELISA, flow cytometry and immunohistochemistry. I have read scientific background paper for Nobel prize and found that almost all references cited for the phage display part were from before year 2000 (references 81-112). How do you write Nobel prize background paper without up-to-date references? Phage display field hasn’t made any progress since then? Actually, phage display guys have been making promises that they will produce high affinity antibodies for all known human proteins and they haven’t done that yet. As for the directed revolution I can’t say anything about enzymes, but I don’t think they are widely used in making high affinity antibodies. The link for the scientific back round paper (pdf, 1MB) is given below.
    https://www.nobelprize.org/uploads/2018/10/advanced-chemistryprize-2018.pdf

    1. Nesprin says:

      No, Phage display isn’t widely used for making high affinity antibodies or the like. Ijnstead phage display is a way to rapidly pick out the targets for developing those antibodies. Its compatibility with complex systems and live animals is truly unique- a well designed phage display screen is truly a thing of beauty.

    2. A Knowing Mess says:

      Phage display is widely used to find initial hits, and it’s also widely used for affinity maturation (by screening sublibraries based on the initial hits) to develop high affinity antibodies from those initial hits. There are a number of important antibodies that have come out of phage display (Humira, for example), although there are still more antibodies going into clinic from immunization approaches.

    3. Druid says:

      I think there would have been more (or more acknowledgment) if not for the threatening patent and licensing situation.

      1. DisplayDude says:

        The patent situation was certainly daunting. Having worked in display in pharma prior to the expiration of the patent life, I can tell you that everyone was doing it, even if they weren’t admitting it (for legal reasons). Now that things are a little cheaper/more open, you’ll note that a huge number of CROs have popped up are offering display services with naive libraries, but more and more frequently with specialized libraries.
        Display (phage or otherwise) is here to stay in the realm of antibody development, and I suspect that more and more therapeutic antibody “discoveries” will be attributed to the technique.

  6. AC says:

    I like how the chemistry Nobel ties in with the physiology/medicine Nobel.

    1. anonymous says:

      Also the Nobel in physics this year is almost chemistry (actually biophysics, but that is essentially chemistry anyway)

  7. Lead Chemist says:

    In 2013-14 Frances Arnold came to our department (top 10) to share her work on directed evolution. She had a difficult time answering technical questions from the audience almost like she didn’t know the work. Her talented postdocs/graduate students are the ones who deserve the nobel.

    1. Ostensibility says:

      “did u try toluene?”
      “nobody thought it could work”
      “was ortho methyl gratified?”

    2. Some Dude says:

      I heard her give a talk at Harvard a few years ago and it was very impressive. She gave insightful and thought provoking answers to the questions from the audience and I walked away thinking that she was extremely competent.

      So it’s possible that she just had a bad day when she gave a talk at your institute. Or of course it’s also possible that you’re a misogynist and/or a troll.

      1. tangent says:

        Nah, nah, let me just search back here for comments by Lead Chemist dinging male profs for their technical grasp of material

        what’s this I’m coming up empty
        shocking

  8. Mellatioredoxx says:

    Maybe next year

  9. PotStirrer says:

    Derek, I like how you worked “gemisch” into your post. Is that actually a term that is used in English (maybe coming from Yiddish?) or is that just a remnant of your days in Germany?

    1. Derek Lowe says:

      I’ve been around several older organic chemists in my career who used it. So it at least has (or has had) a foothold in “chemistry English”. Anyone able to corroborate this?

      1. I use (and used) “Gemisch” all the time. It’s German (and also Yiddish, “געמיש”, “Gemisch” [transliterating the Hebrew characters], probably by derivation from German).

        mischen = to mix
        gemischt = mixed (past tense)
        Gemisch = mixture (but often more in the sense of a jumbled mess)

      2. MM says:

        I’ve heard Steve Weinreb and Sam Danishefsky (both Jewish chemists) use this word more than once.

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