Combinatorial peptide synthesis

Yesterday we talked about a paper in journal club from Nature Chemical Biology. It was one of those combinatorial peptide synthesis papers--in this case to find a inhibitor of a protein in the clotting cascade (a serine protease that activated a precurser of a signalling cascade, I guess). It struck me that all these papers are the same. Do some combinatorial peptide (or peptide analog, or chemical altered peptide with some functional group sidechain), create a library of compounds, screen them, and try to find some compound that is an inhibitor or probe or whatever of some protein of pharmacological or biotechnological relevance. The targets change, the screening methods change, sometimes the synthetic methods change (although it's usually some variant of solid phase peptide synthesis). But the general idea stays the same: boring. There wasn't even any interesting structural biology about how the compounds worked as an inhibitor (my PI suggested that perhaps one of the moeities on a segment of the peptide blocked the catalytic triad--now that sort of hypothesis is something I can actually get into).

I guess I wouldn't be so judgmental about this research if it didn't seem like every issue of Nature Chemical Biology (or ACS Chemical Biology or Chemistry & Biology or ChemBioChem or what have you) had at least one article like this. In the introduction they always introduce their methodology as a novel (novel!?!) modular combinatorial method that is very promising as a way to find compounds of medicinal interest blah blah blah.

There's nothing that is really all that intellectually satisfying about this area of chemical biology to me. It's all the same. There's no narritive story to it--just hammering.

When can we start calling ourselves an "ist"?

I was talking to my friend, and I made the mistake of saying "I think I am more of a chemical biologist than a biochemist in the traditional sense."

He said "You're a fricking undergrad. You're neither. What do you mean by that, that you took a few organic chemistry classes and liked them? That's absurd."

Then I said, "You're absolutely right. Right now I am just a student. But what I mean is how I think about science."

He said, "What do you mean, how you think about science, that is ridiculous. I just don't understand what you're talking about when you say shit like that."

But what I mean, I guess, is that in the biology-chemistry interface-land, what is biology and what is chemistry and what is biochemistry and what is chemical biology is totally artificial. But they are words that we use to describe an approach to solving problems, the way experiments are designed, and a school of thought of training.

I mean, one could say "I just don't think like a cell biologist, I think like a geneticist." This means something to me, even though there is a large degree of overlap between what a cell biologist is and what a geneticist is, and a cell biologist better know genetics and a geneticist better know some cell biology. The way papers in Cell are laid out are just different from the papers in Nature Genetics. And not just visually, in the intellectual approach.

Biochemistry is neither biology nor chemistry (although it's both) in a lot of ways. It's kind of its own thing. It's got it's own kinetics. It's got it's own brand of tedious separation chemistry. It's got it's own sort of sensibility. The mindset that I am in when I read a paper from Organic Letters is totally different from the mindset I am in when I read a paper from ACS Biochemistry.

I feel like by junior year, as a student you have a pretty good sense of what sub-specialty of your science training you are good at and interested in pursuing further and what area you are most "minded" like. And as far as I can tell, I'm most "minded" in this relatively new biology-chemistry hybrid business people refer to as chemical biology. Is that so absurd?

Summer in Germany; Polyketide Biosynthesis

As I may or may not have posted before, this summer I'm going to do a lab internship in Jena Germany at the Hans Knoll Institute: Leibniz Institute for Natural Products Research and Infection Biology in the department of biomolecular chemistry in Christian Hertweck's group.

The story of how this works is the following: I was writing a paper for my biochemistry seminar which focused on chemical biology and I stumbled upon work he was doing with polyketide biosynthetic enzymes in the aureothin (a Streptomyces thioluteus polyketide) pathway. Specifically, AurH, an enzyme catalyzes the chiral oxidation of a THF ring. This paper caught my attention as a mechanistic paper that dissected how the enzyme worked to act as a catalyst and this paper* used the enzyme in a stereospecific total chemoenzymatic synthesis. I read about how they figured which enzyme did the oxidation using molecular biology methods, along with how they figured out how the enzyme worked with biochemical methods, and then their application synthetically. It intrigued me because it was basically exactly the sort of research I want to be doing. It seamlessly integrates biology and chemistry. It relies on both synthetic organic chemistry and molecular biology. Dissecting mechanistically interesting biosynthetic steps that are difficult to mimic with classical reagents is just a really fascinating area of study to me. So I wrote a review paper for my class about research from his lab.

So one day, kind of on a whim I emailed Christian Hertweck, the PI with my CV. He was impressed with my background and my strong desire to do interdisciplinary science and offered me a summer internship at the HKI. I've been in correspondance all year working out the details. So I will be in Germany this summer doing chemical biology research.

It hasn't really hit me that I will be in Germany this summer doing exactly the sort of science I want to be doing. It seems like such a lucky shot in the dark.

I'm so pumped for this summer and next year. I like learning, so classes are alright, but what I really like is doing research. It reminds me "oh yes, this is why I study science."

Also, this will be my fourth consecutive summer in a lab, along with doing research in my prof's lab during the year for a bit and an undergraduate thesis. Although not my motivation for wanting to be in the lab in the summer, that's gotta look attractive to graduate schools, right?

*As a tangent, I also really like the journal ChemBioChem, which is a European chemical biology journal published by Wiley. ACS Chemical Biology puts out a few interesting articles, but it feels uninspiring a lot of the time (and virtually indistinguishable from what goes into ACS Biochemistry), and Nature Chemical Biology seems differently focused. There is some interesting bioorganic work being done here but the the mentality seems different somehow. It seems like the organic community is more seemlessly integrated in this European journal. More on this later.

Polyketides again

I've been thinking lately that I would like to go into polyketide chemistry, lately. I'm going to work in a lab this summer that works with bacterial polyketides, and as far as I can tell, the whole field pretty much brings my all my interests together. Even in light of what I said about combinatorial chemistry (and in this case, biology) which is an aspect of playing around with biosynthetic genes.

It's one area of chemical biology that has caught my interest this year (which is basically when I started browsing the chemical biology lit). It relies heavily on organic and bioorganic chemistry, but also genetics and even tracing evolutionary pathways (like this review that talks about how the classifications of polyketide synthases are a little rigid). There's a med chem/natural products discovery aspect to it, since a lot of these structures are really promising medicinally as antibiotics and chemotherapeutic agents (and like I posted yesterday, the genome-mining approach). There's a synthetic organic aspect because a lot of these structures are good targets for total syntheses due to their medicinal qualities. There's an enzymology aspect because a lot of these biosynthetic enzymes have really interesting proprieties. And then there's even some work on trying to harness enzymes that do mechanistically biosynthetic transformations hard to emulate with classical reagents for use in total synthesis, like this total chemoenzymatic synthesis. There's a structural biology aspect too--like this paper looking the structural basis for polyketide synthases docking and substrate specificity. I suspected there would be some biomimetic organic synthesis based on some of these bacterial polyketide biosynthetic pathways out there, and a quick google search told me that there's is, indeed, loads of work being done in that area.

I've started bookmarking webages of labs that publish in this area (and other areas that look interesting) because...well, I figure if I still want to go into this (kind of specialized) area by the time I decide to apply to grad school in a couple years, that's probably a decent approach. It just seems like such a promising area for me and for my desire to bring all these interests of mine together. And just to see where it goes generally. It's not a cutting-edge new field, but just a field that keeps getting cooler and cooler as our tools to do science get cooler and cooler.

Genome Mining for Natural Products

I've discovered a lot of interesting science in ChemBioChem, a European chemical biology journal. We have more access to more of these journals than most of the Nature journals; it must be because there is some relatively cheap Wiley journal package that comes with Angewandte Chemie, since we basically get all of the European chemistry journals that are published by that group.

But in any case, one pet area that has been fascinating me lately is the convergence of genetics, microbiology, analytical chemistry, and synthetic chemistry to the discovery of new natural products, especially in examining modular biosynthetic polyketide genes. This review that came out a few days ago, Strategies for Discovering New Natural Products through Genome Mining, went through basically what is being done in the field.

The authors explain that natural products discovery has not been favored by pharmaceutical industries for a while as a way to discover new drugs. Most of the 20th century (after penicillin was discovered) is described as the golden age of antibiotics and natural product discovery. It has fallen out of favor because it is time intensive and often leads to discovery of natural products that are already known.

But now, in a post genomics era with so much bioinformatic data out there, we actually have new strategies to approach discovering natural products, especially in examining biosynthetic gene clusters. We can search for PKS (polyketide synthase) domains, we can knockdown genes, and (most exciting to me) you can reconstruct products in vitro to determine if that gene cluster is actually making what you think it is (and then confirm what you have with NMR and MS). Of course, with the reconstruction strategy there are certain problems, like finding the right promoter and so forth, but chemoenzymatic total synthesis to reconstruct biosynthetic pathways has been done in vitro before.

Polyketides are neat from a pharmacological standpoint, because the secondary metabolites tend to have a lot of medicinal properties. They are also neat in that a lot of the genes are modular, so there have been some papers where they re-arrange them essentially doing synthetic chemistry in a cell instead of in an RBF. And sometimes they have neat little genes beyond just PKS genes--I recently wrote a paper for school reviewing research on a gene that was responsible for doing a powerful oxidation to form a chiral THF ring. It seems like a way to both discover new natural products with pharmaceutical value and to generally get a better mechanistic grasp of biosynthesis.

Flourescent Protein Timers

Since Reed doesn't have a subscription to Nature Chemical Biology (I guess I could Interlibrary loan it if I'm really curious--but I still find that incredibly annoying), I'm stuck reading other blogger's accounts of the cool research in there. Like florescent proteins that work as a timer. As far as I can tell, they change color temporally, making them potentially a really powerful tool for cellular tagging and localization studies.

Seriously, though

Apologies for posting here so much; I'm on the last few days of winter break and have the time to do so, I suppose and I'm going a little stirr-crazy.

I was wondering if there are better RSS feeds than the one I have for PNAS, Nature, and Science. All of my ACS journal feeds are quite nice; it gives a full abstract as well as a graphical abstract and makes browsing really easy. And I recently managed to dig up a better feed for Angewandte Chemie (mostly due to reading chemistry blogs of other science people who spend far too much of their life on the interwebs). But I can't find an RSS feed for Cell, and Nature, PNAS and Science suck. No abstract, no nothing but the title and authors. Do biologists spend less time dicking around on the internet? I doubt it. There is way too much down time in molecular biology for that to be true. I gotta do some surfing around to find them.

Unrelated, but I also found it interesting that there was an extensive review article about RNA interference in Angewandte Chemie the other day. The borders of biology and chemistry are becoming very fuzzy indeed.

On Chemical Biology

So I think I mentioned earlier that I'm pretty sure I don't want to go into traditional biochemistry or structural biology because it's not exactly biology-meets-chemistry, it's kind of it's own thing. Here's excerpts from a PDF that I found on the UCSF website somewhere on one of their chemical biology pages:

Is there a problem?
Chemistry is a very mature science compared to biology.
Chemistry graduates continue to grow overall but at modest rates compared to biology graduates. What is making this happen?

...

What is Chemical Biology?
A paradigm shift in allowing scientists systematic access to chemical tools to probe important problems in biology.
It is not the same as biochemistry which uses chemical principles to probe biological molecules.
It is not the same as chemistry which is focused on synthesis and properties of small molecules.
It is not the same as molecular biology which modifies biomolecules to probe cells.

...

"It is different than molecular biology with the use of small molecules to probe biology offering numerous advantages to gene knockout and siRNA knock- downs, the modern tools used by molecular biologists. Proteins contain multiple functional sites and these"ablative tools" do not allow one to dissect individual functions. Moreover, cell signaling events occur quickly often with time-scales on the order of minutes. siRNA usually requires >24 hours to have its maximal effect and even then it usually only ablates 60-80% of the protein. Gene knockouts represent constitutive inactivation, unlike the acute inactivation that can be generated by a small molecule. Not surprisingly these different probes often generated different results. Small molecules represent rapid and dose-dependent probes of cellular function and the information that is generated is more relevant to drug discovery."

This is all very appealing to me. I'm all about small molecules and how they apply to biological systems. That, in my mind, is chemistry-meets-biology. I guess my main problem was that I read a lot of chemical biology papers that felt very...artificial. I think I describe it as "interdisciplinary for the sake of being interdisciplinary rather than having a point" somewhere on this blog, if not, if you know me in person those words definitely have come out of my mouth.

But I guess a lot of that has to do with the fact that trying to define chemical biology as a field is pretty new. I mean, the essence of what it is has been around for a long time called by different names. There has always been a chemistry-biology interface and medicinal chemistry has always been on it; this isn't exactly new. But defining this interface as a true discipline is, and trying to work more on the interplay between in vitro and in vivo with small molecules is definitely new.

I just need to find a corner of it that I feel like has a point and not, like, spend my life making aptamers that will never ever compete with real antibodies unless I find them to be extremely structurally interesting. Not that that is exactly a waste of time per say, just it doesn't seem satisfying to me. There's a lot of room to grow in this discipline, and I think interdisciplinary science is the way of the future.

What is the point of chemical biology?

I am taking a seminar course on chemical biology. Well, it's actually "topics in biochemistry", but every year there is a theme, and this year the theme is chemical biology. We read a couple papers a week and discuss them.

Which leads me to ask--what is the point of chemical biology anyway? All these papers we're reading--especially the ones that self-identify as chemical biology (like Nature Chemical Biology), seem to have these extremely interdisciplinary projects for the sake of...having an extremely interdisciplinary project? A lot of the issues addressed are issues we already have pretty good solutions to (for example, we have a lot of methods for tagging cells and proteins. not that more methods aren't great...but not more methods that have no shot at being as efficient as the ones we already have but are just structurally interesting seem kind of pointless).

The problem I'm finding, is that my interests in different subjects are for different reasons. I like the questions that are posed by molecular biology, and the idea that there are concrete ways to approach these questions in a methodical fashion. What draws me to organic synthesis is the intellectual puzzle of it, as well as that I like to make things (I like making things much more than breaking them apart, which is what you do in biology, but that's another rant). What I like about structural biology that there is a combination of elegance and totally overwhelming complexity in proteins and other biological structures. So, you might say--what if you mash all three together? Shouldn't that be exactly your cup of tea, Connie?

No, not really. The questions posed by chemical biology are boring to me, and the synthesis are buried in the supplemental information if discussed at all. What it basically amounts to, as far as I can tell, is science that is unsatisfying to the molecular biologist and the synthetic chemist in me. And what I do like about it are not the ideas explored and the overall concepts of the papers (well, one was about lipid membrane evolution, and chemical evolution studies are actually pretty cool), but little snippets of sections that were probably done by specialists. Oh, that was a neat series of reactions for the synthesis of n-substituted glycine peptide analogs. Oh that was a cool way to stabilize that protein domain. Oh that's cool that you can stabilize an alpha helix by stapling the end with a Grubbs catalyst.

I mean, isn't it obvious that we are in an interdisciplinary age? Most biomedical labs in particular have an incredible amount of collaboration between specialists. I mean, synthetic organic chemists (supposedly) primarily synthesize compounds with biological relevance (unless they're doing materials science); biology relies on chemical techniques (protein assays, affinity column chromatography, MALDI-TOF MS, etc. etc.). Crystal structures being solved of receptors as well as genetic studies help computational chemists design drugs for the synthetic chemists to make which need to be tested in animals before being put on the market. So what is the point of going out of your way to say "hey! look! look! it's chemical biology! it's chemistry and biology! things are interdisciplinary!" when it's all kind of a natural process anyway? What ends up, as far as I can tell, are a bunch of projects that take really ass-around-your-elbow approaches to problems for the sake of mixing the diciplines, which just seems kind of pointless to me.

Please enlighten me, though, if you think I'm being closed-minded and if there's something I just don't get.