What's the deal with Sirtuins?

Why and how we age is a question that affects all of us. As we get older, the frailty of life becomes all the more poignant. While the concept of aging can seem ephemeral, it also has a very practical side. In fact, researchers all across the world are studying the mechanism of aging and not just how we age but how we can stay young. Humans live a long time and are impractical for the study of the why and the how of aging. For this reason aging researchers use model organisms. C. elegans, for example, is a nematode found in a rotting apple in your back yard. Conveniently, the "worm" lives on average three weeks and has a great number of genes in common with higher organisms. So it is possible to probe conserved signaling pathways in this short lived creature to generate hypotheses that may apply to humans.

Recently, two groups published articles in the journal Nature that concerned the aging process; one story identified a novel way by which the "worm" can live longer, and another suggested an accepted mechanism of longevity was erroneous. Bad news first, always, so here it goes.

Sirtuins are a class of enzymes that are known to be NAD+ dependent deacetylases as well as ribosyl transferases. Originally identified in yeast, sirtuins have been implicated in healthy living in a plethora of model organisms including mice. Resveratrol, a popularized small molecule that might lead to longer life, achieves its beneficial affects in a sirtuin dependent manner. Humans have seven types of sirtuins and understanding the role of these enzymes is of great interest to the medical community.

A few years back one of the four sirtuins in C. elegans was over-expressed, which in turn led to a higher level of the protein SIR-2.1 and a 30% longer lifespan in the "worm". A similar extension in humans would mean a 70 year old man would live to be 91. Unfortunately, the recently published work dampened the enthusiasm for sirtuins as lifespan modulators. It turns out that the way in which the sirtuin enzyme was originally over-expressed brought along another mutated gene that also extends lifespan. The original research team crossed the mutant strain with a non mutated wild type strain 6 times to remove any additional mutations. However, that was not enough. "Back crossing", as this genetic cleaning method is called, has to be done 10 times for an organisms that has 100 million base pairs in its genome. A dye filling mutation (dyf) was very close to the sir-2.1 gene on the C. elegans chromosome and just kept sticking around from generation to generation. All hope is not lost though. When the additional mutation was removed, the over-expressing sirtuins still lived almost 10% longer. That same 70 year old man now lives to be 77, still not too bad. Ultimately, more research is necessary to explore how we can optimize sirtuin activity for healthy living and get some good news out of this.

A joke for every end:

What do you get when you cross a snowman and a vampire?
Frost bite!

Aging

My favorite magazine Proto (free subscription - check it out) had an article in the spring issue about aging. The whole concept of getting older is a tricky one. How can you evaluate life span and tease out the factors that modulate the aging process? Is aging a process at all or just a collection of random degeneration? Is our lifespan dictated by oxidative damage that leads to radicals or something more structured?

These questions were first addressed by a nutritionist at Cornell University, Clive McCay. In the 1930s he put rats on a calorie-restricted diet and saw that they lived 40% longer than other, normally fed, rats. Aging research is perhaps the product of the times and started toward the end of the great depression, as concern about food deprivation and its effect on lifespan was at a high. Surprisingly, in response to dietary limitation life was prolonged.

Since the 1930's the research community has come quite a long way. Last year, the University of Wisconsin published a study that observed rhesus monkeys on a calorie-restricted diet. The dieting monkeys lived 20% longer. Considering rhesus monkeys live on average 27 years, this was an extensive examination and suggests the possibility that caloric restriction might be relevant for primates. Check out these monkeys, can you guess which one is on a diet? (it's the one on the left, both are pretty cute) These results need further validation and leave certain issues unanswered. The calorie-restricted monkeys had more deaths that were considered age unrelated and were excluded from the final statistical analysis. Additionally, the article did not seem to clarify whether the monkeys were kept in isolation or not. A second study is currently in progress sponsored by the National Institutes of Health.

Other researchers utilize model organisms to study the process of aging a little faster. The model organisms C. elegans has a much shorter life expectancy (~30 days), a short generation time (~ 3 days) and a well developed system to study various signalingg pathways. And these nematodes are very cute too (well maybe you have to be there). Nevertheless, it has been shown that even in a simple organism such as C. elegans restricting diet can increase life span through different pathways. Cynthia Kenyon has summarized these observations nicely in a recent review. The timing of the diet has a role in the pathway that leads to life span increase. To clarify, a pathway for life elongation is identified in C. elegans by putting the worm on a diet and then knocking out genes for certain elements of known pathways (i.e. daf-2 is the gene responsible for the insulin/IGF-1 receptor ortholog in the worm). If lifespan elongation is no longer achieved, it is suggested that the mechanism of increase occurs through the role of the gene product. As shown nicely in the chart above the pathways are dramatically different. Mild chronic food limitation acts through sir-2.1, a NAD-dependent histone deacetylase and the putative target of resveratrol, the well known small molecule that is found in red wine (structure on the left). Every other day feeding, however, elongates life through the insulin signaling pathway.

The aging picture is very complex, and the research (as well as more aging themed blog posts) are coming. It is striking that temporal variation in a diet can contribute to the same outcome in such different ways. Imagine varying the type of diet as well. The pathways that are considered in the worms are similar to those found in more complicated organisms such as humans, suggesting that there might be elements in many fundamental pathways, such as insulin signaling or control of gene expression that module life span.

If the science community can properly understand this signaling networks - perhaps humans can live longer healthier lives. It is important to note that health is part of the life elongation process. Interestingly enough, even in the little C. elegans (1mm long) it is possible to differentiate between sickly looking long lived worms and happier long lived worms. The C. elegans community is starting to identify these differences and highlight the pathways that lead to longer lived healthier worms and maybe one day people.

A joke at every end:

Three sisters, a 92, a 94 and a 96 year old, all live together. One day the 96 year old is taking a shower. Suddenly she yells out "hey sisters, can one of you help me? I am in the shower and I don't know whether I am getting in or getting out." So the 94 year old sister starts walking up the stairs to help and suddenly she turns around and yells "hey sisters, can one of you help me? I am walking up the stairs and I don't know if I am going up or coming down?"

The 92 year old sister is sitting at the kitchen table. She mumbles to herself "I hope I never get to be like those two" and knocks on wood for superstition's sake. She yells back "Hold on, I'll be right there as soon as I see who is at the door!"

Whats good...not smoking

It seems like everything is good. It's starting to snow, clementines are back in season and of course science is rocking and rolling. A few interesting studies recently came out about smoking.

Turns out that the first morning cigarette, the one that gets the day going, might be the one that is worst for you. A study at Penn State showed that smokers who had a cigarette within 30 minutes of waking up had a higher level of the nicotine metabolite cotinine (shown on right). The majority of inhaled nicotine is broken down by liver enzymes to cotinine, which serves as a marker of tobacco levels in the blood. Previous research has correlated gender, race and smoking intensity with cotinine levels. This study suggests that the metabolic state of your body might be an important variable in nicotine absorption. The authors admitted that the intensity of inhalation might be the key factor, it just may be that groggy people smoke harder. Either way, if you can't quit cold turkey at least drop that first smoke.

A second study, published in the Environmental Health Perspectives, found DNA from hundreds of bacteria in the content of four popular brand cigarettes. This is the first study to show that cigarettes are contaminated with bacterial human pathogens. Bacteria are everywhere, and further research is needed to explore the feasibility of infection from these organism, but still this is pretty gross.

A joke at every end:

A man walks in to see an eye doctor and says,
"Hey doc, I need some help with my eyes, I think they are getting worse."
The doctor nods his head and says "well ok, let's start with an eye exam. Can you see this sign?"
"What sign?" asks the man.
"The sign that is hanging on this wall," replies the doc.
"What wall?" asks the man.

The Art of Chemistry

To the science of chemistry
In the pursuit of truth
To the art of chemistry
For the welfare of man
To the teaching of youth
In a science
Ministrant of sciences

(quote from the Baker Hall, the home of chemistry, at Cornell University)

It is often difficult to write about science because it moves so fast. Often, a breakthrough one day will be overshadowed by a new story the next. This momentum is important and drives progress. I hope that this blog lets me calm my imagination and put in context some of the things that are in the science air.

Aspirin (pictured on the right) is a wonder drug. It stops headaches, improves outcomes from heart attacks and now can decrease the rate of colon cancer. In a story published last week, 500 people with Lynch syndrome were given aspirin and 500 more were not. Lynch syndrome predisposes one to colon cancer, and in the group taking aspirin the rates of colon cancer decreased.

Despite all the benefit, aspirin would not pass through the intensive drug approval process today. The effect of aspirin is achieved by inhibition of an enzyme called cyclooxygenase (COX) which itself leads to the synthesis of prostaglandins (PG). While inhibition of COX has many positive outcomes it also decreases a specific PG which is responsible for limiting the effect of hydrochloric acid in the stomach. This side effect leads to internal bleeding and would most likely cause a discontinuation of a clinical trial.

Hippocrates used bark from the willow tree as a pain reliever around 500 B.C. The active ingredient was salicylic acid (shown right). This compound was an even worse irritant to the stomach than aspirin. Felix Hoffman added an acetyl group to salicylic acid in 1897 and aspirin was born. We are lucky that a compound like this was discovered in tree bark and also that a scientist came along early enough to push through a drug that now is taken by over 100 million people.

A question lingers, though. Are there compounds currently that are failing safety profiles that could have, one day, the positive contribution of aspirin?

A joke at every end:
What animal do you not want to play cards with?
A cheetah.

Bacteria

I didn't even think of this one and I think about germs a lot. A research team in Colorado has shown that there are bacteria present on our shower heads that could negatively affect those with compromised immunities. This study examined 45 showers in hotels and random houses in various cities. Specifically, the researchers found 100 times more mycobacterium avium, a gram positive mycobacteria, shown on the right, in the water coming out of the shower head than in the water coming into it. Bacteria are classified based on a couple of characteristics, including their ability to absorb a stain called Crystal Violet. The majority of harmful bacteria can not retain this purple stain and are called gram negative. Those in good health should not worry about this germ filled study but those already sick should stick with metal shower heads, as they are less likely to breed bacteria than.

Now bacteria are not all bad. Professor van der Donk at the University of Illinois at Urbana-Champagne is using these tiny organisms to search for compounds that can kill other bacteria. This seems counter intuitive, why would bacteria make antibiotics? Indeed a gram positive bacteria, Lactococcus, is one of many bacteria that produce bacteriocins or toxins that inhibit the growth of similar bacteria. It seems it might help to be the only bully on the block. This is great for us because we can use these bacteria to identify new compounds that are medicinally relevant and most importantly have very creative structures. Nisin, shown on the right, is made by an enzyme in Lactococcus in two steps. While humans have been able to make Nisin in the lab in something like 70 steps. The neat thing about this molecule is that it has been used as an antibacterial in processed food for over 40 years. No resistance has been seen. This is amazing considering the amount of bacterial resistance that we are dealing with in the medical community. Currenlty, the researchers are exploring the relevant chemistry of this compound in order to understand how to make better antibiotics and also to perhaps harness some of these bacterias to make these antibiotics for us.

A joke at every end:

A man is pulled over for driving all over the road.
The cop, suspecting the driver of drinking, walks up to him and says "sir you are going to have to take a breathalyzer test."
"I can't do that," the man responds, "I have asthma and I might start coughing and die."
"Well we have an urine testing kit to measure alcohol level in the back," says the cop."So why don't you pee in a cup for me."
The man says, "I can't do that. I am a diabetic and if I pee I will lose too much sugar, faint, and die."
The cop says, "well then you are gonna have to go the station so we can draw some blood."
The man responds, "well I definitely can't do that. I am a hemophiliac and if I give blood I'll bleed everywhere and die."
"Fine" the cop says, "just get out of the car and walk in a straight line for me."
"I can't do that either," says the man.
"And why the hell not," asks the cop.
"Cause I am drunk," says the man.

Lab is a unicorn

Being a Teaching Assistant is exhilarating and terrifying at the same time. I led my first experimental organic lab this week. It went as well as a first of anything can go. At one point we had 15 steam baths going, none in the hood. My boss walked in and said "Yevgeniy, it's like a sauna in here!" Then he claimed I was putting the students on a steam diet. I am going to a wedding so maybe I was. Next time, we will use hot plates. I might have scared the students with an explosion story that happened when I was in college. A lab partner heated some ether on a hot plate. The ether boiled onto the hot plate, and we are lucky that no one got hurt.

The first lab's goal was to recrystallize benzoic acid (left) in order to separate it from salicylic acid (right). This is a nice starting lab as it reinforces a couple of important concepts and lets one use a lot of different equipment. In fact, the process of recrystallization is often utilized by the pharmaceutical industry to insure purity of their active pharmaceutical ingredient (the key to the pills in our medicine cabinet). The idea behind recrystallization is the following:
more molecules of a certain type (the one to the left or right) dissolve in a hot solvent then in a cold one. If you dissolve a contaminated mix of stuff in as little hot solvent as possible, when the solution is cooled (and the solvent can longer contain the same number of molecules as before) the least soluble compound will crystallize out of solution. If two compounds have very different solubilities this process makes sense.

What happens if two compounds have very similar solubilities? Turns out, if one of the compounds dominates the contaminated mix then when the saturated solution is cooled, the dominant compound will form pure crystals. In chemistry like tends to aggregate with like.

Benzoic acid was an excellent choice for the lab as it is a medically relevant compound, a treatment for various fungal skin diseases.

Did you know that DNA methylation causes DNA condensation and transcriptional silencing. Turns out that adding a carbon with three hydrogens to a base (usually cytosine - as shown on the right, note the extra CH3 group in the second cytosine - or guanisine) blocks RNA polymerase from making RNA. This kind of modification is responsible for the silencing of one out of two X chromosomes in female mammals and what makes calico cats so crazy (see for yourself). The hair pattern is a result of random x-inactivation - all because of a carbon and three hydrogen.

A joke at every end:

What do you get when you cross an insomniac, an agnostic, and a dyslexic?
Someone who lies awake all night long wondering if there really is a Dog.

Reinventing Drug Developement

One of the big challenges in front of the chemical community is to reinvent drug development as we know it. A really cool professor at the University of Michigan named Jason Jestwicki published a research paper in 2009 describing one such approach. His stated goal was to stop cytochrome p 450 from metabolizing an HIV protease inhibitor called amprenavir (right). GlaxoSmithKline, the company producing the drug, has dealt with the metabolism problem by distributing the medication in its prodrug form, fosamprenavir (left - note the addition of the phosphate group in the middle of molecule). The prodrug, digested in the body into the active ingredient, increases the absorption and distribution of amprenavir. Professor Jestwicki, instead of adjusting smaller functional groups, looked to nature as inspiration. Tacrolimus, or FK-506 (lower right), was discovered in soil fungus in 1984. FK-506 is a potent immuno suppresant but defies certain expected drug like properties that have been established over the years. For example, it is bigger and has more hydrogen bond donors and acceptors then the majority of FDA approved drugs. After some work, it was shown that FK-506 accumulates in whole blood by binding to a cellular receptor, FKBP. By hiding in the cellular part of whole blood, FK-506 avoids Cytochrome P450 all together. So Professor Jestwicki tethered the FKBP binding functional group to amprenavir (picture available through the pubmed link above) and created a drug that so far has had a half life of 50 hours in vivo as compared to 7-8 hours for fosamprenavir and 80 fold increase in activity.

The critical element to this study is the thought process behind it. Instead of manipulating well developed and understood chemistry that has historically improved bioavalibility, Jestwicki's group utilized a technique from a drug that seemingly has nothing to do with HIV treatment.

Looking over this novel strategy to fight disease I can't help but imagine a place far away where all diseases have their laboratories. A place where graduate students in diabetes and HIV work together to improve resistance to available medication. Where yearly conferences feature cancers and flu viruses on the same panel because they both have figured out a way to utilize genetic variation to survive. We have come to a point in time where we need to look beyond improving target based therapeutics for each particular disease. The method of success inherent to one therapeutic needs to be categorized and applied to as many diseases as possible. The Jestwicki lab identified one such opportunity by connecting HIV medication and an immuno suppressant. We need to have our pro-health graduate students studying cancers and flu talk together and share their methodology for that might be the key for better drug development.

A joke at every end:

A physicist, biologist, and chemist are sitting on the beach and watching the water.
All of a sudden the physicist can't take it anymore and yells "I have to go examine the sine and cosine curves in those waves!" He runs into the water and drowns.
Next the biologist jumps up and yells "I have to go examine the marine life in this ocean!" He runs into the water and drowns.
Finally, the chemists looks up and says "oh look physicists and biologists are water soluble."

Annals of Medicine: The Cost Conundrum: newyorker.com

Annals of Medicine: The Cost Conundrum: newyorker.com

Shared via AddThis

Atul Gawande, author of the very popular medical books Better and Complications, has just published an article in the New Yorker that explores the rising costs in US health care. Dr. Gawande suggests that the culture of a local medical community can cause a dramatic difference in the cost of care for each patient per year. This article stated some strong facts supporting an inverse relationship between the money spent per patient and the quality of care one receives. This idea makes sense when considering the risks associated with the medical procedures that cause higher costs.

It was surprising that Dr. Gawande's hosts in the various hospitals he visited were mostly unaware of the per patient expenditure of their hospital as compared to that of the national average. Why is Medicare and Medicaid, two government sponsored agencies, not monitoring this more closely?

The article emphasizes the role of the entrepreneurial spirit that is nurtured in some locations, such as McAllen, Texas and is discouraged in others, such as the Mayo Clinic, Minnesota. It seems that doctors should be salaried, so that in no way do their procedures correlate with total income.

Various clinics in the country show that there is a better model to guide doctors. The leaders need to focus the physicians in the community on patient well being and remove per procedure monetary return. However, this concept of care over finance should start in the formative years of a physicians life: Medical School. The application process for medical school is simply too expensive for a college student ($3000-$5000 per application cycle when considering AMCAS, secondary fees and school visits). Most medical students graduate with $200k in loans. Therefore, it is very difficult for professors to instill a disconnect between clinical care and monetary incentive when the student is burdened severely by their monetary obligations.

The government spends almost $400 billion on Medicare and $275 billion on Medicaid per year. There are about 130 accredited medical schools in the US with on average 140 students in each class (560 total at each school). It would cost the US (130 x 560 x 40,000) just under 3 billion dollars (assuming each school costs 40 thousand per year) to offer every accepted student a free medical school education. This is 0.3% of the cost of government provided health care. If the country wants to make a real investment to have cost conscious physicians in the 21st century, removing the monetary pressure from graduating students is an interesting place to start.

Separately, there are other issues that should be considered when discussing health care. Many private physicians outsource their billing services to private companies that have expertise in diagnostic and billing codes. These billing companies receive payment as a percentage of money received from the insurance companies. They, therefore, have an incentive to encourage billing for the highest possible amounts. Therefore, even a well meaning doctor looses some autonomy over costs when utilizing a service that is so focused on maximizing the profit per patient visit.

Health care dialogue is confusing and often convoluted with biased statistics. Insurance companies tend to be demonized as greedy corporations that often refuse to cover vital services to save costs whenever possible. Yet Dr. Gawande moves the dialogue towards the role physicians have in health care's rising costs. The hardest part for physicians, I think, is connecting the check received from Medicare or Blue Cross Blue Shield with the national economy.

The idea of creating an ethical clinical community is an excellent one. We should address the attitudes of practicing doctors, but maybe an investment in the consciousness of medical students would be the wisest change of all.

A joke at every end:

A guy walks into a doctors office with pain in his leg.
The doctor performs some tests and tells the man that he
has a fracture and will need a cast for three months.
The man freaks out and starts yelling,
"oh no this can't be, I want a second opinion!"
"Ok," says the doctor. "You're ugly too!"

Unexpected skaters and sharpies

Some interesting things come out when one looks closely. Recently the BBC world news podcast had a story about Fresno, California. The foreclosure rates in Fresno are extremely high. One of the overlooked side effects of the recession is the growth of unused pools in the nation's warmer cities. Stagnant water leads to a mosquito paradise which lead to scratching and can cause an increasing rate of west nile virus transmission. The causative virion, a strain in the Flaviridae family, relies on mosquitoes to be transported from birds to humans.

Punk rock skateboarders are providing a temporary solution. In fact, there is a growing movement of young boarders who are rolling around Fresno looking for For Sale signs. With an empty house, they break in, drain and clean the pool and skate until they get kicked out by police. While there is no question that these cats are trespassing, they might be doing all of us a favor by getting rid of all the stagnant water overlooked by a failing economy.

Health care reform is a polarizing issue that has an impact on all of us. President Obama's success as a leader will be intimately tied to the revitalization of affordable medical coverage. Medicare is implementing an electronic prescribing incentive program that provides a 2% refund on medicare billing for all physicians that have an accredited electronic prescribing system in place and in use for their medicare covered patients. The refund will turn into a penalty within two years in the hopes of increasing efficiency, decreasing prescription errors, and ultimately lowering costs for government funded coverage.

So wouldn't be nice if there was an easier way to save money? Proto, an excellent quarterly magazine published by the Massacusets General Hospital (sign up for free delivery), noted a study that questioned whether surgeons should be throwing out their sharpies. As per protocol, surgeons mark the site of the incision with a marker and then toss the markers to avoid contamination of one patient with the other's troublesome bacteria. A couple of doctors at the University of Alberta decided to look into this. Considering a sharpie uses alcohol based ink, the study showed that a quick alcohol swipe is all that is needed to disinfect this 2$ per writing tool. On a big scale, this can make a financial difference.

Can the knowledge that alcohol based ink is easier to disinfect be applied to other disciplines? Should we encourage skaters to drain our pools in exchange for a little noise and fun? Let's look around, maybe there are more unexpected opportunities.

A joke at every end:

A newly married man asks his wife, "Would you have married me if my father hadn't left me a fortune?"
"Honey," the woman replied sweetly, "I'd have married you no matter who left you a fortune."

artemisinin

Fig. 1, Artemisinin

This is a historical molecule. The first use of the tri-cyclic peroxy like (two oxygen atoms bonded to each other) structure was noted in 200 BC. Throughout the past 2000 years, Chinese herbalists used the plant from which this molecule derives, Artemisia Annua, for various maladies.

In the 1960s and 1970s the Chinese government established a program exploring the use of some 200 traditional herbs for the treatment of the growing threat of Malaria, a disease most commonly caused by an infection of a parasite called Plasmodium falciparum. Out of those trials, artemisinin was the only one that was turned into a drug.

Artemisinin has an unusual structure for a drug like compound. The double oxygen peroxy group is not very stable. Indeed, the poor bioavalability has to be offset through combination therapies. Derivatives such as artesunate (below, note the extra 4 carbon tail) have also been used as alternative, longer lasting treatments.

Fig. 2, Artesunate

As a side note, this 4 carbon tail is a functional motif found in some hdac inhibitors such as sodium phenylbutyrate and a recent breakthrough drug, vorinostat or SAHA. The side chain increases the hydrophybicity of the molecule and perhaps makes a better binding partner to cellular targets.

Fig. 3, Sodium Phenylbutyrate
Fig. 4, Vorinostat - note the form of the carbon chain

The mechanism of action for artemisinin is not clear, but it seems that the peroxide group is broken by free heme groups that are released by parasitic digestion of hemoglobin.

Recently, the HHV-6 Foundation, a not for profit organization exploring the role of the Human Herpes Virus 6 (HHV-6) in various diseases, has started funding a project to explore the use of artesunate for HHV-6 infection. It is very intriguing that a drug that has been used to disrupt a parasitic infection might also be effective against a viral infection.

There is much more to explore in a post about artemisinin. There are fears right now that monotherapy in third world countries, with artemisinin or its derivatives, is leading to resistance in Plasmodium falciparum. Separately, the synthesis of artemisinin is an important challenge as the extraction and growth of the plant source is impractical to treat the large number of people afflicted by malaria.

A joke at every end:

What do you call a sheep with no legs?
A cloud.

Small Molecules

Small molecules are everywhere. The chemistry community readily uses the term "small molecule" to describe a biologically active compound that is not a protein or a polymer. Chemists are now dedicating their careers to explore the process of using these little guys to solve important biological questions. The New York Academy of Science hosted a seminar recently titled "Accelerating Drug Development with Innovative Discovery Platforms." Representatives from the biotech industry and academia attended. They described innovative research and highlighted small molecule compounds that have been developed into drugs successfully.

The day was started by David J.Bearss, Ph.D. Vice President and Chief Scientist at SuperGen Inc. He suggested that the high cost of drug development in today's market (800 million – 1.2 billion per drug!) is creating a new mood of minimalism in the pharmaceutical community. The big drug companies are scaling back their research efforts and are relying more on smaller companies to develop drug candidates for clinical trials. To fill this niche, SuperGen has developed a new computer algorithm called CLIMB that identifies small molecules that should bind a specified molecular target.

The field of chemical biology has historically relied on high throughput screening to identify drug candidates. In essence, the chemists pours thousands and thousands of chemical molecules, found in a chemical library, over a protein of interest and visualizes the reaction between the compounds. In reality this is a very complex process that relies heavily on the type of chemical library available to the scientist. A good library is made up of small molecules that encompass many different types of chemistry modalities. Yet often times, the best libraries are difficult or too expensive to obtain. Once a type of chemical is established to have reactivity with the chosen target, that chemical type is optimized and similar or "like" compounds are tested for better binding of the selected protein or target. SuperGen Inc. hopes to predict which chemical type will be selected in the first round of screening based on structural data of the molecular target. Their computer program models successful compound interactions and assists the executive in making go/no go decisions regarding further funding of a drug candidate. Thus far, SuperGen Inc. has successfully predicted a PIM kinase inhibitor that causes tumor regression in acute myologenous leukemia (AML) xenograft models (a xenograft model: human tumor tissue or cells are transplanted into mice or rats followed by tumor treatment regimens).

SuperGen's CLIMB technology aims to improve the accepted dogma in small molecule drug development by making the process more efficient. The second speaker, Randal Peterson, Ph.D., assistant professor of medicine at Harvard Medical School, decided to change the process altogether (Fig. 1 below). Dr. Peterson's group injects small molecules into Zebrafish and looks for phenotypes of interest and only then identifies the molecular target involved. Zebrafish are an ideal model organism because they allow for efficient whole organism screening. They are small enough to fit into wells and are conducive to systematic drug treatment. One example of this new process involved Bone Morphogenetic Proteins (BMPs), which have been shown to be implicated in carcinoma and anemia of chronic diseases. BMP's are also involved in various developmental processes in vertebrates. In Zebrafish, BMP are integral to the proper formation of the dorsoventral axis. Genetic studies have shown that antagonism of BMP causes ventralization, increased ventral development at the expense of dorsal structures and inhibition of BMP dorsalizes the Zebrafish organism. Therefore, Dr. Peterson's lab looked for small molecules that dorsalize zebrafish and identified a compound called dorsomorphin (Image 1 below). The compound is now being optimized for further study.

Standard Process for Chemical Screen:

Target --> Modifier (small molecule) -->Phenotype

Process Used by Dr. Peterson:

Phenotype --> Modifier (small molecule) --> Target

Image 1: dorsomorphin

The day finished up with a panel discussion and questions from the audience. The moderator asked the first question: "Is there a clinical trial bottle neck?" The seminar explored all the effort and time spent developing drug candidates in a more efficient and successful manner. The community is now revolutionizing the process of drug development. The goal is to cure disease and treat patients. If these compounds cannot be properly tested through phase III clinical trials, the whole process of drug development becomes moot. The speakers addressed this issue but focused on drug development and the need to have compounds fail earlier in the pipeline. If the drug development process is improved more successful candidates will be tested and hopefully clinical trials will be improved. Everyone agreed, however, that clinical trials are already limited in scope and could someday be the bottleneck of drug development.

Something relevant: An article came out this week in the New York Times discussing the outsourcing of clinical trials.

Something interesting: Pentacosane, a linear small molecule made up of a strand of 25 carbons held together by single covalent bonds, is released by female ants when they are fertile. It was recently shown by a group at Arizona State University that if a queen ant is present, any ants releasing this compound are ostracized and physicaly intimidated by the other worker ants. If there is no monarch, the fertile ladies are left alone.

Something crazy: The American Museum of Natural History in New York is now awarding PhDs in comparative biology!

A joke at every end:

How many graduate students does it take to screw in a light bulb?
Only one, but it may take up to five years for him to get it done.

A week in baseball history

This was a big week for our United States. Children all across the country watched the first black president sworn in to the highest office in the land. Whatever happens, that one moment has already changed everything.

Yesterday, the Yankees baseball team moved offices from one Stadium to another. The stadiums are across the street from each other.

Last week I took a trip down to Shea stadium, the stomping ground for The New York Mets. Shea stadium is being torn down brick by brick in the coming months so that the Mets, like the Yankees, can move into a brand new, state of the art baseball park. If you are interested, this is a nice summary of Shea's great history.

I love Shea stadium. I have been a mets fan since 1993. The day camp I went to took us to a Mets game, where they became, for me, the most lovable losers. That first day, the Mets lost to the expansion Florida Marlins. I started rooting for John Franco's painfully hanging change up, Butch Huskey's slow hussle, and Todd Hundley's big swings. The Mets did sign guys with amazing names, Butch Huskey might be the best sports name period. Rey Ordonez might have been the worst hitting, best fielding short stop you have ever seen. So of course he found a home on the Mets. If Yankee stadium is the house that Ruth built, Shea stadium is the house to which Mike Piazza added an addition. Mike was the first big signing that actually panned out. In 2000, Mike hit a three run home run against the Braves that made Shea stadium shake something special. He was the first player in Baseball to bring some sense of happiness to the country, hitting the game winning home run in the first game after 9/11.

I will always love Shea stadium for its hot dogs, color seats, the huge neon men on the side of the circular stadium. The semi circular nature of the stadium allowed cars driving by on the neighboring roads to catch a glimpse of the game. Shea fit.

The new stadium is called Citi Field. Named in honor of a private bank. The name is a clever one as it integrates itself with the greatest city, as if it was New York Citi and not New York City. The catchy nature of this name troubles me most. Especially in our troubling economic times, it seems odd that we have a local stadium attached to a failing and corrupt economic community.

I am sure I will go to games at Citi Field and love the Mets again. But Shea stadium will always be home for me and I am going to miss it.

Shea and Citi

Citi Field

Shea in its final days

Our Beloved Shea

A joke at every end:

A man walks into a bar and orders 12 shots of vodka.
The bartender pours them all and places the drinks on the bar.
The man starts taking the shot one after the other. Two, Four, Six, Eight shots.
The bartender finally says, "hey buddy, slow down. Why are you drinking so fast?"
The man gets quiet and slowly says "you would too if you had what I have."
The bartender becomes very serious and asks solemnly, "what do you have?"
The man responds, "Seventy five cents!"

Links

Lets call this a link Thursday

http://www.nytimes-se.com/ [The future (crossing fingers)]

http://nymag.com/daily/intel/2008/11/fake_new_york_times_has_a_conn.html [How cool]

http://www.nytimes.com/2008/11/14/health/14hiv.html?_r=1&hp&oref=slogin
[Cure for AIDS, groundbreaking work showing that a stem cell transplant with blood that lacks a co-receptor for HIV, specifically CCR5, can provide immunity to already diseased patients. This is, however, a very risky procedure and too expensive and difficult for most people with HIV. Still pretty incredible]

http://pubs.acs.org/cen/news/86/i45/8645notw1.html[The scientific world has been waiting for Obama]

http://www.vimeo.com/993998 [Pretty neat]

A joke at every end:

Why did the chicken NOT cross the road?
Because it was chicken.

Flu and Google sitting in a tree

Well this is pretty neat: New York Times has noted that Google is getting in on flu tracking. http://www.google.org/flutrends represents Google's non profit side. The company will use key words, relating to flu like symptoms, typed online to track regional outbreaks of influenza.

The flu is caused by a genera of the RNA virus family Orthomyxoviridae. This virus genome is composed of a single negative sense RNA strand, broken into many segments (8). The strains differ every year based on the glycoproteins found in the virus's envelope (or outer cell structure). These glycoproteins allow the viral cell to bind to a human cell (hemagglutinin) and release of the viral cell from the host cell (neuraminidase). A mutation in either one of these "peplomers" creates a new strand of virus.

Ultimately, it is very important to track the influenza virus to implement appropriate vaccine measures and also to identify the most prevalent strand in the years flu outbreak. One of the biggest difficulties in vaccination is that three strains of virus have to be selected 6 months prior to flu season. While Google has validated their keyword based tracking system with the tracking system currently used by the CDC, there is still much more work to do to be able to predict not only where but which strain of the flu is coming for us.

A joke at every end:

A famous champion is in bed with flu. A doctor visits him.

“You’ve got a high fever, my friend,” says the doctor.

“How high?” – asks the champion.

“39.5˚C,” the doctor nods.

“Yeah? And what is the world record?”

Noted

Heparin seized from Cincinnati-based Celsus Laboratories Inc. The WSJ reports that the FDA, after issuing two recommendations for recall, seized two lots of Heparin worth $112,000. While an impressive move, it is quiet alarming that the first letter was sent to Celsus in April.

"The FDA said companies who may have purchased heparin from Celsus should contact the company to determine whether the heparin they purchased was from the seized lots." When it comes to very expensive medication, it seems that these companies might not chose to contact the FDA.

A hospital in Detroit is using the automobile industry to improve efficiency. The Detroit News reports that "lean production" is being applied to the medical system. The Detroit Medical Center, for example, hired automotive consultants to review the patient's trip through the medical system to identify inefficiencies. This has helped save the hospital hundreds of thousands of dollars. Other hospitals, using a similar model of critique, has shortened the average ER wait to under 30 minutes.

A joke at every end:

Little Nancy was in the garden filling in a hole when her neighbor peered over the fence. Interested in what the little girl was up to, he politely asked, "What are you up to there, Nancy?"

"My goldfish died," replied Nancy tearfully, without looking up, "and I've just buried him."

The neighbor was concerned, "That's an awfully big hole for a goldfish, isn't it?"

Nancy patted down the last heap of earth and then replied, "That's because he's inside your stupid cat."

Obama

http://news.bbc.co.uk/2/hi/americas/us_elections_2008/7710079.stm

Heparin II

Previously, I had written about contamination that occurred in a batch of Heparin and caused the death of a number of patients undergoing dialysis. Free Yevgeniy: Heparin To review, Heparin is a natural anticoagulant found in the intestine (lumen) of pigs. Heparin is a variably-sulfated proteoglycan that consists of repeating disaccharide units (pictured to the right). The compound inhibits binding to the clotting factor ATIII and stops the blood clotting process.

Last year there were pediatric deaths that created a commotion in the community and led to the FDA issuing an investigation. One of the academic specialists on Heparin, called to assist in to identify the contaminant, was professor Robert J. Linhardt, at Rensselaer Polytechnic University.

Dr. Linhardt, working with a larger group, helped isolate the contaminant as persulfonated chondroitin, a compound that mimics heparin activity in vitro but causes extreme damage, even death, in vivo.

Heparin is used in dialysis and for invasive hospital tools. Therefore a contaminant was a disaster for the health care community

Dr. Linhardt discussed the need for laboratory made Heparin so that we could better monitor the drug making process and avoid Heparin shortages.

Interesting points made during the talk:

• Pigs in china made four doses of Heparin vs. one dose in America. Turned out Chinese farms are dirtier and cause an increase in mast cell Heparin production as Heparin levels are elevated during a parasitic response
• Heparin was first used in 1926 (prior to FDA existence) and as a compound can not be patented
• While the current process for Heparin production is gruesome (filthy slaughterhouses --> large unregulated factories --> US markets), the contaminant was purposely added to the mix sometime during the process. This is important as the FDA can not allow any inserted contaminant to be present (non process derived), therefore purification is not an option
  
• France continued to use contaminated Heparin, since the alternative was to stop dialysis

Dr. Linhardt, and others, are now involved in commercializing an enzymatic process for Heparin synthesis. The main goal is not to reduce the cost of Heparin, but to create a viable option for the world market that could be better regulated to avoid future shortages.

This meeting was targeted to chemists and business people. Yet, it is an essential concept for all medical doctors to understand. It seems amazing that doctors have so much faith in the prescription pad to provide the right drug. Often generics are recommended because similar efficacy has been shown in trials and cost is decreased. Is quality lost? Cheap sneakers are often of poorer quality then more expensive ones. As a society, we expect our medication to be treated with higher regard then sneakers. However, the FDA is underfunded. Less then 10% of imported drugs are checked when shipments arrive. Until this Heparin crisis occurred, there were no full time FDA officials in China reviewing the manufacturing process. Can physicians rely on the drug market to provide what is prescribed? This continues to be a pivotal issue.

A joke at every end:

Why is Cinderella bad at baseball?
She runs away from the ball and has a pumpkin for a coach.

Who you calling Fat

This week it seems that fat has taken NY by storm.

The May 6th Edition of the Science NY Times had an assortment of fascinating articles that related to fat in some way.

1. Study Finds That Fat Cells Die and Are Replaced
2. Evidence a High-Fat Diet Works to Treat Epilepsy
3. Its Poor Reputation Aside, Our Fat Is Doing Us a Favor (older - Aug 7, 2007)
4. Redefining Disease, Genes and All (separate topic - somewhat related)
   

1. It was previously thought that fat cells developed until puberty, at which point the sex hormones (estrogen) helped direct where in the body the fat deposits went. After puberty, aside from changes due to extreme circumstance (like liposuction), the number of fat cells remained the same. The cells got bigger or smaller as you gained or lost weight. It was even shown that after liposuction, your body somehow regenerated the same # of fat cells as prior to surgery (these new cells were super skinny).

New research is showing that 10% of your fat cells die and are replaced every year. Oddly enough, nuclear bomb testing helped move this stuff forward. The radioactivity released by above ground bombs created a spike in Carbon 14 isotopes in the atmosphere. C14 has 8 protons and 6 electrons (2 more than usual). The natural abundance of C14 in the atmosphere is one in a trillion, therefore, spikes in the atmosphere made an imprint in all things created at that time. The half life of C14 is 5700 years (long enough to not make a difference).

This principal was applied to the whole body, and showed that certain fat cells were very young.

2. A high fat diet showed itself effective in a randomized trial to decrease epilepsy seizures in children. This diet has been evaluated for a long time now. 38 % of kids had 50 % less seizures as compared to only 6% of kids in the control group. On a personal note, my professor and I researched the effects of a high ketone diet on seizure patterns in Mongolian Gerbils.

Ketosis is the state of metabolism when the liver uses fats (instead of glucose) for energy and converts fat into fatty bodies and ketones. Fatty tissue becomes an important source of energy and diet has to maximize fatty intake to maintain ketosis.

To review our basics, a fatty acid is a carbon chain (with double/triple bonds - unsaturated, no double/triple bonds - saturated). Fat tissue tends to be composed of three fatty acids bonded to a carbon backbone. Adipose cells store a lot of fat.

3. This article discusses the important benefits of our fat cells. They protect our organs (visceral fat), provide the bulk under the skin (subcutaneous), store an important energy source, and are critical to supplement disruptions in diet. In addition, these fat cells release different hormones. Too much fat causes a release of inflammatory hormones to decrease obesity, they also release leptin (a compound involved in reproduction). Clearly fat is no joke (line might be stolen from NY Times).

4. Everything is interconnected. Everything. Obesity, Epilepsy, Bipolar disorder, Chronic Fatigue Syndrome. Our gene make up is so complex that undoubtedly relationships can be found and made in disease never before associated by their outward symptoms.

Muscular Distrophy and Heart Attacks share a gene in common. Two genes connect diabetes and prostate cancer.

Nosology - the field of disease classification - is about to get its head knocked. For example, Jonathan Kerr and company [J Infect Dis. 2008 Apr 15;197(8):1171-1184] have published a study of a genomic signature of 55 patients with Chronic Fatigue Syndrome. 88 genes are up regulated. 6 of them have previously been targeted by drugs.

Looking at everything floods the blackboard with an assortment of random thoughts. Once a pattern can be elucidated, though, the most powerful answers can be found.

Ideas:

• Studies show that African Americans and Caucasian populations lose different types of adipose tissue during diet and tend to have different adipose tissue for the same body mass index . These two groups also have different insulin patterns and different diabetic profiles. Fat cells are created every year - can we direct them to different locations? Will they excrete different hormones more conductive to a proper glucose response? What effect will a high fat diet (ketosis) have on the diabetic population (I have a feeling it will be different for African American and Caucasian communities).
  
• Personal story, patient with Chronic Fatigue just started a south beach diet (avoid bad fats and sugars), feels great. How does all this fit in? Separately, if Chronic Fatigue Syndrome is characterized by some inflammation, might fat cells be involved?
  

I need a blackboard and more fat.

A joke at every end:

What do you call a fish with no eyes?
Fsh!

- better said then read [no i(s)]

Methotrexate - some thoughts

Today I wanted to write about a specific. It hasn't been in the news recently but caught my interest because it did something unexpected.

Methotrexate (shown at left) is a very interesting compound. Its history began with FDA approval in 1953 for oncology use.

It gets the job done by inhibiting folic acid breakdown.

Folic Acid or Folate is water soluble vitamin B9 (pictured right). [Note the similar structural elements of methotrexate and Folic Acid] Folic Acid is broken down to form tetrahydrofolate, a metabolite necessary for DNA synthesis, by the enzyme dihydrofolate reductase. Due to their similar structure, methotrexate can bind dihydrofolate reductase, block folic acid breakdown, and slow DNA synthesis. This is preferentially damaging cancer and immune system cells as they grow particularly fast and rely on DNA synthesis for their growth.

Methotrexate therefore has been used for chemotherapy (high dose) and as a treatment for inflammation associated with the autoimmune response (low dose).

A patient mentioned that Methotrexate relieved her symptoms of Fibromyalgia (a disease defined by chronic pain, abnormal pain processing, fatigue, brain fog, etc...). Why did this happen?

The etiology of fibromyalgia is still unknown. However, methotrexate has been used for a similar disease. Behçet's syndrome is characterized by generalized inflammation that causes ulcers, arthritus, and cardiac problems to a name some symptomes. Behçet's syndrome, like Fibromyalgia, is not well understood. The two diseases have overlapping symptoms of pain, fatigue and cognitive difficulties.

Something still doesn't add up. Methotrexate decreases inflammation and relieves symptoms associated with Behçet's syndrome and yet also pain associated with Fibromyalgia?.

Pain is caused by the activation of a nociceptor (pain receptor) by a mechanical or chemical stimuli. The message is passed by the nervous system through the spinal cord to the brain which responds by understanding the impulse as pain. Inflammation, among a variety of things, is known to cause the release of algesic substances which activate the nociceptors. The pictures comes full circle.

The overlap is there. A compound used for anti inflammatory disease helps with pain in disease states that are associated with inflammation. The difficulty is of course to really know whats happening. The woman who mentioned pain improvement was taking the methotrexate for retinal inflammation and happened to have fibromyalgia.

How do we make this connection faster? Is it smart to push for a clinical trial for methotrexate as a pain treatment when resources in the Fibromyalgia community are limited? Yet, it is these random observations that seem important. I guess thats why these are just some thoughts.

A joke at every end:

A blind man walks into a pharmacy with his guide dog.
He lifts his dog and starts spinning the dog by its leash.
A store employee runs up to the man and asks "hey, what are you doing?"
The blind man replies "just looking around."

Memory and Anesthesia

Proc Natl Acad Sci U S A. 2008 February 5; 105(5): 1722–1727.

Sevoflurane (shown to the right) is used in the induction or maintenance of general anesthesia. It boils at 58 degrees Celsius and is administered through an anesthetic vaporizer with a mixture of nitrous oxide and oxygen. The mechanism of action for sevoflurane is yet unknown. It is one molecule in a class of fluorinated methyl ethyl ethers and fluorinated methyl isopropyl ethers that are currently being used for anesthesia. These anesthesia compounds must have at max 4 carbons as their volatility (decreased with increased molecular weight) is necessary for action (Anesthesiology. 2008 Mar;108(3):531-3.) Interestingly, soda lime is used in anesthesiology to absorb exhaled carbon dioxide (reaction shown below) and the anesthetic agents need to be monitored for side reactions with soda lime.

1. CO2 + H2O --> H2CO3
2. H2CO3 + 2 NaOH (or KOH) --> Na2CO3 (or K2CO3) + 2 H2O + Energy
3. Na2CO3 (or K2CO3) + Ca(OH)2 --> CaCO3 + 2 NaOH (or KOH) (source)

Here are the components of soda lime: H2O (water), Ca(OH)2 (third reaction), NaOH (second reaciton- recycled in reaction), KOH (second reaction - recycle). Wet soda lime must be used - to force reaction 2. Otherwise Sevoflurane reacts with dry soda lime to form CF2=C(CF3)OCH2F. It seems this occurs through an elimination reaction with the hydrogen from the carbon neighbored by oxygen and the two fluorinated carbons. A fluorine is a good leaving group and what could abstract this hydrogen? Not H2O, Ca(OH)2 probably could and would form water. Perhaps, extra water would limit this side reaction (equilibrium). Well this is a side track.

I wanted to talk about memory, which is thought to be made through a neurobiological mechanism involving the amygdala. What was really cool about the study mentioned above is that they used no more than 0.25% sevoflurane doses in the study. To make this story short, subjects remembered less traumatic images with this low dose of anesthesia as compared to placebo. The article shows that the anesthesia lowered the metabolic rate of the thalamus (not amygdala) but the suppression was in areas of the brain that "interact with the amygdala and are known to play a role in mediating arousal and controlling the level of consciousness during anesthesia."

Furthermore, two doses 0.2% and 0.25% decreased memory of emotional slides while the o.10% enhanced this recollection. Further work is definitely going to be done to figure out whats going on. This has been mentioned as having the potential to relieve post traumatic stress disorder by breaking the connection of a certain image or thought with the amygdala. There is definitely more work to be done as the implications are very exciting!

A joke at every end:

A panda walks into a bar and orders spaghetti.
After the panda finishes he takes out a bow and arrow and shoots the bartender in the heart.
Next night, the panda walks into the same bar and orders lobster.
After the panda finishes he takes out a gun and pops the new bartender.
The next night, the panda walks in and orders pork chops.
The new bartender says "woh, I am not gonna serve you, you've injured the two previous bartenders, what's your problem panda."
"But I am a panda" says the panda.
"Hey, since when do pandas cause so much trouble! No panda I know" replies the bartender.
"Oh yea, look it up," says the panda "in that dictionary behind you"
The bartender pulls down the dictionary, opens to Panda and reads aloud.
"Panda: eats shoots and leaves."