May 31, 2010
Lots of discussion about resistance lately. Not sure whether the following will help or further confuse the issue, but anyway...
To understand resistance mutations you have to dig out a bit of dusty high school biology. Genetic information (think blueprints) is encoded in DNA/RNA, long molecules made up of 4 types of building blocks (the bases, G,A,T,C). To make life happen something needs to read those blueprints and make machines that will actually get something done (digest lunch, take in some oxygen, sex!). An amazing ancient bit of machinery called the ribosome has been doing that since the days of the primordial ooze in all living cells in essentially the same way. A ribosome reads blueprints and cranks out proteins, molecular machines which are also long chains but made out of 20 types of building blocks (the amino acids alanine. valine, threonine, etc.). Once made, proteins float around in a cell, bumping into other molecules and doing what they know how to do - that's life.
OK enough theory, enter an evil HCV virion from stage right. It only has one goal - make more virus. To do this it enters a cell, unwraps its protective shell, and lets its 9600-long RNA molecule float around the infected cell where it soon runs into a ribosome. The ribosome doesn't know an HCV RNA from a human RNA, reads the blueprint, makes the corresponding machine and calls out 'next'. The resulting viral machine is actually half a dozen machines all stuck together. So before the virus can get anything else done it has to separate these pieces, sort of like unpacking a crate. To do this it relies on 'proteases' proteins that cut up other proteins, starting with some human ones, already floating in the cell, and, after the unpacking has started, using a specialized cutting tool of its own to finish the job. The protein it uses to finish the unpacking/cutting is called NS3A - the HCV protease.
Now enter telaprevir/boceprevir from stage left (accompanied by a greek chorus of eager investors chanting 'inhibit the protease, inhibit the protease'). Unlike the long DNA/RNA or protein chains, these are small molecules - but with a very specific shape. They were carefully designed so that if, as they are floating about in the cell, they bump into an NS3A molecule, they will stick to a specific part of the viral protein. Sure enough, the part they stick to is the very part of the molecule essential to get its job done - think monkey wrench in the transmission. If the protease can't finish its unpacking job the rest of the viral machinery stays in the crate and the viral life cycle (making copies of the viral RNA and of the protective wrapper proteins, assembling the parts to make up fresh new virions and shipping them out of the infected cell) all comes to a screeching halt.
But... the evil virus is wily. It has discovered that a good way to survive is to try lots of different approaches - a variation on the theme of try and try again. So the 9600 bases in the HCV genome are not exactly the same in every virion, and as a result the NS3A proteases are not all the same either. For example, let's look at the A156T virions. These are virions whose RNA is such that their NS3A protein has the amino acid threonine (T) at position 156 instead of the alanine that most healthy virus carry at that spot. Up to now this has been a problem for the poor A156T virions and their descendants. The NS3A protein they produce is not as effective as that of healthy (wild type) virus, and consequently there's a lot fewer of them. The A156T tribe may be less fit, but their 15 minutes of fame has arrived and they are now taking to the spotlight with a vengeance. In cells with boce or tela floating around, A156T virus can still reproduce - but no wild-type HCV virus can. Did tela or boce cause the mutation? - no it was there all along but the drugs screened out everything else so the A156T (or similar mutations) are the only ones left standing.
At this point it may help to look at the image posted in my photographs list. The telaprevir molecule is shown in magenta. It's bound to the viral NS3A protease most of which is shown in gray in a summary shorthand ( with loops, arrows and helices) used to represent protein structure. The parts of NS3A where mutation can interfere with tela/boce are in color (green, yellow, pink, etc.) Note that it's easy to see why position 156 is so crucial - it's right at the core of where tela sticks to the protease - make a change there and tela would just float off instead of binding. In fact the A156T mutation is one of the strongest in disabling tela effectiveness.
Questions for homework : what killed off the A156T virus in Jack who SVR'ed ? (hint think soc) What happened to the mix of A156T and wild-type virus in Jill who relapsed ? (hint remember A156T's fitness problem)