Protease resistance explained

[Mr Liver]

This is a very informative paper on protease and to a lesser degree, polymersae inhibitors. It covers the issue of cross-resistance between boceprivir and telaprivir,along with all other protease inhibitiors. The paper contains svr rates using various regimens taken from several trials. In spite of being a medical paper, it turned out to be a fairly easy read which offered clear explanations. - ML

http://www.springerlink.com/content/e665j00852110q19/fulltext.pdf

[RobertBeWell]

Excellent!

It seems the site now lets me get to the paper for free. I'm not really sure what happened, but for the last two days, when I would try that link, I would get a login screen, and a blurb that said "This article is available to download for $34.00".

Today, however, I tried it from another computer, and it brought it right up. I must have been doing something wrong. Thanks for the links though, I'm adding them to my ever growing HepC favorites folder.

Can't wait till the day I can delete it.

Robert

[willing]

if you can't find a free copy of that paper, here's another, free-access one,
covering the same ground:

"Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naïve patients."
http://www.ncbi.nlm.nih.gov/pubmed/19026009

Checking  the pubmed related citations section should turn up lots of others; this issue has been covered extensively over the past couple of years.

From a patient perspective,  what's missing is a commercially available way to (a) test for presence/frequency of resistant mutations prior to committing to  a given PI (b) monitoring decline of unfit but resistant mutations after a failed PI tx. I believe (a) is available and used in HIV tx planning.

[RobertBeWell]

Apparently, this site wants $34.00 to read this article now. Anyone have a copy they saved when this thread was current?

[mikesimon]

Thanks.
Mike

[Willy50]

Mike, I was joking about not knowing where that leaves us.  I have always argued against alcohol use, even moderate drinking.  I confess though that I'm not so dogmatic about it so as to prohibit a toast at a wedding or funeral if one's histology supports it.  I'm still a little bewildered; I would have thought that more quasi-species = greater viability and resistance to the immune system or TX.

Provide a link?  
Sure, at the risk of going slightly off topic.
Great paper by Schiff

http://pubs.niaaa.nih.gov/publications/arh27-3/232-239.htm
(This appears about half way down the page;)

"Mutations of the HCV virus (forming what are known as quasi–species). Alcoholics infected with HCV show greater quasi–species complexity than do nonalcoholics with HCV infection. In alcoholic HCV patients, such increased viral complexity might make it difficult for the immune system to control the mutated viruses, leading to progressive injury (Takahashi et al. 2001).
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Willy

[mikesimon]

Could you provide a citation to the article regarding alcohol and quasi-species.
I do not recall seeing it.
Mike

[Willy50]

I also thought the same.  In a older alcohol thread I found an article which said that the use of alcohol created more quasi-species of HCV.  My argument was that this was not a good thing, even if one could not prove damage from a few drinks, promoting the growth of more quasi-species surely would be a bad thing.

I'm not sure where that leaves us now.  ; )

Willy

[mikesimon]

At first glance I also thought it was counter-intuitive. But, after  reading the article and thinking about it, the conclusion seems logical, give the fact that there are always going to be quasi-species in response to treatment.
How this information might increase treatment efficacy eludes me.
Mike

[Mr Liver]

Hey Mike,
This is just as good as any place for your post. I have read this study and a few others with basically the same findings. At first glance it can appear counter-intuitive that those patients with an HCV virus that has the most QS diversity would have the higher EVR rates than for those who show less heterogeneity in QS population. It's logical to think that the HCV virus that produces the most mutants (decoys) would have the most success against our immune defenses. But, as the study you posted and others, this is surprisingly not the case. Here is a great study out of those that have had similar results that offers some explanation for these findings. An excerpt:

"We previously found that HCV sequences from patients who responded well to pegylated IFN-α and ribavirin were more variable than were poor responders in genes implicated in counteracting the type 1 IFN response (17). We interpreted this to mean that viral isolates with a relatively tight genetic distribution around an optimum sequence were more able to withstand the pressures induced by therapy, and those that were more distant from this optimum were less able to survive, presumably as a result of the presence of multiple variations that each reduced the overall efficacy of the viral proteins. Here, we found that genome-wide networks of covarying amino acids existed, that the connections within the networks (connectivity) were different in the responders and nonresponders, and that the nonresponder networks had many more hydrophobic amino acid pairs than did the responder networks. "

http://www.jci.org/articles/view/37085#B19

Great topic. Thanks for the post. - ML

[mikesimon]

It's not exactly on topic but this is the only place I could think of to put it.

High diversity of hepatitis C viral quasispecies is associated with early virological response in patients undergoing antiviral therapy.

Fan X, Mao Q, Zhou D, Lu Y, Xing J, Xu Y, Ray SC, Di Bisceglie AM.

Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Louis University School of Medicine, St. Louis, MO.

Differential response patterns to optimal antiviral therapy, peginterferon alpha plus ribavirin, are well documented in patients with chronic hepatitis C virus (HCV) infection. Among many factors that may affect therapeutic efficiency, HCV quasispecies (QS) characteristics have been a major focus of previous studies, yielding conflicting results. To obtain a comprehensive understanding of the role of HCV QS in antiviral therapy, we performed the largest-ever HCV QS analysis in 153 patients infected with HCV genotype 1 strains. A total of 4,314 viral clones spanning hypervarible region 1 were produced from these patients during the first 12 weeks of therapy, followed by detailed genetic analyses. Our data show an exponential distribution pattern of intrapatient QS diversity in this study population in which most patients (63%) had small QS diversity with genetic distance (d) less than 0.2. The group of patients with genetic distance located in the decay region (d>0.53) had a significantly higher early virologic response (EVR) rate (89.5%), which contributed substantially to the overall association between EVR and increased baseline QS diversity. In addition, EVR was linked to a clustered evolutionary pattern in terms of QS dynamic changes. Conclusion: EVR is associated with elevated HCV QS diversity and complexity, especially in patients with significantly higher HCV genetic heterogeneity.(HEPATOLOGY 2009;50:1765-1772.).

PMID: 19937690 [PubMed - in process]

http://www.ncbi.nlm.nih.gov/pubmed/19937690?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=1

[Mr Liver]

While total eradication of the virus without using the current SOC may not be possible yet I share your excitement that one day it will be a reality. My doc told me a few years back that he expects research to show that IFN will be able to be reduced by as much as half in some patients when used with protease inhibitors and do so without compromising their SVR rates. Of course, like everyone else's, he is world famous. haha

One exciting aspect of the current research is the ability to determine SVR rates not as a group as its done now, but for each and every individual based on their own unique HCV resistance profile This will eventually lead to the ability to a) spare someone the rigors of tx if failure is certain, and b) develop drugs that will work in concert or alone to target the exact areas of resistance.

It is a well written paper (concisely referenced, succinct, etc) . You described some of the highlights of the paper very well . Much of the specualtive reasoning a good paper can create will often lead to interesting "what if" scenarios that can certainly be thought-provoking. Thanks for your reply, Trish.  -  ML

[Trish77]

Mr. Liver...thank you for posting this article.  It contains SO MUCH valuable information.  It took me awhile to respond as, when I started to read it, there was so much valuable information that I needed time to digest it properly.  I ended up printing it out and reading it slowly and carefully with a highlighter so that I could mark the parts that were especially significant for future reference. I know I will refer to this one ongoing.
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Newleaf:   "My take on the article is that Teleprevir and Boceprevir and the other current PI's attack the same protease (NS3/4A) necessary for viral replication and if patient does not respond to teleprevir or boceprevir, the other will be no more effective, since they are both causing mutations of the virus in the same location on the virus.  Peg and riba are still absolutely necessary and neither therapy is successful without them because the peg/riba can still knock out the protease-resistant variants that arise.  There is another PI, ITMN-191, that attacks the same protease (NS3/4A), but causes a mutation in a different place than those seen with teleprevir and boceprevir.  That will be the one to watch for those who were unable to succeed with teleprevir or boceprevir.  "

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I was encouraged by the mention that ITMN-191 only shares one resistance overlap with Telaprevir and Boceprevir, while Telaprevir and Boceprevir share similar resistance mutation positions.  This finding is significant and noteworthy to me as those who have not responded to Telaprevir OR Boceprevir who have previously thought that they may do better with either/or may in fact be better off to wait on the development of ITMN-191 as a more effective PI for their particular pathology:

"ITMN-191 is another inhibitor of the NS3/4A protease with potent antiviral activity in vitro [22]. A single mutation associated with resistance to ITMN-191 was found
in the replicon system (Table 1). Results from the phase 1b study in patients with chronic hepatitis C are not yet available [23]. A single mutation associated with resistance has been reported at position 168 in the replicon system. A resistance mutation at this position has not been found during treatment with telaprevir and boceprevir. Therefore, ITMN-191 has the potential to be effective against HCV
variants resistant to telaprevir and boceprevir. However, this hypothesis needs further evaluation in clinical trials."

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ML:  "Perhaps two different PI's could run concurrently or even consecutively with SOC. "

What I found bloody exciting were the results from a combination of protease inhibitor and polymerase inhibitor - and that it seems to indicate that SOC may not be required and that we might be able to get rid of that nasty Interferon eventually:

"Protease inhibitors, nucleoside analogue polymerase inhibitors, and nonnucleoside polymerase have NONOVERLAPPING (emphasis is mine) resistance profiles and therefore should be promising combinations for treatment of patients with chronic hepatitis C."

"The double combination of the nonnucleoside analogue polymerase inhibitor A-782759 with the protease inhibitor ciluprevir was investigated in vitro [25]. Treatment
of replicon cells for about 16 days resulted in HCV RNA declines of 5.1 log10 IU/mL with A-782759 and 3.9 log10 IU/mL with ciluprevir, but undetectable levels were not
achieved with either compound.

>>>>>>>"The combination of the two resulted in a stronger decline of HCV RNA (> 7 log10)to undetectable replicon RNA after 16 days of treatment.The study indicates that double combination therapy using a polymerase inhibitor with a protease inhibitor reduces the likelihood of developing resistance and maybe a promising combination therapy in vivo."  <<<<<<<<  (Again, emphasis is mine.)"

This combination of both of them resulted in UND after 16 days of treatment.  This is with no INF and no ribavirin.  I find that bloody exciting along with the fact that they have non-overlapping resistance profiles.  While the article bears out that a PI is not yet effective without the combination of INF and riba, the possibility exists that the combination of a protease and polymerase inhibitor could potentially change that.  I look forward to further study on this, which will be important - great that it results in UND 16 days after treatment .. it's the SVR rates that I want to see as this goes along.  Still...bloody exciting!!!

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In the meantime, as studies continue on the two PI's - polymerase and protease inhibitors, what I think is also important to note is that the role ribavirin plays is borne out in the various studies this article covers.  Over and over, the importance of a sufficient dosage of ribavirin comes through.  Reduced ribavirin dosages directly co-relates to reduction in SVR due to relapse - interesting to note that it's relapse and not non-response:

"In the PROVE2 trial, the sustained virologic response rate in patients treated with telaprevir and peginterferon alfa-2a without ribavirin for 12 weeks was lower than in
patients treated with telaprevir and peginterferon alfa-2a plus ribavirin. The lower sustained virologic response rate in the arm without ribavirin mostly resulted from a higher relapse rate. In the SPRINT-1 trial, the virologic response rate in the triple-therapy arm with peginterferon alfa-2b, low-dose ribavirin (400–1000 mg), and boceprevir was lower than in the triple-therapy arm using standard-dose ribavirin. These results indicate that ribavirin remains crucial in achieving high sustained virologic response rates by reducing relapse rates."

I think of my own situation with a PI - the Phase IIb polymerase inhibitor R1626 where the trial was stopped across the board due to adverse effects on the immune system.  I was at 34 weeks when the trial was stopped.  My INF dosage turned out to be at half for the first 12 weeks and at Week 25 and onward, I was at 3/4 dosage of INF.  My ribavirin was reduced for one week only at Week 13 - just after Week 12, a point at which one can sustain up to a one week reduction in ribavirin without too much concern.  I remained at full dosage ribavirin otherwise - thanks to procrit/eprex.  Despite stopping treatment at 34 weeks, I've got my SVR.  Thank you, ribavirin and thank you, PI.  I begrudgingly thank Interferon as I'm left with thyroid issues (manageable so far) and most of my more impacting side effects were due to the Interferon but the absence of Interferon would not have been effective, I'm convinced of that.  I'm just not as affectionate towards it. :)

I look forward to the possibility of treatment that includes neither ribavirin or INF, although I confess a particular affection for my riba...just will be nice when people don't have to subject themselves to either.

Trish

[Mr Liver]

One point that is made is that the mutants or quasi-species (QS) of the virus were present before any treatment of any kind started. The selection pressure caused by the PI merely determined which mutant becomes dominant enough to create the most resistance. Its known that when the wild-type virus is placed under pressure QS variability and production is increased. When the pressure lets up, the wild-type virus returns to its 'ancestral home' on the genome. In the study I referenced above it was found that after resistance to the PI was established when they discontinued the PI the successful mutant virus disappears as the wild-type virus becomes the dominant strain once again. If the new PI used has a similar profile to the old one the resistance will take hours, not days to develop. As you noted this would be the case if the two used in this example were teleprivir and boceprivir. Since they can test for resistance in vitro it is possible that more than one PI could be used in a single tx.
Perhaps two different PI's could run concurrently or even consecutively with SOC. Thanks for your reply. ML

[newleaf09]

More than a little interesting.  Thanks for posting.  My take on the article is that Teleprevir and Boceprevir and the other current PI's attack the same protease (NS3/4A) necessary for viral replication and if patient does not respond to teleprevir or boceprevir, the other will be no more effective, since they are both causing mutations of the virus in the same location on the virus.  Peg and riba are still absolutely necessary and neither therapy is successful without them because the peg/riba can still knock out the protease-resistant variants that arise.  There is another PI, ITMN-191, that attacks the same protease (NS3/4A), but causes a mutation in a different place than those seen with teleprevir and boceprevir.  That will be the one to watch for those who were unable to succeed with teleprevir or boceprevir.   Looking forward to what happens next.