January 2011


For over 60 years, the use of microbially-produced or semi-synthetic antibiotics has helped to cure life-threatening bacterial diseases in many millions of people. The development of drugs to effectively combat viral diseases, however, has proven to be much more difficult. But advances in understanding the detailed molecular biology of virus replication cycles, coupled with determination of detailed three dimensional structures of viral molecules, are now making possible the development of highly specific and effective anti-viral drugs.

In principle, a molecule can act as an anti-viral drug if it inhibits some stage of the virus replication cycle, without being too toxic to the body's cells. The possible modes of action of anti-viral agents would include being able to ...

1. Inactivate extracellular virus particles.
2. Prevent viral attachment and/or entry.
3. Prevent replication of the viral genome.
4. Prevent synthesis of specific viral protein(s).
5. Prevent assembly or release of new infectious virions.

The first types of somewhat effective anti-viral drugs were nucleoside analogues, developed several decades ago, which are able to interfere with viral genome replication. The 1990's saw the development of the first specific inhibitors of viral protease activity. The 2000's have seen the development of a few new enzyme-inhibitor type drugs and research on the possibility of short-length RNA molecules being able to inhibit viral gene expression.

As we investigate how some of these drugs work at the molecular level, we must keep in mind that the potential problem of the emergence of mutant virus strains resistant to a drug is always a concern.

1. How do nucleoside analogues, particularly acyclovir (against HSV) and AZT (against HIV), work?

Here is a figure showing the structures of various nucleoside analogues. All of these analogues lack a 3' OH. Thus, if they get incorporated into a growing nucleic acid strand, no further elongation will be possible, because all nucleic acid synthesis requires a 3' OH site for adding the NEXT nucleotide. (This is the same molecular situation as the use of dideoxynucleotides for DNA sequencing.)

Here is a figure showing how acyclovir and AZT work.
Note both the similarities and the differences.

The effectiveness of acyclovir at preventing person-to-person transmission of HSV was presented in a 2004 editorial in NEJM by Crumpacker titled "Use of Antiviral Drugs to Prevent Herpesvirus Transmission."

2. What are the structures of some protease inhibitors, and how do they work?

Here is a figure showing the chemical structures of inhibitors of HIV protease.

These are "designed" drugs, i.e., designed to block the active site of a specific protease. The development of these HIV protease inhibitors could not occur until the 3-D stucture of the HIV protease was determined (~1990). Some early version inhibitors (early 1990's) had too much cellular toxicity for clinical use. Variations of these first drugs led to several promising molecules;"ritonavir" and "indinavir" were approved by the FDA in 1996. Other similar molecules have been approved since then.

The HIV protease inhibitors can greatly reduce the levels of virus replication in HIV-positive individuals. A reasonable concentration of one of the protease inhibitors in an infected cell will inhibit the action of the enzyme. The gag and gag-pol polyproteins will not get proteolytically cut (by protease) into their final proteins, which (as you know) are the viral core structural proteins and the copies of integrase, reverse transcriptase, and protease itself for assembly into new virus particles. Because these cleavages occur during the late stages of virus assembly and are essential for infectivity of the new virions, the effect of the drug is to inhibit the production of new infectious virus particles.

The action of these HIV protease inhibitors is powerful and specific enough that, when typically combined with two nucleoside analogues in a triple drug "cocktail", the reproduction level (and hence the "viral load") of HIV in a person can be lowered by several orders of magnitude. (We will look at the clinical aspects of this in more detail in a few weeks.)

What about the possible use of protease inhibitors against other viruses? In theory, specific protease inhibitors could be developed for any virus which uses protease action to cut a polyprotein into individual viral proteins. For example, the new drug named rupintrivir (Phizer) is an inhibitor of rhinovirus protease 3C, and the journal Antimicrobial Agents and Chemotherapy has a 2005 article titled "Conservation of Amino Acids in Human Rhinovirus 3C Protease Correlates with Broad-Spectrum Antiviral Activity of Rupintrivir, a Novel Human Rhinovirus 3C Protease Inhibitor". The structure of the drug bound to the protease is shown in Figure 1 in this article.


3. What about the influenza neuraminidase-inhibitors such as oseltamivir?

There are four drugs, in two categories, that can somewhat lessen the severity of influenza. These include the "entry inhibitors" amantidine and rimantidine and the "release inhibitors" oseltamavir and zanamavir. Oseltamivir and zanamivir were designed and first synthesized in the late 1990's, to be able to bind to the active site of viral neuraminidase and block its activity. When new influenza virions are produced, by cores budding through plasma membrane patches containing HA and NA, the new virions tend to stick onto the cell or to each other, due to HA binding to sialic acid residues. Neuraminidase cuts the sialic acid, thus releasing the virion. So, inhibiting NA activity slows down the spread of the infection. (NEJM figure).

How useful can a drug such as oseltamavir be? Here is a 2004 article from J. of Infectious Diseases: " Management of influenza in households: a prospective, randomized comparison of oseltamivir treatment with or without postexposure prophylaxis."


4. What are some 2011 updates on research on antiviral agents?

Every month, the journal Antimicrobial Agents and Chemotherapy has a section titled "Antiviral Agents". Taking a look at the titles of some of these articles for the early months of 2011 provides a sense of the scope of research going on in this area.