NUST CENTRE OF VIROLOGY AND IMMMUNOLOGY

Antiviral Drugs
Pathway; Production; Prospects
Submitted to : Dr. Abdul Ghafoor Khan, General Virology Submitted by: Shehroze Ameen, UG-3, Section A

It is submitted that the undersigned is the sole author of this assignment and has not indulged in plagiarism during the course of the writing of this assignment. All references have been made.

Table of Contents
Introduction: ................................................................................................................................................. 1 Part I: Life cycle of Virus and Antiviral Drug Pathway ................................................................................... 2 Part II: Drug Designing and Bioinformatics ................................................................................................... 6 Part III: Future Prospects .............................................................................................................................. 9 Works Cited................................................................................................................................................. 10

Introduction

Introduction:
Antiviral Drugs are synthetically designed drugs which act on viruses by blocking specific virus targets i.e. viral life cycle steps, hence decreasing the pathogenesis of the virus. The importance of antiviral drugs arises because of the rise of mutagenic viruses, most notably HIV, Hepatitis among others. During the course of this document we shall be discussing the following aspects of these drugs: 1. 2. 3. 4. Mechanisms blocked by antiviral drugs Drug Designing traditional and modern The importance of Bioinformatics in the production of Antiviral Drugs Future prospects of Antiviral Drugs

Bibliography

Part I: Life cycle of Virus and Antiviral Drug Pathway

A Virus is a very versatile pathogen. This is because of its simple morphology and its complex replication machinery. The Baltimore Classification divides the virus according to its replication technique. It is classified as: I. II. III. IV. V. VI. VII. Double Stranded DNA Virus Single Stranded DNA Virus Positive Polarity Single Stranded RNA Virus Negative Polarity Single Stranded RNA Virus Double Stranded RNA Virus Reverse Transcriptase RNA Virus Partially Double Stranded DNA Virus

While the medium and modus replica is different for these viruses, their general life cycle is the same: 1) The virus attaches to the cell membrane of the host. This attachment is very specific, due to complementarity of the virus glycoproteins with the cell membrane receptors. E.g. HIV have gp120 receptors which can only bind with CD4 receptors on white blood cells 2) After attachment, the virus capsid is injected into the cell cytoplasm (for enveloped viruses) from where it travels to the nucleus and injects the virus genome; or the virus genome is injected into the cytoplasm (for non-enveloped viruses) from where it begins replication. The former is the case with Baltimore classes I, II, VII, and VI. The latter are the case with Baltimore classes III,IV and V 3) The virus undergoes protein synthesis and replication. Both occur simultaneously as the host immune response is activated in deactivating viral machinery, particularly for RNA Viruses. To protect themselves from such a situation, the virus makes a monocistronic mRNA from which it is able to form its protein components. The replication can occur either in the cytoplasm or in the nucleus, and the modus replica is unique for every Baltimore class. 4) The components are assembled and virions are formed

5) These virions are released from the host cell and target other hosts.

Bibliography However, this is a very broad generalization. It is made complex because of the following factors: A. Replication is a major factor in virus survival. Some viral techniques for evading antiviral response are: a. Positive Polarity RNA Viruses are very poisonous because they can undergo translation directly (the genome is an mRNA, and thus can proceed directly to protein synthesis) thus it undergoes replication and assembly rapidly. This is the case with flaviviruses, which are the cause of yellow fever. b. Double stranded and Single stranded DNA both integrate with the host cell genome and proceed with latent replication, and are lysogenic. Unless they revert to the lytic phase it is very difficult to detect DNA Viruses c. Class VII viruses include hepadna viruses, of which Hepatitis C is a famous example. These viruses require an RNA intermediate to form their DNA genome. B. Another complexity is that all viruses are specific to their hosts and thus the virus attacks only specific regions of the body. Therefore each virus has a specific pathogenesis C. Another factor is the virulent or temperate phases of the viruses. These phases (better known as lytic or lysogenic) are the most crucial factors affecting the survival of a virus. Very often the virus remains in the lysogenic stage and only enters the lytic stage (if it does) after it has produced an ample number of virions D. Often it is the antiviral response which is targeted and affected. With the rise of Hepatitis C Virus, HIV, Paramoxviruses (Respiratory syncytial virus), Herpesviruses (Cytomegalovirus, Herpes Simplex Virus), Arena Viruses (Lymphocytic choriomeningitis virus) it is necessary to produce antiviral drugs which will in effect stop specific virus life cycle portions. The regions that can be stopped for a virus to become ineffective are: I. II. III. The attachment site of virus The protein capsid The replication process a. Introduction of nucleoside analogues to prevent mRNA from being synthesized b. Prevention of viral genome from integrating with host cell genome c. Prevention of synthesis of proteins The synthesis of the viral apparatus Assembly Release

IV. V. VI.

These steps are kept under control as provided below:

Bibliography

Again it is pertinent to mention that viral modus replica varies for all virus classes. However, antiviral drugs are unique in being broad spectrum and can stop viruses from their specific life cycle portions. The antiviral drugs can be classified as: A. Co-Receptor Antagonists: These antivirals prevent the virus from binding to the cell membrane of the host. This is achieved by the antiviral in two ways a. By making the virus bind with a receptor analogue b. By forming permanent complementary bonds with the viral receptor and thus preventing the virus from attaching with the cell membrane B. Fusion Inhibitors: The fusion inhibitors prevent the virus from injecting its genome into the host cell. This is achieved by forming inhibitory bonds with the envelope or protein coat. This prevents the injection of the capsid (in the case of the envelope) or the genome (in the case of the protein coat) 4

Bibliography C. Reverse Transcriptase Inhibitors: These work specifically for RNA Viruses. They include the following catagories: a. Nucleoside-analogue Reverse Transcriptase Inhibitors (NRTIs): These antiviral drugs present themselves as nucleotides that bind onto their complementary bases on the viral genome. However, upon binding, they nullify the mRNA formed, as a result of which the virus cannot proceed with protein synthesis. b. Non Nucleoside-analogue Reverse Transcriptase Inhibitors (NNRTIs): These behave in a similar way to NRTIs except that they do not bind at the nucleotide-binding site of the enzyme. They act as non-competitive inhibitors and thus, suppress enzyme activity D. Integrase Inhibitors: These act against DNA Viruses and Class VI and VII Viruses. They prevent the viral genome from binding with the host cell genome by clipping the complementary base pairs of the viral genome. Alternatively it binds onto the complementary regions of the DNA and prevents the Viral Genome from binding with the DNA E. Protease Inhibitors: This inhibitor prevents the protease enzymes from cutting the polypeptide formed by the viral monocistronic mRNA. This is done by forming non-competitive inhibition of the enzymes themselves. It is pertinent to mention however that multiple antivirals are prescribed to patients. This is because of: a) Mutation Rate of Virus b) Fitness of Virus against Antiviral c) Replication of Wild Genotype Virus An excellent example can be found in Acyclovir resistance of herpes simplex virus; for acyclovir to function effectively, the thymidine kinase is needed. Wild types of Herpes Simplex can function without this enzyme and can easily be identified. These mutations cause a change in the viral DNA polymerase gene, which alters the polymerase such that they have reduced ability to incorporate the phosphorylated drug into DNA. Another problem is that the drugs inhibit replication at host cell level it does not affect those cells containing latent virus. Thus the virus is not completely removed from the host.

Bibliography

Part II: Drug Designing and Bioinformatics

Thus, what can we do? How can we suppress virus activity in the host? What improvements can be made to the drugs themselves such that they are more effective against the virus against which they were designed to act? This is where in silico techniques of antiviral drug designing and manufacture come in. When we say in silico we refer to the utilization of IT to create a virtual image of the drug itself. Through this method, we pass our virtual drug through a series of tests (i.e. demo runs) through which we determine which regions of the virus are most effective, and what further improvements can be made to the drug such that it can have a high infectivity index and a low toxicity index. Once the antiviral drug passes these tests, the drug is then presented for approval for in vitro testing, followed by in vivo analysis. Only after it has been thoroughly analyzed is it approved for clinical trails.

Prior to in silico technique, the drugs were made through in vitro method and trail-and-error basis. Drugs made were often rejected before they reached the clinical trails phase. Viruses are resistant to

Bibliography many drugs made during this period (such as AZT, Acyclovir, ganciclovir) which makes the need of drug designing and the importance of bioinformatics even more important.

As can be seen from the diagram above, in (a) we have an AZT model which is manipulated to form the drugs saquinavir and indinavir (b). The in silico treatment of the drugs makes creation of antiviral drugs much more easier because a basic model of the drug can then be manipulated. Bioinformatics is even more important because the drug should affect the infected cells of the host and not the non-infected cells of the host. Also, bioinformatics allows researchers to produce drugs with as low a toxicity index as is possible for the drug. The regions which can be most affected by an antiviral drug are:

This is important to mention because previously the drugs had many side affects which would drastically corrode the physiological condition of patient.

Bibliography Furthermore, bioinformatics has been a crucial step in determining virus transmission and pathogenesis. Responses to antiviral drugs provides numerous opportunities to analyze the virus, both to overcome it and at the same time in the prospective utilization of the virus itself. It was the use of bioinformatics which identified retroviruses and their advantages in genetics, biochemistry, pharmacology and other biological fields. Also, the use of bioinformatics has resulted in an improved analysis of viruses (e.g. BLAST aids in the study of virus genome). The basic medicines from which drug derivatives are made are: Name Acyclovir Type Nucleoside Analogue Target Viral Polymerase Virus Herpes Simplex Virus (HSV)

AZT

Nucleoside-analogue Reverse Transcriptase Inhibitor (NRTI)

Reverse Transcriptase Retrovirus (e.g. HIV)

Delaviridine Non-nucleoside analogue Reverse Transcriptase Retrovirus (e.g. HIV) Reverse Transcriptase Inhibitors (NNRTI) Ritovirin Protein Inhibitors (Peptide Analogues) Broad Spectrum HIV Protease Retrovirus (e.g. HIV)

Ribavirin

RNA Mutagen

HCV, HSV, measles, mumps Influenza A Influenza A and B

Armatadine Tricyclic Amine Relenza Neuraminic acid mimetic

Haemagglutinin Neuraminidase inhibitor Small cyclic

Pleconaril

Blocks attachment and uncoating

Rhinoviruses

Interferons Cell defense proteins activated protein Fuzeon Inhibits fusion of HIV to cell 11 membrane Peptide

Hepatitis B& C HIV

Bioinformatics also determines the method by which the drug is administered. This could be tablet, injection, or liquid medium (drinking). In the case of antiviral drugs, the medium is either tablet or injection. 8

Bibliography

Part III: Future Prospects

In many ways, antiviral drugs provide lucrative and interesting results. Antiviral drugs are important because: Aid in understanding viral growth mechanism and proteins involved Use of selective antiviral drugs, coupled with viral mutations that confer drug resistance, can help to identify the roles of viral proteins and assimilate details of how these proteins act Such mutations can also provide selectable markers for viral genetics, and thus aid in drug designing. Antivirals can be taken during the disease, while vaccines are only effective before advent of viral disease. Vaccines cannot be developed for certain mutagenic viruses (e.g. retrovirus HIV, rhinovirus etc), also reassortment (e.g. influenza A) and immunosuppressive diseases (AIDS) can nullify vaccine efficacy

Bioinformatics has been a crucial factor determining the efficacy of antiviral drugs. Furthermore, it is crucial to understand the flaws of antiviral drugs as well. These are Antiviral Drugs are expensive. This is not surprising considering the effort cost and time needed in their manufacture Antiviral Drugs are Virus Activity-centric. This means that the antiviral drug will only stop a specific portion of the virus. Antivirals, therefore, are not broad-spectrum, Ribavarin being an exception. Antiviral Drugs are ineffective if they cannot deliver. Often, Antiviral analogues fail to reach their target because of improper formulation Antiviral Drugs are limited in number, and are effective against a select number of viruses. To date, antiviral drugs still have to be developed for: Human T-lymphotropic virus type I (retrovirus); BK and JC virus (polyoma virus); B-19 Parvovirus; Epstein-Barr virus (Herpesvirus) among others. Antiviral Drugs, unlike vaccines, cannot confer long-term immunity. It is often advised to patients to undergo combinatorial therapy so as to decrease the onset of the disease.

However, antiviral drugs are more versatile and can be better manipulated by researchers to not only understand virus pathogenesis but also to attain a degree of immunity against other fresh viruses and to improve the physiological defense of patients against existing viruses.

Bibliography

Works Cited
Carter, J., & Saunders, V. (2007). Virology - Principles and Application. Chichester, West Sussex: John Wiley & Sons Ltd. Flint, S. J., Enquist, W. L., Racaniello, V. R., & Skalka, A. M. (2009). Principles of Virology : Third Edition. Washington DC: ASM Press. Microbiology, A. S. (2008). Nature Reviews (Drug Discovery). New York City, New York, USA. Microbiologybytes. (n.d.). Antiviral Drugs. Retrieved September 30, 2010, from Microbiologybytes: http://www.microbiologybytes.com/virology/Antivirals.html

10