<\/p>\n

Today, small molecules are commonly used as antiviral drugs, generally leading to the inhibition of some viral protein or enzyme.\u00a0 When we say ‘small molecule’ we are referring to molecules of a low molecular weight.\u00a0 Small molecules are not the only option in drug therapy.\u00a0 There are lots of high molecular weight molecules used, like biologics.\u00a0 Biologics are derivatives of natural products used to treat diseases.\u00a0 They include proteins, enzymes, vaccines, blood products, antibodies, etc.\u00a0 So, why use small molecules for antiviral drug therapy and not large molecules?<\/span><\/p>\n

 <\/p>\n

Small molecules offer many advantages over large molecules.\u00a0 Small molecules are easily manufactured and have a low production cost.\u00a0 Large molecules, on the other hand, can have very difficult, time-consuming, expensive methods of production\/collection.\u00a0 Small molecules have good oral bioavailability.\u00a0 Proteins (large molecules) are subject to proteolytic degradation, and have low oral bioavailability.\u00a0 Biologics often must be injected directly.\u00a0 Small molecules diffuse easily, giving them access to intracellular targets.\u00a0 Large molecules do not diffuse easily.\u00a0 Another advantage that small molecules have over large ones is that they do not elicit an immune response.\u00a0 The half-life of many large molecules is drastically reduced by anti-drug antibodies.\u00a0 Also, small molecules are species independent and can be tested on rodents.\u00a0 Because biologics are species-specific, toxicity studies relevant to humans should be performed on other primates.\u00a0 These advantages are summarized in the table that follows.<\/span><\/p>\n

 <\/p>\n

 <\/p>\n

\u00a0Advantages of Small Molecules Over Large Molecules:<\/span><\/strong><\/p>\n

 <\/p>\n\n\n\n\n\n\n\n\n

Small Molecules<\/span><\/strong><\/td>\n	\u00a0Large Molecules\/ Biologics<\/span><\/strong> \n<\/span><\/td>\n<\/tr>\n
Low cost and easy to produce<\/td>\n	Difficult and costly to manufacture<\/td>\n<\/tr>\n
Oral bioavailability<\/td>\n	Subject to proteolytic degradation, so they may need to be injected directly into the blood stream<\/td>\n<\/tr>\n
Diffuse easily (access to intracellular targets)<\/td>\n	Low rate of diffusion<\/td>\n<\/tr>\n
No immune response<\/td>\n	Immunogenicity (Anti-drug antibodies can reduce the half-life)<\/td>\n<\/tr>\n
Species independent (facilitates testing on rodents)<\/td>\n	Species-specific (testing relevant to humans requires primates)<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n  <\/p>\n  <\/p>\n  <\/p>\n Small molecules aren’t perfect though.\u00a0 One of the main disadvantages of small molecules is that they are readily metabolized, and their metabolites can often be active and\/or toxic.\u00a0 Because small molecules are processed by the biliary and renal systems, they can often be very hard on the liver and kidneys.<\/span><\/p>\n <\/h2>\n The most common antivirals available today are against human immunodeficiency virus (HIV), herpesvirus, hepatitis B and C viruses, and influenza A and B.\u00a0 While many other disease-causing viruses are completely without antivirals, even these highly studied ones have no cure.\u00a0 Effective treatments for these and many other viruses have yet to be discovered.\u00a0 This is not as easy as it sounds.\u00a0 Besides overcoming the difficulties of finding inhibitors that bind the active sites of proteins, maximizing bioavailability, and avoiding toxicity to the host, which are problems that occur in all drug design, antivirals face their own unique problems.\u00a0 Viruses have a very short replication cycle.\u00a0 In only hours (or even minutes), one virus can produce hundreds of infectious copies of itself.\u00a0 This extremely fast replication allows viruses to mutate constantly and for new strains to become prevalent very quickly.\u00a0 Mutated viruses, if still functional, have the advantage of avoiding the host immune system (if antibodies no longer recognize a viral antigen, for example) or drugs that were once effective inhibitors.\u00a0 This leads to the major problem with antiviral drug therapy: drug-resistance.\u00a0 When a virus has mutated to the point that a once effective drug no longer works, that virus strain is said to be drug-resistant.\u00a0 A single virus strain can become resistant to several different drugs.\u00a0 This is termed multidrug-resistance.\u00a0 Another major problem facing antiviral drugs is cross-resistance.\u00a0 When a virus becomes resistant to a drug after contact with a similar drug, it is displaying cross-resistance to a series of drugs.<\/span><\/p>\n  <\/p>\n <\/h2>\n <\/h2>\n Techniques used in design of anti-viral therapies<\/h1>\n  <\/p>\n  <\/p>\n There are many techniques used during the process of finding and evaluating new compounds for use as small molecule treatments for viral disease. Through automation, many techniques that\u00a0were once\u00a0obsolete are now the preferred and standard procedures used in labs around the world.\u00a0 To begin, high-throughput screening (HTS) is a very powerful tool for medicinal chemists to find new lead compounds for potential drug development. Basically, HTS works by allowing a large number of compounds to react with a specific entity for a relatively short period of time, and then the reactivity of the compounds with the entity is measured. The reactivity of the compound with the entity is referred to as bioactivity, and bioactivity can be measured numerous ways depending on the entity that is being tested on.<\/span><\/p>\n \u00a0<\/span><\/p>\n Enzyme\/substrate interactions: If the entity that is being tested is an enzyme and you are testing compounds for inhibitory activity against this enzyme, one would begin the HTS by placing standardized quantities of the enzyme into multi-welled plates. Then one would add the potentially inhibitory compound as well as modified enzyme substrate. The substrate is generally modified in such a way that after interaction with the enzyme, it either fluoresces, radiates, or gives off some kind of measureable reading. Thus, by using a spectrophotometer, or other third party device that can be incorporated directly into the HTS apparatus, one can obtain a measurement of how well a given compound can inhibit the enzyme.\u00a0In other words,\u00a0the fluorescence emitted from a given well is inversely proportional to the tested compounds ability to inhibit the entity. So, the more fluorescence the worse the inhibitory activity of the compound.<\/span><\/p>\n \u00a0<\/span><\/p>\n Immunoassays are another method of indirectly measuring a drug’s activity. They can be used in cases where a drug is suspected to inhibit production of a specific cellular component or cell type, as long as it can generate an immune response. Then, specific antibodies are developed against the cellular component or cell type that you are trying to inhibit (i.e. rabbit antivirus protein). Subsequently, you develop antibodies against the constant regions of the antibodies you developed against the protein you are trying to inhibit. These are referred to as secondary antibodies and are of the form of pig anti-rabbit. You then label these secondary antibodies with a group that can be registered either by radiation, fluorescence, or something else that is measurable. After you have completed these steps, you would proceed with the HTS by placing both entities and potential drugs into a multi-welled plate. Upon sufficient incubation time, you would incubate the drug-exposed entities with the primary antibody, which should bind to any of the protein that you are trying to inhibit. You would then wash your sample, thereby removing excess rabbit antivirus protein antibody, and add the pig anti-rabbit antibody. You would then wash away the excess enzyme once again and take a reading of the intensity of the fluorescence, radiation, or other measurable parameter. This measurement is once again inversely proportional to the effectiveness of the drug as an inhibitor of protein production or proliferation of the specific type of cell in question.\u00a0<\/span><\/p>\n  <\/p>\n Examples of high-throughput screening apparatuses.<\/p>\n  <\/p>\n \u00a0\u00a0\u00a0\u00a0 <\/p>\n  <\/p>\n  <\/p>\n There are also several other computer based techniques that\u00a0are widely used in the development of new\u00a0drugs.\u00a0Particularly, structure activity relationship (SAR) and quantative structure activity relationship (QSAR) studies can be powerful weapons in the arsenal of the medicinal chemist. <\/span>SAR is used to map the biological activity of a compound to its structure.\u00a0Thus, by making small changes to a compound’s structure and measuring the change in biological activity associated with that change, scientists can make inferences about the best types of functional groups to be placed at each position on a drug’s skeleton. At first, substitutions of broad groups would be made. One would switch a hydrophobic group for a hydrophilic group to see the effects on the drug’s activity. This will indicate which is more favorable depending on which type of group had the higher activity, but it will not give insight into the best hydrophobic or hydrophilic group to place at that particular position. Hence, one would carry out these types of general substitutions until the general makeup of the most active compound has been mapped. After the general substitutions are completed one can then create a library of the most potentially active compounds with this particular pharmacophore as a map. Then these compounds can be tested for biological activity and side effects.<\/span><\/p>\n  <\/p>\n QSAR is another technique used in the design of small molecules. This is a technique with similar results as a SAR study, but QSAR generally leads to more specific results in a shorter period of time and can also lend more predictive power than SAR. QSAR is a quantitative technique. This means that it uses calculable numbers to find the best possible design of a potential drug. QSAR assumes that there is a series of calculable descriptors that will best define the activity of a drug in a biological setting.\u00a0The descriptors are features of the potential drug, such as lipophilicity, number of hydrogen bond donors and accepters, electronic properties, and hydrophilicity.\u00a0 These are used to determine how the drug will act in a biological system. The structure part of \u201cQSAR\u201d comes from the fact that the numbers representing each descriptor depend on the structure of the compound. Thus, a scientist can manipulate a QSAR study to find the best set of possible descriptors to represent the most appropriate features that a drug would need to interact within a given biological system. These descriptors are then used to build an equation, and the equation can be optimized to find the structure of the drug that would be most active in the setting.<\/span><\/p>\n  <\/p>\n  <\/p>\n  <\/p>\n  <\/p>\n Hepatitis C Virus<\/h1>\n <\/h2>\n Hepatitis C virus (HCV) is a member of the Flaviviridae<\/em> family. It is an enveloped virus that has a plus-sense, single-stranded, RNA molecule as its genetic material. The hepatocytes of the liver are the host cells of HCV,\u00a0explaining why HCV can cause liver cirrhosis and liver cancer. Furthermore,\u00a0because hepatocytes are the host cells, the blood of an infected individual still carries a viral load; thus, if one comes into contact with infected blood, there is a\u00a0high probability\u00a0of horizontal transmission.<\/span> \u00a0<\/span><\/p>\n <\/div>\n Hepatitis C is very rarely diagnosed early in the infection cycle, as infection of the HCV has very few symptoms, most of which are very mild. Only when liver malady has reached an aggravated state does a diagnosis of HCV as the causative agent become likely; only at this point are specialty tests run. <\/span>These specialty tests include anti-HCV immuno assays, which look <\/span>for a<\/span>n\u00a0<\/span>immune response to HCV proteins. Also PCR or RT-PCR can be used to <\/span>scan blood samples for HCV RNA, which is indicative of <\/span>acute and chronic infection.<\/span><\/span><\/div>\n <\/div>\n There are several new classes of small molecules that are being <\/span>tested for treatment of HCV. Most of these molecules are targeted for inhibition of non-structural proteins that play a role in the HCV replication cycle.<\/span><\/span>\u00a0 The current gold standard of HCV treatment is combinatorial therapy using ribavirin and peg-interferon. Ribavirin is a pro-drug that metabolizes into a nucleoside analogue when it is metabolized.<\/span><\/div>\n \u00a0\u00a0 \u00a0\u00a0 \u00a0<\/span><\/div>\n <\/div>\n \u00a0\u00a0\u00a0\u00a0 \u00a0\u00a0\u00a0 \u00a0 \u00a0 Ribavirin<\/div>\n <\/div>\n Nucleoside analogues, such as ribavirin, are drugs that look very much like a nucleoside, but when incorporated into newly synthesized DNA or RNA they are different enough that the resulting nucleic acid strand is non-functional. One can see how this could cause a potential problem, as there is no particular way to target this drug to soley HCV RNA synthesis, and as such, there are some severe consequences to use of this drug.<\/span>\u00a0 Ribavirin has a very long list of side effects. They include \u201c<\/span>fever<\/span><\/a><\/span>, <\/span>anorexia<\/span><\/a><\/span>, vomiting, emotional lability, <\/span>fatigue<\/span><\/a><\/span>, <\/span>dyspepsia<\/span><\/a><\/span>, <\/span>arthralgia<\/span><\/a><\/span>, <\/span>insomnia<\/span><\/a><\/span>, irritability, impaired concentration, <\/span>dyspnea<\/span><\/a><\/span>, and pruritus\u201d (<\/span>rebetol_ad.htm#AR<\/span><\/a>http:\/\/www.rxlist.com\/cgi\/generic\/<\/a>).<\/span><\/div>\n <\/div>\n Interferon, the other type of drug used to treat HCV, is a natural glycoprotein that is produced to aid in an immune response to foreign infections. When a cell detects dsRNA, which is only present in a eukaryotic cell during viral infection, that cell produces and releases interferons. These interferons act as early warning signals and trigger signal transduction pathways that eventually lead to the inhibition of host transcription factors and thus, shut down host replication equipment that is necessary for viral proliferation.<\/span>\u00a0 However, most hepatitis C patients are given peg-interferon and not normal interferon. Peg-interferon is a normal interferon with polyethylene glycol (PEG) side chains added to it. The addition of these PEG side-chains reduces the solubility of the interferon, leading to slower drug-uptake from the bloodstream. PEG increases the half-life of interferon from just a few hours to 20-50 hours, reducing the frequency of interferon injections from 2-3 times each week to only once.<\/span>\u00a0 Also, note that once again this is not a targeted therapy against HCV. This again poses the problem of causing most cells in the body to elicit a response to interferon. Because of this, interferon also produces a large number of side effects most of which are very similar to the ribavirin side effects.<\/span><\/div>\n <\/div>\n  <\/p>\n New Treatments for HCV<\/h2>\n  <\/p>\n Ideally, an anti-HCV treatement should target a process only preformed by HCV. This\u00a0minimizes the chances of\u00a0the drug having cytotoxic effects on host cells. This being said, there are serveral candidate HCV proteins\u00a0being studied as potential targets for anti-viral therapy. One of these proteins is non-structural protein 5 B (NS5B), the viral polymerase which uses RNA as a template and makes a complimentary RNA strand. This process is completely foreign to hepatocytes and all other cells in the human body,\u00a0and as such, it makes a\u00a0prime candidate for drug research.\u00a0<\/span><\/p>\n <\/p>\n  <\/p>\n In analogy, the structure of NS5B, the HCV RNA polymerase, is often compared to a hand. The palm region carries the catalytic polymerase activity of the protein, and the “thumb and fingers” of the protein interact with the template RNA and the newly synthesised<\/span> RNA. There are two loop regions on the “fingers” that interact with the “thumb”\u00a0to confer the protein into a barrel-like conformation. NS5B\u00a0can also adapt to a more open conformation where the\u00a0“thumb and “finger” regions do not interact, but this inactivates the protein.<\/span><\/p>\n  <\/p>\n One new series of drugs being developed for inhibiton of this protein is anthranilic acid derivatives.\u00a0They\u00a0are\u00a0allosteric inhibitors of the protein, meaning that\u00a0they do not function by blocking the active site of NS5B like a competitive inhibitor, but\u00a0rather\u00a0they work by binding to a different area on the protein and causing a conformational change that disrupts its function. Typically allosteric inhibition of a protein is more effective than competitive inhibition, as the allosteric inhibitors do not have to\u00a0“fight” with the natural substrate of the enzyme (i.e. there is less chance of the allosteric inhibitor not being able to bind to the enzyme).<\/span><\/p>\n  <\/p>\n In particular, the work being done by\u00a0Nittoli et al.<\/em> is very promising, as their last publication yielded\u00a0two allosteric inhibitors of this class that have in vitro<\/em> IC50s\u00a0in the 10-17 nM range. They began with a lead compound refered to as “3a”, which was identified through high-thoughput screening of the Wyeth compound library. \u00a0<\/span><\/p>\n  <\/p>\n  <\/p>\n  <\/p>\n  <\/p>\n <\/p>\n  <\/p>\n From this lead compound, many analogues were developed. These compounds bind approximately 7<\/span>.5 \u00c5 from the NTP\u00a0binding site of the NS5B active site; NTPs are nucleotide triphosphates, the natural substrate used by NS5B to make the sister strand to the RNA that it is copying. Through the use of SAR techniques, Nittoli et al.<\/em> were able\u00a0to determine the most important, potency enhancing\u00a0characteristics of the molecules.<\/span><\/span><\/span><\/p>\n \u00a0<\/h2>\n <\/p>\n Diagram exhibiting the quasi-tricyclic nature of the\u00a0compounds.<\/span><\/p>\n  <\/p>\n  <\/p>\n They discovered that\u00a0 much of the potency of this class of inhibitors was due to the drug being in a quasi-tricyclic conformation, held by intramolecular hydrogen bonding between the H of the amino group, the O of the Carboxylic acid, and the linker atom located at the Y position. Thus, removing or changing any of these groups or atoms can have severe consequences for the potency of the inhibitor. This can be seen in the IC50 values of other derivitives where the carboxylic acid\u00a0group is moved from the 2 position, as in 3b and 3c, and also when the H-bonding ability of the carboxylic acid is compromised, as in 3d. Also, by comparing\u00a03a, 3f, 13, and 14, they were able to evaluate the\u00a0best linker molecules as being\u00a0\u00a0N > O and O > S.\u00a0<\/span><\/p>\n <\/p>\n  <\/p>\n  <\/p>\n  <\/p>\n They also studied the effect of substituting the methylene linker and found that S\u00a0methylation\u00a0of the linker, as in compound 17a, was very favorable when compared with no methylation, as in 3a, and also that R methylation was unfavorable due to strong steric interactions with the enzyme. This is also the reasoning behind the low activity of 3h.<\/span><\/p>\n  <\/p>\n Through similar reasoning processes, they discovered that the most active inhibitor was one that would be tri-subsituted on the phenoxy ring with 3 electro-negative groups or atoms. They found the most potent inhibiton to be derived from a\u00a02, 4, 5 tri-chloro substitution, as this phenoxy ring sits in a spherical binding pocket and chloro-substituents at these locations provided the stongest binding of the drug into the allosteric site.<\/span><\/p>\n  <\/p>\n From all of these observations, they were able to design two very potent inhibitors of the NS5B polymerase. These two compounds embody all of the favorable SARs that they documented in the course of their experiments and as predicted had the lowest IC50 of all the compounds designed. They have a carboxylic acid located at the 2 position on the “B” ring and\u00a0have a N for the linker atom. They are also tri-substituted on the anilino-ring; however, they noticed that placing an othro-acetyl group on the anilino ring significantly increased activity of the compound, as did having\u00a0the anilino ring hetero disubstituted with chloro and fluoro groups or bromo and fluoro groups.<\/span><\/p>\n  <\/p>\n <\/h2>\n <\/a><\/h2>\n <\/a><\/h2>\n  <\/p>\n  <\/p>\n <\/a>Human Immunodeficiency Virus Type-1<\/h1>\n  <\/p>\n <\/h2>\n Human immunodeficiency virus type-1\u00a0\u00a0 \u00a0Representation of HIV-1 Structure<\/h2>\n  <\/p>\n Human Immunodeficiency Virus Type-1 (HIV-1) is a retrovirus of the lentivirus family.\u00a0 The name lentivirus comes from the Latin word \u2018lentis\u2019, meaning slow, and refers to the slow progression of disease.\u00a0 HIV-1 infects cells of the immune system, including macrophages and helper T cells.\u00a0 As the host immune system becomes progressively weakened, the host develops an increased susceptibility to opportunistic infections and is then said to have acquired immunodeficiency syndrome (AIDS).\u00a0 <\/span><\/p>\n  <\/p>\n The\u00a0Joint United Nations Programme on HIV\/AIDS (UNAIDS) reports that as of 2005, roughly 40 million people were infected and living with HIV.\u00a0 Since the discovery of the virus in 1981, 65 million people have been infected, and 25 million people have died from AIDS-related illnesses.\u00a0 As of 2007, HIV-1 newly infects 14000 people every day.\u00a0<\/span><\/p>\n  <\/p>\n The current treatment for HIV infection is highly active antiretroviral treatment (HAART).\u00a0 HAART uses a combination of three or more drugs from multiple drug classes to target several different proteins involved in various stages of the HIV replication cycle.\u00a0 There are currently four FDA-approved drug classes used in HAART:<\/span><\/p>\n  <\/p>\n 1) nucleoside reverse transcriptase inhibitors (NRTIs)<\/strong> \u2013 Reverse transcriptase is a viral enzyme necessary for replication; it converts the single-stranded RNA genome into double-stranded DNA.\u00a0 There are no host enzymes capable of doing this.\u00a0 NRTIs inhibit reverse transcriptase by acting as nucleoside analogues that, once incorporated into the growing DNA strand, will terminate further polymerization.\u00a0 NRTIs can lead to multi-drug resistant strains of HIV and can be toxic to cell mitochondria.<\/span><\/p>\n  <\/p>\n 2) non-nucleoside reverse transcriptase inhibitors (NNRTIs)<\/strong> \u2013 NNRTIs inhibit reverse transcriptase by binding to an allosteric site near reverse transcriptase\u2019s active site.\u00a0 NNRTIs have led to many drug-resistant HIV strains.<\/span><\/p>\n <\/p>\n HIV Reverse Transcriptase<\/p>\n  <\/p>\n <\/p>\n HIV-1 life cycle showing reverse transcription<\/p>\n  <\/p>\n 3) protease inhibitors (PIs)<\/strong> \u2013 Many of HIV\u2019s genes are translated into polyproteins.\u00a0 HIV\u2019s protease is an aspartic acid protease required to cleave the polyproteins into individual, functional proteins.\u00a0 This step is necessary for virus production.\u00a0 All of the current FDA approved PIs are peptidomimetic nonhydrolyzable analogues.\u00a0 These drugs have many disadvantages: they increase drug-resistance, they have low oral bioavailability, and they are the most toxic of all available anti-HIV drugs.<\/span><\/p>\n  <\/p>\n 4) fusion inhibitors<\/strong> \u2013 When HIV\u2019s envelope glycoprotein gp120 has bound the host receptor CD4 and a co-receptor (either CCR5 or CXCR4), the viral glycoprotein gp41 is inserted into the cell membrane and fusion occurs.\u00a0 Enfuvirtide (ENF) or fuzeon is currently the only fusion inhibitor that has gained FDA approval.\u00a0 It inhibits viral entry by binding to one region of gp41, preventing the glycoprotein from binding its other regions, ultimately changing its conformation.\u00a0 ENF is only used as a last resort, because it has low bioavailability and a high production cost.\u00a0<\/span><\/p>\n  <\/p>\n \u00a0\u00a0\u00a0\u00a0\u00a0 <\/p>\n HIV Protease with Glaxo Wellcome inhibitor in active site.\u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0\u00a0 \u00a0\u00a0\u00a0 \u00a0 \u00a0\u00a0 Enfuvirtide<\/p>\n  <\/p>\n  <\/p>\n  <\/p>\n New prospects for the treatment of HIV-1<\/h2>\n  <\/p>\n Integrase inhibitors<\/strong> \u2013 Integrase is HIV\u2019s third enzyme that is necessary for replication.\u00a0 The integrase enzyme integrates the new ds-DNA virus genome into the host genome, where the host cellular machinery can replicate the virus.\u00a0 By inhibiting integrase, HIV is unable to replicate.\u00a0 Because nothing similar to integrase can be found in mammalian cells, integrase inhibitors should be expected to have low toxicity to humans.\u00a0 In October of this year, Raltegravir (a small molecule) became the first integrase inhibitor to receive FDA approval, and can now be used as a part of HAART therapy.\u00a0 However, it has only been approved for patients whose infection shows resistance to other HAART drugs.\u00a0 There are other integrase inhibitors in various stages of clinical trials and many others being developed.<\/span><\/p>\n \u00a0<\/span><\/p>\n Entry inhibitors<\/strong> \u2013 Entry inhibitors block virus entry into a cell, thereby preventing the spread of infection.\u00a0 Most entry inhibitors being developed will only prevent the spread of infection within an already infected individual and not from person-to-person.\u00a0 Entry inhibitors can target several different proteins, including viral adhesins, like gp120 and gp41, host cell receptors, like CD4, and host co-receptors, like CCR5 and CXCR4 (both are normally chemokine receptors).\u00a0 In August of 2007, Maraviroc gained FDA approval.\u00a0 It is the first drug of its class to do so.\u00a0 Maraviroc (a small molecule) is a CCR5 antagonist.\u00a0 It binds the CCR5 host receptor and interferes with the host-virus interaction, thereby preventing infection.\u00a0 It is also used in HAART.\u00a0 There are many other entry inhibitors with various targets currently being developed.<\/span><\/p>\n \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 <\/p>\n Raltegravir\u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0\u00a0\u00a0 \u00a0 Maraviroc<\/p>\n  <\/p>\n  <\/p>\n Topical microbicides<\/strong> \u2013 A new area being researched is small molecule inhibitors that can be used in topical microbicides to prevent the spreading of HIV infection from person-to-person.\u00a0 In order to be used in a topical, these entry inhibitors must be able to inhibit virus entry without interacting with the host cell receptors.\u00a0 Therefore, these small molecules must render a virus particle non-infectious after binding only a viral adhesion.\u00a0 Because 80% of HIV infections are transmitted sexually, the development of anti-HIV topical microbicides could drastically reduce the number of people being newly infected.\u00a0 <\/span><\/p>\n \u00a0<\/span><\/p>\n Cell splicing equipment inhibitors<\/strong> \u2013 When the HIV genome is transcribed, the initial product is a single strand of genome-length pre-mRNA.\u00a0 This pre-mRNA is then spliced by the host splicing equipment, producing 40 different functional mRNAs.\u00a0 If the host\u2019s splicing machinery has been inhibited, HIV cannot successfully replicate.\u00a0 This theory has lead to a new study researching small molecule inhibitors of splicing equipment.\u00a0 Scientists have begun researching the inhibition of host proteins in an attempt to reduce drug-resistance.\u00a0 The idea is that it would be highly unlikely that a virus could mutate to compensate for a host deficiency.\u00a0 Therefore, a virus couldn\u2019t gain resistance to drugs that inhibit host proteins and enzymes, like splicing equipment.\u00a0 These drugs would be extremely useful for patients with multidrug-resistant HIV infections.\u00a0 However, because these drugs are targeting the host, they have the potential to be highly toxic.<\/span><\/p>\n  <\/p>\n  <\/p>\n <\/h2>\n Influenza Virus<\/h1>\n  <\/p>\n Influenza viruses are members of the Orthomyxoviridae<\/em> virus family. They are enveloped, negative sense RNA viruses that use the cells of the lungs as host cells. There are 3 types of common influenza viruses that infect humans, deemed influenza A, B, and C. Each of these subtypes can be further classified into specific serotypes, which are classed based on the two types of outer membrane proteins found on the virus. The two outer membrane proteins that determine viral serotype are hemagglutinine and neuraminidase.\u00a0 Because there are several types of both, viral hemagglutinine and neuraminidase, there are many different viral serotypes.<\/span><\/p>\n  <\/p>\n <\/span><\/p>\n Representation of typical Influenza A Virus structure<\/p>\n  <\/p>\n Hemagglutinine is used by the virus to gain entry into the host cells. It binds to receptors that contain sialic-acid on the host cell surface and causes the virus to become endocytosed. After the endocytosis the virus cell is able to unwrap from its membrane and begin host infection. Neuraminidase is used by the virus when it is time to bud from the host cell membrane. Neuraminidase is an enzyme that will sever the last remaining sialic-acid residue tying the newly formed progeny virus to the host, thus causing the release of the virus and allowing it to infect a new host cell. Because both of these proteins are located on the viral outer membrane, they commonly illicit a host immune response, and this makes them good targets for anti-viral vaccine treatments. Also, since both of these proteins are critical to viral admission and departure from the cell, they each become superior targets for small molecule anti-viral therapies.<\/span><\/p>\n The first class of drugs used to treat viruses of the Orthomyxoviridae<\/em> family was matrix protein (M2) inhibitors. M2 inhibitors, such as amantadine and rimantadine, block a viral ion channel that is necessary for virus proliferation. However, the efficacy of this drug was short lived, as a very small mutation of this protein instilled the virus with complete immunity to the drug. Some work was done on finding M2 inhibitor analogues that would circumvent this mutation, but after several unproductive years the effort was stopped and focus was turned to other viral targets.<\/span><\/p>\n \u00a0\u00a0\u00a0 \u00a0\u00a0\u00a0\u00a0\u00a0 \u00a0\u00a0 <\/span> <\/span><\/p>\n \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 \u00a0\u00a0 Amantadine\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 \u00a0 \u00a0\u00a0\u00a0 Rimantadine<\/span><\/p>\n  <\/p>\n There are currently several different small molecule inhibitors of the influenza neuraminidase. Zanamivir was designed in the late 1960\u2019s and was found to be a very potent competitive inhibitor. However, it had horrible bioavailability and had to be administered through inhalation to direct it to the site of viral infection. Peramivir was another potent competitive inhibitor that was developed some time later, but it also had very low bioavailability; work is currently being done to develop an intravenous treatment with this drug. However, there was one drug that did show promise – Tamiflu.\u00a0 Tamiflu is a potent neuraminidase inhibitor with an effective bioavailability, but there are some down sides to Tamiflu that were underestimated until the late 1990\u2019s, when Tamiflu was being regarded as the number one reactionary drug to a possible influenza pandemic.<\/span><\/p>\n \u00a0\u00a0 \u00a0\u00a0 \u00a0 \u00a0\u00a0 <\/p>\n  <\/p>\n <\/p>\n Zanamivir \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0\u00a0 \u00a0\u00a0\u00a0 \u00a0\u00a0\u00a0 \u00a0\u00a0\u00a0 \u00a0\u00a0\u00a0 \u00a0\u00a0\u00a0 \u00a0\u00a0\u00a0 \u00a0 \u00a0\u00a0\u00a0 \u00a0\u00a0\u00a0 \u00a0\u00a0 Peramivir \u00a0\u00a0\u00a0 \u00a0\u00a0\u00a0 \u00a0\u00a0\u00a0 \u00a0\u00a0\u00a0 \u00a0\u00a0\u00a0 \u00a0\u00a0\u00a0 \u00a0\u00a0 \u00a0 \u00a0\u00a0 \u00a0\u00a0\u00a0 \u00a0\u00a0\u00a0 \u00a0 \u00a0 \u00a0\u00a0 Tamiflu<\/span><\/p>\n The first problem with Tamiflu lays not in the drug itself, but rather in its target, neuraminidase. Neuraminidase is a highly mutagenic protein undergoing antigenic shift on an almost yearly basis. This presents a major problem for any drug that acts as a competitor to it. At the time of a flu pandemic, there will be no guarantee that the pandemic strain of flu will not have mutated outside the influence of Tamiflu, rendering the drug useless. This is not a good scenario for the \u201cmost promising\u201d drug in our influenza arsenal. <\/span><\/p>\n Tamiflu also has a very delicate synthesis process. Currently, the starting reagent, shikimic acid, is only effectively isolated from the ancient Chinese cooking spice Star Anise. Star Anise is only grown in ~ 6 provinces in China, and 90% of the plant is already being utilized by Roche, the pharmaceutical company responsible for Tamiflu, to synthesize Tamiflu. Hence, another strike against Tamiflu: if there was ever a pandemic, it would be nearly impossible to scale up the production of of the drug to match the demand that would be needed to combat such a large scale viral infection.<\/span><\/p>\n <\/p>\n <\/p>\n  <\/p>\n Star anise fruits (Illicium verum<\/em>)\u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0\u00a0 \u00a0 \u00a0 \u00a0\u00a0 \u00a0 Shikimic acid<\/p>\n The next problem with Tamiflu is with the current dosage regime. It is thought by many that the current recommended dosage of Tamiflu, which is commonly prescribed, is much too low, and as a result, Tamiflu is not obliterating viral populations. The remaining viruses may be more resistant to Tamiflu\u2019s mode of action.\u00a0 These more resistant viruses will then be the ones that re-establish infection in a Tamiflu treated host. Thus, this makes a second round of Tamiflu treatment useless if the virus has achieved resistance or immunity.<\/span><\/p>\n Finally, Tamiflu has been reported to have some severe psychological effects on teenage recipients, such as hallucination and delirium. However, it is not clear whether these effects are due to the drug or if they are side effects of the influenza infection. In 2006, a study done by a professor at a Japanese university reported that Tamiflu had no apparent psychological side effects on the ~3000 children monitored in the study. It was, however, later found that the Roche had made significant donations to the department of the university where the principal investigator worked, and with this information in mind one must ask him\/herself exactly how objective the study was.<\/span><\/p>\n  <\/p>\n <\/p>\n Tamiflu (Oseltamivir) pills<\/p>\n  <\/p>\n  <\/p>\n  <\/p>\n Flaviviruses<\/h1>\n  <\/p>\n <\/p>\n \u00a0 \u00a0 \u00a0 \u00a0<\/em><\/p>\n  <\/p>\n \u00a0\u00a0\u00a0 \u00a0\u00a0 Aedes aegypti<\/em> mosquito<\/p>\n  <\/p>\n A genus of the family Flaviviridae, flaviviruses contain (+)stranded RNA and replicate in the host cytoplasm.\u00a0 The flaviviruses cause a variety of diseases.\u00a0 They are spread by insect bites or contact with contaminated blood.\u00a0 The genus includes (but is not limited to) the following virus:<\/span><\/p>\n \u00a0<\/span><\/p>\n Dengue fever virus<\/strong> \u2013 Dengue fever causes fever, joint pain, and severe flu-like symptoms.\u00a0 It can often progress to dengue hemorrhagic fever, which is characterized by internal bleeding and circulatory failure.\u00a0 Infection with the virus has a 5% mortality rate.\u00a0 This may seem low, but more than 50 million people are infected every year.\u00a0 The disease is caused from infection by one of four different virus serotypes, so many people remain susceptible to infection even after outbreaks of the disease, and new outbreaks occur roughly every five years.<\/span><\/p>\n \u00a0<\/span><\/p>\n West Nile virus<\/strong> \u2013 West Nile virus (WNV) infects birds and mammals.\u00a0 In humans, infection by WNV can have no symptoms, cause fever and flu-like symptoms, or lead to West Nile encephalitis or West Nile meningitis.\u00a0 Though the majority of people infected show either no symptoms or non-severe ones, one in 150 people develop the far more serious encephalitis or meningitis, which can be fatal.\u00a0 There are currently no drugs to treat West Nile encephalitis.<\/span><\/p>\n \u00a0<\/span><\/p>\n Yellow fever virus<\/strong> \u2013 This virus causes severe flu-like symptoms.\u00a0 15% of infected patients will develop yellow fever, which is named for the jaundice that occurs with the disease.\u00a0 Along with flu-like symptoms and jaundice, the disease causes haemorrhaging and kidney malfunction.\u00a0 Roughly 7% of infected individuals die.\u00a0 Though there is an effective vaccine, yellow fever is prominent in Africa and South America.\u00a0 There is currently no cure for the disease.<\/span><\/p>\n  <\/p>\n \u00a0\u00a0 \u00a0\u00a0\u00a0 <\/p>\n Dengue fever virus\u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0\u00a0 \u00a0\u00a0\u00a0 \u00a0 \u00a0 West Nile virus\u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0 \u00a0\u00a0 \u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 \u00a0\u00a0 Yellow fever virus<\/p>\n  <\/p>\n  <\/p>\n  <\/p>\n World Community Grid<\/h2>\n  <\/p>\n The World Community Grid is a non-profit organization that uses grid computing for scientific research projects that can benefit humanity.\u00a0 Grid computing joins individual computers together into a \u2018grid\u2019 to increase computational power.\u00a0 Anyone can register their computer with World Community Grid, and computational analyses will be run on these computers when they are idle.\u00a0 <\/span><\/p>\n \u00a0<\/span><\/p>\n The World Community Grid launched a new project in August called \u2018Discovering Dengue Drugs \u2013 Together\u2019.\u00a0 The goal of this project is to find new small molecule inhibitors of viruses in the Flaviviridae family, more specifically Dengue fever virus, West Nile virus, Yellow fever virus, and Hepatitis C virus.\u00a0 These viruses contain a common target for small molecule inhibition, the NS3 protease, which is essential for virus replication.\u00a0 The amino acid sequence and atomic structure of the NS3 protease is very similar in all four viruses, and its structure is known.\u00a0 This allows the computational analyses of one protein structure to be meaningful for all of the viruses.\u00a0 <\/span><\/p>\n \u00a0<\/span><\/p>\n So how is the Discovering Dengue Drugs project finding new drug leads against the NS3 protease?\u00a0 Their method can be divided into two phases.\u00a0 First, they determine the binding orientation of a given small molecule into the active site of the NS3 protease.\u00a0 They do this using mean-field molecular dynamics algorithms and AutoDock, a docking program.\u00a0 Docking is the process of bringing two molecules together.\u00a0 They determine the orientation of the small molecule by maximizing favourable interactions with the protease\u2019s active site and minimizing unfavourable ones.\u00a0 Millions of small molecules are screened through this process.\u00a0 The molecules that appear to have protease inhibitor qualities are advanced to the next phase.<\/span><\/p>\n \u00a0<\/span><\/p>\n In the second phase, the molecules are analyzed in CHARMM, a molecular dynamics program.\u00a0 The binding free energies of the molecules and the protein are calculated<\/span> using the binding orientations determined in phase one.\u00a0 The binding free energy is a thermodynamic measure of the energy difference between the bound and unbound state.\u00a0 This phase is much more precise than phase one, but requires significantly more time.\u00a0 This is why molecules are first screened through phase one.\u00a0 Overall, this process drastically reduces the time required to find potential dengue drug leads.\u00a0 After the second phase is completed any molecules that appear to be good drug leads are tested in labs, where actual antiviral activity is determined.<\/span> <\/span><\/p>\n <\/p>\n  <\/p>\n Yellow fever virus NS3 protease<\/p>\n  <\/p>\n  <\/p>\n  <\/p>\n References<\/h1>\n  <\/p>\n Acheson, N.\u00a0 (2007)\u00a0 Human Immunodeficiency Virus type I.\u00a0 Ed: Witt, K.\u00a0 Fundamentals of Molecular Virology<\/em> (pp 284-293).\u00a0 USA: John Wiley & Sons.<\/p>\n  <\/p>\n Bakkour, N., Y. Lin, S. Maire, L. Ayadi, F. Mahuteau-Betzer, C. Nguyen, C. Mettling, P. Portales, D. Grierson, B. Chabot, P. Jeanteur, C. Branlant, P. Corbeau, and J. Tazi.\u00a0 2007.\u00a0 Small-molecule inhibition of HIV pre-mRNA splicing as a novel antiretroviral therapy to overcome drug resistance.\u00a0 PLoS Pathogens <\/em>3<\/strong>:1530-1539<\/p>\n  <\/p>\n De Francesco R., and G. Migliaccio.\u00a0 2005. Challenges and successes in developing new therapies for hepatitis C.\u00a0 Nature<\/em>.\u00a0 436<\/strong>: 953-960<\/p>\n  <\/p>\n Duong, Y., D. C. Meadows, I. K. Srivastava, J. Gervay-Hague, and T. W. North.\u00a0 2007.\u00a0 Direct inactivation of human immunodeficiency virus type 1 by a novel small-molecule entry inhibitor, DCM205.\u00a0 Antimicrob. Agents Chemother<\/em>. 51<\/strong>: 1780-1786<\/p>\n  <\/p>\n Hartsough, M.\u00a0 Nonclinical development of biotechnology-derived products and small molecules: What are the differences?\u00a0 <http:\/\/www3.niaid.nih.gov\/research\/topics\/radnuc\/PDF\/Hartsough.pdf><\/p>\n  <\/p>\n Meadows, D.C., and J. Gervay-Hague.\u00a0 2006.\u00a0 Current developments in HIV chemotherapy.\u00a0 ChemMedChem<\/em> 1<\/strong>:16-29<\/p>\n  <\/p>\n Nittoli, T., K. Curran, S. Insaf, M. DiGrandi, M. Orlowski, R. Chopra, A. Agarwal, A. Howe, A. Prashad, M. Floyd, B. Johnson, A. Sutherland, K. Wheless, B. Feld, J. O\u2019Connell, T. Mansour, and J. Bloom. 2007.\u00a0 Identification of anthranilic acid derivatives as a novel class of allosteric inhibitors of hepatitis C NS5B polymerase.\u00a0 J. Med. Chem<\/em>. 50<\/strong>: 2108-2116<\/p>\n  <\/p>\n NSW Department of Health\u00a0 <http:\/\/www.ncahs.nsw.gov.au\/sexual-health\/index.php?pageid=275&siteid=154><\/p>\n  <\/p>\n Patrick: Introduction to Medicinal Chemistry – Chapter 17 <http:\/\/www.oup.com\/uk\/orc\/bin\/9780199275007\/patrick_ch17.pdf><\/p>\n  <\/p>\n Wikipedia – Hepatitis C virus\u00a0 <http:\/\/en.wikipedia.org\/wiki\/Hepatitis_C_virus><\/p>\n  <\/p>\n Wikipedia \u2013 Influenza\u00a0 <http:\/\/en.wikipedia.org\/wiki\/Flu><\/p>\n  <\/p>\n Wikipedia – Interferon\u00a0 <http:\/\/en.wikipedia.org\/wiki\/Interferon><\/p>\n  <\/p>\n Wikipedia – Ribavirin\u00a0\u00a0 <http:\/\/en.wikipedia.org\/wiki\/Ribavirin><\/p>\n  <\/p>\n World Community Grid\u00a0 <http:\/\/www.worldcommunitygrid.org\/index.jsp><\/p>\n  <\/p>\n UNAIDS.\u00a0 2006.\u00a0 2006 report on the global AIDS epidemic: Executive summary. <http:\/\/data.unaids.org\/pub\/GlobalReport\/2006\/2006_GR-ExecutiveSummary_en.pdf><\/p>\n","protected":false},"excerpt":{"rendered":" \u00a0Small Molecules as Antiviral Drugs   Today, small molecules are commonly used as antiviral drugs, generally leading to the inhibition of some viral protein or enzyme.\u00a0 When we say ‘small molecule’ we are referring to molecules of a low molecular weight.\u00a0 Small molecules are not the only option in drug therapy.\u00a0 There are lots of… Continue reading Small Molecules as Antiviral Drugs<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"open","ping_status":"open","template":"","meta":{"footnotes":""},"_links":{"self":[{"href":"https:\/\/amcrasto.theeurekamoments.com\/wp-json\/wp\/v2\/pages\/1122"}],"collection":[{"href":"https:\/\/amcrasto.theeurekamoments.com\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/amcrasto.theeurekamoments.com\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/amcrasto.theeurekamoments.com\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/amcrasto.theeurekamoments.com\/wp-json\/wp\/v2\/comments?post=1122"}],"version-history":[{"count":1,"href":"https:\/\/amcrasto.theeurekamoments.com\/wp-json\/wp\/v2\/pages\/1122\/revisions"}],"predecessor-version":[{"id":1123,"href":"https:\/\/amcrasto.theeurekamoments.com\/wp-json\/wp\/v2\/pages\/1122\/revisions\/1123"}],"wp:attachment":[{"href":"https:\/\/amcrasto.theeurekamoments.com\/wp-json\/wp\/v2\/media?parent=1122"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}