Current Pharmaceutical Design - Volume 20, Issue 21, 2014

HIV protease (PR) is a key target for antiviral drugs, and HIV protease inhibitors (PIs) are a prime example of successful structure-based drug design. PIs show clear therapeutic benefits, but their efficacy can be compromised by poor bioavailabilitity, unwanted side effects, and most importantly, development of antiviral drug resistance. Therefore, the quest for novel, highly active compounds with improved resistance profiles, better pharmacokinetic properties, and fewer adverse effects continues. In particular, the problem of cross-resistance could be circumvented by identifying novel compounds that show different binding modes to HIV PR than the current clinical inhibitors.

Despite the fact that HIV-Protease is an over 20 years old target, computational approaches to rational design of its inhibitors still have a great potential to stimulate the synthesis of new compounds and the discovery of new, potent derivatives, ever capable to overcome the problem of drug resistance. This review deals with successful examples of inhibitors identified by computational approaches, rather than by knowledge-based design. Such methodologies include the development of energy and scoring functions, docking protocols, statistical models, virtual combinatorial chemistry. Computations addressing drug resistance, and the development of related models as the substrate envelope hypothesis are also reviewed. In some cases, the identified structures required the development of synthetic approaches in order to obtain the desired target molecules; several examples are reported.

Viral DNA integration into the infected cell genome is an essential step in the HIV-1 life cycle. Hence, the viral integrase enzyme has become an important target for antiviral therapy. The integrase's activity action relies on the binding to its cellular partners, therefore the knowledge of the structural determinants is very important from a therapeutic perspective. Here we first review published computer-aided structural predictions of HIV-1 integrase in complex with its interactors. These include DNA and the human HAT protein. Next, we present a prediction of the complex between HIV-1 integrase with the human prolyl-isomerase-1 (hPin1) enzyme. Interaction with hPin1 is crucial for efficient HIV-1 infection and it increases integrase stability (Manganaro et. al 2010, Nat. Med. 16, 329). The modeling presented here, which is validated against experimental data, provides a rationale for a variety of viral protein's mutations which impair protein function and HIV-1 virus replication in vivo without significantly affecting enzymatic activity.

Even though a number of groups have identified peptidic inhibitors for DENV and WNV proteases, and several high throughput screening campaigns have been performed, the progress towards drug candidates has been very slow. This is in stark contrast to the related NS3/NS4A protease of HCV for which two peptidomimetic drugs were approved in 2011. In this review we will compare the NS3 proteases of the flaviviruses WNV and DENV with that of HCV, and answer the question whether the flavivirus proteases are inherently more challenging, or whether the lack of success is simply due to the limited resources that have so far been invested in these neglected disease targets.

Viruses belonging to the Flaviviridae family primarily spread through arthropod vectors, and are the major causes of illness and death around the globe. The Flaviviridae family consists of 3 genera which include the Flavivirus genus (type species, yellow fever virus) as the largest genus, the Hepacivirus (type species, hepatitis C virus) and the Pestivirus (type species, bovine virus diarrhea). The flaviviruses (Flavivirus genus) are small RNA viruses transmitted by mosquitoes and ticks that take over host cell machinery in order to propagate. However, hepaciviruses and pestiviruses are not antropod-borne. Despite the extensive research and public health concern associated with flavivirus diseases, to date, there is no specific treatment available for any flavivirus infections, though commercially available vaccines for yellow fever, Japanese encephalitis and tick-born encephalitis exist. Due to the global threat of viral pandemics, there is an urgent need for new drugs. In many countries, patients with severe cases of flavivirus infections are treated only by supportive care, which includes intravenous fluids, hospitalization, respiratory support, and prevention of secondary infections. This review discusses the strategies used towards the discovery of antiviral drugs, focusing on rational drug design against Dengue virus (DENV), West Nile virus (WNV), Japanese encephalitis virus (JEV), Yellow Fever virus (YFV) and Hepatitis C virus (HCV). Only modified peptidic, nonpeptidic, natural compounds and fragment-based inhibitors (typically of mass less than 300 Da) against structural and non-structural proteins are discussed.

Hepatitis C virus (HCV) is the major etiological agent of human non-A and non-B hepatitis, affecting more than 170 million people worldwide. While the current standard of care for the treatment of HCV infection is ribavirin in combination with interferon-α (IFN-α), this therapeutic regimen presents several drawbacks, mainly related to important and serious side effects, to resistance issues, and to the lack of efficacy for the treatment of specific viral genotypes. In 2011, the FDA approved two HCV-targeted antivirals, namely boceprevir and telaprevir. These two drugs inhibit the protease activity of the viral enzyme NS3/4A, and in Phase III clinical trials proved to be effective in achieving sustained virological response rate up to 75%. However, problems associated with these therapeutic regimens still exist and need to be addressed. Intense research efforts in the field are aimed at discovering small-molecule inhibitors of HCV enzymes and proteins such as NS5B and NS5A and at developing NS3 protease inhibitors active against resistant viruses expressing mutated NS3 protease. The most recent advances for the rational drug design of such inhibitors are here reviewed.

Hepatitis C virus (HCV) infections are a serious viral health problem globally, causing liver cirrhosis and inflammation that can develop to hepatocellular carcinoma and death. Since the HCV NS3/4A protease complex cleaves the scissile peptide bond in the viral encoded polypeptide to release the non-structural proteins during the viral replication process, this protease is then an important target for drug design. The computer-aided drug design and screening targeted at NS3/4A protease of HCV were reviewed. In addition, using steered molecular dynamics simulations, potent inhibitors of the NS3/4A complex were searched for by screening the ZINC database based upon the hypothesis that a high rupture force indicates a high binding efficiency. Nine top-hit compounds (59500093, 59784724, 13527817, 26660256, 29482733, 25977181, 28005928, 13527826 and 13527826) were found that had the same or a greater maximum rupture force (and so assumed binding strength and inhibitory potency) than the four current drugs and so are potential candidates as anti- HCV chemotherapeutic agents. In addition, van der Waals interactions were found to be the main contribution in stabilizing the ligand- NS3/4A complex.

The outbreak of avian influenza A (H5N1) virus has raised a global concern for both the animal as well as human health. Besides vaccination, that may not achieve full protection in certain groups of patients, inhibiting neuraminidase or the transmembrane protein M2 represents the main measure of controlling the disease. Due to alarming emergence of influenza virus strains resistant to the currently available drugs, development of new neuraminidase N1 inhibitors is of utmost importance. The present paper provides an overview of the recent advances in the design of new antiviral drugs against avian influenza. It also reports findings in binding free energy calculations for nine neuraminidase N1 inhibitors (oseltamivir, zanamivir, and peramivir -carboxylate, -phosphonate, and -sulfonate) using the Linear Interaction Energy method. Molecular dynamics simulations of these inhibitors were performed in a free and two bound states – the so called open and closed conformations of neuraminidase N1. Obtained results successfully reproduce the experimental binding affinities of the already known neuraminidase N1 inhibitors, i.e. peramivir being a stronger binder than zanamivir that is in turn stronger binder than oseltamivir, or phosphonate inhibitors being stronger binders than their carboxylate analogues. In addition, the newly proposed sulfonate inhibitors are predicted to be the strongest binders – a fact to be confirmed by their chemical synthesis and a subsequent test of their biological activity. Finally, contributions of individual inhibitor moieties to the overall binding affinity are explicitly evaluated to assist further drug development towards inhibition of the H5N1 avian influenza A virus.

Viral diseases have been affecting the human race since ancient times. Currently, a long list of diseases caused by the viruses is available and extensive research in this area has resulted in understanding the finest details of the molecular mechanism of pathogenesis caused by these pathogens. Side by side, efforts have been made towards the search and design of antiviral agents that could interfere with viral pathogenesis. As a result of these efforts a number of effective antiviral agents have been developed and are available in the market. However, the high cost and lengthy protocol of the drug discovery process are some of the major limiting factors in the development of new and more effective antiviral agents. Considering the above fact, presently the research community is trying to integrate short and cost effective techniques in the modern drug discovery process for the identification and design of novel antiviral agents. Computeraided drug design (CADD), which comprises of various techniques like molecular docking, virtual screening, three dimensional quantitative structure activity relationship (3D-QSAR) studies and many more, has the capability to speed up the antiviral drug development process. Successful design of antiviral drugs like Relenza, Saquinavir and Tamiflu have validated application of these techniques and holds a bright future in drug discovery protocol. This review explores the role of CADD in antiviral drug development and highlights the recent advances in antiviral drug research using computer-aided structure based approaches.