Current Pharmaceutical Biotechnology - Volume 14, Issue 5, 2013

Among the currently available options for the treatment of chronic myeloid leukemia (CML), ATP-competitive tyrosine kinases inhibitors (Gleevec®, Dasatinib® and Nilotinib®) represent one of the most promising therapeutic approaches developed in the last 10-15 years. However, the initial enthusiasm generated by the high response rate to these drugs has been dampened by the development of resistance. The T315I mutation at the gatekeeper residue is very frequent in advanced phases of the disease and is one of the main causes of resistance, disrupting important contact points between the inhibitors and the enzyme. Different strategies have been implemented to overcome this resistance, such as the recent development of more selective non-ATP competitive inhibitors targeting sites outside the ATP-binding cleft. Some of these allosteric inhibitors alter the kinase conformation, while others directly compete with the protein substrates. Another interesting family of allosteric inhibitors is represented by those compounds targeting the myristate-pocket of Bcr-Abl (myristate-pocket binders). The binding of these inhibitors blocks the Bcr-Abl kinase in the inactive conformation and provides an advantage in overcoming drug resistance due to kinase mutations. This review reports the last findings in the development of novel myristate-pocket binders of Bcr-Abl as promising anti-leukemia agents.

The multiple therapeutic approaches developed so far to cope HIV-1 infection, such as anti-retroviral drugs, germicides and several attempts of therapeutic vaccination have provided significant amelioration in terms of life-quality and survival rate of AIDS patients. Nevertheless, no approach has demonstrated efficacy in eradicating this lethal, if untreated, infection. The curative power of gene therapy has been proven for the treatment of monogenic immunodeficiensies, where permanent gene modification of host cells is sufficient to correct the defect for life-time. No doubt, a similar concept is not applicable for gene therapy of infectious immunodeficiensies as AIDS, where there is not a single gene to be corrected; rather engineered cells must gain immunotherapeutic or antiviral features to grant either short- or long-term efficacy mostly by acquisition of antiviral genes or payloads. Anti-HIV/AIDS gene therapy is one of the most promising strategy, although challenging, to eradicate HIV-1 infection. In fact, genetic modification of hematopoietic stem cells with one or multiple therapeutic genes is expected to originate blood cell progenies resistant to viral infection and thereby able to prevail on infected unprotected cells. Ultimately, protected cells will re-establish a functional immune system able to control HIV-1 replication. More than hundred gene therapy clinical trials against AIDS employing different viral vectors and transgenes have been approved or are currently ongoing worldwide. This review will overview anti-HIV-1 infection gene therapy field evaluating strength and weakness of the transgenes and payloads used in the past and of those potentially exploitable in the future.

Peptides are ideally suited to mimic natural ligands and thereby function in an antagonistic or agonistic way. Furthermore they are able to physiologically disrupt functional complexes due to their small size and specific binding properties. Proteins form homo- or heteromeric (macro)molecular complexes and intricate networks by interacting with small molecules, peptides, nucleic acids or other proteins. On average, five interaction partners have been estimated for any given cellular protein, illustrating the complexity of the formed ‘interactomes’ and the impact of their investigation. Many protein-protein interactions are mediated by hot-spots, which comprise only a small part of the large binding interface but account for 80% of the binding energy. Thus, these hot spots provide an ‘Achilles heel’ for pharmaceutical interventions aiming at the disruption of functional protein-protein complexes. Methods to select peptides for defined target structures include display technologies on phages, ribosomes or yeast, and the yeast-two-hybrid system. Once selected, these peptides can be optimized for their binding affinity using peptide arrays. Stabilization of biologically unstable peptides is achieved by the introduction of non-natural amino acids to form so-called peptidomimetics that are resistant to cellular proteases. Moreover, lipocalins and peptide aptamers represent scaffolded binding structures with unique binding characteristics and enhanced stability. In case of extracellular targets, like cell surface receptors or pathogens in patients` plasma, peptide inhibitors have direct access. Addressing intracellular targets with peptides is more difficult since short hydrophilic peptides generally do not cross plasma membranes on their own. However, intracellular uptake of peptides can be achieved by coupling to carrier systems like liposomes or nanoparticles or upon fusion to a protein transduction domain. Alternatively, peptides may be expressed within cells after transduction with viral vectors in a gene therapy setting. This review will summarize the broad potential of peptides as drugs, with special emphasis on peptides which inhibit protein-protein interactions.

In general, drug discovery in the therapeutic field of infectious disease has a stellar track record. And yet, subsets of pathogens, for example many classes of viruses other than HIV, HSV, influenza, and HCV, have been poorly addressed. In addition, the development of resistance remains a specter of great concern for almost all current chemotherapy directed against infectious diseases, including viruses. Within the viral lifecycle, capsid assembly stands out as a step occurring in all viruses, which has not been the subject of extensive drug discovery programs. Until recently, the common view of assembly was that all the necessary information for assembly was contained in the sequence of the viral protein, in other words, the capsid self-assembles. In the last few years, a body of data has opened new opportunities for antiviral pharmaceutical research. Evidence that host proteins may play catalytic or essential structural roles in viral capsid assembly suggests that these host proteins and their functions are novel targets for small molecule therapeutics. Here we review the current understanding of the capsid assembly process with emphasis on recent data that demonstrate the essential role of host proteins in capsid assembly. Furthermore, this dependency of assembly on host factors appears quite sensitive to small molecule intervention. Implications of this alternate mechanism of capsid assembly are also considered. For example, the dependency on host factors could impose a potent barrier to development of viral resistance to a host-targeted anti-capsid chemotherapeutic. Finally, we give specific examples of the current state of drug discovery programs that have focused on therapeutic inhibition of host-assisted viral capsid assembly.

Poly(ADP-ribose) polymerases (PARPs) and poly(ADP-ribosylation) play essential roles in several biological processes, among which neoplastic transformation and telomere maintenance. In this paper, we review the poly(ADPribosylation) process together with the highly appealing use of PARP inhibitors for the treatment of cancer. In addition, we report our results concerning poly(ADP-ribosylation) in a cellular model system for neoplastic transformation developed in our laboratory. Here we show that PARP-1 and PARP-2 expression increases during neoplastic transformation, together with the basal levels of poly(ADP-ribosylation). Furthermore, we demonstrate a greater effect of the PARP inhibitor 3-aminobenzamide (3AB) on cellular viability in neoplastically transformed cells compared to normal fibroblasts and we show that prolonged 3AB administration to tumorigenic cells causes a decrease in telomere length. Taken together, our data support an active involvement of poly(ADP-ribosylation) in neoplastic transformation and telomere length maintenance and confirm the relevant role of poly(ADP-ribosylation) inhibition for the treatment of cancer.

Knowledge of three-dimensional structures of biological macromolecules is essential for a complete understanding of many biological processes. X-ray crystallography is the most widely used technique in structural biology and can provide highly detailed structures of proteins, nucleic acids or macromolecular complexes without any size limit. In the past decade, several recent advances in biological crystallography and automation of data collection and structure solution allowed extraordinary progresses and now more than 93 000 crystal structures have been deposited into the Protein Data Bank. This wealth of structural data significantly helped the elucidation of many biological processes and led to the development of new drugs. In this review we will show how of X-ray crystallography can provide insights into the mechanism of action of biological processes and can contribute to the rationale development of ligands through structure-based drug design.

Drug development is a long and expensive process. It starts from the identification of a small molecule (hit compound) endowed with the ability to suppress a cellular or viral enzyme essential for the development of a given disease and proceeds through subsequent rounds of structural changes and optimization until the desired pharmacological properties are reached (lead compound). At any point of the hit-to-lead optimization process, it is of essence to monitor the behavior of the intermediate molecules with respect to their molecular targets. This involves precise mechanism of action studies as well as quantitative measurement of the performance of the compound against its target. Enzyme kinetic studies are thus an essential component of the drug development process. Relevant examples of the power of enzyme kinetics in the antiviral drug development process will be discussed in the context of anti-HIV chemotherapy.

Highly active antiretroviral therapy (HAART) dramatically has changed the course of HIV infection. Currently, this therapy involves the use of agents from at least two distinct classes of antivirals: a protease inhibitor in combination with two nucleoside/nucleotide reverse transcriptase inhibitors (N(t)RTIs), or a non-nucleoside reverse transcriptase inhibitor (NNRTI) in combination with NRTIs. Recently, the third family of antivirals started to be used clinically, with the advent of enfuvirtide, the first fusion inhibitor. This broad spectrum of anti-HIV agents recently was extended with compounds inhibiting HIV integrase and vital entry. But these advances did not come without a cost: there were the short- and long-term drug toxicities, emergence of drug resistance, and persistence of viral reservoirs. For these reasons, there is a pressing need for novel anti-HIV drugs, particularly those that have a novel action mechanism, as these might be less likely to show cross-resistance with current therapies. The field of bioinformatics has become a major part of the drug discovery pipeline playing a key role in improvement and acceleration of the time and money consuming process of the drug development. Here we review the application of the EIIP/AQVN (Electron-Ion Interaction Potential, EIIP; Average Quasi Valence Number, AQVN) bioinformatics concept in the development of new anti-HIV drugs and propose a simple theoretical criterion for a virtual screening of molecular libraries for promising lead anti-HIV compounds and refinement of selected lead compounds in order to increase their biological activity.