Frontiers in Medicinal Chemistry

HIV-1 integrase is a multidomain enzyme which is required for the integration of viral DNA into the host genome. It is one of three enzymes of HIV, the others being Reverse Transcriptase and Protease. It is an attractive target for therapeutic drug design. The enzyme consists of three domains. The N-terminal domain has a His2Cys2 motif which chelates zinc, the core domain has the catalytic DDE motif which is required for its enzymatic activity, and the C-terminal domain has an SH3-like fold which binds DNA nonspecifically. We review the structures of various integrase fragments, the core domain with inhibitors bound, and propose a model for DNA binding.

Currently, 20 drugs have been approved for Human Immunodeficiency Virus type-1 (HIV-1) clinical therapy. These drugs inhibit HIV-1 reverse transcriptase, protease, or virus entry. Introduction of a combination therapy with reverse transcriptase inhibitors and protease inhibitors has resulted in a drastic decrease in HIV-1 related mortality. Although the combination therapy can suppress viral replication below detection levels in current available assays, low levels of on-going viral replication still persist in some patients. Long-term administration of the combination therapy may increase selective pressure against viruses, and subsequently induce emergence of multiple drug-resistant HIV-1 variants. Attempts have been made to design novel antiretroviral drugs that would be able to suppress replication of the resistant variants. At present, several investigational drugs are being tested in clinical trials. These drugs target not only the resistant variants, but also improvement in oral bioavilability or other viral proteins such as HIV-1 integrase, ribonuclease H, and HIV-1 entry (CD4 attachment inhibitors, chemokine receptors antagonists, and fusion inhibitors). Understanding mechanism(s) of action of the drugs and mechanisms of drug resistance is necessary for successful designs in the next generation of anti-HIV-1 drugs. In this review, the mechanisms of action of reverse transcriptase- and protease-inhibitors, and the mechanism of resistance to these inhibitors, are described.

Gene therapy is a rapidly evolving field of medicine, which potentially offers new treatments for cardiovascular diseases. With the use of gene transfer methods it is possible to modify somatic cells in blood vessels and myocardium to overexpress or inhibit pathologically important proteins and achieve therapeutic effects. Prevention of restenosis after vascular interventions such as percutanous coronary angioplasty (PTCA), percutanous peripheral angioplasty (PTA) or stent implantation, prevention of venous grafts failure and therapeutic angiogenesis are the major aims of experimental studies and clinical gene therapy. The promise of gene therapy in the treatment of cardiovascular diseases remains high. Experimental studies have established the proof of principle that gene transfer to cardiovascular system can achieve therapeutic effects. First human clinical trials provided the initial evidence of the feasibility and safety of the novel therapy. There are also first successful reports on the prevention of neointimal hyperplasia and promotion of therapeutic angiogenesis in clinical trials. However, there are still important questions regarding utility, efficiency and safety of gene therapy in the treatment of cardiovascular diseases. In this review we discuss the rapid progress in cardiovascular gene therapy, the development of delivery systems and vectors, most promising therapeutic genes and results of the recent human clinical trials.

Heart failure is a common condition, associated with both poor prognosis and poor quality of life. In contrast to all other cardiovascular diseases, the prevalence of heart failure is increasing in the western world, and is likely to continue to do so as the population ages. In the UK, a significant proportion of patients with heart failure come from South Asian and African Caribbean ethnic groups. A large body of evidence exists that there may be epidemiological and pathophysiological differences between patients with heart failure from different ethnic groups. Treatments such as ACE inhibitors, which are now part of standard heart failure therapy, have an evidence base consisting of trials in patients of almost exclusively white ethnicity. Such treatments may not be equally effective in patients from other ethnic groups. This review will discuss the current evidence for heart failure management with respect to ethnicity, and consider the implications for future drug development and implications for antihypertensive therapy.

Peptidomimitism is applied to the medicinal chemistry in order to synthesize drugs that devoid of the disadvantages of peptides. AT1 antagonists constitute a new generation of drugs for the treatment of hypertension designed and synthesized to mimic the C-terminal segment of Angiotensin II and to block its binding action on AT1 receptor. An effort was made to understand the molecular basis of hypertension by studying the conformational analysis of Ang II and its derivatives as well as the AT1 antagonists belonging to SARTANs class of molecules. Such studies offer the possibility to reveal the stereoelectronic factors responsible for bioactivity of AT1 antagonists and to design and synthesize new analogs. An example will be given which proves that drugs with better pharmacological and financial profiles may arise based on this rational design.

Cardiac arrhythmias represent a major area of cardiovascular research, and for drug therapy, a large choice of antiarrhythmic agents have been available. However, clinical trials with antiarrhythmic drugs have recently indicated that serious side effects may considerably limit the use of various antiarrhythmic agents, in particular, for preventing arrhythmia-related mortality. Amiodarone with its complex mode of action, while exerting a strong and favorable antiarrhythmic action, posseses extracardiac untoward side effects originating from its chemical structure.

In this paper, we report on our attempt to develop conceptually new, therapeutically valuable antiarrhythmic compounds, in which Class I/B and Class III features were combined into single molecules bearing no structural resemblance to amiodarone. Synthesis and pharmacological screening of series of N- (phenylalkyl)-N-(phenoxyalkyl)amines led us to discover some new promising compounds with the required dual mode of action. GYKI-16638, selected for further investigation, was also found to possess a remarkable in vivo antiarrhythmic effect, and it is now considered as a safe new antiarrhythmic drug candidate.

Adenosine receptors are widely distributed in the body and modulate numerous physiological processes. Four receptor subtypes (termed A1, A2A, A2B and A3) have been identified based on their pharmacological profile and cloning. Activation of the A1 adenosine receptors produces a number of effects including a reduction in heart rate and atrial contractility, the attenuation of the stimulatory actions of catecholamines on the heart as well as a reduction of lipolysis in adipose tissue. As a result, A1AR agonists have been targeted as anti-arrhythmic and cardioprotective agents. This review discusses the synthesis, structure-activity relationships and therapeutic potential of A1AR agonists.

Most drugs with central nervous system (CNS) activity enter the brain either by diffusing across the membranes which comprise the blood-brain barrier (BBB) or by being transported by carrier systems across those membranes. Substances which cannot cross the BBB by one of these mechanisms, like serum albumin, are virtually excluded from the CNS. However, this exclusion is not absolute. Cerebrospinal fluid (CSF) levels of albumin, for example, are about 0.5% those of serum levels. Albumin enters the CNS through a variety of pathways collectively termed the extracellular pathways. Any circulating substance can, in theory, use these pathways to enter the CNS. But, traditional drug development has ignored this pathway. To approach even the CSF/serum ratio of 0.5%, a candidate therapeutic would need to meet several criterion: long half-life in blood, small volume of distribution, high potency in the CNS, and absence of brain-to-blood efflux. Two emerging therapeutics which are likely exerting their CNS effects by way of the extracellular pathways are antibodies directed against amyloid beta protein (ABP) and erythropoietin (Epo) used in the treatment of stroke. These examples suggest that the extracellular pathways are an option for the delivery of certain therapeutics to the brain.

The brain remains an area where little corrective surgery can be performed and the reversal of damage is almost impossible. Recently, reports of agents offering neuroprotection have begun to appear in the literature. The concept of neuroprotection is the administration of some agent, which should reverse some of the damage or prevent further damage. Some agents offer protection against cell degeneration to the neuronal cells. Still other agents specifically protect the dopamine neurons and the retina. The majority of neuroprotective agents are antioxidants. An immunosuppressive immunophilin ligand, NOS inhibitor, σ-1 modulator, AMPA antagonist and Ca2+ channel blocker have all shown neuroprotective activity. An oestrogen agonist and two glycoprotein IIb/IIIa antagonists also exhibit neuroprotective activity. Most of the synthetic compounds presented were not originally designed as neuroprotective agents but were found to possess neuroprotective activity in later studies. Many of these compounds are biologically active natural products, either plant extracts or endogenous peptides/proteins. This chapter will present the most recent reports on these agents.

In the last decade, nicotinic acetylcholine receptors (nAChRs) have emerged as important targets for drug discovery. The therapeutic potential of nicotinic agonists depends substantially on the ability to selectively activate certain receptor subtypes that mediate beneficial effects. The design of such compounds has proceeded in spite of a general shortage of data pertaining to subtype selectivity. Medicinal chemistry efforts have been guided principally by binding affinities to the α4β2 and/or α7 subtypes, even though these are not predictive of agonist activity at either subtype. Nevertheless, a diverse family of nAChR ligands has been developed, and several analogs with promising therapeutic potential have now advanced to human clinical trials. This paper provides an overview of the structure-affinity relationships that continue to drive development of new nAChR ligands.

First described by Alois Alzheimer in 1907, Alzheimer's disease (AD) is the most common dementia type, affecting approximately 20 million people worldwide. As the population is getting older, AD is a growing health problem.

AD is currently treated by symptomatic drugs, the acetylcholinesterase inhibitors, based on the cholinergic hypothesis (1976).

During the past decade, advances in neurobiology have conducted to the identification of new targets. Although some of these innovative approaches tend to delay onset of AD, others are still symptomatic.

In this review, we present an overview of the several strategies and new classes of compounds against AD.

The melanocortin pathway consists of endogenous agonists, antagonists, G-protein coupled receptors (GPCRs), and auxiliary proteins. This pathway has been identified to participate physiologically in numerous biological pathways including energy homeostasis, pigmentation, sexual function, inflammation, cardiovascular function, adrenal function, sebaceous gland lipid production, just to list a few. During this past decade, a clear link between the melanocortin-4 receptor (MC4R) and obesity, in both mice and humans via the regulation of food intake and energy homeostasis, has made this pathway the target of many academic and industrial research endeavors in attempts to develop potent and selective MC4R small molecules as anti-obesity therapeutic agents. Herein, we attempt to summarize the known proteins that constitute the melanocortin system and discuss advances in peptide and non-peptide drug discovery.

Type 2 diabetes is a prevalent disease which afflicts over 150 million people worldwide and there is a great medical need for new therapeutic agents to treat it. Inhibition of protein tyrosine phosphatase 1B (PTP1B) has emerged as a highly validated, attractive approach for the treatment of not only type 2 diabetes but also obesity. Discovery of small-molecule inhibitors has been pursued extensively in both academia and industry and a number of very potent and selective inhibitors have been identified. With X-ray crystallography, the binding modes of several classes of inhibitors have been elucidated. This has resulted in significant progress in understanding important interactions between inhibitors and specific residues of PTP1B, which could help the design of future inhibitors. However, since the active site of PTP1B that most of these inhibitors bind to is highly hydrophilic, it remains a challenge to identify inhibitors with both excellent in vitro potency and drug-like physiochemical properties, which would lead to significant in vivo activities.

Falling infection rates in the developed world are being matched by a rapidly rising incidence of allergic and autoimmune diseases. This review explores the hypothesis that there is a causal link between these phenomena and that infections can prevent the onset of autoimmune disease. The hypothesis is discussed with particular reference to Type I diabetes in the NOD mouse and the ability of the helminth infection Schistosoma mansoni to prevent its onset. The article addresses the possible mechanisms that underly this protection. The effects of protective pathogen-derived agents on key cells of the innate immune system such as dendritic cells are distinct and include the production of anti-inflammatory cytokines such as IL-10. The most likely mechanisms by which these innate changes prevent the subsequent adaptive autoimmune destruction are: (1) the production of systemically high levels of cytokines that oppose the production of cytokines that drive the autoimmune process - possibly via the action of natural killer T (NKT) cells (2) the induction of regulatory T cells that inhibit the action of autoreactive cells and (3) the production of pathogen-specific T cells that are not autoreactive and compete with autoreactive cells for survival signals such as cytokines and T cell receptor ligation.

The analysis of the molecular basis of autoimmune diseases is currently under intense investigation. The identification of novel mechanisms underlying the pathogenesis of these diseases generates the possibility for the development of new therapeutic agents. In this review we summarize the results leading to novel insights concerning the molecular processes involved in the pathogenesis of rheumatoid arthritis, systemic lupus erythematodes, multiple sclerosis and diabetes type 1. We focus on the role of transcription factors such as nuclear factor kappa B, activator protein 1, peroxisome proliferator-activated receptor, vitamin D receptor and the glucocorticoid receptor that mediate pro- and anti-inflammatory effects and therefore represent direct or indirect targets for therapeutic intervention.

Activating mutations of FLT3 (FMS-Like Tyrosine kinase-3) are the most common molecular abnormality in acute myeloid leukemia (AML). Their presence is associated with a worse prognosis, and the recognition of this has led to the development of several new small molecule FLT3 tyrosine kinase inhibitors. In this review, we summarize these developments and compare and contrast these novel agents both with regards to the assays used to characterize them as well as to their clinical potential.

Ca2+ signalling is involved in virtually all cellular processes: among the others, it controls cell survival, proliferation and death regulating a plethora of intracellular enzymes located in the cytoplasm, nucleus and organelles.

Changes in the cytosolic free Ca2+ concentration may be due either to release from the intracellular Ca2+ stores or to influx from the extracellular medium, through the opening of plasmamembrane calcium-permeable channels. In particular, Ca2+ entry from the extracellular space is a mechanism able to sustain long lasting intracellular Ca2+ elevations: this signal, activated by many growth factors and mitogens in normal and tumoral tissues, is linked to DNA transcription and duplication, finally leading to cell proliferation.

In the last years many informations have been provided about the transduction mechanisms related to Ca2+ entry induced by mitogenic factors, mostly binding to tyrosine kinase receptors, but also to G-protein coupled ones. Nevertheless, some key points remain to be fully clarified: among them, the molecular structure of the Ca2+ channels involved, their regulation by intracellular messengers, and the modes through which specificity is achieved.

The increasing knowledge on Ca2+ entry-dependent control of proliferation may provide a more satisfactory understanding of pathological alterations, including cancer progression and angiogenesis. A detailed description of the mechanisms that trigger Ca2+ entry, and in particular the definition of calcium-permeable channels and their modulators at the molecular levels, will greatly improve our possibility to take advantage of Ca2+ entry regulation as a therapeutic approach for the control of cell proliferation, designing antibodies or molecules with low side effects and specific channel blocker functions. The review will focuse on this topic.

The contribution of small molecular weight chemoattractant cytokines (chemokines) and their receptors in the trafficking of tumor, immune and vascular cells pertaining to the development and progression of cancer has begun to be investigated. The current literature indicates that interactions between the immune network, angiogenic and cell survival cascades are important for the trafficking and progression of human cancer and that chemokines and chemokine receptors play a central role in these complex inter-related pathways. Several therapeutic approaches have been reviewed and suggest that the most promising arise from the development of combinations of chemokine receptor antagonists.

During the last two decades, the number of sequence-known proteins has increased rapidly. In contrast, the corresponding increment for structureknown proteins is much slower. The unbalanced situation has critically limited our ability to understand the molecular mechanism of proteins and conduct structurebased drug design by timely using the updated information of newly-found sequences. Therefore, it is highly desired to develop an automated method for fast deriving the 3D (dimensional) structure of a protein from its sequence. Under such a circumstance, the structural bioinformatics was emerging naturally as the times required. In this review, three main strategies developed in structural bioinformatics, i.e., pure energetic approach, heuristic approach, and homology modeling approach, as well as their underlying principles, are briefly introduced. Meanwhile, a series of demonstrations are presented to show how the structural bioinformatics has been applied to timely derive the 3D structures of some functionally important proteins, helping to understand their action mechanisms and stimulating the course of drug discovery. Also, the limitation of these approaches and the future challenges of structural bioinformatics are briefly addressed.

Chemical genomics, which utilizes specially designed small chemical compounds early in the discovery phase of new drugs to explore the life science at various levels, can address biological questions that are not amenable to genetic manipulation or functional genomics/proteomics approaches. Following the development of HT phenotypic assays and DNA expression analysis, the integration of cell-based assays with activity / affinity-based approaches allows us to interrogate the cells by analyzing phenotypic alterations, changes of transcript signature or detecting the differences in protein expression levels. Furthermore, activity / affinitybased techniques directly provide a druggable subset of gene products which interact with small molecules, greatly reducing the complexity of analyzing the proteome. In this paper, we give an account of the recent advances (approaches and strategies) in the field of chemical genomics, and discuss how these approaches enable the investigator to obtain a novel therapeutically relevant target as well as drug candidates acting on them in a target-specific manner. This novel post-genomic discovery strategy, where target identification/ validation is carried out by interactions with small molecules, could significantly reduce the time-scale for early drug discovery, and increase the success rate of finding novel, druggable targets, as well as more specific drug candidates.

A major goal in contemporary drug design is to develop new ligands with high affinity of binding toward a given protein receptor. Pharmacophore, which is the three-dimensional arrangement of essential features that enable a molecule to exert a particular biological effect, is a very useful model for achieving this goal. If the three-dimensional structure of the receptor is known, pharmacophore is a complementary tool to standard techniques, such as docking. However, frequently the structure of the receptor protein is unknown and only a set of ligands together with their measured binding affinities towards the receptor is available. In such a case, a pharmacophore-based strategy is one of the few applicable tools.

Here, we present a broad, yet concise, guide to pharmacophore identification and review a sample of applications for drug design. In particular, we present the framework of the algorithms, classify their modules and point out their advantages and challenges.

A large number of computational methodologies have been used to predict, and thus help explain, the metabolism catalysed by the enzymes of the cytochrome P450 superfamily (P450s). The methodologies and resulting models are summarized. This illustrates that investigations so far have focused on a small number of the many P450s; specifically those that are involved in drug metabolism. The models have evolved from simple comparisons of known substrates to more elaborate experiments that require considerable computer power. These models help to explain and, more importantly, predict the involvement of P450s in the metabolism of specific compounds.

The goal of this paper is to review the variety of approaches used to improve lead generation, in terms of cost, time and risk management. Our analysis shows that successful lead generation requires not only an accurate definition of the needs (to define the most relevant assay protocols and readouts), but most of all a good hit as a starting point. It also appears that teams where techniques and knowledge are combined, are more successful in that difficult game.

Virtual screening, especially the structure-based virtual screening, has emerged as a reliable, cost-effective and time-saving technique for the discovery of lead compounds. Here, the basic ideas and computational tools for virtual screening have been briefly introduced, and emphasis is placed on aspects of recent development of docking-based virtual screening, scoring functions in molecular docking and ADME/Tox-based virtual screening in the past three years (2000 to 2003). Moreover, successful examples are provided to further demonstrate the effectiveness of virtual screening in drug discovery.

Heme is an essential molecule with contradictory biological functions. In hemoproteins such as hemglobin and cytochromes protein-bound heme is a prosthetic group serving physiological functions as a transporter for oxygen and electrons. On the other hand free heme can have deleterious effects by generating reactive oxygen species that cause oxidative stress. Consequently, heme homeostasis of the cell must be tightly controlled via regulation of its enzymatic biosynthesis and degradation that are differentially regulated in liver and erythroid cells. Accumulating evidence indicates that heme has potent proinflammatory effects and is involved in the pathogenesis of diseases such as rhabdomyolysis, sickle cell disease and atherosclerosis. The regulation of gene expression by heme in yeast and mammals and the underlying molecular mechanisms are presented. Finally, we discuss the functional significance of the heme-degrading enzyme heme oxygenase-1 and that of heme-binding proteins for the regulation of heme homeostasis.