Current Pharmaceutical Design - Volume 11, Issue 3, 2005

Advances in protein crystallography and molecular simulations have greatly aided computer aided drug design paradigms and the accuracy of binding affinity predictions. The methods used in the discovery and / or optimization of a lead inhibitor have ranged from graphical visualization of the ligand in the binding site to calculation of relative binding affinities using molecular dynamics simulations in conjunction with the Free Energy Perturbation (FEP) approach. The aim of the Computer Aided Drug Design (CADD) issue of Current Pharmaceutical Design is to provide computational chemists and medicinal chemists with a comprehensive review of the methods used for drug design. While the FEP approach remains the method that consistently generates the most accurate free energies, its high CPU requirements and inability to evaluate compounds that differ significantly in structure, clearly limit the impact and value of FEP calculations on drug design. Accordingly, efforts are ongoing to develop faster methods such as high-throughput docking, molecular mechanics methods, etc. that have the potential to evaluate a large number of compounds qualitatively. The first article focuses on lead inhibitor optimization strategies using the free energy perturbation approach and molecular mechanics methods and evaluates the merits of each method for predicting relative binding affinities of fructose 1,6- bisphosphatase inhibitors. The second article summarizes all the published structural information for matrix metalloprotease inhibitor complexes and the design of specific matrix metalloproteinase inhibitors using structure-based drug design methods. The third article focuses on various computational aspects of docking-based virtual screening of small molecule databases. In addition the article discusses the fundamental issues and challenges associated with various docking methods. The fourth article describes several computational techniques such as high-throughput docking and similarity searching to identify potential lead MurB inhibitors. The fifth article describes computer-based strategies for modeling the interaction of agouti-related protein (AGRP) and related peptide ligands with the AGRP-binding site of murine melanocorin receptors. The final article describes efforts to design and prepare fumagillin and curcumin analogs and the antiangiogenic activities for a promising anti-cancer treatment discovered using CADD methods. Overall, this issue provides an extensive overview of the scope and limitations of CADD methods. The authors contributing to this issue are well-recognized leaders in this field of research representing both academic institutions and pharmaceutical industry. As an Executive Editor of Current Pharmaceutical Design, I would like to thank the authors for their contributions. I would also like to thank Dr. Mark Erion for his helpful suggestions and his encouragement and support in editing this CADD issue.

Computational assessment of the binding affinity of enzyme inhibitors prior to synthesis is an important component of computer-aided drug design (CADD) paradigms. The free energy perturbation (FEP) methodology is the most accurate means of estimating relative binding affinities between two inhibitors. However, due to its complexity and computation-intensive nature, practical applications are restricted to analysis of structurally-related inhibitors. Accordingly, there is a need for methods that enable rapid assessment of a large number of structurally-unrelated molecules in a suitably accurate manner. In this review, the FEP method is compared with molecular mechanics (MM) methods to assess the advantages of each in the estimation of relative binding affinities of inhibitors to an enzyme. Qualitative predictions of relative binding free energies of fructose 1, 6-bisphosphatase inhibitors using MM methods are discussed and compared with the corresponding FEP results. The results indicate that the MM based methods and the FEP method are useful in the qualitative and quantitative assessment of relative binding affinities of enzyme inhibitors, respectively, prior to synthesis.

It has been 10 years since a 3-dimensional structure of the catalytic domain of a Matrix Metalloprotease (MMP) was revealed for the first time in 1994. More than 80 structures of different MMPs in apo and inhibited forms, determined by X-ray crystallography and NMR methods, have been published by the end of year 2003. A large number of very potent inhibitors have been disclosed in published and patent literature. Several MMP inhibitors entered clinical trials for the treatment of cancer and arthritis. Most of the first generation inhibitors have hydroxamic acid as the Zinc-binding group and have limited specificity. With the failure of these inhibitors in clinical trials, more efforts have been directed to the design of specific inhibitors with different Zn-binding groups in recent years. This review will summarize all the published structural information and focus on the inhibitors that were designed to take advantage of the nonprime side of the MMP active site using structural information and computational analysis. Representative structures from all MMPs are aligned to a target structure to provide a better understanding of the similarities and differences of the active site pockets. This analysis supports the view that the differences in the nonprime side pockets provide better opportunities for designing inhibitors with higher specificity. Published information on all the Zinc-binding groups of MMP inhibitors is reviewed for the first time. Pros and cons of inhibitors with non-hydroxamate Zinc-binding groups in terms of specificity, toxicity and pharmacokinetic properties are discussed.

The state of the art of various computational aspects of docking-based virtual screening of database of small molecules is presented. The review encompasses the different search algorithms and the scoring functions used in docking methods and their applications to protein and nucleic acid drug targets. Recent progress made in the development and application of methods to include target flexibility are summarized. The fundamental issues and challenges involved in comparing various docking methods are discussed. Limitations of current technologies as well as future prospects are presented.

Small research-based pharmaceutical start-ups often lack the budget and do not have the infrastructure available to apply all possible techniques for compound selection. This review details our use of a range of techniques such as high-throughput docking and similarity searching to maximize the success rate when attempting to identify pharmaceutically relevant ligands in a resource-constrained environment.

The hypothesis that the interaction of agouti-related protein (AGRP) and the melanocortin-4 receptor (MC4R) modulates feeding behavior in humans has stimulated the synthesis of conformationally constrained peptides, peptoids and small molecules in efforts to identify novel compounds that can potentially be used in the clinical treatment of obesity and related eating disorders. In addition, the availability of a high-resolution NMR structure for the MC4R-binding domain of AGRP, and studies employing site-specific murine MC4R mutants have identified key intermolecular AGRP / MC4R interactions. It is therefore surprising that only one, relatively unsophisticated, computer-based study has been reported to obtain a model for the AGRP / mMC4R complex. In this review we outline computer-based strategies for building models of the AGRP / mMC4R and related peptide / mMC4R complexes, and illustrate the strengths and limitations of sophisticated molecular dynamics methods in obtaining information that might form the basis of rational efforts to discover novel drugs that selectively interact with melanocortin receptors.

Cancer is a general term used to describe many disease states, each of which are characterized by abnormal cell proliferation. The causes which bring about this abnormal cellular behavior are specific to each type of cancer. The success of tumor-targeted therapy is limited by this diversity. One common denominator for all types of cancer is the requirement of a suitable blood supply. Therefore, tumor vasculature has emerged as a potential target for therapeutic intervention. New blood vessel growth from preexisting vasculature stimulated by biochemical signals is termed angiogenesis. Tumor masses require a constant supply of oxygen and nutrients, and a means of efficient waste removal to ensure sustained development. Diffusion from nearby capillaries can supply adequate nutrition for tumors less than 2 mm in size, but for continued growth the tumors must develop their own blood supply. Alteration of the delicate balance of angiogenic stimulating factors and angiogenic inhibitors results in the phenotypic change from quiescence to active endothelial proliferation. To date, this angiogenic switch is not completely understood. The goal of antiangiogenic therapy is to interfere with these mechanisms and prevent tumor cells from developing a viable blood supply. Fumagillin is a naturally occurring antifungal agent. Curcumin is a natural product isolated from the spice turmeric. Both compounds have been shown to have antiangiogenic properties in vitro and in vivo. This paper describes efforts to design and prepare fumagillin and curcumin analogs and evaluate their corresponding antiangiogenic activities.

Synthetic gene delivery vectors are gaining increasing importance in gene therapy as an alternative to recombinant viruses. Among the various types of non-viral vectors, cationic lipids are especially attractive as they can be prepared with relative ease and extensively characterised. Further, each of their constituent parts can be modified, thereby facilitating the elucidation of structure-activity relationships. In this forward-looking review, cationic lipid-mediated gene delivery will mainly be discussed in terms of the structure of the three basic constituent parts of any cationic lipid: the polar headgroup, hydrophobic moiety and linker. Particular emphasis will be placed on recent advances in the field as well as on our own original contributions. In addition to reviewing critical physicochemical features (such as headgroup hydration) of monovalent lipids, the use of headgroups with known nucleic-acid binding modes, such as linear and branched polyamines, aminoglycosides and guanidinium functions, will be comprehensively assessed. A particularly exciting innovation in linker design is the incorporation of environment-sensitive groups, the intracellular hydrolysis of which may lead to more controlled DNA delivery. Examples of pH-, redox- and enzyme-sensitive functional groups integrated into the linker are highlighted and the benefits of such degradable vectors can be evaluated in terms of transfection efficiency and cationic lipid-associated cytotoxicity. Finally, possible correlations between the length and type of hydrophobic moiety and transfection efficiency will be discussed. In conclusion it may be foreseen that in order to be successful, the future of cationic lipid-based gene delivery will probably require the development of sophisticated virus-like systems, which can be viewed as “programmed supramolecular systems” incorporating the various functions required to perform in a chronological order the different steps involved in gene transfection.

Thalidomide was developed in the 1950s as a sedative drug and withdrawn in 1961 because of its teratogenic effects, but has been rediscovered as an immuno-modifying drug. It has been administered successfully for the treatment of erythema nodosum leprosum, aphthous ulceration in HIV disease, inflammatory bowel diseases, and multiple myeloma. So far, investigations into the mode of action of thalidomide have focused on lymphocytes and vascular endothelial cells and have shown that this agent inhibits the production of tumor necrosis factor (TNF)-α and is an inhibitor of tumor angiogenesis. Recently, other immunological effects of this drug have been gaining attention, including attenuation of neutrophil activation and inhibition of myelo-proliferative responses. In autoimmune diseases, inflammation is characterized by an influx of granulocytes, and the association of granulocytes with gastrointestinal ulcer formation or rheumatic arthritis has been well documented. The suppressive effect of thalidomide on the activation of the nuclear transcription factor NF-κB may explain these effects of thalidomide. NF-κB is retained in the cytoplasm with IκBα, and is activated by a wide variety of inflammatory stimuli including TNF, IL-1 and endotoxin followed by its translocation to the nucleus. Constitutive activation of NF-κB has been detected in various inflammatory diseases, while angiogenesis and organogenesis also require NF-κB activation. Thalidomide, on the other hand, has been shown to selectively suppress NF-κB activation induced by inflammatory mediators. NF-κB is known to be located downstream of proliferative and / or survival signaling induced by growth factors, which regulate anti-apoptotic genes. Myeloid cells in vitro, however, have been found to proceed to apoptosis as the result of the treatment with thalidomide and subsequent inactivation of NF-κB. These findings are consistent with clinical symptoms that showed the recovery from leukocytosis and / or neutrophilia after the administration of thalidomide. These findings shed new light on the anti-inflammatory properties of thalidomide and suggested that they may inhibit granulocyte-mediated tissue injury.

The migration of tumor cells is a prerequisite for tumor cell invasion and metastasis development, which accounts for over 90% of cancer mortality. Therefore a major focus of current tumor biological research is the study of those factors that regulate tumor cell migration. Those chemokines and neurotransmitters that bind to G-protein coupled receptors (also known as serpentine receptors) are the most prominent of these factors. Neurotransmitters have been identified that have not only a stimulatory (e.g. norepinephrine) effect, but an inhibitory effect (e.g. GABA) as well. This is an especially fortuitous development, because many known agonists and antagonists of neurotransmitter receptors are currently being successfully used in the treatment of other pathological conditions (e.g. β-blockers in the treatment of cardiovascular diseases). Likewise, chemokine receptor antagonists, which are under development for the treatment of HIV or rheumatoid arthritis, may be effective tools for the inhibition of chemokine-driven tumor cell migration as well. A further approach to inhibit tumor cell migration arises from the investigation of the relevant signal transduction pathways. The PKC alpha, for example, is a key enzyme in the regulation of tumor cell migration, but not of leukocyte migration. It thus offers a selective target opportunity for specific pharmacological agents to interfere with tumor cell migration. In this review we therefore summarize the current findings on those serpentine receptors involved in the neurotransmitter- and chemokine-regulated tumor cell migration, on the underlying signal transduction pathways, and on the opportunities to inhibit tumor cell migration and ultimately metastasis development with pharmaceutical agents.