Combinatorial chemistry as a tool for drug discovery

The formation of right-handed and left-handed chiral nanopores within a single domain during amino acid self-assembly on Au(111)

We report the formation of both right- and left-handed chiral nanopores within a single domain during the self-assembly of an amino acid derivative on an inert Au(111) surface using STM. DFT calculations employed to rationalize this unusual result identified that intermolecular interactions between chiral, windmill-shaped tetramers are crucial for self-assembly.

Combinatorial synthesis of functionalized spirooxindole-pyrrolidine/pyrrolizidine/pyrrolothiazole derivatives via three-component 1,3-dipolar cycloaddition reactions

A series of diverse polycyclic heterocycles containing spirooxindole, pyridine/thiophene, and pyrrolidine/pyrrolizidine/pyrrolothiazole rings have been synthesized through the 1,3-dipolar cycloaddition of azomethine ylides generated in situ by the condensation of dicarbonyl compounds (isatin or acenaphthenequinone) and secondary amino acids with dipolarophiles. The method is simple and provides diverse and biologically interesting products with excellent yields.

Polychlorinated biphenyls impair blood–brain barrier integrity via disruption of tight junction proteins in cerebrum, cerebellum and hippocampus of female Wistar rats

Polychlorinated biphenyls (PCBs) comprise a ubiquitous class of toxic substances associated with carcinogenic and tumor-promoting effects as well as neurotoxic properties. Reactive oxygen species, which is produced from PCBs, alters blood–brain barrier (BBB) integrity, which is paralleled by cytoskeletal rearrangements and redistribution and disappearance of tight junction proteins (TJPs) like claudin-5 and occludin. Quercetin, a potent antioxidant present in onion and other vegetables, appears to protect brain cells against oxidative stress, a tissue-damaging process associated with Alzheimer’s and other neurodegenerative disorders. The aim of this study is to analyze the role of quercetin on oxidative stress markers and transcription of transmembrane and cytoplasmic accessory TJPs on cerebrum, cerebellum and hippocampus of female rats exposed to PCBs. Rats were divided into the following four groups. Group I: received only vehicle (corn oil) intraperitoneally (i.p.); group II: received Aroclor 1254 at a dose of 2 mg/kg body weight (bwt)/day (i.p); group III: received Aroclor 1254 (i.p.) and simultaneously quercetin 50 mg/kg bwt/day through gavage and group IV: received quercetin alone gavage. From the experiment, the levels of hydrogen peroxide, lipid peroxidation and thiobarbituric acid reactive substances were observed to increase significantly in cerebrum, cerebellum and hippocampus as 50%, 25% and 20%, respectively, after exposure to PCB, and the messenger RNA expression of TJP in rats exposed to PCBs is decreased and is retrieved to the normal level simultaneously in quercetin-treated rats. Hence, quercetin can be used as a preventive medicine to PCBs exposure and prevents neurodegenerative disorders.

Pfizer Global Virtual Library (PGVL): a chemistry design tool powered by experimentally validated parallel synthesis information

An unprecedented amount of parallel synthesis information was accumulated within Pfizer over the past 12 years. This information was captured by an informatics tool known as PGVL (Pfizer Global Virtual Library). PGVL was used for many aspects of drug discovery including automated reactant mining and reaction product formation to build a synthetically feasible virtual compound collection. In this report, PGVL is discussed in detail. The chemistry information within PGVL has been used to extract synthesis and design information using an intuitive desktop Graphic User Interface, PGVL Hub. Several real-case examples of PGVL are also presented.

PGVL Hub: An integrated desktop tool for medicinal chemists to streamline design and synthesis of chemical libraries and singleton compounds

PGVL Hub is an integrated molecular design desktop tool that has been developed and globally deployed throughout Pfizer discovery research units to streamline the design and synthesis of combinatorial libraries and singleton compounds. This tool supports various workflows for design of singletons, combinatorial libraries, and Markush exemplification. It also leverages the proprietary PGVL virtual space (which contains 10(14) molecules spanned by experimentally derived synthesis protocols and suitable reactants) for lead idea generation, lead hopping, and library design. There had been an intense focus on ease of use, good performance and robustness, and synergy with existing desktop tools such as ISIS/Draw and SpotFire. In this chapter we describe the three-tier enterprise software architecture, key data structures that enable a wide variety of design scenarios and workflows, major technical challenges encountered and solved, and lessons learned during its development and deployment throughout its production cycles. In addition, PGVL Hub represents an extendable and enabling platform to support future innovations in library and singleton compound design while being a proven channel to deliver those innovations to medicinal chemists on a global scale.

Synthesis of 2-(N-Benzylpyrrolyl)-benzimidazoles Using Polyphosphoric Acid Prompted Cyclocondensation

Synthesis of a series of 2-substituted benzimidazoles was carried out for screening anti-inflammatory activities. 2-(N-benzylpyrrolyl)-benzimidazoles 9a-k were synthesized from N-benzyl-2-pyrrole carboxylic acids 8a-d and 4-substituted-1,2-phenylenediamines by cyclocondensation utilizing polyphosphoric acid (PPA) as condensing agent. The N-benzyl-2-pyrrole carboxylic acids were prepared by standard method of N-benzylation of 2-pyrrole carboxylate using NaH/DMF and appropriately substituted benzyl halides followed by alkaline hydrolysis.

Cancer cell-based genomic and small molecule screens

This chapter focuses on the promising post-genomic technologies being used for discovery of new, safer, and better cancer drugs and drug targets. Since cancer is largely a disease of the cell, usually involving unrestricted cell proliferation as a result of heritable genetic changes such as mutation, this chapter will focus on cell-centric technologies and their utility in addressing major questions in cancer biology. Recent advances in cell-based technology, including phenotypic assays, image-based readouts, primary tumor cell growth and maintenance in vitro, gene and small molecule delivery tools, and automated systems for cell manipulation, provide a novel means to understand the etiology and mechanisms of cancer as never before. In addition to the abundant tool sophistication, many aspects of cancer can be emulated and monitored in cell systems, which makes them ideal vehicles for exploitation to discover new targets and drugs. This chapter will first handle nomenclature and provide a context for a "good drug target" within the framework of the human genome, then overview functional genomic gene-based library screening approaches with specific applications to cancer target discovery. Second, small molecule screening applications will be handled, with an emphasis on the new paradigm of massively parallel screening and resultant multidimensional dataset analysis approaches to identify drug candidates, assign mechanism of action, and address problems in deriving selective and safe chemical entities.

Evolutionary computation and multimodal search: a good combination to tackle molecular diversity in the field of peptide design

The awesome degree of structural diversity accessible in peptide design has created a demand for computational resources that can evaluate a multitude of candidate structures. In our specific case, we translate the peptide design problem to an optimization problem, and use evolutionary computation (EC) in tandem with docking to carry out a combinatorial search. However, the use of EC in huge search spaces with different optima may pose certain drawbacks. For example, EC is prone to focus a search in the first good region found. This is a problem not only because of the undesirable and automatic rejection of potentially good search space regions, but also because the found solution may be extremely difficult to synthesize chemically or may even be a false docking positive. In order to avoid rejecting potentially good solutions and to maximize the molecular diversity of the search, we have implemented evolutionary multimodal search techniques, as well as the molecular diversity metric needed by the multimodal algorithms to measure differences between various regions of the search space.

The role of functional and molecular imaging in cancer drug discovery and development

Studies of pharmacokinetics (which is what the body does to the drug) and pharmacodynamics (which is what the drug does to the body) are essential components of the modern process of cancer drug discovery and development. Defining the precise relationship between pharmacokinetics and pharmacodynamics is critical. It is especially important to establish a well understood pharmacological "audit trail" that links together all of the essential parameters of drug action, from the molecular target to the clinical effects. The pharmacological audit trail allows us to answer two absolutely crucial questions: (1) how much gets there; and (2) what does it do? During the pre-clinical drug discovery phase, it is essential that pharmacokinetic/pharmacodynamic (PK/PD) properties are optimized, so that the best candidate can be selected for clinical development. As part of contemporary mechanistic, hypothesis-testing clinical trials, construction of the pharmacological PK/PD audit trail facilitates rational decision-making. However, PK/PD endpoints frequently require invasive sampling of body fluids and tissues. Non-invasive molecular measurements, e.g. using MRI or spectroscopy, or positron emission tomography, are therefore very attractive. This review highlights the need for PK/PD endpoints in modern drug design and development, illustrates the value of PK/PD endpoints, and emphasises the importance of non-invasive molecular imaging in drug development. Examples cited include the use of PK/PD endpoints in the development of molecular therapeutic drugs such as the Hsp90 molecular chaperone inhibitor 17AAG, as well as the development of SR-4554 as a non-invasive probe for the detection of tumour hypoxia.

Cassette dosing pharmacokinetics of a library of 2,6,9-trisubstituted purine cyclin-dependent kinase 2 inhibitors prepared by parallel synthesis

Determination of pharmacokinetic properties in the intact animal remains a major bottleneck in drug discovery. Cassette dosing involves administration of a cocktail of drugs to individual animals. Here we describe the cassette dosing properties of a 107-membered library of 2,6,9-trisubstituted purine cyclin-dependent kinase 2 (CDK2) inhibitors. A three-step parallel synthesis approach produced compounds with purity ranging from 63% to 100%. Cassette dosing was validated by comparing the pharmacokinetic parameters obtained following i.v. administration of a mixture of olomoucine, R-roscovitine (CYC202), and bohemine, each at 16.6 mg/kg, with results for administration of single agents at 50 mg/kg. No significant difference was observed between the pharmacokinetic parameters of agents when dosed in combination compared with those of individual compounds. CYC202 showed the highest area under the curve (AUC) and the longest elimination half-life (t1/2). Further cassettes evaluated the library of trisubstituted purines with CYC202 and purvalanol A included as pharmacokinetic standards in a validated limited sampling strategy. The ratios of pharmacokinetic parameters to that of CYC202 [AUC, maximum concentration (Cmax), and t1/2] remained similar when compounds were tested in two different cassettes or as individual compounds. Following dosing of the same cassette on three different days, there was less than 20% variation in pharmacokinetic parameters between days. The structure-pharmacokinetics relationship showed that the favored purine substituents are benzylamine and veratrylamine at position 6, amino-2 propanol at position 2, and methylpropyl or hydroxyethyl at position 9. Without cassette dosing, this study would have used 3 times as many animals and would have taken 4 times longer, illustrating the power of this method in lead optimization.

A combinatorial biocatalysis approach to an array of cholic acid derivatives

A 39-member library of bile acid derivatives was prepared starting from 3alpha,7alpha,12alpha-trihydroxy-5beta-cholan-24-oic acid methyl ester using a combinatorial biocatalytic approach. A regioselective oxidation step, catalyzed by hydroxysteroid dehydrogenases, followed by an acylation step with a series of different acyl donors catalyzed by Candida antarctica lipase B, led to the modification of the bile acid scaffold. Each member of the library was obtained in high purity and good yield.

Inhibitors of cell migration that inhibit intracellular paxillin/alpha4 binding: a well-documented use of positional scanning libraries

Screening combinatorial libraries for inhibition of Paxillin binding to the cytoplasmic tail of the integrin alpha4 provided the first inhibitors of this protein-protein interaction implicated in enhanced rates of cell migration and chronic inflammation. The preparation of substructure analogs of the lead identified features required for activity, those available for modification, and those that may be removed. The most potent lead structure was shown to inhibit alpha(4)beta(1)-mediated human Jurkat T cell migration in a dose-dependent manner, validating the intracellular Paxillin/alpha4 interaction as a useful and unique target for therapeutic intervention. Moreover, the lead structure emerged from a library that was prepared in two formats: (1) a traditional small mixture format composed of 100 mixtures of 10 compounds and (2) a positional scanning library. Their parallel testing provided the rare opportunity to critically compare two approaches.

Identification of selective inhibitors of acetylcholinesterase from a combinatorial library of 2,5-piperazinediones

The potentiation of central cholinergic activity has been proposed as a therapeutic approach for improving cognitive function in patients with Alzheimer's disease. Increasing the acetylcholine concentration in brain by modulating acetylcholinesterase (AChE) activity is among the most promising strategies. We have used a combinatorial approach to identify different 2,5-piperazinediones (DKP) with AChE inhibitory activity. Our goal was to find inhibitors exhibiting high AChE/BuChE (butyrylcholinesterase) selectivity, in order to reduce the undesirable side effects elicited by most of the inhibitors that have been developed to date. Screening of a DKP library constructed on solid-phase using the multiple parallel synthesis format, resulted in the identification of several compounds with moderate efficacy on AChE. In particular, DKP-80 had an IC50 = 2.2 microM with no significant inhibitory activity on BuChE. Moreover, estimated values of Clog P and log BB for the most active compounds fulfilled the bioavailability requirements for enzyme inhibitors acting on the central nervous system. In order to understand the inhibitory properties of the ligand at the molecular level, molecular dynamics simulations were computed on DKP-80 complexed to AChE, and the most relevant binding interactions of this inhibitor to the active center of the enzyme were characterized. Overall the present results indicate that the DKP-based compounds identified are novel AChE inhibitors which may be considered likely lead compounds for further development of drug candidates against Alzheimer's disease.

Barriers to Alzheimer disease drug discovery and development in the biotechnology industry

The major barrier to Alzheimer disease (AD) drug discovery and development in the biotechnology industry is scale. Most biotechnology companies do not have the personnel or expertise to carry a drug from the bench to the market. Much effort in the industry has been directed toward the elucidation of molecular mechanisms of AD and the identification of new targets. Advances in biotechnology have generated new insights into disease mechanisms, increased the number of lead compounds, and accelerated biologic screening. The majority of costs associated with drug development are in clinical testing and development activities, many of which are driven by regulatory issues. For most biotechnology companies, the costs of such trials and the infrastructure necessary to support them are prohibitive. Another significant barrier is the definition of therapeutic benefit for AD drugs; Food and Drug Administration (FDA) precedent has established that a drug must show superiority to placebo on a performance-based test of cognition and a measure of global clinical function. This restrictive definition is biased toward drugs that enhance performance on memory-based tests. Newer AD drugs are targeted toward slowing disease progression; however, there is currently no accepted definition of what constitutes efficacy in disease progression. Despite these obstacles, the biotechnology industry has much to offer AD drug discovery and development. Biotechnology firms have already developed essential technology for AD drug development and will continue to do so. Biotechnology companies can move more quickly; of course, the trick is to move quickly in the right direction. Speed may offset some of the problems associated with lack of scale. Additionally, biotechnology companies can afford to address markets that may be too restricted for larger pharmaceutical companies. This advantage will have increasing importance, as therapies are developed to address subtypes of AD.

Erythropoietin mimetics derived from solution phase combinatorial libraries

The erythropoietin receptor (EPOr) is activated by ligand-induced homodimerization, which leads to the proliferation and differentiation of erythroid progenitors. Through the screening of combinatorial libraries of dimeric iminodiacetic acid diamides, novel small molecule binders of EPOr were identified in a protein binding assay. Evaluation of a series of analogues led to optimization of binding subunits, and these were utilized in the synthesis of higher order dimer, trimer, and tetramer libraries. Several of the most active EPOr binders were found to be partial agonists and induced concentration-dependent proliferation of an EPO-dependent cell line (UT-7/EPO) while having no effect on a cell line lacking the EPOr (FDC-P1). An additional compound library, based on a symmetrical isoindoline-5,6-dicarboxylic acid template and including the optimized binding subunits, was synthesized and screened leading to the identification of additional EPO mimetics.

Development of a solid-phase binding assay and identification of nonpeptide ligands for the FynB Src homology 2 domain

The nonreceptor tyrosine kinase FynB is known to be required in the induction of long-term potentiation (LTP), a cellular mechanism for learning and memory. Ligands of the FynB SH2 domain as a possible FynB activator are, thus, of great interest. In this study, a solid-phase ligand binding assay was established to meet the screening requirement of high-throughput and ease of use, and in an attempt to find the specific ligands for the FynB SH2 domain. This assay measures the competitive inhibition of the binding of the biotinylated phosphopeptide (GGSETDDY*AEIID), derived from a binding sequence in human focal adhesion kinase, to the SH2 domain of FynB precoated as a glutathione S-transferase fusion protein on a solid-phase. Using this high-throughput screening method for SH2 ligands, a modest size of chemical library was screened, and two non-peptide compounds, 4-acetamidobenzene sulfinic acid and 1-allylpyridinium 3-sulfonate, were identified by their strong binding affinity to the FynB SH2 domain. This result demonstrates the feasibility of the developed assay in high-throughput screening. Further studies on the molecular structures of the identified SH2-binding ligands will allow presentation of specific models for ligand-domain complexes for improving the ligands and will help to develop a potential lead compound for improving LTP.

Mass spectrometry and combinatorial chemistry: a short outline

The rapid evolution of combinatorial chemistry in recent years has led to a dramatic improvement in synthetic capabilities. The goal is to accelerate the discovery of molecules showing affinity against a target, such as an enzyme or a receptor, through the simultaneous synthesis of a great number of structurally diverse compounds. This is done by generating combinatorial libraries containing as many as hundreds or thousands of compounds. The need to test all these compounds led to the development of high-throughput screening (HTS) techniques, and also high-throughput analytical techniques capable of assessing the occurrence, structure and purity of the products. In order to be applied effectively to the characterization of combinatorial libraries, an analytical technique must be adequately sensitive (to analyse samples which are typically produced in nanomole amounts or less), fast, affordable and easy to automate (to minimize analysis time and operator intervention). Although no method alone can meet all the analytical challenges underlying this task, the recent progress in mass spectrometric (MS) instrumentation renders this technique an essential tool for scientists working in this area. We describe here relevant aspects of the use of MS in combinatorial technologies, such as current methods of characterization, purification and screening of libraries. Some examples from our laboratory deal with the analysis of pooled oligomeric libraries containing n x 324(n = 1, 2) compounds, using both on-line high-performance liquid chromatography/MS with an ion trap mass spectrometer, and direct infusion into a triple quadrupole instrument. In the first approach, MS and product ion MS/MS with automatic selection of the precursor were performed in one run, allowing library confirmation and structural elucidation of unexpected by-products. The second approach used MS scans to characterize the entire library and also precursor ion and neutral loss scans to detect selectively components with given structural characteristics.

Tracelessness Unmasked: A General Linker Nomenclature

Nowadays it is rare to find an issue of a major chemistry journal without at least one article on solid-phase synthesis. This is hardly surprising: the technique promises an end to arduous work-up procedures and the ability to facilitate the creation of vast libraries of compounds using combinatorial techniques. No longer is the technique only of interest to those involved in peptide synthesis: an enormous variety of product classes have now been prepared on and isolated from the solid phase. It is the "linker" which is the focus of this article. The linker's ultimate function is to release a product from the support into solution: it does this, without exception, with a chemical change to the product at the former linkage site. Some linkers, apparently, are "traceless". But what, in fact, is "tracelessness"? Twenty years ago, in a climate where cleavage of a linker resulted in formation of a polar carboxylic acid as the vestige of the support, the concept was attractive. Today the chemist is faced with a myriad of novel linkers which have the ability to release products bearing most major functionalities at the former linkage site and we will argue here that the term "traceless", although currently in widespread use, is meaningless. Instead, we propose a new categorization of linkers based on the functionality they release upon cleavage, and suggest a nomenclature to underpin this categorization. We anticipate that the article will also serve to highlight areas of linker technology in need of further research.

Identification of a novel class of small-molecule antiangiogenic agents through the screening of combinatorial libraries which function by inhibiting the binding and localization of proteinase MMP2 to integrin alpha(V)beta(3)

The process of new blood vessel growth from existing vasculature, known as angiogenesis, is critical to several pathological conditions, most notably cancer. Both MMP2, which degrades the extracellular matrix (ECM), and integrin alpha(V)beta(3), which contributes to endothelial cell attachment to the ECM, are critically involved in this process. Recent findings have shown that MMP2 is localized in an active form on the surface of invasive endothelial cells based on its ability to directly bind integrin alpha(V)beta(3), suggesting that disrupting this protein--protein interaction may represent a new target for the development of angiogenesis inhibitors. The screening of small molecule libraries led to the identification of compounds which disrupt the MMP2--alpha(V)beta(3) interaction in an in vitro binding assay. A prototypical inhibitor was further found to prevent the degradation of the protein matrix without directly inhibiting MMP2 activity or disrupting the binding of alpha(V)beta(3) to its classical ECM ligand, vitronectin. The synthesis and screening of analogues and substructures of this lead compound allowed the identification of requisite structural features for inhibition of MMP2 binding to alpha(V)beta(3). This led to the synthesis of a more water-soluble derivative which maintains the in vitro biological properties and has potent antiangiogenic and antitumor activity in vivo, validating the target as one useful for therapeutic intervention.

Rapid estimation of hydrophobicity for virtual combinatorial library analysis

Novel NPH (Nonpolar, Polar, Hydrogen) descriptors for rapid estimation of hydrophobicity, amenable for filtering extremely large virtual combinatorial libraries (VCL) are proposed, based on atom counts: P_at, the sum of polar atoms (sum of oxygen, nitrogen, phosphorus and sulfur); NP_at, the sum of non-polar atoms (the sum of carbons and halogens minus P_at); SHDA (the sum of hydrogen bond donors and acceptors). In combination with molecular weight, the following related parameters are defined: MWP_at (the "polar" molecular weight); MWNP_at (the "nonpolar" molecular weight); and MWSHDA (the "hydrogen bonding" molecular weight). The NPH descriptors provide moderate-to-good predictive PLS models when external prediction is evaluated against measured logP values (q2 pred > 0.5, n = 7954) or against calculated logP values (q2 pred > 0.6, n = 18 991). Related to hydrophobicity, the NPH descriptors are intended for fast analyses of extremely large VCLs (10(6)-10(12) compounds), even before the enumeration of reactants into products occurs.

The potential of alkaloids in drug discovery

Alkaloids are an important group of diversely distributed, chemically, biologically and commercially significant natural products. This article suggests why now, with the presently available technology, and the remaining biome available and reasonably accessible, is an opportune moment to consciously focus on the discovery of further alkaloids with pharmacophoric utility.

Development of inhibitors for protein tyrosine kinases

In the last 5 years, through combinatorial chemistry, high-throughput screening, computational chemistry, and traditional medicinal chemistry, numerous inhibitors for various protein tyrosine kinases (PTKs) have been developed. The majority of these compounds are small molecules that compete at the ATP binding site of the catalytic domain of the enzymes. Some compounds such as pseudosubstrate-based peptide inhibitor binds to the peptide/protein substrate site of the catalytic domain. Some inhibitors, primarily monoclonal antibodies, bind to the extracellular domain of receptor tyrosine kinases. Some of these inhibitors are highly potent and selective. Several are currently undergoing clinical trials for a number of diseases such as cancer.