Combinatorial Chemistry & High Throughput Screening

ISSN: 1386-2073

Combinatorial Chemistry & High Throughput Screening
Volume 11, Number 6, July 2008

Contents

GPCR High Throughput Screening (Part 2)
Guest Editors: David P. Siderovski and Francis S. Willard


Development of Selective High Affinity Antagonists, Agonists, and Radioligands for the P2Y₁ Receptor Pp. 410-419
Dayle Houston, Stefano Costanzi, Kenneth A. Jacobson and T. Kendall Harden
[Abstract]


Massively Parallel Screening of the Receptorome Pp . 420-426
Niels H. Jensen and Bryan L. Roth
[Abstract]


Affinity Selection-Mass Spectrometry and its Emerging Application to the High Throughput Screening of G Protein-Coupled Receptors Pp. 427-438
Charles E. Whitehurst and D. Allen Annis
[Abstract]


Over-Expression, Solubilization, and Purification of G Protein-Coupled Receptors for Structural Biology Pp. 439-462
Mark L. Chiu, Cindy Tsang, Nelson Grihalde and Maria P. MacWilliams
[Abstract]


Antibodies Against G-Protein Coupled Receptors: Novel Uses in Screening and Drug Development Pp. 463-467
Achla Gupta, Andrea S. Heimann, Ivone Gomes and Lakshmi A. Devi
[Abstract]


Meet the Guest Editors Pp . 468


General Articles


Applications of High Throughput Microsomal Stability Assay in Drug Discovery Pp. 469-476
Li Di, Edward H. Kerns, Xuewen JoAnn Ma, Youping Huang and Guy T. Carter
[Abstract]


Similarity Analysis of Protein Sequences Based on the Normalized Relative-Entropy Pp . 477-481
Chun Li, Jùn Wang, Yi Zhang and Jun Wang
[Abstract]


How Large Does a Compound Screening Collection Need To Be? Pp. 482-493
Michael J. Lipkin, Adrian P. Stevens, David J. Livingstone and C. John Harris
[Abstract]




Abstracts

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Development of Selective High Affinity Antagonists, Agonists, and Radioligands for the P2Y₁ Receptor
Dayle Houston, Stefano Costanzi, Kenneth A. Jacobson and T. Kendall Harden

The P2Y₁ receptor is a member of the P2Y family of nucleotide-activated G protein-coupled receptors, and it is an important therapeutic target based on its broad tissue distribution and essential role in platelet aggregation. We have designed a set of highly selective and diverse pharmacological tools for studying the P2Y₁ receptor using a rational approach to ligand design. Based on the discovery that bisphosphate analogues of the P2Y₁ receptor agonist, ADP, are partial agonists/competitive antagonists of this receptor, an iterative approach was used to develop competitive antagonists with enhanced affinity and selectivity. Halogen substitutions of the 2-position of the adenine ring provided increased affinity while an N⁶ methyl substitution eliminated partial agonist activity. Furthermore, various replacements of the ribose ring with symmetrically branched, phosphorylated acyclic structures revealed that the ribose is not necessary for recognition at the P2Y₁ receptor. Finally, replacement of the ribose ring with a five member methanocarba ring constrained in the Northern conformation conferred dramatic increases in affinity to both P2Y₁ receptor antagonists as well as agonists. These combined structural modifications have resulted in a series of selective high affinity antagonists of the P2Y₁ receptor, two broadly applicable radioligands, and a high affinity agonist capable of selectively activating the P2Y₁ receptor in human platelets. Complementary receptor modeling and computational ligand docking have provided a putative structural framework for the drug-receptor interactions. A similar rational approach is being applied to develop selective ligands for other subtypes of P2Y receptors.


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Massively Parallel Screening of the Receptorome
Niels H. Jensen and Bryan L. Roth

The National Institute of Mental Health (NIMH) Psychoactive Drug Screening Program (PDSP) is a resource that provides free screening of novel compounds to academic investigators. This program differs from other public-sector screening programs in that compounds are screened against a large panel of transmembrane receptors, channels, and transporters, a selection that currently includes a large portion of the whole neuro-receptorome. This review discusses the research areas that can profit from this resource, exemplified by recent findings. The first area is the identification of side effects of medications. Examples include the identification of the histamine H₁ receptor as being responsible for weight gain under antipsychotic treatment and the association of 5 HT_2B receptor agonism with cardiac valvulopathy, which led to the removal of several medications. A second area is the identification of mechanisms of actions of medications and natural products. Examples are the finding that the kappa opioid receptor is the pharmacological target of the potent hallu-cinogen salvinorin A, that ephedrine and related compounds are not acting through direct sympathomimetic action, the identification of a strong dopaminergic action of WAY 100635, a compound that had been used as a selective 5 HT_1A antagonist, and the discovery that the metabolite desmethylclozapine activates M₁ muscarinic receptors, an activity that might contribute to the clinical efficacy of the antipsychotic drug clozapine. A third, relatively new area is the identification of inert compounds as agonists for engineered designer receptors that no longer respond to their natural ligand (DREADDs) but exhibit unchanged signaling properties.


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Affinity Selection-Mass Spectrometry and its Emerging Application to the High Throughput Screening of G Protein-Coupled Receptors
Charles E. Whitehurst and D. Allen Annis

Advances in combinatorial chemistry and genomics have inspired the development of novel affinity selection-based screening techniques that rely on mass spectrometry to identify compounds that preferentially bind to a protein target. Of the many affinity selection-mass spectrometry techniques so far documented, only a few solution-based implementations that separate target-ligand complexes away from unbound ligands persist today as routine high throughput screening platforms. Because affinity selection-mass spectrometry techniques do not rely on radioactive or fluorescent reporters or enzyme activities, they can complement traditional biochemical and cell-based screening assays and enable scientists to screen targets that may not be easily amenable to other methods. In addition, by employing mass spectrometry for ligand detection, these techniques enable high throughput screening of massive library collections of pooled compound mixtures, vastly increasing the chemical space that a target can encounter during screening. Of all drug targets, G protein coupled receptors yield the highest percentage of therapeutically effective drugs. In this manuscript, we present the emerging application of affinity selection-mass spectrometry to the high throughput screening of G protein coupled receptors. We also review how affinity selection-mass spectrometry can be used as an analytical tool to guide receptor purification, and further used after screening to characterize target-ligand binding interactions, enabling the classification of orthosteric and allosteric binders.


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Over-Expression, Solubilization, and Purification of G Protein-Coupled Receptors for Structural Biology
Mark L. Chiu, Cindy Tsang, Nelson Grihalde and Maria P. MacWilliams

With the advent of the recent determination of high-resolution crystal structures of bovine rhodopsin and human β2 adrenergic receptor (β2AR), there are still many structure-function relationships to be learned from other G protein-coupled receptors (GPCRs). Many of the pharmaceutically interesting GPCRs cannot be modeled because of their amino acid sequence divergence from bovine rhodopsin and β2AR. Structure determination of GPCRs can provide new avenues for engineering drugs with greater potency and higher specificity. Several obstacles need to be overcome before membrane protein structural biology becomes routine: over-expression, solubilization, and purification of milligram quantities of active and stable GPCRs. Coordinated iterative efforts are required to generate any significant GPCR over-expression. To formulate guidelines for GPCR purification efforts, we review published conditions for solubilization and purification using detergents and additives. A discussion of sample preparation of GPCRs in detergent phase, bicelles, nanodiscs, or low-density lipoproteins is presented in the context of potential structural biology applications. In addition, a review of the solubilization and purification of successfully crystallized bovine rhodopsin and β2AR highlights tools that can be used for other GPCRs.


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Antibodies Against G-Protein Coupled Receptors: Novel Uses in Screening and Drug Development
Achla Gupta, Andrea S. Heimann, Ivone Gomes and Lakshmi A. Devi

Antibodies are components of the body’s humoral immune system that are generated in response to foreign pathogens. Modern biomedical research has employed these very specific and efficient molecules designed by nature in the diagnosis of diseases, localization of gene products as well as in the rapid screening of targets for drug discovery and testing. In addition, the introduction of antibodies with fluorescent or enzymatic tags has significantly contributed to advances in imaging and microarray technology, which are revolutionizing disease research and the search for effective therapeutics. More recently antibodies have been used in the isolation of dimeric G protein-coupled receptor (GPCR) complexes. In this review, we discuss antibodies as powerful research tools for studying GPCRs, and their potential to be developed as drugs themselves.


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Applications of High Throughput Microsomal Stability Assay in Drug Discovery
Li Di, Edward H. Kerns, Xuewen JoAnn Ma, Youping Huang and Guy T. Carter

High throughput in vitro microsomal stability assays are widely used in drug discovery as an indicator for in vivo stability, which affects pharmacokinetics. This is based on in-depth research involving a limited number of model drug-like compounds that are cleared predominantly by cytochrome P450 metabolism. However, drug discovery compounds are often not drug-like, are assessed with high throughput assays, and have many potential uncharacterized in vivo clearance mechanisms. Therefore, it is important to determine the correlation between high throughput in vitro microsomal stability data and abbreviated discovery in vivo pharmacokinetics study data for a set of drug discovery compounds in order to have evidence for how the in vitro assay can be reliably applied by discovery teams for making critical decisions. In this study the relationship between in vitro single time point high throughput microsomal stability and in vivo clearance from abbreviated drug discovery pharmacokinetics studies was examined using 306 real world drug discovery compounds. The results showed that in vitro Phase I microsomal stability t_1/2 is significantly correlated to in vivo clearance with a p-value < 0.001. For compounds with low in vitro rat microsomal stability (t _1/2 < 15 min), 87% showed high clearance in vivo (CL > 25 mL/min/kg). This demonstrates that high throughput microsomal stability data are very effective in identifying compounds with significant clearance liabilities in vivo. For compounds with high in vitro rat microsomal stability (t _1/2 > 15 min), no significant differentiation was observed between high and low clearance compounds. This is likely owing to other clearance pathways, in addition to cytochrome P450 metabolism that enhances in vivo clearance. This finding supports the strategy used by medicinal chemists and drug discovery teams of applying the in vitro data to triage compounds for in vivo PK and efficacy studies and guide structural modification to improve metabolic stability. When in vitro and in vivo data are both available for a compound, potential in vivo clearance pathways can be diagnosed to guide further discovery studies.


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Similarity Analysis of Protein Sequences Based on the Normalized Relative-Entropy
Chun Li, Jùn Wang, Yi Zhang and Jun Wang

Based on the classification of 20 amino acids, we reduce a protein primary sequence to six (0,1) sequences. For each of them, two so-called normalized relative-entropies are calculated and thus a 12-D vector is constructed to describe the protein primary sequence. The examination of similarities/dissimilarities among eight different proteins illustrates the utility of the approach.


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How Large Does a Compound Screening Collection Need To Be?
Michael J. Lipkin, Adrian P. Stevens, David J. Livingstone and C. John Harris

Increasingly, chemical libraries are being produced which are focused on a biological target or group of related targets, rather than simply being constructed in a combinatorial fashion. A screening collection compiled from such libraries will contain multiple analogues of a number of discrete series of compounds. The question arises as to how many analogues are necessary to represent each series in order to ensure that an active series will be identified. Based on a simple probabilistic argument and supported by in-house screening data, guidelines are given for the number of compounds necessary to achieve a “hit”, or series of hits, at various levels of certainty. Obtaining more than one hit from the same series is useful since this gives early acquisition of SAR (structure-activity relationship) and confirms a hit is not a singleton. We show that screening collections composed of only small numbers of analogues of each series are suboptimal for SAR acquisition. Based on these studies, we recommend a minimum series size of about 200 compounds. This gives a high probability of confirmatory SAR (i.e. at least two hits from the same series). More substantial early SAR (at least 5 hits from the same series) can be gained by using series of about 650 compounds each. With this level of information being generated, more accurate assessment of the likely success of the series in hit-to-lead and later stage development becomes possible.