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1.  AAPS pharmSci: An advanced publication forum has matured 
AAPS PharmSci  2003;5(2):86-87.
doi:10.1208/ps050216
PMCID: PMC2751524  PMID: 12866943
2.  A semiautomated approach to gene discovery through expressed sequence tag data mining: Discovery of new human transporter genes 
AAPS PharmSci  2003;5(1):1-18.
Identification and functional characterization of the genes in the human genome remain a major challenge. A principal source of publicly available information used for this purpose is the National Center for Biotechnology Information database of expressed sequence tags (dbEST), which contains over 4 million human ESTs. To extract the information buried in this data more effectively, we have developed a semiautomated method to mine dbEST for uncharacterized human genes. Starting with a single protein input sequence, a family of related proteins from all species is compiled. This entire family is then used to mine the human EST database for new gene candidates. Evaluation of putative new gene candidates in the context of a family of characterized proteins provides a framework for inference of the structure and function of the new genes. When applied to a test data set of 28 families within the major facilitator superfamily (MFS) of membrane transporters, our protocol found 73 previously characterized human MFS genes and 43 new MFS gene candidates. Development of this approach provided insights into the problems and pitfalls of automated data mining using public databases.
doi:10.1208/ps050101
PMCID: PMC2751469  PMID: 12713273
Major facilitator superfamily; transporters; superfamily analysis; expressed sequence tags; data mining
3.  Pharmacogenomics: The implementation phase 
AAPS PharmSci  2002;4(2):1-6.
Pharmacogenomics makes use of genetic and genomic principles to facilitate drug discovery and development, and to improve drug therapy. Its goal is to attain optimal therapy for the individual patient. This article analyzes current trends in pharmacogenomics and asks how this new science affects drug development in the pharmaceutical industry and the clinical use of drugs.
doi:10.1208/ps040210
PMCID: PMC2751290  PMID: 12102619
4.  Single nucleotide polymorphisms of the human M1 muscarinic acetylcholine receptor gene 
AAPS PharmSci  2001;3(4):57-61.
The gene encoding the human muscarinic receptor, type 1 (CHRM1), was genotyped from 245 samples of the Coriell Collection (Coriell Institute for Medical Research, Camden, NJ). Fifteen single nucleotide polymorphisms (SNPs) were discovered, 9 of which are located in the coding region of the receptor. Of these, 8 represent synonymous SNPs, indicating that CHRM1 is highly conserved in humans. Only a single allele was found to contain a nonsynonymous SNP, which encodes an amino acid change of Cys to Arg at position 417. This may have functional consequences because a C417S point mutation in rat M1 was previously shown to affect receptor binding and coupling. Furthermore, 0 of 4 SNPs within CHRM1 previously deduced from sequencing of the human genome were found in this study despite a prediction that a majority of such inferred SNPs are accurate. The consensus sequence of CHRM1 obtained in our study differs from the deposited reference sequence (AC NM_000738) in 2 adjacent nucleotides, leading to a V173M change, suggesting a sequencing error in the reference sequence. The extraordinary sequence conservation of the CHRM1 gene-coding region was unexpected as M1-knockout mice show only minimal functional impairments.
doi:10.1208/ps030431
PMCID: PMC2751220  PMID: 12049494
pharmacogenetics; muscarinic acetylcholine; receptor; single nucleotide polymorphism; G protein coupled receptor; CHRM1
5.  Genetic variations in human G protein-coupled receptors: Implications for drug therapy 
AAPS PharmSci  2001;3(3):54-80.
Numerous genes encode G protein-coupled receptors (GPCRs)-a main molecular target for drug therapy. Estimates indicate that the human genome contains approximately 600 GPCR genes. This article addresses therapeutic implications of sequence variations in GPCR genes. A number of inactivating and activating receptor mutations have been shown to cause a variety of (mostly rare) genetic disorders. However, pharmacogenetic and pharmacogenomic studies on GPCRs are scarce, and therapeutic relevance of variant receptor alleles often remains unclear. Confounding factors in assessing the therapeutic relevance of variant GPCR alleles include 1) interaction of a single drug with multiple closely related receptors, 2) poorly defined binding pockets that can accommodate drug ligands in different orientations or at alternative receptor domains, 3) possibility of multiple receptor conformations with distinct functions, and 4) multiple signaling pathways engaged by a single receptor. For example, antischizophrenic drugs bind to numerous receptors, several of which might be relevant to therapeutic outcome. Without knowing accurately what role a given receptor subtype plays in clinical outcome and how a sequence variation affects drug-induced signal transduction, we cannot predict the therapeutic relevance of a receptor variant. Genome-wide association studies with single nucleotide polymorphisms could identify critical target receptors for disease susceptibility and drug efficacy or toxicity.
doi:10.1208/ps030322
PMCID: PMC2751017  PMID: 11741273
G Protein-Coupled; Receptors; Drug Therapy; Pharmacogenomics; Pharmacogenetics
6.  The venus flytrap of periplasmic binding proteins: An ancient protein module present in multiple drug receptors 
AAPS PharmSci  1999;1(2):7-26.
Located between the inner and outer membranes of Gram-negative bacteria, periplasmic binding proteins (PBPs) scavenge or sense diverse nutrients in the environment by coupling to transporters or chemotaxis receptors in the inner membrane. Their three-dimensional structures have been deduced in atomic detail with the use of X-ray crystallography, both in the free and liganded state. PBPs consist of two large lobes that close around the bound ligand, resembling a Venus flytrap. This architecture is reiterated in transcriptional regulators, such as the lac repressors. In the process of evolution, genes encoding the PBPs have fused with genes for integral membrane proteins. Thus, diverse mammalian receptors contain extracellular ligand binding domains that are homologous to the PBPs; these include glutamate/glycine-gated ion channels such as the NMDA receptor, G protein-coupled receptors, including metabotropic glutamate, GABA-B, calcium sensing, and pheromone receptors, and atrial natriuretic peptide-guanylate cyclase receptors. Many of these receptors are promising drug targets. On the basis of homology to PBPs and a recently resolved crystal structure of the extracellular binding domain of a glutamate receptor ion channel, it is possible to construct three-dimensional models of their ligand binding domains. Together with the extensive information available on the mechanism of ligand binding to PBPs, such models can serve as a guide in drug discovery.
doi:10.1208/ps010202
PMCID: PMC2761117  PMID: 11741199

Results 1-6 (6)