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PubMed2000

Creating addressable aqueous microcompartments above solid supported phospholipid bilayers using lithographically patterned poly(dimethylsiloxane) molds

Herein we report the use of microcontact displacement (microCD) to generate addressable arrays of aqueous solutions above fluid lipid bilayers by bringing a patterned PDMS mold into conformal contact with a phospholipid membrane on a solid supported substrate. Epifluorescence microscopy established that the bilayer material was displaced in regions where contact between the mold and substrate was made. Photobleaching experiments confirmed that the bilayer sectors remained individually fluid but completely separated. The microcompartments created by microCD could be individually injected with aqueous solutions that remained sealed from their neighbors. This procedure was then exploited for screening a small library of aqueous-phase molecules for their ability to inhibit binding between surface-bound ligands and soluble protein receptors.

Journal Article↗
PubMed2001

Substrate specificity of the integral membrane protease OmpT determined by spatially addressed peptide libraries.

Escherichia coli outer membrane protease T (OmpT) is an endopeptidase that specifically cleaves between two consecutive basic residues. In this study we have investigated the substrate specificity of OmpT using spatially addressed SPOT peptide libraries. The peptide acetyl-Dap(dnp)-Ala-Arg/Arg-Ala-Lys(Abz)-Gly was synthesized directly onto cellulose membrane. The peptide contained the aminobenzoyl (Abz) fluorophore, which was internally quenched by the dinitrophenyl (dnp) moiety. Treatment of the SPOT membrane with the small, water-soluble protease trypsin resulted in highly fluorescent peptide SPOTs. However, no peptide cleavage was observed after incubation with detergent-solubilized OmpT, a macromolecular complex with an estimated molecular mass of 180 kDa. This problem could be solved by the introduction of a long, polar polyoxyethylene glycol linker between the membrane support and the peptide. Peptide libraries for the P(2), P(1), P(1)', and P(2)' positions in the substrate were screened with OmpT, and peptides of positive SPOTs were resynthesized and subjected to kinetic measurements in solution. The best substrate Abz-Ala-Lys-Lys-Ala-Dap(dnp)-Gly had a turnover number k(cat) of 40 s(-)(1), which is 12-fold higher than the starting substrate. Peptides containing an acidic residue at P(2) or P(2)' were not substrates for OmpT, suggesting that long-range electrostatic interactions are important for the formation of the enzyme-substrate complex. OmpT was highly selective toward L-amino acids at P(1) but was less so at P(1)' where a peptide with D-Arg at P(1)' was a competitive inhibitor (K(i) of 19 microM). An affinity chromatography resin based on these findings was developed, which allowed for the one-step purification of OmpT from a bacterial lysate. The implications of the determined consensus substrate sequence (Arg/Lys)/(Arg/Lys)-Ala for the proposed biological function of OmpT in defense against antimicrobial peptides are discussed.

Bacterial Outer Membrane Proteins↗
PubMed2000

Parallel electrosynthesis of alpha-alkoxycarbamates, alpha-alkoxyamides, and alpha-alkoxysulfonamides using the spatially addressable electrolysis platform (SAEP)

The spatially addressable electrolysis platform (SAEP) has been designed and constructed. It is demonstrated that the advantages of electrochemistry can be readily adapted to combinatorial chemistry and parallel synthesis formats. Parallel electrosynthesis of alpha-alkoxycarbamates, alpha-alkoxyamides, and alpha-alkoxysulfonamides via anodic oxidation of carbamates, amides, and sulfonamides, respectively, highlights the main features of the SAEP.

Journal Article↗
PubMedDate not supplied

2D and 3D spatially addressed arrays for high-throughput automated synthesis of combinatorial libraries.

One of the key elements in the drug discovery process is the use of automation to synthesize libraries of compounds for biological screening. The "split-and-mix" approaches in combinatorial chemistry have been recognized as extremely powerful techniques to access large numbers of compounds, while requiring only few reaction steps. However, the need for effective encoding/deconvolution strategies and demands for larger amounts of compounds have somewhat limited the use of these techniques in the pharmaceutical industry. In this paper, we describe a concept of directed sort and combine synthesis with spatially arranged arrays of macroscopic supports. Such a concept attempts to balance the number of reaction steps, the confidence in compound identity, and the quantity of synthesized compounds. Using three-dimensional arrays of frames each containing a two-dimensional array of macroscopic solid supports, we have conceptualized and developed a modular semiautomated system with a capacity of up to 100 000 compounds per batch. Modularity of this system enables flexibility either to produce large diverse combinatorial libraries or to synthesize more focused smaller libraries, both as single compounds in 12-15 micromol quantities. This method using sortable and spatially addressed arrays is exemplified by the synthesis of a 15 360 compound library.

Journal Article↗
PubMedDate not supplied

Further development of a robust workup process for solution-phase high-throughput library synthesis to address environmental and sample tracking issues.

During further improvement of a high-throughput, solution-phase synthesis system, new workup tools and apparatus for parallel liquid-liquid extraction and evaporation have been developed. A combination of in-house design and collaboration with external manufacturers has been used to address (1) environmental issues concerning solvent emissions and (2) sample tracking errors arising from manual intervention. A parallel liquid-liquid extraction unit, containing miniature high-speed magnetic stirrers for efficient mixing of organic and aqueous phases, has been developed for use on a multichannel liquid handler. Separation of the phases is achieved by dispensing them into a newly patented filter tube containing a vertical hydrophobic porous membrane, which allows only the organic phase to pass into collection vials positioned below. The vertical positioning of the membrane overcomes the hitherto dependence on the use of heavier-than-water, bottom-phase, organic solvents such as dichloromethane, which are restricted due to environmental concerns. Both small (6-mL) and large (60-mL) filter tubes were developed for parallel phase separation in library and template synthesis, respectively. In addition, an apparatus for parallel solvent evaporation was developed to (1) remove solvent from the above samples with highly efficient recovery and (2) avoid the movement of individual samples between their collection on a liquid handler and registration to prevent sample identification errors. The apparatus uses a diaphragm pump to achieve a dynamic circulating closed system with a heating block for the rack of 96 sample vials and an efficient condenser to trap the solvents. Solvent recovery is typically >98%, and convenient operation and monitoring has made the apparatus the first choice for removal of volatile solvents.

Amides↗
PubMed2001

Addressing uncertainty and conflicting cost estimates in revising the arsenic MCL.

The current effort to revise the arsenic drinking water standard is one of the first times that the promulgation of a Maximum Contaminant Level (MCL) for drinking water has been influenced explicitly by benefit-cost considerations. Different stakeholders have developed different estimates of the costs, benefits, and appropriate decision-making criteria for a lower standard. In this study, alternative analyses prepared by the U.S. EPA and by independent researchers are compared. The large discrepancies in the aggregate national cost estimates are shown to result largely from differences in the engineering cost estimates for arsenic treatment processes. Further research is needed to resolve these discrepancies. Alternative regulatory approaches, such as providing point-of-use treatment or exempting water systems with high household compliance costs, yield only modest improvement in the overall cost-effectiveness of lower standards but are effective at addressing serious affordability problems for the small percentage of (primarily small) water systems where these problems are predicted to occur. The U.S. EPA may wish to provide more explicit guidance to state regulators and to water utilities as to the conditions under which these options will be acceptable.

Arsenic↗
PubMed2005

Building addressable libraries: the use of electrochemistry for spatially isolating a heck reaction on a chip.

Pd(0) was generated at preselected sites on an electrochemically addressable chip and then utilized to effect a Heck reaction. The Pd(0) was confined to the preselected electrodes with the use of allylmethyl carbonate. Unlike most mediated electrochemical reactions, the electrolysis in this case was not used to convert a stoichiometric process into a catalytic one by recycling the metal. Instead, the unique environment of the chip was used to interfere with a catalytic process to make it stoichiometric. This was done to gain spatial control over the reaction. The development of a strategy for conducting Pd(0)-catalyzed reactions on the chips should greatly expand the synthetic chemistry available for building chip-based libraries.

Combinatorial Chemistry Techniques↗
PubMed2004

Building addressable libraries: the use of electrochemistry for generating reactive Pd(II) reagents at preselected sites on a chip.

A Pd(II) reagent has been generated at preselected sites on an electrochemically addressable chip. The reagent was used to effect the Wacker oxidation of an olefin substrate bound to the chip near the electrode. The use of ethyl vinyl ether in the solution above the chip effectively kept the Pd(II) reagent generated at the preselected electrode from migrating to neighboring electrodes and initiating Wacker oxidations at unwanted sites on the chip.

2,4-Dinitrophenol↗
PubMed2006

Building addressable libraries: spatially isolated, chip-based reductive amination reactions.

A Pd(II) reagent has been generated at preselected sites on an electrochemically addressable chip and used to effect the oxidation of the neighboring alcohols on the polymer coating the chip's surface. The resulting carbonyls were then used to accomplish site-selective reductive amination reactions on the chips. The work demonstrates that the confinement strategy developed for spatially isolated Wacker oxidations to specific sites on the chips is general and can be used for other Pd(II)-based reactions.

Alcohols↗
PubMed2006

Building addressable libraries: The use of a mass spectrometry cleavable linker for monitoring reactions on a microelectrode array.

Time-of-flight secondary ion mass spectrometry (TOF SIMS) has been used in conjunction with a mass spectrometry cleavable linker to determine the percent conversion of reactions that were conducted site-selectively on an addressable microelectrode array. When combined with fluorescence techniques for analysis of the reactions, the TOF SIMS experiment provides a means for optimization of both reaction confinement and reaction efficiency on the microelectrode arrays.

Calibration↗
PubMed1995

Probes for narcotic receptor-mediated phenomena. 20. Alteration of opioid receptor subtype selectivity of the 5-(3-hydroxyphenyl)morphans by application of the message-address concept: preparation of delta-opioid receptor ligands.

Derivatives of racemic and optically active 5-(3-hydroxyphenyl)-2-methylmorphan (5-(3-hydroxyphenyl)-2-methyl-2-azabicyclo[3.3.1]nonane, 1) were synthesized containing additional aromatic moieties, as an application of the message-address concept targeted at producing delta-opioid receptor selective ligands. In vitro radioreceptor binding studies in rat brain revealed that both of the parent enantiomers, (-)- and (+)-1, had a high affinity for the mu-opioid receptor (21 nM), a slight affinity for kappa 1-opioid receptors (approximately 800-900 nM), and less than 1000 nM affinity for the delta-opioid receptor (mu/delta IC50 ratio of < 0.02 for both). A derivative of (-)-1 containing an indole moiety fused at the C6-C7 position of the phenylmorphan nucleus, (-)-11, displayed a > 180-fold increase in affinity for the delta-opioid receptor with an IC50 value of 6 nM. The parent compound (-)-1 had only 26% agonist activity at 30 microM in the mouse vas deferens (delta) bioassay, whereas compound (-)-11 had an IC50 of 393 nM in this preparation, indicating the importance of the indole moiety in imparting delta-opioid agonist activity to the phenylmorphan (-)-11. A structure-activity relationship (SAR) study of N-alkyl derivatives of the racemic nor 11 indicated similarities between the interaction of various derivatives with the mu- and delta- but not the kappa 1-opioid receptor. As studies on the molecular basis of the interaction of opioid ligands with their respective receptors continue to gain momentum, the SAR data described herein for the synthetic phenylmorphans will prove useful for further studies.

Animals↗
PubMed1994

Structure-activity relationship of N17'-substituted norbinaltorphimine congeners. Role of the N17' basic group in the interaction with a putative address subsite on the kappa opioid receptor.

A series of norbinaltorphimine congeners (2-12) which contain different groups at the N17'-position have been synthesized in order to evaluate the role of N17' in conferring kappa opioid antagonist selectivity at opioid receptor sites. The compounds that contain a basic N17' nitrogen (2-9) were found to be selective kappa antagonists. Amidation of N17' afforded congeners 10-12 with feeble kappa antagonist potency and low selectivity. The fact that potent antagonism and selectivity were observed only when members of the series contain a basic N17' nitrogen suggests that it interacts with extracellular domains of the kappa receptor that contain acidic amino acid residues. The N-terminal domain and extracellular loop 2, both of which contain acidic residues, are candidates for this interaction and may be components of the kappa address subsite of the receptor.

Animals↗
PubMed1993

Synthesis and kappa-opioid antagonist selectivity of a norbinaltorphimine congener. Identification of the address moiety required for kappa-antagonist activity.

Compound 2, which represents a structurally simplified congener of norbinaltorphimine 1a, was synthesized in order to evaluate the role of its second basic nitrogen in conferring kappa-opioid receptor antagonist selectivity. Congener 2 was found to be at least twice as selective as 1a as a kappa antagonist, while its N-carbobenzoxy derivative (3) was inactive at kappa-receptors. This study establishes the importance of the second basic nitrogen of 1a for kappa-receptor recognition. It is proposed that this basic group mimics the guanidinium moiety of Arg7, which may be the key kappa-address component of dynorphin.

Animals↗
PubMed2004

Importance of phenolic address groups in opioid kappa receptor selective antagonists.

In vitro characterization and comparison of JDTic, its dehydroxy analogue and nor-BNI, and its dehydroxy analogue demonstrates that the N-substituted 3,4-dimethyl-(3-hydroxyphenyl)piperidine-derived antagonist, JDTic, relies more heavily on its phenol address group for affinity and antagonist activity relative to the corresponding naltrexone derived antagonists, nor-BNI. The structural flexibility of the former class of compound relative to the latter is postulated to underlie the difference.

Animals↗
PubMed2005

"In situ cross-docking" to simultaneously address multiple targets.

In standard docking, every target structure requires separate docking calculations. To overcome this limitation, an approach is presented by which multiple proteins can be addressed simultaneously in a single docking run. This "in situ cross-docking" is built on a grid-based docking method and follows the idea that grids calculated for single binding sites may be joined to one common grid. Docking then allows for a direct selection of the optimal target by the ligand being docked. The approach is technically feasible and can lead to significant time savings over conventional cross-docking.

Algorithms↗
PubMed2005

[Nalpha-benzylTyr1,cyclo(D-Asp5,Dap8)]- dynorphin A-(1-11)NH2 cyclized in the "address" domain is a novel kappa-opioid receptor antagonist.

The cyclic dynorphin A analogue [N(alpha)-benzylTyr(1),cyclo(D-Asp(5),Dap(8))]dynorphin A-(1-11)NH(2) (Dap = 2,3-diaminopropionic acid) exhibits nanomolar affinity (30 nM) and high selectivity (K(i) ratio (kappa/mu/delta) = 1/194/330) for kappa-opioid receptors. This analogue antagonizes dynorphin A-(1-13)NH(2) at kappa-opioid receptors in the adenylyl cyclase assay (K(B) = 84 nM). This is the first dynorphin A-based antagonist with modifications in the C-terminal "address" domain that alter efficacy and thus represents a novel selective kappa-opioid receptor antagonist.

Adenylyl Cyclases↗
PubMed1996

Opioid antagonist activity of naltrexone-derived bivalent ligands: importance of a properly oriented molecular scaffold to guide "address" recognition at kappa opioid receptors.

The presence of a molecular scaffold to orient a basic group is important for potent and selective kappa opioid antagonist selectivity. An attempt to determine how the geometry of the scaffold affects this selectivity has led to the synthesis of a bivalent ligand (5) whose linker constrains the N17' basic nitrogen (the "address") to a position that is 6.5 A from N17' in the kappa antagonist norBNI (1) when these molecules are superimposed. The fact that compound 5 was found to be a highly selective and potent mu-selective antagonist supports the idea that the position of N17' in 5 precludes effective ion pairing with the nonconserved residue Glu297 on outer loop 3 of the kappa opioid receptor. The high mu receptor binding affinity and in vitro pharmacological selectivity of 5 coupled with its presumed low central nervous system bioavailability suggest that it may be a useful antagonist for the investigation of peripheral mu opioid receptors.

Animals↗
PubMed1997

Address and message sequences for the nociceptin receptor: a structure-activity study of nociceptin-(1-13)-peptide amide.

Nociceptin (NC) and some of its fragments as well as nociceptin-(1-13)-peptide amide [NC- (1-13)-NH2] and a series of its analogues were prepared and tested in the mouse vas deferens in an attempt to identify the sequences involved in the activation (message) and in the binding (address) of nociceptin to its receptor. The NC receptor that inhibits the electrically evoked twitches of the mouse vas deferens was demonstrated to be distinct from the delta opioid receptor, since naloxone and Dmt-Tic-OH (a selective delta opioid receptor antagonist) block the delta opioid receptor but have no effect on the nociceptin receptor. Results from structure-activity experiments suggest that (a) the entire sequence of NC may not be required for full biological activities, since NC(1-13)-NH2 is as active as NC; (b) fragments of NC have however to be amidated as in NC(1-13)-NH2 in order to be protected from degradation by proteases; (c) cationic residues (as Arg8,12, Lys9,13) appear to play a functional role, since their replacement with Ala in the sequence of NC(1-13)-NH2 leads to inactivity; (d) the N-terminal tetrapeptide Phe-Gly-Gly-Phe is essential for activity: its full length and flexibility appear to be required for NC receptor activation and/or occupation; (e) Phe4 and not Phe1 appears to be the residue involved in receptor activation, since the replacement of Phe1 with Leu has no effect, while that of Phe4 leads to inactivity. Results summarized in this paper indicate that the structural requirements of NC for occupation and activation of its receptor are different from that of opioids, particularly delta agonists.

Amino Acid Sequence↗