2004 publications:
J Comb Chem.
2004 Mar-Apr;6(2):255-61
High-throughput purification of combinatorial libraries I: a high-throughput purification system using an accelerated retention window approach.
Yan B, Collins N, Wheatley J, Irving M, Leopold K, Chan C,
Shornikov A, Fang L, Lee A, Stock M, Zhao J.
Discovery Chemistry Division, Discovery Partners
International, Inc., 385 Oyster Point Boulevard, South San
Francisco, CA 94080, USA.
We have developed a high-throughput purification system to purify combinatorial libraries at a 50-100-mg scale with a throughput of 250 samples/instrument/day. We applied an accelerated retention window method to shorten the purification time and targeted one fraction per injection to simplify data tracking, lower QC workload, and simplify
the postpurification processing. First, we determined the
accurate retention time and peak height for all compounds
using an eight-channel parallel LC/UV/MS system, and
calculated the specific preparative HPLC conditions for
individual compounds. The preparative HPLC conditions include
the compound-specific gradient segment for individual
compounds with a fixed gradient slope and the compound-
specific UV or ELSD threshold for triggering a fraction
collection device. A unique solvent composition or solvent
strength was programmed for each compound in the
preparative HPLC in order to elute all compounds at the same
target time. Considering the possible deviation of the
predicted retention time, a 1-min window around the target
time was set to collect peaks above a threshold based on
UV or ELSD detection. Dual column preparative instruments
were used to maximize throughput. We have purified more
than 500 000 druglike compounds using this system in the past
3 years. We report various components of this high-throughput
purification system and some of our purification results.
Drug Discov Today.
2004 Apr 15;9(8):358-65
The evolution of microarrayed compound screening.
Hoever M, Zbinden P.
Discovery Partners International AG, Gewerbestrasse 16, CH-4123 Allschwil, Switzerland.
mhoever@discoverypartners.com
This review describes recent developments in the evolutionary process of microarrayed compound screening (microARCS
to become a robust and efficient ultra-high-throughput screening technology. Improvements in compound spotting
(including new quality-control methods), gel casting and imaging, together with software capable of automatic
analysis and deconvolution of images, have helped to streamline the screening process. A variety of screening
projects using cell-based and non-cell-based approaches have been successfully concluded using microARCS. Comparison
of hits derived from standard microtitre-plate-based screening and from microARCS reveals excellent overlap.
Furthermore, there seems to be no bias towards finding compounds within a particular range of logP values, even
though compounds are solubilized from a dry state during the course of the assay.
Curr Opin Chem Biol.
2004 Jun;8(3):281-6
Libraries from natural product-like scaffolds.
Boldi AM.
Discovery Partners International, Discovery Chemistry Division, 385 Oyster Pt Blvd, Suite 1, South San Francisco,
California 94080 USA. boldi@chemrx.com
Natural products are an attractive source of varied structures that exhibit potent biological activities, and
desirable pharmacological profiles. Since the relatively recent advent of high-throughput organic synthesis in the
drug discovery process, several design approaches have been applied to the construction of screening libraries.
Libraries of natural-product derivatives, natural-product-like compounds prepared by total synthesis, and libraries
derived from natural-products are several types that have been reported.
J Comb Chem.
2004 Jul-Aug;6(4):478-86
High-throughput purification of combinatorial libraries II: Automated separation of single diastereomers from a
4-amido-pyrrolidone library containing intentional diastereomer pairs.
Irving M, Krueger CA, Wade JV, Hodges JC, Leopold K, Collins N, Chan C, Shaqair S, Shornikov A, Yan B.
ChemRx Division, Discovery Partners International, Inc., 385 Oyster Point Blvd., South San Francisco, California
94080, USA.
A 4-amido-pyrrolidone library that was intentionally synthesized as pairs of diastereomers was produced by
solution-phase parallel syntheses and purified by an automated high-throughput purification system. A total of 2592 4-amido-pyrrolidinones were ultimately isolated as single diastereomers from a matrix of 1920 syntheses. After the four-step synthesis and HPLC purification, the average yield of a single diastereomer was 36.6%. The average
chemical purity was >90%, and the average diastereomeric purity was >87%. The choice of chiral amines used to make
amides with heterocyclic acid chlorides had a dramatic effect on success. Analysis of the relationship between
amines used for synthesis and the diastereomeric separation showed that amides made from chiral 1,2-amino alcohols
gave superior separation to amides from chiral morpholines. The presence of a hydrogen bond donor on the amide side
chain seems to be required for a better diastereomeric separation.
J Comb Chem.
2004 Jul-Aug;6(4):487-96
Solid-phase synthesis of 1-substituted tetrahydroisoquinoline derivatives employing BOC-protected
tetrahydroisoquinoline carboxylic acids.
Bunin BA, Dener JM, Kelly DE, Paras NA, Tario JD, Tushup SP.
ChemRx Division, Discovery Partners International, 385 Oyster Point Boulevard, Suite 1, South San Francisco,
California 94080, USA.
Compounds containing the tetrahydroisoquinoline ring system were prepared using solid-supported ester derivatives on
a nucleophile-sensitive resin, starting from the corresponding BOC-protected amino acids. The key heterocyclic
intermediates were obtained from the Pictet-Spengler reaction between ethyl glyoxylate or methyl 4-formylbenzoate
and dopamine or 3-hydroxyphenethylamine. After the resulting amino esters were converted to the BOC derivatives, the
phenolic hydroxyl groups were alkylated with a series of alkyl halides to afford the corresponding ethers. Ester
hydrolysis afforded the BOC-protected tetrahydroisoquinoline carboxylic acid scaffolds, which were then attached to
(4-hydroxyphenyl)sulfide resin (Marshall linker) as the corresponding ester. The BOC group was removed under acidic
conditions, and the resulting support-bound amine hydrochlorides were converted to the corresponding amides using a set of carboxylic acids. The support-bound amides were liberated with amines to produce the desired
tetrahydroisoquinoline carboxamides. Optimization of the resin loading conditions is described in addition to the
identification of impurities observed during the development of the optimum conditions for solid-phase synthesis.
J Comb Chem. 2004
Jul-Aug;6(4):564-72
Solid-phase synthesis of 1,2,3,4-tetrahydroisoquinoline derivatives employing support-bound tyrosine esters in the
Pictet-Spengler reaction.
Kane TR, Ly CQ, Kelly DE, Dener JM.
Discovery Partners International, ChemRx Division, 385 Oyster Point Boulevard, Suite 1, South San Francisco,
California 94080, USA.
The solid-phase synthesis of 1,2,3,4-tetrahydroisoquinoline-3-carboxamides employing carboxyl-supported, o-alkylated
tyrosine esters in a Pictet-Spengler reaction is described. Esterification of [4-(hydroxyphenyl)thiomethyl]polystyrene (Marshall resin) with ethers of N-BOC-L-tyrosine using
diisopropylcarbodiimide (DIC) and 4-dimethylaminopyridine (4-DMAP) afforded the solid-supported ester derivatives.
Removal of the BOC group with trifluoroacetic acid (TFA) afforded the carboxyl-supported tyrosine ester, which was
then treated with paraformaldehyde and TFA to afford the desired solid-supported counterpart. Acylation of the
secondary amine with arylsulfonyl chlorides followed by reaction with amines resulted in the formation of the
desired 2-arylulfonyl-7-alkoxy-1,2,3,4-tetrahydroisoquinoline-3-carboxamides. Alternatively, the support-bound
tetrahydroisoquinoline-3-carboxylate derivatives could be treated with an aldehyde and a reducing agent to give the
corresponding support-bound tertiary amine. Exposure of these resin-bound products to amines afforded the
corresponding 2-alkyl-7-alkoxy-1,2,3,4-tetrahydroisoquinoline-3-carboxamides after cleavage from the resin.
Alternative routes to the desired chemotypes, as well optimization of the conditions for the Pictet-Spengler
reaction and the conditions for the acylation and reductive amination of the support-bound secondary amines, are
also described.
Curr Med Chem. 2004
Nov;11(22):2911-77
The design, structure, and clinical update of small molecular weight matrix metalloproteinase inhibitors.
Skiles JW, Gonnella NC, Jeng AY.
Discovery Partners International, 9640 Towne Centre Drive, San Diego, CA 92121, USA. jskiles@cytrxlabs.com
Matrix metalloproteinases (MMPs) are a family of zinc-containing enzymes involved in the degradation and remodeling
of extracellular matrix proteins. Under normal physiological conditions, the activities of these enzymes are
well-regulated by endogenous tissue inhibitors of metalloproteinases (TIMPs). Chronic stimulation of MMP activities due to an imbalance in the levels of MMPs and TIMPs has been implicated in the pathogenesis of a variety of diseases such as cancer, osteoarthritis, and rheumatoid arthritis. Thus, MMP inhibitors are expected to be useful for the treatment of these disorders. Because of their importance in a variety of pathological conditions, a number of small
molecular weight MMP inhibitors have entered clinical trials in humans. However, the results of these trials have
been extremely disappointing and have led many investigators to conclude that MMP inhibitors have no therapeutic
benefit in human cancer. To date, the first generation MMP inhibitors exhibited poor bioavailability while
second-generation compounds revealed that prolonged treatment caused musculoskeletal pain and inflammation or had a
lack of efficacy. This article describes the design of small molecular weight MMP inhibitors, a brief description of
available three-dimensional MMP structures, a review of the proposed therapeutic utility of MMP inhibitors, and a
clinical update of compounds that have entered clinical trials in humans. The experimentally determined structures
used in the structure-based design of MMP inhibitors are thoroughly covered. Major emphasis is on recently published
and/or patented potent MMP inhibitors, from approximately January 2000 to April 2003, and their pharmacological
properties. Protein inhibitors of these proteolytic enzymes, i.e. TIMPs, will not be discussed.
Comb Chem High Throughput Screen.
2004 Dec;7(8):745-56
High throughput screening of beta-amyloid secretion inhibitors using homogenous time-resolved fluorescence.
Albrecht H, Zbinden P, Rizzi A, Villetti G, Riccardi B, Puccini P, Catinella S, Imbimbo BP.
Discovery Partners International, Integrated Drug Discovery Division, Allschwil, Switzerland.
A cell-based assay using homogeneous time-resolved fluorescence has been developed for high throughput screening of putative beta-amyloid (Abeta)production inhibitors. In this assay, total Abeta is detected by simply adding two
commercially available antibody complexes. The first was a biotinylated monoclonal antibody (4G8), specifically
recognizing an epitope comprising the residues 17-24 of the Abetapeptide, complexed with europium
cryptate-streptavidin conjugate. The second was a polyclonal antibody (BioS-N), raised against the N-terminus of the
Abeta peptide, complexed with an allophycocyanin-anti rabbit antibody conjugate. Binding of the two complexes to the
Abeta peptide brought europium cryptate (fluorescence donor) and allophycocyanin (fluorescence acceptor) into close
proximity, consequently a fluorescent resonance energy transfer signal was produced upon excitation at 337 nm. The
resulting fluorescence signal (665 nm) was then detected using a Discovery or a ViewLux reader. Detection of Abeta
by the proposed method is possible at concentrations of approximately 1 nM. The method was employed for the
detection of Abeta secreted from a stable transfected human neuroglioma cell line (H4) overexpressing a mutated form
of the human amyloid precursor protein (APP695NL) and developed for robotic automation. At optimized conditions,
signal-to-background ratios exceeding 5 and Z' factors around 0.7 were achieved in a 384-well format. High
throughput screening of 56,913 potential Abeta production inhibitors led to identification of new non-cytotoxic and
cell permeable compounds with potencies in the submicromolar range. |
