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New antibiotics are urgently needed to address increasing rates of multidrug resistant infections. Seventy-six diversely functionalized compounds, comprising five structural scaffolds, were synthesized and tested for their ability to inhibit microbial growth. Twenty-six compounds showed activity in the primary phenotypic screen at the Community for Open Antimicrobial Drug Discovery (CO-ADD). Follow-up testing of active molecules confirmed that two unnatural dipeptides inhibit the growth of Cryptococcus neoformans with a minimum inhibitory concentration (MIC) ≤ 8 μg/mL. Syntheses were carried out by undergraduate students at five schools implementing Distributed Drug Discovery (D3) programs. This report showcases that a collaborative research and educational process is a powerful approach to discover new molecules inhibiting microbial growth. Educational gains for students engaged in this project are highlighted in parallel to the research advances. Aspects of D3 that contribute to its success, including an emphasis on reproducibility of procedures, are discussed to underscore the power of this approach to solve important research problems and to inform other coupled chemical biology research and teaching endeavors.

Remote amide bonds in simple N-acyl amino acid amide or peptide derivatives 1 can be surprisingly unstable hydrolytically, affording, in solution, variable amounts of 3 under mild acidic conditions, such as trifluoroacetic acid/water mixtures at room temperature. This observation has important implications for the synthesis of this class of compounds, which includes N-terminal-acylated peptides. We describe the factors contributing to this instability and how to predict and control it. The instability is a function of the remote acyl group, R(2)CO, four bonds away from the site of hydrolysis. Electron-rich acyl R(2) groups accelerate this reaction. In the case of acyl groups derived from substituted aromatic carboxylic acids, the acceleration is predictable from the substituent's Hammett σ value. N-Acyl dipeptides are also hydrolyzed under typical cleavage conditions. This suggests that unwanted peptide truncation may occur during synthesis or prolonged standing in solution when dipeptides or longer peptides are acylated on the N-terminus with electron-rich aromatic groups. When amide hydrolysis is an undesired secondary reaction, as can be the case in the trifluoroacetic acid-catalyzed cleavage of amino acid amide or peptide derivatives 1 from solid-phase resins, conditions are provided to minimize that hydrolysis.

A new solid-phase synthesis efficiently incorporates three different substituents (from R(1)-X, R(2)-CO(2)H, and R(3)-NH(2)) into a glycine-based peptidomimetic scaffold. The synthetic sequence is general and is typically accomplished in >50% overall isolated yield. Alkylating agents with a range of reactivities and normal and branched primary amines give good results. Utility was demonstrated by the synthesis of a series of protected phosphotyrosine mimetics.

Chiral tertiary alpha-hydroxy esters of known stereochemical configuration were transformed to alpha-azido esters by Mitsunobu reaction with HN3. Optimization of this reaction was shown to proceed at room temperature with high chemical yield using 1,1-(azodicarbonyl)dipiperidine (ADDP) and trimethylphosphine (PMe3). Complete inversion of configuration was observed at the alpha-carbon. Several alpha,alpha-disubstituted amino acids were synthesized in high overall chemical yield and optical purity.

For the successful implementation of Distributed Drug Discovery (D(3)) (outlined in the accompanying Perspective), students, in the course of their educational laboratories, must be able to reproducibly make new, high quality, molecules with potential for biological activity. This article reports the successful achievement of this goal. Using previously rehearsed alkylating agents, students in a second semester organic chemistry laboratory performed a solid-phase combinatorial chemistry experiment in which they made 38 new analogs of the most potent member of a class of antimelanoma compounds. All compounds were made in duplicate, purified by silica gel chromatography, and characterized by NMR and LC/MS. As a continuing part of the Distributed Drug Discovery program, a virtual D(3) catalog based on this work was then enumerated and is made freely available to the global scientific community.

Distributed Drug Discovery (D(3)) proposes solving large drug discovery problems by breaking them into smaller units for processing at multiple sites. A key component of the synthetic and computational stages of D(3) is the global rehearsal of prospective reagents and their subsequent use in the creation of virtual catalogs of molecules accessible by simple, inexpensive combinatorial chemistry. The first section of this article documents the feasibility of the synthetic component of Distributed Drug Discovery. Twenty-four alkylating agents were rehearsed in the United States, Poland, Russia, and Spain, for their utility in the synthesis of resin-bound unnatural amino acids 1, key intermediates in many combinatorial chemistry procedures. This global reagent rehearsal, coupled to virtual library generation, increases the likelihood that any member of that virtual library can be made. It facilitates the realistic integration of worldwide virtual D(3) catalog computational analysis with synthesis. The second part of this article describes the creation of the first virtual D(3) catalog. It reports the enumeration of 24,416 acylated unnatural amino acids 5, assembled from lists of either rehearsed or well-precedented alkylating and acylating reagents, and describes how the resulting catalog can be freely accessed, searched, and downloaded by the scientific community.

Natural organic matter (NOM) is an important constituent of aquatic environments; however, its influence on aquatic biota remains poorly studied. In the current study, NOM was isolated from nine different sites in southern Ontario, Canada, by the on-site treatment of water by reverse osmosis, followed by cation exchange. NOM from each site was reconstituted to 10 mg of C/L and pH 7.0 and exposed to either adult rainbow trout implanted with indwelling catheters or to in vitro primary cultures of the gill epithelium grown on semipermeable membranes. In both the in vivo and in vitro preparations, NOM was found to hyperpolarize transepithelial potential (TEP), with the magnitude of this change correlating extremely well to the absorptivity of the NOM at 340 nm, which is an index of its aromaticity. Gill hyperpolarization appeared to be independent of Ca2+ complexation by the NOM in all but two samples tested. We argue that NOM has direct actions on the ionic transport and/or permeability properties of fish gills. While NOM effects on the bioavailability of contaminants are well-known, NOM actions on such fundamental physiological properties of the gills have previously been overlooked. These may be of comparable or greater magnitude than commonly reported for other water-quality variables (e.g., hardness, pH, salinity) and therefore of critical importance in ecological understanding and risk assessment.

A wide variety of highly substituted lactam containing peptidomimetic scaffolds are prepared by solid-phase synthesis from a single, versatile class of resin-bound aldehyde intermediates (1). These include monocyclics 3, bicyclics 4, tricyclics 5, and tetracyclics 6. The key intermediate 1 is readily synthesized from resin-bound natural or unnatural alpha-amino acids. The synthetic procedures permit the construction of a large diversity of substitution patterns for ready use in combinatorial chemistry. In every case, the release of final products from resin is by a cyclitive cleavage process. Since this depends on successful completion of multiple intermediate synthetic steps, the products are often quite pure, even though previous steps involve only a filtration workup. The mild conditions for many of these synthetic procedures offer the promise of using this chemistry in peptide fragment condensations to produce modified peptides, at either the N-terminus or C-terminus, or as individually assembled peptide segments with a wide variety of conformationally restricted peptidomimetic linkers at the point of juncture.

A new, general, and practical procedure for the asymmetric synthesis of 4-alkylidenyl glutamic acid derivatives via a catalytic enantioselective tandem conjugate addition-elimination on allylic acetates under chiral phase-transfer conditions is reported. A variety of structural types of allylic acetates have been reacted with the benzophenone imine of glycine tert-butyl ester to give the products in good to excellent yields and enantioselectivities (63-92% yield, 80-97% ee, 8 cases).

The development and application of chiral phase-transfer catalysis (PTC) for the enantioselective synthesis of optically active alpha-amino acid derivatives using achiral Schiff base esters developed in the author's laboratory and by others is reviewed. Phase-transfer catalysts derived from the Cinchona alkaloids have been exploited as inexpensive and attractive organocatalysts in the chiral PTC process. The recent evolution and use of these and other catalytic systems is described.

Lactams are key components of many peptidomimetic structures. Five- and six-membered lactam peptidomimetics with hydrogen or amino acid side chains at the alpha-position can be constructed from peptide precursors during a solid-phase synthesis. There is no significant racemization of remote stereocenters during synthesis.

Optically active syn- or anti-beta-substituted-alpha-amino acid derivatives are prepared in 94 to >/=99% ee and 66-98% ds by reaction of the Schiff base acetate of glycine tert-butyl ester with chiral, nonracemic B-alkyl-9-BBN derivatives in the presence of the Cinchona alkaloid, cinchonidine (CdOH) or cinchonine (CnOH), base, and lithium chloride.

Optically active (S)-alpha-amino acids are prepared in 54-95% ee (12 cases) by reaction of the Schiff base acetate of glycine tert-butyl ester with B-alkyl-9-BBN derivatives in the presence of the Cinchona alkaloid, cinchonidine, and base. The enantiomeric (R)-alpha-amino acids are available in 59-92% ee (3 cases) by using cinchonine as the chiral control element.

Reacting imine derivatives of resin-bound amino acids with alpha,omega-dihaloalkanes provides highly versatile intermediates to racemic alpha,alpha-disubstituted amino acids with a wide variety of side-chain functionality. Two strategies were developed to convert the intermediate omega-chloro or omega-bromo derivatives to the desired products. Together, they allow the creation of amino acids with diverse functionalities (omega-chlorides, nitriles, azides, acetates, thioacetates, thioethers, secondary and tertiary aliphatic amines, and anilines) placed at varying chain lengths (2-5) from the alpha-center of the amino acid.

The solid-phase synthesis of "unnatural" amino aldehydes, amino ketones, peptide aldehydes, and peptide ketones was accomplished from commercially available resin in a series of room temperature reactions. The initial step involved addition of an "unnatural" side chain to the N-terminus of a benzophenone imine-activated Weinreb resin-bound amino acid or peptide derivative. The alkylated imine was hydrolyzed, and the amine was converted to the Boc-, Cbz-, or naphthoyl derivative. The resin-bound substrate was then cleaved with DIBAL-H or a Grignard reagent to give the amino aldehyde, amino ketone, peptide aldehyde, or peptide ketone products. Twenty-four reactions were carried out simultaneously using a "Billboard" reaction apparatus to give products in 27-87% (59% average) isolated yield.

A method is described for the covalent attachment of DNA to a solid surface at high density for hybridization detection by mass spectrometry. A silicon wafer is functionalized to place an amino group on the surface; a heterobifunctional cross-linking agent is then reacted with the primary amine to incorporate an iodoacetamido group. An oligodeoxynucleotide containing a 3'- or a 5'-disulfide is treated with a reducing agent, resulting in a terminal free thiol, which is then coupled to the iodoacetamido surface. Analysis of the surface reveals that the amount of covalently bound oligodeoxynucleotide is 250 fmol of DNA/mm(2) with ∼40% of the immobilized oligodeoxynucleotides available for hybridization. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometric (MALDI-TOF MS) analysis reveals that the covalent linkage to the support remains intact, only the annealed strand is desorbed by the laser, and the amount of DNA hybridized to the array is sufficient for detection.