The Distributed Drug Discovery (D3) program trains students in three drug discovery disciplines (synthesis, computational analysis, and biological screening) while addressing the important challenge of discovering drug leads for neglected diseases. This article focuses on implementation of the synthesis component in the second-semester undergraduate organic laboratory. The educational program was started at IUPUI in 2003 and has been carried out over 23 semesters with 65 lab sections by >1200 students. Since the chemistry component is most advanced, it serves as a model for the computational and biological modules in development. Synthetic procedures are based on well-documented, reproducible solid-phase combinatorial chemistry. They are carried out in a 2 × 3 combinatorial grid (Bill-Board) to create a control molecule and five new products (50 μmol scale, ∼10–20 mg product, typically high LC/MS purity). The first of these synthetic procedures (D3 Lab 1) utilizes a protected and activated derivative of glycine that is converted in a five-step synthetic sequence (alkylation, hydrolysis, neutralization, acylation, and cleavage from the resin) to N-acylated unnatural amino acids containing two variable diversity elements: a new α-side chain and an N-acyl group. Based on these combinatorial procedures, large virtual libraries/catalogs of student-accessible molecules can be created and computationally analyzed. Selected molecules are then synthesized and screened by D3 students. Active classroom learning experiences and recorded lectures or demonstrations are used to teach fundamental knowledge and skills in synthesis while enabling students to pursue, with no predetermined outcome, multidisciplinary, distributed, research-based experiments toward drug-lead discovery.
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, R2CO, four bonds away from the site of hydrolysis. Electron-rich acyl R2 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.
Syntheses of various isomeric dihydropiperazines can be approached successfully by taking advantage of the regioselective monothionation of their respective diones. Preparation of the precursor unsymmetrical N-substituted piperazinediones from readily available diamines is key to this selectivity. The dihydropiperazine ring system, as exemplified in 1-[(6-chloropyridin-3-yl)methyl]-4-methyl-3-oxopiperazin-2-ylidenecyanamide (4) and 1-[(2-chloro-1,3-thiazol-5-yl)methyl]-4-methyl-3-oxopiperazin-2-ylidenecyanamide (25), has been shown to be a suitable bioisosteric replacement for the imidazolidine ring system contained in neonicotinoid compounds. However, placement of the cyanoimino electron-withdrawing group further removed from the pyridine ring, as in 4-[(6-chloropyridin-3-yl)methyl]-3-oxopiperazin-2-ylidenecyanamide (3a), or relocation of the carbonyl group, as in 1-[(6-chloropyridin-3-yl)methyl]-4-methyl-5-oxopiperazin-2-ylidenecyanamide (5), results in significantly decreased bioisosterism. The dihydropiperazine ring system of 4 and 25 also lends a degree of rigidity to the molecule that is not offered by the inactive acyclic counterpart 2-[(6-chloropyridin-3-yl)-methyl-(methyl)amino]-2-(cyanoimino)-N,N-dimethylacetamide (6). A pharmacophore model is proposed that qualitatively explains the results on the basis of good overlap of the key pharmacophore elements of 4 and imidacloprid (1); the less active regioisomers of 4 (3a, 5, and 6) feature a smaller degree of overlap.
An experiment for the synthesis of N-acyl derivatives of natural amino acids has been developed as part of the Distributed Drug Discovery (D3) program. Students use solid-phase synthesis techniques to complete a three-step, combinatorial synthesis of six products, which are analyzed using LC−MS and NMR spectroscopy. This protocol is suitable for introductory organic laboratory students and has been successfully implemented at multiple academic sites internationally. Accompanying prelab activities introduce students to SciFinder and to medicinal chemistry design principles. Pairing of these activities with the laboratory work provides students an authentic and cohesive research project experience.
It has been shown that oxidation at the alpha-carbon of N-(4-chloro-3-methyl-5-isothiazolyl)-2-[p-[(alpha,alpha, alpha-trifluoro-p-tolyl)oxy]phenyl]acetamide (1) is conveniently brought about using dimethylformamide dimethylacetal to give N-(4-chloro-3-methyl-5-isothiazolyl)-beta-(dimethylamino)-p-[(alpha, alpha,alpha-trifluoro-p-tolyl)oxy]atropamide (2), which has served as a common starting point for a variety of functional group transformations. These transformations were found to proceed in moderate to good yields to give derivatives of 1 that retained much of the efficacy associated with the parent amide and have allowed for an expansion of the SAR to be developed. Examples of enamines, enols, enol (thio)ethers, oximes, and hydrazones were prepared. In particular, the enamines derived from low molecular weight amines and amino acids were most active as broad-spectrum insecticides and were found to be even more active than 1 on root-knot nematode.
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