Solid phase synthesis of heterocyclic compounds from linear peptides: Cyclic ureas and thioureas

Synthesis of Diazacyclic and Triazacyclic Small-Molecule Libraries Using Vicinal Chiral Diamines Generated from Modified Short Peptides and Their Application for Drug Discovery

Small-molecule probes are powerful tools for studying biological systems and can serve as lead compounds for developing new therapeutics. Especially, nitrogen heterocycles are of considerable importance in the pharmaceutical field. These compounds are found in numerous bioactive structures. Their synthesis often requires several steps or the use of functionalized starting materials. This review describes the use of vicinal diamines generated from modified short peptides to access substituted diaza- and triazacyclic compounds. Small-molecule diaza- and triazacyclic compounds with different substitution patterns and embedded in various molecular frameworks constitute important structure classes in the search for bioactivity. The compounds are designed to follow known drug likeness rules, including "Lipinski's Rule of Five". The screening of diazacyclic and traizacyclic libraries has shown the utility of these classes of compounds for the de novo identification of highly active compounds, including antimalarials, antimicrobial compounds, antifibrotic compounds, potent analgesics, and antitumor agents. Examples of the synthesis of diazacyclic and triazacyclic small-molecule libraries from vicinal chiral polyamines generated from modified short peptides and their application for the identification of highly active compounds are described.

Fused Ring Molecular Scaffold with 3D Architecture for Constrained Peptidomimetics: Polymer-Supported Stereoselective Synthesis of Tetrahydrobenzo[e]pyrazino[2,1-c][1,2,4]thiadiazinone 6,6-dioxide via N-Acyl Iminiums

3,4,4a,5-Tetrahydrobenzo[e]pyrazino[2,1-c][1,2,4]thiadiazin-1(2H)-one 6,6-dioxides, molecular scaffolds with 3D architecture, were synthesized on solid supports via tandem N-acyl iminium ion cyclization followed by nucleophilic addition. The modular synthesis proceeded under mild conditions using commercially available building blocks and provided crude products with respectable purity. The synthesized compounds are applicable as fused nitrogenous heterocyclic compounds in drug discovery and as constrained peptidomimetics incorporated into a peptide backbone.

Simple, versatile, and chemoselective reduction of secondary amides and lactams to amines with the Tf2O–NaBH4 or Cp2ZrHCl–NaBH4 system

A convenient method for the direct reduction of secondary amides and lactams to amines is reported.

A novel method for the determination of isokinetic ratios and its application in the synthesis of two new positional scanning libraries

A novel method for the direct evaluation of the equimolarity of the compounds contained in a mixture is presented. We applied the method toward calculating isokinetic ratios for the reaction between the amine termini of a resin bound peptide fragment and a sulfonyl chloride to produce equal molar mixtures of sulfonamides. The results of this study and the application of the method to the synthesis of two new positional scanning synthetic combinatorial libraries (PS-SCL) are discussed.

Multi-chelation approach towards natural product-like skeletons: one-pot access to a nitrogen-containing tetracyclic framework from AlaAla dipeptide

Reductive transformation of the dipeptide BocAlaAlaOMe to a complex, internally charge-stabilized, natural product-like skeleton in one synthetic step is discussed. Stepwise replacement of the B-H bonds in borane by B-N or B-O resulted in incorporation of three boron atoms in a tetracyclic framework whereby one is stereogenic!

Small molecule functional analogs of peptides that inhibit lambda site-specific recombination and bind Holliday junctions

Our lab has isolated hexameric peptides that are structure-selective ligands of Holliday junctions (HJ), central intermediates of several DNA recombination reactions. One of the most potent of these inhibitors, WRWYCR, has shown antibacterial activity in part due to its inhibition of DNA repair proteins. To increase the therapeutic potential of these inhibitors, we searched for small molecule inhibitors with similar activities. We screened 11 small molecule libraries comprising over nine million individual compounds and identified a potent N-methyl aminocyclic thiourea inhibitor that also traps HJs formed during site-specific recombination reactions in vitro. This inhibitor binds specifically to protein-free HJs and can inhibit HJ resolution by RecG helicase, but only showed modest growth inhibition of bacterial with a hyperpermeable outer membrane; nonetheless, this is an important step in developing a functional analog of the peptide inhibitors.

Preparation, isolation, and characterization of Nalpha-Fmoc-peptide isocyanates: solution synthesis of oligo-alpha-peptidyl ureas

The N(alpha)-Fmoc-peptide isocyanates 3a-q, 4a-c, and 5a-c were prepared by the Curtius rearrangement of N(alpha)-Fmoc-peptide acid azides in toluene under thermal, microwave, and ultrasonic conditions. All the N(alpha)-Fmoc-oligo-peptide isocyanates made were isolated as stable crystalline solids with 71 to 94% yield and were fully characterized by 1H NMR, 13C NMR, and mass spectroscopy. Their utility for the synthesis of oligo-alpha-peptidyl ureas 7a-f and 8a-c by the divergent coupling approach was demonstrated. The coupling of N(alpha)-Fmoc-dipeptide isocyanates with amino acid ester or with N,O-bis(trimethylsilyl)amino acids resulted in N(alpha)-Fmoc-tripeptidyl urea ester and acids containing one each of peptide bond and urea bond. The divergent approach is extended to the synthesis of tetrapeptidyl ureas by the 2 + 2 strategy using bis-TMS-peptide acid as an amino component. To incorporate urea bonds in adjacent positions, N(alpha)-Fmoc-peptidyl urea isocyanates 9a-d were prepared and employed in the synthesis of three tetrapeptidyl ureas 10a-b and 11 containing one peptide bond and two urea bonds in series from the N-terminal end. The protocol was then employed for the synthesis of five urea analogues 13-15, 18, and 21 of [Leu5]enkephalin containing urea bonds at the 2, 3, 4 positions as well as at the 2, 4 and 2, 3, 4 positions. The analogue 2l was made by the convergent synthesis by the N --> C terminal chain extension. Finally, two urea analogues 22 and 23 of repeat units of bioelasto polymers, namely Val-Pro-Gly-Val-Gly-OH and Pro-Gly-Val-Gly-Val-OH, were synthesized incorporating the urea bond by the concomitant isocyanate generation and urea bond formation under thermal conditions.

In vitro and direct in vivo testing of mixture-based combinatorial libraries for the identification of highly active and specific opiate ligands

The use of combinatorial libraries for the identification of novel opiate and related ligands in opioid receptor assays is reviewed. Case studies involving opioid assays used to demonstrate the viability of combinatorial libraries are described. The identification of new opioid peptides composed of L-amino acids, D-amino acids, or L-, D-, and unnatural amino acids is reviewed. New opioid compounds have also been identified from peptidomimetic libraries, such as peptoids and alkylated dipeptides, and those identified from acyclic (eg, polyamine, urea) and heterocyclic (eg, bicyclic guanidine) libraries are reviewed.

Solid Phase Synthesis of 3,4,7-Trisubstituted 4,5,8,9-Tetrahydro-3H-imidazo[1,2-a][1,3,5]triazepin-2(7H)-thiones and N-Alkyl-4,5,7,8-tetrahydro-3H-imidazo[1,2-a][1,3,5]triazepin-2-amines

The solid-phase parallel synthesis of 3,4,7-trisubstituted 4,5,8,9-tetrahydro-3H-imidazo[1,2-a][1,3,5]triazepin-2(7H)-thiones and N-alkyl-4,5,7,8-tetrahydro-3H-imidazo[1,2-a][1,3,5]triazepin-2-amines starting from resin-bound dipeptides is described. The key synthetic steps involve the cylization of an amino and a guanidino functionality using thiocarbonyldiimidazole and the subsequent transformation of the resulting thiourea moiety to a substituted guanidine group using HgCl(2) and various amines. Following cleavage from the resin, the desired products were obtained in good yields and good to moderate purities, depending on the building blocks employed.

Solid phase synthesis and application of trisubstituted thioureas

Resin-bound amines 1a-e condense with isothiocyanates to give thiourea resins 2a-i. Resins 2a-g subsequently react with iodomethane followed by cleavage affording S-methyl isothioureas 4a-g, and resins 2a-b,h-i react with acyl chlorides to afford N-acylated thioureas 6a-d. N-Acylthioureas 8a-f (R(2) = H) were prepared directly from resin-bound amines 1a-d with acyl isothiocyanates. N-Acylthioureas 8a-d,f(R(2) = H) were used for the preparation of S-methyl-N-acylisothioureas 10a-e. Alkylation was performed using methyl iodide. Resin-bound S-methyl-N-acylisothioureas 10a,b,d are converted by an action of hydrazines into 3-amino-1,2,4-triazoles 13a-d. Condensation of resins 8a-e (R(2) = H) with 2-bromoacetophenones in the presence of TEA affords thiazoles 15 a-e. All transformations proceeded in high yields and gave products of good purities.

Solid phase synthesis of mixture-based acyclic and heterocyclic small molecule combinatorial libraries from resin-bound polyamides

The development of soluble mixture-based heterocyclic combinatorial libraries derived from amino acids and peptides is described. Starting with a "toolbox" of various chemical transformations, including alkylations, reductions, acylations, and the use of a variety of bifunctional reagents, the "libraries from libraries" concept has been expanded to encompass the development of more than fifty positional scanning combinatorial libraries each composed of tens of thousands of low molecular weight acyclic and heterocyclic compounds.

Novel strategies for solid-phase construction of small-molecule combinatorial libraries

During the past decade we witnessed a rapid advance in the new field of chemical science, combinatorial chemistry. The pharmaceutical industries invested heavily in accelerating the development of this new technology. As a result, it has become an extremely important tool in lead identification and optimization in current pharmaceutical research. It also quickly crossed the boundaries of the original chemical discipline and demonstrated great potential in many other important areas, such as searching for novel and highly efficient catalysts and superconductive material. Researchers from both academic and industrial laboratories have directed great effort towards the development of novel strategies for combinatorial synthesis.

A mild and general solid-phase method for the synthesis of chiral polyamines. Solution studies on the cleavage of borane-amine intermediates from the reduction of secondary amides

A mild oxidative workup protocol using iodine in an acetic acid-acetate buffer solution is described for the cleavage of borane-amine adducts arising from the borane-promoted reduction of polyamides supported onto practical trityl-based resins. Chiral polyamines with diverse side-chain functionalities can be generated as free bases without premature release from the solid support and with essentially no racemization using this method. A series of model oligomeric secondary diamides 6 containing various alpha-amino acid residues (Val, Phe, Tyr, Ser, Cys, Met, Gln, Trp) provided triamine products 8 in high yields and good to excellent purity. On the other hand, a substrate containing a tertiary amide (15) formed a rather unusual triaminoborane intermediate that required more stringent workup conditions to liberate the polyamine product 20. The reduction of oligomeric tertiary amides such as 9 was found sluggish, but these compounds could nonetheless be obtained in high purity from in situ reductive amination of the corresponding secondary amines. Control studies, carried out in solution with model secondary amide 23, confirmed the efficiency of the buffered iodine solution and highlighted several advantages (no heating necessary, no need for strong bases or acids) over existing methods for the cleavage of borane-amine adducts. A possible mechanism involving all buffer components (iodine, acetic acid, and acetate ion) is proposed in which borane-amine adducts are transformed first to the monoiodoborane-amine and then to the corresponding acetoxyborane-amine adduct of much weaker coordination affinity. The latter would dissociate readily and get trapped by the acetic acid to provide the desired secondary amine. This reduction/oxidative workup protocol is useful as a general method for the facile solid-phase synthesis of polyamines for eventual release in solution and use in various applications. It is also potentially very useful toward the synthesis and screening of bead-supported libraries of free oligoamines assembled through split-pool methods.

Solid-phase synthesis of bis-heterocyclic compounds from resin-bound orthogonally protected lysine

An efficient method for the solid-phase synthesis of bis-heterocyclic compounds from resin-bound orthogonally protected lysine is presented. The initial reaction step involves the exhaustive reduction of resin-bound tetra-amides using borane-THF, followed by cyclization of the resulting tetra-amine with either carbonyldiimidazole, thiocarbonyldiimidazole, or oxalyldiimidazole to generate resin-bound bis-cyclic ureas, bis-cyclic thioureas, and bis-cyclic diketopiperazines, respectively. Cleavage from the solid support using hydrogen fluoride, followed by extraction and lyophilization, yields the desired bis-heterocyclic compounds in excellent yield and high purity.

Solid-phase synthesis of bis-2-imidazolidinethiones from resin-bound tripeptides

The exhaustive reduction of resin-bound tripeptides with borane afforded three secondary amines and one primary amine. The treatment of the solid-support polyamines with thiocarbonyldiimidazole afforded, following cleavage of the solid support, the corresponding bis-cyclic thiourea in good purity and yield.

Drug discovery and vaccine development using mixture-based synthetic combinatorial libraries

The approaches and concepts that encompass combinatorial chemistry represent a paradigm shift in drug discovery and basic research. Viewed initially as a curiosity by the pharmaceutical industry, combinatorial chemistry approaches are now recognized as essential drug discovery tools that decrease the time taken for discovery and increase the throughput of chemical screening by as much as 1000-fold. Although the use of mixture-based synthetic combinatorial libraries was one of the first approaches presented, its inherent strengths are only recently being recognized. Numerous mixture-based libraries of peptides, peptidomimetics and heterocycles have been synthesized and deconvoluted using the positional scanning approach. Mixture-based library approaches for drug discovery and vaccine development will be reviewed herein.

New opioid peptides, peptidomimetics, and heterocyclic compounds from combinatorial libraries

Here we review the use of combinatorial libraries in opioid receptor assays. Following a brief description of the history of the combinatorial field, methods for the generation of synthetic libraries and the deconvolution of mixture-based libraries are presented. Case studies involving opioid assays used to demonstrate the viability of combinatorial libraries are described. The identification of new opioid peptides from combinatorial libraries is reviewed. The peptides found are composed of L-amino acids, D-amino acids, or L-, D-, and unnatural amino acids, and range from tetrapeptides to decapeptides. Likewise, new opioid compounds identified from peptidomimetic libraries, such as peptoids and alkylated dipeptides, and those identified from acyclic (e.g., polyamine, urea) and heterocyclic (e.g., bicyclic guanidine) libraries, are reviewed.

Combinatorial chemistry: Polymer supported synthesis of peptide and non-peptide libraries

In recent years, combinatorial chemistry has emerged as a powerful tool for accelerating drug discovery. While industry is rapidly embracing the technology, researchers continue to develop novel library methods including resins, linkers, tagging and deconvolution techniques. Newer strategies involving computer-customized combinatorial libraries offer enormous potential for the design of more "focused" and "smart" chemical libraries with maximal diversity. In addition, miniaturized systems for synthesizing chemical libraries are also being developed, which has made it possible to carry out reactions at submicroliter volumes.

Tight-binding streptavidin ligands from a cyclic peptide library

During the screening of a soluble library of cyclo(AXXXXXAE)K-CONH2, a cyclic peptide cyclo(AHPQFPAE)K-CONH2 was identified as a tight-binding ligand (IC50 = 128 nM) and found to bind 1000-fold more tightly than its linear peptide to streptavidin. The results of this study suggest that library screening of conformationally constrained cyclic peptides can be an effective means for the discovery of high affinity ligands.