Synthetic chemical diversity: solid phase synthesis of libraries of C2 symmetric inhibitors of HIV protease containing diamino diol and diamino alcohol cores

Stereoselective Synthesis and Catalytical Application of Perillaldehyde-Based 3-Amino-1,2-diol Regioisomers

A library of regioisomeric monoterpene-based aminodiols was synthesised and applied as chiral catalysts in the addition of diethylzinc to benzaldehyde. The synthesis of the first type of aminodiols was achieved starting from (-)-8,9-dihydroperillaldehyde via reductive amination, followed by Boc protection and dihydroxylation with the OsO4/NMO system. Separation of formed stereoisomers resulted in a library of aminodiol diastereoisomers. The library of regioisomeric analogues was obtained starting from (-)-8,9-dihydroperillic alcohol, which was transformed into a mixture of allylic trichloroacetamides via Overman rearrangement. Changing the protecting group to a Boc function, the protected enamines were subjected to dihydroxylation with the OsO4/NMO system, leading to a 71:16:13 mixture of diastereoisomers, which were separated, affording the three isomers in isolated form. The obtained primary aminodiols were transformed into secondary derivatives. The regioselectivity of the ring closure of the N-benzyl-substituted aminodiols with formaldehyde was also investigated, resulting in 1,3-oxazines in an exclusive manner. To explain the stability difference between diastereoisomeric 1,3-oxazines, a series of comparative theoretical modelling studies was carried out. The obtained potential catalysts were applied in the reaction of aromatic aldehydes and diethylzinc with moderate to good enantioselectivities (up to 94% ee), whereas the opposite chiral selectivity was observed between secondary aminodiols and their ring-closed 1,3-oxazine analogues.

Synthesis and Investigation of Pinane-Based Chiral Tridentate Ligands in the Asymmetric Addition of Diethylzinc to Aldehydes

A library of pinane-based chiral aminodiols, derived from natural (−)-β-pinene, were prepared and applied as chiral catalysts in the addition of diethylzinc to aldehydes. (−)-β-Pinene was reacted to provide 3-methylenenopinone, followed by a reduction of the carbonyl function to give a key allylic alcohol intermediate. Stereoselective epoxidation of the latter and subsequent ring opening of the resulting oxirane with primary and secondary amines afforded aminodiols. The regioselectivity of the ring closure of the N-substituted secondary aminodiols with formaldehyde was examined and exclusive formation of oxazolidines was observed. Treatment of the allylic alcohol with benzyl bromide provided the corresponding O-benzyl derivative, which was transformed into O-benzyl aminodiols by aminolysis. Ring closure of the N-isopropyl aminodiol derivative with formaldehyde resulted in spirooxazolidine. The obtained potential catalysts were applied in the reaction of both aromatic and aliphatic aldehydes to diethylzinc providing moderate to good enantioselectivities (up to 87% ee). Through the use of molecular modeling at an ab initio level, this phenomenon was interpreted in terms of competing reaction pathways. Molecular modeling at the RHF/LANL2DZ level of theory was successfully applied for interpretation of the stereochemical outcome of the reactions leading to display excellent (R) enantioselectivity in the examined transformation.

Methods and Approaches for the Solid-Phase Synthesis of Peptide Alcohols

Many methods have been developed for attaching an alcohol functionality to a solid support. However, not all of these methods are used to obtain peptide alcohols. In this Minireview, we will discuss several of the most important methods and approaches for the synthesis of peptide alcohols and the attachment of hydroxy groups to a solid support for the synthesis of cyclic peptides. Some of the methods include the use of functionalized Wang resin and the attachment of an alcohol to an enol ether resin. We also discuss the use of the chlorotrityl resin, one of the most common linkers used to obtain peptide alcohols. In addition, we outline the recently developed resins with the Rink, Ramage and Sieber handles. The majority of these methods have been used to synthesize many important drugs, such as octreotide and the antibiotic peptaibols.

Recent advances in the Overman rearrangement: synthesis of natural products and valuable compounds

This review documents the reports since 2005 on the Overman rearrangement, an important C–N bond forming reaction that has been profoundly used in the synthesis of natural products, synthetic intermediates, building blocks and valuable compounds.

(1S,2R,4S)-1-[(Benzyl-amino)-meth-yl]-4-(prop-1-en-2-yl)cyclo-hexane-1,2-diol

The title compound, C₁₇H₂₅NO₂, was synthesized by epoxidation of the double bond of (S)-perillyl alcohol [(S)-4-isopropenyl-1-cyclo­hexenyl­methanol], followed by the oxirane ring-opening by benzyl­amine using [Ca(CF₃CO₂)₂] as catalyst under solvent-free condition at 313 K. The mol­ecular conformation is stabilized by an intra­molecular O—H⋯N hydrogen bond. In the crystal, mol­ecules are linked by inter­molecular N—H⋯O hydrogen bonds, forming chains parallel to the a axis, which are further connected by O—H⋯O hydrogen bonds into sheets parallel to (010). The absolute configuration of the mol­ecule is known from the synthetic procedure.

An efficient procedure based on a MW-assisted Horner-Wadsworth-Emmons reaction for the synthesis of (Z)-3,3-trisubstituted-alpha,beta-unsaturated esters

A microwave-assisted HWE olefination process of readily accessible aryl-alkyl ketones has been developed to provide a rapid access to (Z)-3,3-trisubstituted-alpha,beta-unsaturated methyl esters, key building blocks for the synthesis of biologically active compounds.

Microwave-assisted combinatorial synthesis of polysubstituent imidazo[1,2-a]quinoline, pyrimido[1,2-a]quinoline and quinolino[1,2-a]quinazoline derivatives

A series of unusual fused heterocyclic compound derivatives, consisting of a pyridine and a imidazole or pyrimidine core, with a bridgehead nitrogen, were successfully synthesized by a microwave-assisted, three-component domino reaction of aldehydes, enaminones, and malononnitrile. In this one-pot reaction, up to five new bonds were formed accompanied by generating the lactam group. This method has the advantages of short synthetic route, operational simplicity, increased safety for small-scale high-speed synthesis, and minimal environment impact.

Indium(III)-Catalyzed Addition of Diethyl Acetamidomalonate to Terminal Alkynes: An Efficient Approach to β-Branched α-Amino Acids

The indium(III)-catalyzed Markovnikov addition of active methylene compounds to terminal alkynes has been expanded further to include diethyl acetamidomalonate. This reaction has been studied, and a practical approach to beta-branched alpha-amino acids was developed.

ULTRAMINE: a high-capacity polyethylene-imine-based polymer and its application as a scavenger resin

The synthesis of a novel high-loading polyethylene-imine resin (ULTRAMINE) is described, and its application as a scavenger resin in various acylation reactions is demonstrated. The inverse suspension polymerization technique was used for the synthesis of well-defined spherical polymer beads. Polymer beads with different cross-linking densities were synthesized according to the degree of acryloylation of the polyethylene-imine polymer. The resin was characterized by various spectroscopic techniques. The size, shape, and morphological features of the resin were demonstrated by microscopy. The resin showed excellent swelling properties in both polar and nonpolar solvents. The chemical stability of the resin in various reagents and solvents was investigated and monitored by IR spectroscopy. The mechanical stability of the beads was determined by a single-bead compressive experiment. The ULTRAMINE beads can be used as an excellent scavenger for excess acylating reagent, as demonstrated for a variety of reactions. ULTRAMINE-red resin was derived from ULTRAMINE through exhaustive reduction of the amide carbonyl groups to yield an all-amine resin.

Efficient Solid-Phase Synthesis of Trifunctional Probes and Their Application to the Detection of Carbohydrate-Binding Proteins

[structure: see text] An efficient solid-phase synthesis of trifunctional probes containing a photoreactive group, a reporter tag, and a carbohydrate ligand was developed. Labeling studies with these probes demonstrate that specific lectins can be labeled with high sensitivity and selectivity. This technique serves as a powerful tool for the rapid detection and profiling of lectins.

A quick diversity-oriented amide-forming reaction to optimize P-subsite residues of HIV protease inhibitors

We report a new simple method that allows rapid preparation in solution of a library of compounds for in situ high-throughput screening to identify new inhibitors of HIV-1 protease. The method is based on the amide-forming reaction of a C(2)-symmetrical diamino diol core with various carboxylic acids, followed by a direct assay of the inhibition activity without product isolation. Sixty-two compounds were made and screened in less than 1 hr. The utility of this method is demonstrated by the identification of new P3-P3' residues that convert a transition state analog core from a poor binding molecule (1, K(i) > 2 microM) to a potent inhibitor (AB1, K(i) = 2 nM) against the wild-type, and the inhibition activities against resistant mutants are better than those of two existing drugs. This method reduces the time required for synthesis and testing of a large number of characterized inhibitors and should find useful applications in other enzyme systems.

A combinatorial library of indinavir analogues and its in vitro and in vivo studies

A combinatorial library of 300HIV protease inhibitors has been synthesized. The library was screened against recombinant wild-type and mutant HIV-1 protease enzymes. The pharmacokinetics of the library was evaluated by dosing in dogs. Compounds that are notably more potent than indinavir and have favorable pharmacokinetic properties were identified.

Tracelessness Unmasked: A General Linker Nomenclature

Nowadays it is rare to find an issue of a major chemistry journal without at least one article on solid-phase synthesis. This is hardly surprising: the technique promises an end to arduous work-up procedures and the ability to facilitate the creation of vast libraries of compounds using combinatorial techniques. No longer is the technique only of interest to those involved in peptide synthesis: an enormous variety of product classes have now been prepared on and isolated from the solid phase. It is the "linker" which is the focus of this article. The linker's ultimate function is to release a product from the support into solution: it does this, without exception, with a chemical change to the product at the former linkage site. Some linkers, apparently, are "traceless". But what, in fact, is "tracelessness"? Twenty years ago, in a climate where cleavage of a linker resulted in formation of a polar carboxylic acid as the vestige of the support, the concept was attractive. Today the chemist is faced with a myriad of novel linkers which have the ability to release products bearing most major functionalities at the former linkage site and we will argue here that the term "traceless", although currently in widespread use, is meaningless. Instead, we propose a new categorization of linkers based on the functionality they release upon cleavage, and suggest a nomenclature to underpin this categorization. We anticipate that the article will also serve to highlight areas of linker technology in need of further research.

A picomolar inhibitor of resistant strains of human immunodeficiency virus protease identified by a combinatorial approach

In order to identify inhibitors of various drug-resistant forms of the human immunodeficiency virus protease (HIV PR), we have designed and synthesized pseudopeptide libraries with a general structure Z-mimetic-Aa1-Aa2-NH2. Five different chemistries for peptide bond replacement have been employed and the resulting five individual sublibraries tested with the HIV PR and its drug-resistant mutants. Each mutant contains amino acid substitutions that have previously been shown to be associated with resistance to protease inhibitors, including Ritonavir, Indinavir, and Saquinavir. We have mapped the subsite preferences of resistant HIV PR species with the aim of selecting a pluripotent pharmaceutical lead. All of the enzyme species in this study manifest clear preference for an L-Glu residue in the P2' position. Slight, but significant, differences in P3' subsite specificity among individual resistant PR species have been documented. We have identified three compounds, combining the most favorable features of the inhibitor array, that exhibit low-nanomolar or picomolar Ki values for all three mutant PR species tested.

Combinatorial chemistry as a tool for drug discovery

The question 'will combinatorial chemistry deliver real medicines' has been posed [96]. First it is important to realise that the chemical part of the drug discovery process cannot stand alone; the integration of synthesis and biological assays is fundamental to the combinatorial approach. The results presented in Tables 3.1 to 3.8 suggest that so far smaller directed combinatorial libraries have obtained equivalent results to those obtained previously from traditional medicinal chemistry analogue programs. Unfortunately, because of the long time it takes to develop pharmaceutical drugs there are no examples yet of marketed drugs discovered by combinatorial methods. There are interesting examples where active leads have been discovered from the screening of the same library against multiple targets (e.g. libraries 13, 39, 43, 66, 71 and 76). It is now possible to handle much larger libraries of non-oligomeric structures and the chemistry required for such applications is becoming available. Whether combinatorial approaches can also be adapted to deal with all the other requirements of a successful pharmaceutical (lack of toxicity, bioavailability etc.) is open to question but there are already examples such as cassette dosing [235-237]. However we can still be optimistic about the possibility of larger libraries producing avenues of investigation for the medicinal chemist to develop into real drugs. Combinatorial chemistry is an important tool for the medicinal chemist.

Combinatorial library of serine and cysteine protease inhibitors that interact with both the S and S' binding sites

A combinatorial library of 400 inhibitors has been synthesized and screened against several serine and cysteine proteases including plasmin, cathepsin B, and papain. The inhibitors are based upon a cyclohexanone nucleus and are designed to probe binding interactions in the S2 and S2' binding sites. This methodology has led to the discovery of inhibitor 15A, which incorporates Trp at both the P2 and P2' positions and has an inhibition constant against plasmin of 5 microM. Data from screening of the library shows that plasmin has a strong specificity for Trp at the S2 subsite and prefers to bind hydrophobic and aromatic amino acids such as Ile, Phe, Trp, and Tyr at the S2' subsite. In contrast, the S2' subsites of cathepsin B and papain do not show a strong preference for any particular amino acid.

Combinatorial mixture synthesis and biological evaluation of dihydrophenyl triazine antifolates

The traditional 'one-pot' three component synthesis was adapted successfully for combinatorial mixtures synthesis of dihydrophenyl triazines, which are nonclassical, dihydrofolate reductase (DHFR) inhibitors. Each library was designed to comprise eight reaction mixture pots and in every pot there were three dihydrophenyl triazines. A total of three libraries were synthesized and the final number of compounds harvested was 64. The products precipitated out of the reaction mixture and could be collected easily and cleansed by washing. Solid supports and further purification processes were not required. The reactions were monitored by TLC and a HPLC method was developed to determine the number of products in each pot. All 24 pots were screened for inhibitory activity against the rat liver DHFR. Two pots showed good inhibitory activity and the products in them were individually synthesized, characterized and biologically tested again. One lead compound was identified amongst all the compounds synthesized, and would be further optimized.

Comprehensive survey of chemical libraries yielding enzyme inhibitors, receptor agonists and antagonists, and other biologically active agents: 1992 through 1997

This review is a historical accounting of chemical libraries from which biologically active agents have been obtained. The comprehensive tabulation includes citations as early as 1992, when the first descriptions of biologically active libraries were disclosed, and continues through 1997. Four tables are provided listing libraries screened against (1) proteolytic enzymes, (2) non-proteolytic enzymes, (3) G-protein coupled receptors (GPCRs), and (4) other targets not classified in the first three tables (e.g. non-GPCRs, integrins, antiinfectives). A name, generic structure, and size is provided for each library citation, accompanied by the molecular screen and the structure and potency of the most active library member. In total, 86 libraries are presented with 60% of the contributions reported from pharmaceutical and biotechnology companies. Approximately 70% of the libraries have used alpha-amino acid synthons in their construction and 85% of the libraries include one or more amide bonds.

Discovery of protease inhibitors using targeted libraries

There continues to be considerable effort towards the construction of compound libraries targeted for the inhibition of protease enzymes. New tag-encoding methods for library deconvolution have been applied to this problem and there has been particular interest in novel solid-phase linkers for the introduction of key pharmacophore groups required for protease inhibition. Recent reports have tended to focus on nonpeptidic libraries, and, notably, structure-based design methods are now being applied to direct library design.

Discovery of enzyme inhibitors through combinatorial chemistry

This review serves to highlight the recent examples of combinatoric methodology as applied to the discovery and optimization of enzyme inhibitors. Early research efforts focused on the identification of polypeptides from libraries as inhibitors of proteases. As solution- and solid-phase chemistries gain in sophistication, libraries containing less peptidic structural motifs have been created. A recurring design stratagem relies on the synthesis of libraries incorporating pharmacophores with known affinity for the target enzyme. Screening of these structure-based libraries has led to the discovery of small-molecule inhibitors of both proteolytic and non-proteolytic enzymes alike. Two tables are provided listing the enzyme targeted libraries through 1996. A name, generic structure and size is given for each library citation, accompanied by the enzyme screen and the structure and potency of the most active library member.

PRO_SELECT: combining structure-based drug design and combinatorial chemistry for rapid lead discovery. 1. Technology

This paper describes a novel methodology, PRO_SELECT, which combines elements of structure-based drug design and combinatorial chemistry to create a new paradigm for accelerated lead discovery. Starting with a synthetically accessible template positioned in the active site of the target of interest, PRO_SELECT employs database searching to generate lists of potential substituents for each substituent position on the template. These substituents are selected on the basis of their being able to couple to the template using known synthetic routes and their possession of the correct functionality to interact with specified residues in the active site. The lists of potential substituents are then screened computationally against the active site using rapid algorithms. An empirical scoring function, correlated to binding free energy, is used to rank the substituents at each position. The highest scoring substituents at each position can then be examined using a variety of techniques and a final selection is made. Combinatorial enumeration of the final lists generates a library of synthetically accessible molecules, which may then be prioritized for synthesis and assay. The results obtained using PRO_SELECT to design thrombin inhibitors are briefly discussed.