Comprehensive survey of combinatorial library synthesis: 2000

Sulfur(VI) Fluoride Exchange Chemistry in Solid-Phase Synthesis of Compound Arrays: Discovery of Histone Deacetylase Inhibitors

Multistep synthesis performed on solid support is a powerful means to generate small-molecule libraries for the discovery of chemical probes to dissect biological mechanisms as well as for drug discovery. Therefore, expansion of the collection of robust chemical transformations amenable to solid-phase synthesis is desirable for achieving chemically diverse libraries for biological testing. Here, we show that sulfur(VI) fluoride exchange (SuFEx) chemistry, exemplified by pairing phenols with aryl fluorosulfates, can be used for the solid-phase synthesis of biologically active compounds. As a case study, we designed and synthesized a library of 84 hydroxamic acid-containing small molecules, providing a rich source of inhibitors with diverse selectivity profiles across the human histone deacetylase enzyme family. Among other discoveries, we identified a scaffold that furnished inhibitors of HDAC11 with exquisite selectivity in vitro and a selective inhibitor of HDAC6 that was shown to affect the acetylation of α-tubulin over histone sites H3K18, H3K27, as well as SMC3 in cultured cells. Our results encourage the further use of SuFEx chemistry for the synthesis of diverse small-molecule libraries and provide insight for future design of selective HDAC inhibitors.

Effects of indole derivatives from Purpureocillium lilacinum in controlling tobacco mosaic virus

There are various types of compounds studied and applied for plant disease management, and some of them are environment friendly and suitable in organic production. An example is indole-3-carboxaldehyde (A1) and indole-3-carboxylic acid (A2) derived from Purpureocillium lilacinum H1463, which have shown a strong activity in the control of tobacco mosaic virus (TMV). In this study, the effects of these compounds were studied on suppressing TMV and corresponding mechanism. Both A1 and A2 exhibited strong anti-TMV activities in vitro and in vivo. They fractured TMV virions and forced the fractured particles agglomerated. A1 and A2 also induced immune responses or resistance of tobacco to TMV infection, including expressing hypersensitive reaction (HR), increasing defense-related enzymes and overexpressing pathogenesis-related (PR) proteins. The upregulation of salicylic acid (SA) biosynthesis genes PAL, ICS, and PBS3 confirmed that SA served as a defense-related signal molecule. Therefore, indole derivatives have a potential for activating defense of tobacco against TMV and other pathogens and can be used for disease control.

DBU-catalyzed dearomative annulation of 2-pyridylacetates with α,β-unsaturated pyrazolamides for the synthesis of multisubstituted 2,3-dihydro-4H-quinolizin-4-ones

DBU-catalyzed dearomative [3 + 3] annulation of 2-pyridylacetates and α,β-unsaturated pyrazolamides for the synthesis of multisubstituted 2,3-dihydro-4H-quinolizin-4-ones was developed.

In silico identification of angiotensin-1 converting enzyme inhibitors using text mining and virtual screening

Cardiovascular diseases are the world's leading cause of death. Hypertension is an important risk factor for cardiovascular and renal diseases. Angiotensin-converting enzyme (ACE) can be a possible therapeutic target for managing angiotensin I conversion to angiotensin II and ultimately controlling hypertension. Indole is an significant fragment used in many medicines approved by FDA. For this reason, the molecules in their fragments containing" indol" keywords were taken from the Specs-SC (small compound) database. The predicted therapeutc activity values (TAV) of these compounds against hypertension were evaluated using binary models of QSAR by MetaCore/MetaDrug. For the 26 separate QSAR models of toxicity, molecules with measured TAV greater than 0.5 were used. 3792 non-toxic compounds were investigated by molecular docking study and molecular dynamics simulations for their ACE inhibitory activity. Glide standard precision (SP) of Maestro Molecular Modeling pocket was used to perform molecular docking. Short molecular dynamics (MD) simulations (5-ns) were carried out by initiating the top docking poses of selected 40 molecules. To quantitatively evaluate the predicted binding affinity of a screened compound, average MM/GBSA scores of screened ligands were calculated and based on their binding free energy values, hit compounds were identified for the long (100-ns) MD simulations. Root mean square deviation and root mean square fluctuations were also calculated to assess the structural characteristics and observe fluctuations of the 100-ns time scale. Thus, with the application of text mining and integrated molecular modeling we reported novel indole-based hit inhibitors for ACE-1.Communicated by Ramaswamy H. Sarma.

Discovery of novel indole derivatives containing dithioacetal as potential antiviral agents for plants

Thirty unreported indole derivatives containing dithioacetal moiety were synthesized and evaluated for anti-plant viral activity. Bioassay results displayed that some of the target compounds showed better activities against tobacco mosaic virus (TMV) than the commercial Ribavirin in vivo. In particular, anti-TMV curative, protective and inactivating activity of 4p were 55.1, 57.2, and 80.3%, respectively, and EC₅₀ value for inactivating activity was 88.5 μg/mL. The observation of transmission electron microscope showed that 4p may have a certain destructive effect on TMV particles. To further study, microscale thermophoresis analysis result also demonstrated that 4p powerfully interacted with TMV coat protein in vitro. Hence, this study provides a strong evidence suporting that indole derivatives might be applied as new antiviral agents.

Synthesis, Antiviral Activity, and Induction of Plant Resistance of Indole Analogues Bearing Dithioacetal Moiety

A series of compounds with potential activity to induce plant resistance was synthesized from indole and thiol compounds and methodically evaluated for antiviral activity. The results indicated that some of the synthesized compounds had high antipotato virus Y (PVY), anticucumber mosaic virus, and antitobacco mosaic virus activities. Notably, compound D21 exhibited the best activity against PVY among these compounds in vivo, and the 50% effective concentrations (EC50) of protection activity is 122 μg/mL, which was distinctively better than the corresponding values for ribavirin (653 μg/mL), Ningnanmycin (464 μg/mL), and Xiangcaoliusuobingmi (279 μg/mL). Interestingly, we found that the protection activity of D21 was associated with improvement of chlorophyll content and defense-related enzyme activities. Moreover, D21 could trigger the malate dehydrogenase (MDH) signaling pathway, as further confirmed by the MDH activity evaluation. Hence, D21 can protect plants against viral activity and has potential as a novel activator for plant resistance induction.

One-pot synthesis of isoxazolines and isoxazoles using soluble polymer-supported aldehyde

Liquid-phase synthesis of isoxazoles and isoxazolines through a 1,3-dipolar of nitrile oxides is described. Soluble polymer-supported nitrile oxides generated in situ react with dipolarophiles to afford isoxazoles and isoxazolines in good yields and purity.

Combinatorial library of peptidotriazoles: identification of [1,2,3]-triazole inhibitors against a recombinant Leishmania mexicana cysteine protease

A library consisting of about half of 800 000 possible peptidotriazoles on 450 000 beads was prepared by solid-phase peptide synthesis combined with a regiospecific copper(I)-catalyzed 1,3-dipolar cycloaddition between a resin-bound alkyne and a protected amino azide. The central [1,2,3]-triazole was flanked on each side by two randomized amino acids introduced in a combinatorial approach. Importantly, the formation of the triazole could be performed quantitatively in a randomized fashion. The library was screened on solid phase for inhibitory effect against a recombinant cysteine protease, Leishmania mexicana CPB2.8DeltaCTE and sorted by a high-throughput instrument, COPAS beadsorter (up to 200 000 beads/h). Forty-eight hits were analyzed by MALDI-TOF MS providing structural information about the protease specificity, and 23 peptidotriazoles were resynthesized and evaluated in solution, with the best inhibitor displaying a K(i) value of 76 nM. A one-pot procedure was used to convert Fmoc-amino azides into their corresponding Boc derivatives. The crucial influence of weak interactions with a spacer used for detection by MALDI-TOF MS on screening results was observed.

Biomolecular recognition at the cellular level: geometrical and chemical functionality dependence of a low phototoxic cationic probe for DNA imaging

Potential application of a biocompatible and low phototoxic cationic stain with semilunar geometry for longer duration visualization of cellular DNA is reported.

A review on recent developments of indole-containing antiviral agents

Indole represents one of the most important privileged scaffolds in drug discovery. Indole derivatives have the unique property of mimicking the structure of peptides and to bind reversibly to enzymes, which provide tremendous opportunities to discover novel drugs with different modes of action. There are seven indole-containing commercial drugs in the Top-200 Best Selling Drugs by US Retail Sales in 2012. There are also an amazing number of approved indole-containing drugs in the market as well as compounds currently going through different clinical phases or registration statuses. This review focused on the recent development of indole derivatives as antiviral agents with the following objectives: 1) To present one of the most comprehensive listings of indole antiviral agents, drugs on market or compounds in clinical trials; 2) To focus on recent developments of indole compounds (including natural products) and their antiviral activities, summarize the structure property, hoping to inspire new and even more creative approaches; 3) To offer perspectives on how indole scaffolds as a privileged structure might be exploited in the future.

Biomedical importance of indoles

The indole nucleus is an important element of many natural and synthetic molecules with significant biological activity. This review covers some of the relevant and recent achievements in the biological, chemical and pharmacological activity of important indole derivatives in the areas of drug discovery and analysis.

Diversity oriented synthesis of a vinblastine-templated library of 7-aryl-octahydroazonino[5,4-b]indoles via a three-component reaction

A vinblastine-templated library of 7-aryl-octahydroazonino[5,4-b]indoles was prepared by a three-component reaction from indolizino[8,7-b]indoles, chloroformates, and activated arenes via a chloroformate mediated fragmentation of the indolizinoindole nucleus followed by insertion of an activated arene. In addition to N3-carbamoyl-7-aryl-octahydroazonino[5,4-b]indoles prepared in one step, a wide range of N3-substituted substrates were synthesized in one pot via the derivatization of a versatile N3-H-azonino[5,4-b]indole intermediate generated in situ by application of the same strategy. A subset of 308 compounds out of a virtual library of 3216, representing 13 different chemotypes, was prepared by high throughput solution-phase synthesis and subsequently purified by mass-triggered high performance liquid chromatography (HPLC). A total of 188 compounds with a minimum purity of 80% by UV214 nm and 85% by evaporative light scattering detection (ELSD) was isolated for primary screening.

Parallel chemistry in the 21st century

The tool chest of techniques, methodologies, and equipment for conducting parallel chemistry is larger than ever before. Improvements in the laboratory and developments in computational chemistry have enabled compound library design at the desks of medicinal chemists. This unit includes a brief background in combinatorial/parallel synthesis chemistry, along with a discussion of evolving technologies for both solid- and solution-phase chemistry. In addition, there are discussions on designing compound libraries, acquisition/procurement of compounds and/or reagents, the chemistry and equipment used for chemical production, purification, sample handling, and data analysis.

High Throughput Chemistry in Drug Discovery

This chapter outlines the evolution of high throughput chemistry from its origins in the genome revolution of the early 1990's to its current practice as an integral tool in drug discovery, via the concept of the large “universal library” to the practice of small targeted arrays for structure–activity relationship generation. The technologies developed as part of this evolution are also outlined including early ACT peptide synthesisers and other automated and non-automated devices for both solid-supported and solution-based approaches. Finally, the chapter outlines several case studies of the application of high throughput synthesis to drug discovery.

Methods for combinatorial and parallel library design

Diversity has historically played a critical role in design of combinatorial libraries, screening sets and corporate collections for lead discovery. Large library design dominated the field in the 1990s with methods ranging anywhere from purely arbitrary through property based reagent selection to product based approaches. In recent years, however, there has been a downward trend in library size. This was due to increased information about the desirable targets gleaned from the genomics revolution and to the ever growing availability of target protein structures from crystallography and homology modeling. Creation of libraries directed toward families of receptors such as GPCRs, kinases, nuclear hormone receptors, proteases, etc., replaced the generation of libraries based primarily on diversity while single target focused library design has remained an important objective. Concurrently, computing grids and cpu clusters have facilitated the development of structure based tools that screen hundreds of thousands of molecules. Smaller "smarter" combinatorial and focused parallel libraries replaced those early un-focused large libraries in the twenty-first century drug design paradigm. While diversity still plays a role in lead discovery, the focus of current library design methods has shifted to receptor based methods, scaffold hopping/bio-isostere searching, and a much needed emphasis on synthetic feasibility. Methods such as "privileged substructures based design" and pharmacophore based design still are important methods for parallel and small combinatorial library design. This chapter discusses some of the possible design methods and presents examples where they are available.

Bis-enaminone based parallel solution-phase synthesis of 1,4-dihydropyridine derivatives

Two variations of a parallel solution-phase synthesis of N-substituted dimethyl 4-oxo-1,4-dihydropyridine-3,5-dicarboxylates 4 and methyl 3-oxo-3,5-dihydro-2H-pyrazolo[4,3-c]pyridine-7-carboxylates 9 from dimethyl acetone-1,3-dicarboxylate (1) were developed. The first synthetic method comprises preparation of the bis-enaminone reagents 2 and 8 and their cyclization with primary amines 3 via double substitution of both dimethylamino groups to give dihydropyridines (DHPs) 4 and 9, respectively. Another variation consists of preparation of the monoenaminone reagents 5 and 10, followed by substitution of the dimethylamino group with primary amines 3, and cyclization of the so formed intermediates 6 with N,N-dimethylformamide dimethylacetal (DMFDMA). In this manner, a library of 46 analytically pure compounds, 24 intermediates 6, 11, and 13, and 22 final dihydropyridines 4 and 9 was obtained employing just a simple filtration workup.

Distributed Drug Discovery, Part 2: global rehearsal of alkylating agents for the synthesis of resin-bound unnatural amino acids and virtual D(3) catalog construction

Distributed Drug Discovery (D³) 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 D³ 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 D³ catalog computational analysis with synthesis. The second part of this article describes the creation of the first virtual D³ 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.

Synthesis of Novel N-Rich Polycyclic Skeletons Based on Azoles and Pyridines

An efficient method for the synthesis of new polycyclic skeletons: triaza-benzofluorenes and triaza-pentalenonaphthalene from bicyclic privileged structures imidazopyridine and imidazothiazole, respectively, has been described using the Pictet-Spengler cyclization.

Survey of the diversity space coverage of reported combinatorial libraries

Courtesy of the annual collections reported by Roland E. Dolle in the Journal of Combinatorial Chemistry, all three-point diverse libraries reported in the literature since 1992 have been evaluated according to their similarity at the library level (the Diversity Space approach).1 This comparison enabled the identification of several particularly promising scaffold hopping opportunities and highlighted a number of optimal libraries (surrogates) expected to reveal binding information characteristic of an entire area of chemical space. As highlighted herein, future library design pursuits would benefit from a methodology such as the Diversity Space approach to ensure access to novel areas within the chemical landscape, thereby avoiding the expenditure of additional resources to cover a previously explored region.

Combinatorial solution-phase synthesis of (2S,4S)-4-acylamino-5-oxopyrrolidine-2-carboxamides

Solution-phase combinatorial synthesis of (2S,4S)-4-acylamino-5-oxopyrrolidine-2-carboxamides was studied. First, di-tert-butyl (2S,4S)-4-amino-5-oxopyrrolidine-1,2-dicarboxylate hydrochloride was prepared as the key intermediate in five steps from (S)-pyroglutamic acid. Acylation of the amino group followed by acidolytic deprotection gave (2S,4S)-4-acylamino-5-oxopyrrolidine-2-carboxylic acids, which were then coupled with amines to furnish a library of (2S,4S)-4-acylamino-5-oxopyrrolidine-2-carboxamides. Four coupling reagents, BPC, EEDQ, TBTU, and PFTU, were tested for the amidation reactions in the final step. Amidations with EEDQ and TBTU led to the desired carboxamides. On the other hand, BPC and PFTU were not suited, since diketopiperazines were sometimes obtained instead of the desired carboxamides.

SHOP: scaffold HOPping by GRID-based similarity searches

A new GRID-based method for scaffold hopping (SHOP) is presented. In a fully automatic manner, scaffolds were identified in a database based on three types of 3D-descriptors. SHOP's ability to recover scaffolds was assessed and validated by searching a database spiked with fragments of known ligands of three different protein targets relevant for drug discovery using a rational approach based on statistical experimental design. Five out of eight and seven out of eight thrombin scaffolds and all seven HIV protease scaffolds were recovered within the top 10 and 31 out of 31 neuraminidase scaffolds were in the 31 top-ranked scaffolds. SHOP also identified new scaffolds with substantially different chemotypes from the queries. Docking analysis indicated that the new scaffolds would have similar binding modes to those of the respective query scaffolds observed in X-ray structures. The databases contained scaffolds from published combinatorial libraries to ensure that identified scaffolds could be feasibly synthesized.

Unambiguous structural characterization of hydantoin reaction products using 2D HMBC NMR spectroscopy

Data from two-dimensional (2D) NMR experiments were used to identify the reaction products resulting from the opening of pyroglutamates with isocyanates or thioisocyanates. The reaction has the potential to produce compounds that would have very similar one-dimensional proton ((1)H) or carbon-13 ((13)C) NMR spectra. Careful analysis of (1)H--(1)H COSY, (1)H--(1)H NOESY, and HMBC data, including chemical shifts and coupling constants, were used to distinguish correctly between carbamoyl-2-pyrrolidinone, hydantoin, and perhydro-1,3-diazepine-2,4-dione type structures that could result from this reaction. This work describes their preparation and subsequent identification using 2D NMR spectroscopy, and includes complete (13)C assignments of the reaction products. The 2D NMR techniques and analysis described here can be applied successfully to other synthetic reactions with the potential to produce isomeric products.

PNA encoding (PNA=peptide nucleic acid): from solution-based libraries to organized microarrays

Microarray-based technologies have attracted attention in chemical biology by virtue of their miniaturized format, which is well suited to probe ligand-protein interactions or investigate enzymatic activity in complex biological mixtures. A number of research groups have reported the preparation of surfaces on microarrays with specific functional groups to chemoselectively attach small molecules from libraries. We have developed an alternative method whereby libraries are encoded with peptide nucleic acid (PNA), such that libraries which exist as mixtures in solution self-assemble into an organized microarray through hybridization to produce readily available DNA arrays. This allows libraries synthesized by split and mix methods to be decoded in a single step. An asset of this method compared to direct spotting is that libraries can be used in solution for bioassays prior to self-assembly into the microarray format.