Solid phase synthesis of complex natural products and libraries thereof.

Natural products have served as an important source of medicinal compounds and pharmaceutical leads over the last century. Within the last 10 years, significant interest has developed in applying combinatorial chemistry techniques to the study of natural products and their biological activities. In this review, we examine several representative efforts wherein natural product skeletons have been constructed or immobilized on solid support and subsequently derivatized, giving rise to analog libraries useful in understanding the structure-activity relationships of the parent natural product. Issues such as target selection, library design, linker development, automation, and library characterization are addressed.     

Combinatorial solid phase peptide synthesis and bioassays

Solid phase peptide synthesis method, which was introduced by Merrifield in 1963, has spawned the concept of combinatorial chemistry. In this review, we summarize the present technologies of solid phase peptide synthesis (SPPS) that are related to combinatorial chemistry. The conventional methods of peptide library synthesis on polymer support are parallel synthesis, split and mix synthesis and reagent mixture synthesis. Combining surface chemistry with the recent technology of microelectronic semiconductor fabrication system, the peptide microarray synthesis methods on a planar solid support are developed, which leads to spatially addressable peptide library. There are two kinds of peptide microarray synthesis methodologies: pre-synthesized peptide immobilization onto a glass or membrane substrate and in situ peptide synthesis by a photolithography or the SPOT method. This review also discusses the application of peptide libraries for high-throughput bioassays, for example, peptide ligand screening for antibody or cell signaling, enzyme substrate and inhibitor screening as well as other applications.     

Natural products and combinatorial chemistry: back to the future

The introduction of high-throughput synthesis and combinatorial chemistry has precipitated a global decline in the screening of natural products by the pharmaceutical industry. Some companies terminated their natural products program, despite the unproven success of the new technologies. This was a premature decision, as natural products have a long history of providing important medicinal agents. Furthermore, they occupy a complementary region of chemical space compared with the typical synthetic compound library. For these reasons, the interest in natural products has been rekindled. Various approaches have evolved that combine the power of natural products and organic chemistry, ranging from the combinatorial total synthesis of analogues to the exploration of natural product scaffolds and the design of completely unnatural molecules that resemble natural products in their molecular characteristics.     

Immobilized catalysts in combinatorial chemistry

As a new methodology for library synthesis in combinatorial chemistry, the use of immobilized catalysts and multi-component reactions is focused. In the past two years, many advances have been made in this emerging field, leading to the efficient library synthesis of, for example, quinolines, amino ketones and amino esters.     

Combinatorial chemistry,automation and molecular diversity: new trends in the pharmaceutical industry

Combinatorial chemistry has emerged as a set of novel strategies for the synthesis of large sets of compounds (combinatorial libraries) for biological evaluation. Within a few years combinatorial chemistry has undergone a series of changes in trends, which are closely related to two important factors in libraries: numbers and quality. While the number of compounds in a library may be easily expressed, it is a lot more difficult to indicate the degree of quality of a library. This degree of quality can be split into two aspects : purity and diversity. The changing trends in combinatorial chemistry with respect to the strategies, the technologies, the libraries themselves (numbers and purity aspects) and the molecular diversity are outlined in this paper.     

Parallel and combinatorial approaches for synthesis of ligands

Although new detection screening methods must still be developed, the actual main limitation in combinatorial chemistry seems to be the diversity of ligands that can be generated in terms of real structural and chemical diversity. Thus, there is a strong interest for the development of different strategies for the parallel or combinatorial synthesis of ligands. We report here a selection of recent attempts proposing 'open' approaches able to increase the diversity of molecular architecture truly accessible via parallel or combinatorial processes.     

Studies of Asymmetric Styrene Cyclopropanation with a Rhodium(II) Metallopeptide Catalyst Developed with a High‐Throughput Screen

Dirhodium metallopeptides have been developed as selective catalysts for asymmetric cyclopropanation reactions. A selective ligand sequence has been identified by screening on‐bead metallopeptide libraries in a 96‐well plate format. Efficient ligand synthesis and screening allows a 200‐member library to be created and assayed in less than three weeks. These metallopeptides catalyze efficient cyclopropanation of aryldiazoacetates, providing asymmetric access to cyclopropane products in high diastereoselectivity. Chirality 25:493–497, 2013. © 2013 Wiley Periodicals, Inc.     

Solution-phase combinatorial synthesis and evaluation of piperazine-2,5-dione derivatives

An efficient one-pot synthesis of a 61-membered combinatorial chemistry library of piperazine-2,5-diones was accomplished. Results of combinatorial synthesis, purification, analysis, and biological evaluation are described.     

A road less traveled by: exploring a decade of Ellman chemistry

The Ellman group has been one of the most influential in the development and widespread adoption of combinatorial chemistry techniques for biomedical research. Their work has included substantial methodological development for library synthesis with a particular focus on new scaffolds rationally targeted to biomolecules of interest and biologically relevant natural products. Herein we analyze a representative set of libraries from this group with respect to their biological and biomedical relevance in comparison to existing drugs and probe compounds. This analysis reveals that the Ellman group has not only provided new methodologies to the community but also provided libraries with unique potential for further biological study.     

High-speed combinatorial synthesis utilizing microwave irradiation

Recent advances in microwave-assisted combinatorial chemistry include high-speed solid-phase and polymer-supported organic synthesis, rapid parallel synthesis of compound libraries, and library generation by automated sequential microwave irradiation. In addition, new instrumentation for high-throughput microwave-assisted synthesis continues to be developed at a steady pace. The impressive speed combined with the unmatched control over reaction parameters justifies the growing interest in this application of microwave heating.     

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.     

Solid-phase synthesis: a paradigm shift.

A personal review by the first graduate student of Professor R. Bruce Merrifield of the evolution of solid-phase synthesis and its acceptance by various subsets of the chemistry community. Solid-phase synthesis, as currently practised in the synthesis of biopolymers, combinatorial solid-phase organic chemistry, synthesis of natural products, catalyst selection, chemical ligation and materials development, has proven a paradigm shift for the chemistry community.     

Combinatorially-generated library of 6-fluoroquinolone analogs as potential novel antitubercular agents: a chemometric and molecular modeling assessment

The virtual combinatorial chemistry approach as a methodology for generating chemical libraries of structurally-similar analogs in a virtual environment was employed for building a general mixed virtual combinatorial library with a total of 53.871 6-FQ structural analogs, introducing the real synthetic pathways of three well known 6-FQ inhibitors. The druggability properties of the generated combinatorial 6-FQs were assessed using an in-house developed drug-likeness filter integrating the Lipinski/Veber rule-sets. The compounds recognized as drug-like were used as an external set for prediction of the biological activity values using a neural-networks (NN) model based on an experimentally-determined set of active 6-FQs. Furthermore, a subset of compounds was extracted from the pool of drug-like 6-FQs, with predicted biological activity, and subsequently used in virtual screening (VS) campaign combining pharmacophore modeling and molecular docking studies. This complex scheme, a powerful combination of chemometric and molecular modeling approaches provided novel QSAR guidelines that could aid in the further lead development of 6-FQs agents.     

Trifluoromethylpyrimidine-based inhibitors of proline-rich tyrosine kinase 2 (PYK2): structure-activity relationships and strategies for the elimination of reactive metabolite formation

The synthesis and SAR for a series of diaminopyrimidines as PYK2 inhibitors are described. Using a combination of library and traditional medicinal chemistry techniques, a FAK-selective chemical series was transformed into compounds possessing good PYK2 potency and 10- to 20-fold selectivity against FAK. Subsequent studies found that the majority of the compounds were positive in a reactive metabolite assay, an indicator for potential toxicological liabilities. Based on the proposed mechanism for bioactivation, as well as a combination of structure-based drug design and traditional medicinal chemistry techniques, a follow-up series of PYK2 inhibitors was identified that maintained PYK2 potency, FAK selectivity and HLM stability, yet were negative in the RM assay.     

Combinatorial synthesis of CCR5 antagonists

Herein we report the preparation of a combinatorial library of compounds with potent CCR5 binding affinity. The library design was aided by SAR generated in a traditional medicinal chemistry effort. Compounds with novel combinations of subunits were discovered that have high binding affinity for the CCR5 receptor. A potent CCR5 antagonist from the library, compound 11 was found to have moderate anti-HIV-1 activity.     

Synthesis of a statistically exhaustive fluorescent peptide substrate library for profiling protease specificity

A statistically exhaustive, 8800 compound tripeptidal amidomethylcoumarin library was synthesized as discreet compounds using solid-phase combinatorial chemistry. A subset of the compounds was purified by HPLC and tested in a high-throughput fluorometric assay against several known serine and cysteine proteases to demonstrate the utility of this library for profiling protease substrate specificity.     

用混合氨基酸接肽的方法合成OX型肽亚库

肽库合成是药物研究组合化学策略的重要技术之一。建立合成OX型肽亚库的固相合成方法 ,接肽反应采用等摩尔的Fmoc氨基酸混合物和DIC HOBt缩合方法 ,以高浓度的缩合剂和不断缩减溶剂的策略促进偶联反应进行完全。产物的氨基酸组成分析结果显示 ,所使用的常见氨基酸都能以相近的摩尔比例接肽至X位置。推测经多次接肽后最终形成的肽亚库中 ,含低活力氨基酸较多的肽其浓度虽然会较低一些 ,但影响不会太大 ,且本合成方法成本相对较低 ,故可为抗原表位分析、多肽药物筛选及构效关系分析提供一种有用的工具。     

Sulfonamido-aryl ethers as bradykinin B1 receptor antagonists

The synthesis and identification of sulfonamido-aryl ethers as potent bradykinin B1 receptor antagonists from a ～60,000 member encoded combinatorial library are reported. Two distinct series of compounds exhibiting different structure–activity relationships were identified in a bradykinin B1 whole-cell receptor-binding assay. Specific examples exhibit K_i values of ～10 nM.     

Diversity-oriented synthesis: exploring the intersections between chemistry and biology

Diversity-oriented synthesis (DOS) is an emerging field involving the synthesis of combinatorial libraries of diverse small molecules for biological screening. Rather than being directed toward a single biological target, DOS libraries can be used to identify new ligands for a variety of targets. Several different strategies for library design have been developed to target the biologically relevant regions of chemical structure space. DOS has provided powerful probes to investigate biological mechanisms and also served as a new driving force for advancing synthetic organic chemistry.     

Light directed massively parallel on-chip synthesis of peptide arrays with t-Boc chemistry

Peptide and peptidomimetic molecule arrays are emerging powerful tools for parallel screening of binding in proteomics and pharmaceutical discovery research. Up to now the common method of preparing peptide arrays was based on spotting on glass using a library of presynthesized peptides. However, due to the large number of monomers (amino acids) it is not possible to have combinatorial libraries which include all combinations of natural and synthetic amino acids. We describe a very flexible on-chip oligopeptide synthesis method which uses the well developed t-Boc based solid state synthesis chemistry. A very high degree of flexibility is achieved by using light photo generated acids and maskless projection lithography for spatially directed deprotection. Use of microfluidic chips enables moderately high densities, short reaction times and off-the-shelf chemicals. Examples are given from synthesis of metal ion binding peptides and epitope binding assays.