Skeletally diverse small molecules using a build/couple/pair strategy

IntraMolecular Diels–Alder Reactions of Vinylarenes and Alkynyl Arenes (the IMDAV Reaction)

This comprehensive review summarizes the published literature data concerning the intramolecular Diels–Alder reactions of vinylarenes (the IMDAV reaction) and alkynyl arenes from 1970 to 2019, and covers mainly intramolecular [4+2] cycloaddition reactions of vinyl- or acetylene-substituted furans, thiophenes, pyrroles, indoles, imidazoles, benzenes, and naphthalenes, in which the unsaturated substituent is linked directly to an arene moiety. The selected area of the Diels–Alder reaction differs from other forms of [4+2] cycloadditions due to the uniqueness of the diene fragment, which, along with an exocyclic multiple bond, includes the double bond of an aromatic or heteroaromatic nucleus in its system. Thus, during the formation of the [4+2] cycloaddition intermediate, the aromaticity of furan, thiophene and even benzene rings is broken, leading, as a rule, to the formation of heterocyclic structures rarely accessible by other methods, in contrast to the majority of intermolecular Diels–Alder reactions, with the highest degree of chemo-, regio-, and diastereoselectivity. Therefore, the IMDAV approach is often used for the synthesis of naturally occurring and bioactive molecules, which are also discussed in this review alongside other applications of this reaction. Whenever possible, we have tried to avoid examples of radical, photochemical, oxidative, precious-metal-complex-catalyzed cyclizations and other types of formal [4+2] cycloadditions, focusing on thermal Diels–Alder reactions in the first step, according to the classical mechanism. The second stage of the process, aromatization, is unique for many initial substrates, and hence considerable attention in this overview is given to the detailed description of the reaction mechanisms.

1 Introduction

2 IMDAV Reactions of Vinylfurans

2.1 Alkenes as Internal Dienophiles

2.2 Alkynes and Allenes as Internal Dienophiles

3 IMDAV Reactions of Vinylthiophenes

3.1 Alkenes as Internal Dienophiles

3.2 Alkynes as Internal Dienophiles

4 IMDAV Reactions of Vinylbenzothiophenes

5 IMDAV Reactions of Vinylpyrroles

6 IMDAV Reactions of Vinylindoles

6.1 Alkenes as Internal Dienophiles

6.2 Alkynes as Internal Dienophiles

7 IMDAV Reactions of Styrenes and Vinylnaphthalenes

7.1 Alkenes as Internal Dienophiles

7.2 Alkynes as Internal Dienophiles

7.3 Alkynes as Internal Dienophiles in Aryl Acetylenes (the Intramolecular Dehydro Diels–Alder Reaction)

8 IMDAV Reactions of Vinylimidazoles, Vinylisoxazoles and Vinylpyridines

9 Conclusion

10 Abbreviations

Chemoinformatics-based enumeration of chemical libraries: a tutorial

Virtual compound libraries are increasingly being used in computer-assisted drug discovery applications and have led to numerous successful cases. This paper aims to examine the fundamental concepts of library design and describe how to enumerate virtual libraries using open source tools. To exemplify the enumeration of chemical libraries, we emphasize the use of pre-validated or reported reactions and accessible chemical reagents. This tutorial shows a step-by-step procedure for anyone interested in designing and building chemical libraries with or without chemoinformatics experience. The aim is to explore various methodologies proposed by synthetic organic chemists and explore affordable chemical space using open-access chemoinformatics tools. As part of the tutorial, we discuss three examples of design: a Diversity-Oriented-Synthesis library based on lactams, a bis-heterocyclic combinatorial library, and a set of target-oriented molecules: isoindolinone based compounds as potential acetylcholinesterase inhibitors. This manuscript also seeks to contribute to the critical task of teaching and learning chemoinformatics.

Computational-aided design of a library of lactams through a diversity-oriented synthesis strategy

Small molecule libraries for virtual screening are becoming a well-established tool for the identification of new hit compounds. As for experimental assays, the library quality, defined in terms of structural complexity and diversity, is crucial to increase the chance of a successful outcome in the screening campaign. In this context, Diversity-Oriented Synthesis has proven to be very effective, as the compounds generated are structurally complex and differ not only for the appendages, but also for the molecular scaffold. In this work, we automated the design of a library of lactams by applying a Diversity-Oriented Synthesis strategy called Build/Couple/Pair. We evaluated the novelty and diversity of these compounds by comparing them with lactam moieties contained in approved drugs, natural products, and bioactive compounds from ChEMBL. Finally, depending on their scaffold we classified them into β-, γ-, δ-, ε-, and isolated, fused, bridged and spirolactam groups and we assessed their drug-like and lead-like properties, thus providing the value of this novel in silico designed library for medicinal chemistry applications.

Synthesis of functionalized tetrahydropyrans via cascade cycloaddition involving silyloxyallyl cation intermediates

An expedient synthesis of highly substituted tetrahydrobenzofuran via an unsymmetrical silyloxyallyl cation is reported.

SD, Verho O, Dandapani S, Wagner BK, Clemons PA, Booker-Milburn K, Boskovic ZV, Schreiber SL. Real-Time Biological Annotation of Synthetic Compounds

Organic chemists are able to synthesize molecules in greater number and chemical complexity than ever before. Yet, a majority of these compounds go untested in biological systems, and those that do are often tested long after the chemist can incorporate the results into synthetic planning. We propose the use of high-dimensional "multiplex" assays, which are capable of measuring thousands of cellular features in one experiment, to annotate rapidly and inexpensively the biological activities of newly synthesized compounds. This readily accessible and inexpensive "real-time" profiling method can be used in a prospective manner to facilitate, for example, the efficient construction of performance-diverse small-molecule libraries that are enriched in bioactives. Here, we demonstrate this concept by synthesizing ten triads of constitutionally isomeric compounds via complexity-generating photochemical and thermal rearrangements and measuring compound-induced changes in cellular morphology via an imaging-based "cell painting" assay. Our results indicate that real-time biological annotation can inform optimization efforts and library syntheses by illuminating trends relating to biological activity that would be difficult to predict if only chemical structure were considered. We anticipate that probe and drug discovery will benefit from the use of optimization efforts and libraries that implement this approach.

Towards vast libraries of scaffold-diverse, conformationally constrained oligomers

There is great interest in the development of probe molecules and drug leads that would bind tightly and selectively to protein surfaces that are difficult to target with traditional molecules, such as those involved in protein-protein interactions. The currently available evidence suggests that this will require molecules that are larger and have quite different chemical properties than typical Lipinski-compliant molecules that target enzyme active sites. We describe here efforts to develop vast libraries of conformationally constrained oligomers as a potentially rich source of these molecules.

Modular, One-Pot, Sequential Aziridine Ring Opening-S(N)Ar Strategy to 7-, 10-, and 11-Membered Benzo-Fused Sultams

The generation of common and stereochemically rich medium-sized benzo-fused sultams via complementary pairing of heretofore-unknown (o-fluoroaryl)sulfonyl aziridine building blocks with an array of amino alcohols/amines in a modular one-pot, sequential protocol using an aziridine ring opening and intramolecular nucleophilic aromatic substitution is reported. The strategy employs a variety of amino alcohols/amines and proceeds with 6 + 4/6 + 5 and 6 + 1 cycloetherification pathways in a highly chemo- and regioselective fashion to obtain skeletally and structurally diverse, polycyclic, 10- to 11- and 7-membered benzo-fused sultams for broad-scale screening.

Combining the Petasis 3-component reaction with multiple modes of cyclization: a build/couple/pair strategy for the synthesis of densely functionalized small molecules

A build/couple/pair strategy for the synthesis of complex and densely functionalized small molecules is presented. The strategy relies on synthetically tractable building blocks (build), that is, diversely substituted hydrazides, α-hydroxy aldehydes, and boronic acids, which undergo Petasis 3-component reactions (couple) to afford densely functionalized anti-hydrazido alcohols. The resulting scaffolds can subsequently be converted via chemoselective cyclization reactions (pair), including intramolecular Diels-Alder or Ru-alkylidene catalyzed ring-closing metathesis, into sets of structurally diverse heterocycles in good yields in only 3-4 steps.

Switchable stereocontrolled divergent synthesis induced by aza-Michael addition of deactivated primary amines under acid catalysis

Switchable tandem intramolecular aza-Michael/Michael and double aza-Michael reactions allow the oriented synthesis of highly functionalised cyclic skeletons. Conjugate addition of deactivated anilines triggers chemo- and stereo-divergent ring-closure reaction pathways with a striking selectivity depending on reaction conditions.

Synthesis of a natural product-like compound collection through oxidative cleavage and cyclization of linear peptides

Massive efforts in molecular library synthesis have strived for the development of synthesis methodology which systematically delivers natural product-like compounds of high spatial complexity. Herein, we present a conceptually simple approach that builds on the power of solid-phase peptide synthesis to assemble precursor peptides (oligomers) designed to undergo oxidative cascade reactions. By harnessing the structural side-chain diversity and inherent stereochemical features offered by readily available amino acids (monomers), a proof-of-concept collection of 54 skeletally and stereochemically diverse compounds was generated, and selected compounds were elaborated into isoform-selective metalloprotease inhibitors.

Macrocyclic drugs and synthetic methodologies toward macrocycles

Macrocyclic scaffolds are commonly found in bioactive natural products and pharmaceutical molecules. So far, a large number of macrocyclic natural products have been isolated and synthesized. The construction of macrocycles is generally considered as a crucial and challenging step in the synthesis of macrocyclic natural products. Over the last several decades, numerous efforts have been undertaken toward the synthesis of complex naturally occurring macrocycles and great progresses have been made to advance the field of total synthesis. The commonly used synthetic methodologies toward macrocyclization include macrolactonization, macrolactamization, transition metal-catalyzed cross coupling, ring-closing metathesis, and click reaction, among others. Selected recent examples of macrocyclic synthesis of natural products and druglike macrocycles with significant biological relevance are highlighted in each class. The primary goal of this review is to summarize currently used macrocyclic drugs, highlight the therapeutic potential of this underexplored drug class and outline the general synthetic methodologies for the synthesis of macrocycles.

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.

A biomimetic polyketide-inspired approach to small-molecule ligand discovery

The discovery of new compounds for the pharmacological manipulation of protein function often embraces the screening of compound collections, and it is widely recognized that natural products offer beneficial characteristics as protein ligands. Much effort has therefore been focused on “natural product-like” libraries, yet the synthesis and screening of such libraries is often limited by one or more of the following: modest library sizes and structural diversity, conformational heterogeneity, and the costs associated with the substantial infrastructure of modern high-throughput screening centers. Here, we describe the design and execution of an approach to this broad problem by merging principles associated biologically-inspired oligomerization and the structure of polyketide-derived natural products. A novel class of chiral and conformationally-constrained oligomers is described (termed “chiral oligomers of pentenoic amides” – COPAs) that offers compatibility with split-and-pool methods and can be screened en masse in a batch mode. We demonstrate that a COPA library containing 160,000 compounds is a useful source of novel protein ligands by identifying a non-covalent synthetic ligand to the DNA-binding domain of the p53 transcription factor.

A modular reaction pairing approach to the diversity-oriented synthesis of fused- and bridged-polycyclic sultams

A reaction pairing strategy centered on utilization of a reaction triad (sulfonylation, S(N)Ar addition and Mitsunobu alkylation) generating skeletally diverse, tricyclic and bicyclic benzofused sultams is reported. Pairing sulfonylation and S(N)Ar reactions yields bridged, tricyclic and bicyclic benzofused sultams. Application of the Mitsunobu reaction in a sulfonylation-Mitsunobu-S(N)Ar pairing allows access to benzthiazocine-1,1-dioxides, while a simple change in the order of pairing to sulfonylation-S(N)Ar-Mitsunobu affords structurally different, bridged tricyclic benzofused sultams.

Practical asymmetric synthesis of β-hydroxy γ-amino acids via complimentary aldol reactions

Orthogonally protected chiral β-hydroxy-γ-amino acids can be accessed in >100 g quantities from readily available starting materials and reagents in 3-4 steps. These chiral synthons contain two adjacent stereocenters along with suitably protected functional groups (O-TBS, N-Boc) for downstream reactivity. Implementation of two existing aldol technologies allows rapid access to all possible stereoisomers of 1. The guiding principles during reaction optimization were reaction scalability and operational efficiency. Conversion of the amino acids to a variety of chiral building blocks in 1-2 steps demonstrates their synthetic utility.

An aldol-based build/couple/pair strategy for the synthesis of medium- and large-sized rings: discovery of macrocyclic histone deacetylase inhibitors

An aldol-based build/couple/pair (B/C/P) strategy was applied to generate a collection of stereochemically and skeletally diverse small molecules. In the build phase, a series of asymmetric syn- and anti-aldol reactions were performed to produce four stereoisomers of a Boc-protected γ-amino acid. In addition, both stereoisomers of O-PMB-protected alaninol were generated to provide a chiral amine coupling partner. In the couple step, eight stereoisomeric amides were synthesized by coupling the chiral acid and amine building blocks. The amides were subsequently reduced to generate the corresponding secondary amines. In the pair phase, three different reactions were employed to enable intramolecular ring-forming processes: nucleophilic aromatic substitution (S(N)Ar), Huisgen [3+2] cycloaddition, and ring-closing metathesis (RCM). Despite some stereochemical dependencies, the ring-forming reactions were optimized to proceed with good to excellent yields, providing a variety of skeletons ranging in size from 8- to 14-membered rings. Scaffolds resulting from the RCM pairing reaction were diversified on the solid phase to yield a 14 400-membered library of macrolactams. Screening of this library led to the discovery of a novel class of histone deacetylase inhibitors, which display mixed enzyme inhibition, and led to increased levels of acetylation in a primary mouse neuron culture. The development of stereo-structure/activity relationships was made possible by screening all 16 stereoisomers of the macrolactams produced through the aldol-based B/C/P strategy.

Stereochemical and skeletal diversity arising from amino propargylic alcohols

An efficient synthetic pathway to the possible stereoisomers of skeletally diverse heterocyclic small molecules is presented. The change in shape brought about by different intramolecular cyclizations of diastereoisomeric amino propargylic alcohols is quantified using principal moment-of-inertia (PMI) shape analysis.