Scaffold Flatness: Reversing the Trend

A stepwise dearomatization/nitration/enantioselective homoenolate reaction of quinolines to construct C3-nitro-substituted tetrahydroquinolines

Herein, we describe a stepwise 1,2-reductive dearomatization/selective C3-nitration of quinoline and a subsequent catalytic enantioselective homoenolate addition reaction using a NHC catalyst strategy to construct N-acetyl 3,4-disubstituted tetrahydroquinoline in good yields with remarkably high diastereo- and enantioselectivities (dr >99 : 1, ee up to >99%). An efficient metal- and base-free method for 3-nitroquinoline synthesis from readily accessible quinoline has also been realized.

Steric Activation in the Nazarov Cyclization of Fully Substituted Divinyl Ketones

Fully substituted divinyl ketones (fsDVKs) have long been regarded as resistant to Nazarov cyclization (NC) unless they contain strategically positioned electronically activating substituents. Here, however, we show that fsDVKs bearing only electronically neutral alkyl or aryl groups actually undergo facile NC due to steric crowding in the pentadienyl cation intermediate, which raises its energy and reduces the barrier height to cyclization. Strongly ionizing and suitably bulky acid moieties further increase the energy of this intermediate cation, favoring cyclization. These features enable NCs of fsDVKs to be employed in the ready construction of multiple contiguous all-carbon quaternary stereocenters under mild conditions, in the absence of electronically activating groups.

3-Diazopiperidine-2,4-diones as Convenient Precursors to Rare Polysubstituted Spiro Bis-β,γ-lactams and 2-Oxopyrrolidine-3-carboxylic Acid Derivatives via the Thermally Promoted Wolff Rearrangement

Herein, we describe a diastereoselective and straightforward synthetic approach to polysubstituted spirocyclic bis-lactams bearing both β- and γ-lactam cores with diverse substitution patterns. The method developed is based on a microwave-assisted Wolff rearrangement/Staudinger [2 + 2] cycloaddition sequence involving 3-diazopiperidine-2,4-diones and imines. The corresponding reaction tolerates a wide range of functionalities in both substrates, giving the target bis-lactams in generally high yields. The synthetic utility of the thermally promoted Wolff rearrangement has been extended to the interaction of 3-diazopiperidine-2,4-dione-derived ketenes with various nucleophiles leading to derivatives of 2-oxopyrrolidine-3-carboxylic acids. Our findings potentially pave an avenue for designing new compounds with a high degree of medicinal relevance by means of the processes studied.

Access to Spiro Bis-β-lactams via a Metal-Free Microwave-Assisted Wolff Rearrangement/Staudinger [2+2] Cycloaddition Cascade Involving 3-Diazotetramic Acids and Imines

Herein, we report the study of the thermally promoted reaction of 3-diazotetramic acids with imines as a rapid route to a novel spiro heterocyclic scaffold, spiro bis-β-lactams (2,6-diazaspiro[3.3]heptane-1,5-diones). The transformation proceeds via metal-free microwave-assisted Wolff rearrangement of the diazo reagent followed by Staudinger [2+2] cycloaddition of the heterocyclic ketenes with Shiff bases. This methodology enables the preparation of diastereomerically pure spiro bis-β-lactams in high yields and provides an avenue for exploring new versions of the privileged β-lactam core for drug design.

Utilizing Allenic Acids and Heterocyclic Diazo Compounds in the Synthesis of Polysubstituted Spirocyclic Butenolides and β-Methylidene 2-Furanones

Herein, we report a novel approach for the assembly of spirocyclic Δα,β-butenolides and β-methylidene 2-furanones via Rh(II)-catalyzed O-H insertion of heterocyclic diazo compounds into allenic acids followed by base-promoted cyclization. Utilizing various diazo heterocycles, including α-diazo homophthalimides, 3-diazo tetramic acids, and diazo oxindoles, diverse spirocyclic scaffolds were produced. The research revealed that the allenic acid substitution pattern is decisive for the product type, enabling extraordinary target compound switching between two types of spirocyclic 2-furanones with exo- and endocyclic C═C bonds.

Recent Strategies in the Nucleophilic Dearomatization of Pyridines, Quinolines, and Isoquinolines

Dearomatization reactions have become fundamental chemical transformations in organic synthesis since they allow for the generation of three-dimensional complexity from two-dimensional precursors, bridging arene feedstocks with alicyclic structures. When those processes are applied to pyridines, quinolines, and isoquinolines, partially or fully saturated nitrogen heterocycles are formed, which are among the most significant structural components of pharmaceuticals and natural products. The inherent challenge of those transformations lies in the low reactivity of heteroaromatic substrates, which makes the dearomatization process thermodynamically unfavorable. Usually, connecting the dearomatization event to the irreversible formation of a strong C-C, C-H, or C-heteroatom bond compensates the energy required to disrupt the aromaticity. This aromaticity breakup normally results in a 1,2- or 1,4-functionalization of the heterocycle. Moreover, the combination of these dearomatization processes with subsequent transformations in tandem or stepwise protocols allows for multiple heterocycle functionalizations, giving access to complex molecular skeletons. The aim of this review, which covers the period from 2016 to 2022, is to update the state of the art of nucleophilic dearomatizations of pyridines, quinolines, and isoquinolines, showing the extraordinary ability of the dearomative methodology in organic synthesis and indicating their limitations and future trends.

Development of trisubstituted thiophene-3-arboxamide selenide derivatives as novel EGFR kinase inhibitors with cytotoxic activity

Overexpression of EGFR is one of the eminent oncogenic drivers detected in the development of several human cancers. The increasing incidences of mutation-based resistance in the tyrosine kinase domain call upon the need for the development of a newer class of small-molecule TK inhibitors. Accordingly, a new series of symmetrical trisubstituted thiophene-3-carboxamide selenide derivatives was developed via the hybridization of complementary pharmacophores. Most of the compounds showed a modest to excellent antiproliferative action at 20 μM concentration. The utmost antiproliferative activity was portrayed by compound 16e on the selected cancer cell lines with IC50 < 9 μM, the lowest being 3.20 ± 0.12 μM in the HCT116 cell line. Further, it also displayed an impressive EGFR kinase inhibition with an IC50 value of 94.44 ± 2.22 nM concentration. As a corollary of the reported EGFR inhibition, the nature, energy, and stability of the binding interactions were contemplated via in silico studies.

Absorption matters: A closer look at popular oral bioavailability rules for drug approvals

This study examines how two popular drug-likeness concepts used in early development, Lipinski Rule of Five (Ro5) and Veber's Rules, possibly affected drug profiles of FDA approved drugs since 1997. Our findings suggest that when all criteria are applied, relevant compounds may be excluded, addressing the harmfulness of blindly employing these rules. Of all oral drugs in the period used for this analysis, around 66 % conform to the RO5 and 85 % to Veber's Rules. Molecular Weight and calculated LogP showed low consistent values over time, apart from being the two least followed rules, challenging their relevance. On the other hand, hydrogen bond related rules and the number of rotatable bonds are amongst the most followed criteria and show exceptional consistency over time. Furthermore, our analysis indicates that topological polar surface area and total count of hydrogen bonds cannot be used as interchangeable parameters, contrary to the original proposal. This research enhances the comprehension of drug profiles that were FDA approved in the post-Lipinski period. Medicinal chemists could utilize these heuristics as a limited guide to direct their exploration of the oral bioavailability chemical space, but they must also steer the wheel to break these rules and explore different regions when necessary.

Diazo Tetramic Acids Provide Access to Natural-Like Spirocyclic Δα,β-Butenolides through Rh(II)-Catalyzed O-H Insertion/Base-Promoted Cyclization

3-Diazotetramic acids were found to be valid substrates for the recently discovered approach toward natural-like Δα,β-spirobutenolides via Rh(II)-catalyzed O-H insertion into propiolic acids followed by base-promoted intramolecular Michael addition. The target Δα,β-spirobutenolides were obtained in generally high yields and, in the case of chiral 5-monosubstituted 3-diazotetramic acids, high diastereoselectivity. The synthesis of Δα,β-spirobutenolides that we report here was virtually insensitive to the structure of the propiolic acids though it was somewhat sensitive to the structure of the 3-diazotetramic acids, thereby demonstrating quite a large scope. Thus, a new class of α-diazocarbonyl compounds suitable for the realization of the approach outlined above was identified.

Exploration of Spirocyclic Derivatives of Ciprofloxacin as Antibacterial Agents

The previously reported as well as newly synthesized derivatives of the 1-oxa-9-azaspiro[5.5]undecane were employed in the synthesis of thirty-six derivatives of ciprofloxacin using commercially available 7-chloro-1-cyclopropyl-6-fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylic acid and the literature protocol involving the preparation of boron chelate complex to facilitate nucleophilic aromatic substitution. All new fluoroquinolone derivatives were tested against two gram-positive as well as three gram-negative strains of bacteria. With the activity spectrum of the new derivatives being substantially narrower than that of ciprofloxacin, compounds were distinctly active against two of the five strains: gram-negative Acinetobacter baumannii 987^® and gram-positive Bacillus cereus 138^®. Towards these two strains, a large group of compounds displayed equal or higher potency than ciprofloxacin.

Puckering the planar landscape of fragments: design and synthesis of a 3D cyclobutane fragment library

Fragment‐based drug discovery (FBDD) has a growing need for unique screening libraries. The cyclobutane moiety was identified as an underrepresented yet attractive three‐dimensional (3D) scaffold. Synthetic strategies were developed via a key 3‐azido‐cyclobutanone intermediate, giving potential access to a range of functional groups with accessible growth vectors. A focused set of 33 novel 3D cyclobutane fragments was synthesised, comprising three functionalities: secondary amines, amides, and sulfonamides. This library was designed using Principal Component Analysis (PCA) and an expanded version of the rule of three (RO3), followed by Principal Moment of Inertia (PMI) analysis to achieve both chemical diversity and high 3D character. Cis and trans ring isomers of library members were generated to maximise the shape diversity obtained, while limiting molecular complexity through avoiding enantiomers. Property analyses of the cyclobutane library indicated that it fares favourably against existing synthetic 3D fragment libraries in terms of shape and physicochemical properties.

Recent Advances in the Tandem Copper-Catalyzed Ullmann-Goldberg N-Arylation–Cyclization Strategies

N‒Aryl bond formation under copper catalysis has been playing a pivotal role and has been extensively used as a key step in the total syntheses of several therapeutic molecules. The...

Photochemical Formal (4 + 2)-Cycloaddition of Imine-Substituted Bicyclo[1.1.1]pentanes and Alkenes

Amines containing bridged bicyclic carbon skeletons are desirable building blocks for medicinal chemistry. Herein, we report the conversion of bicyclo[1.1.1]pentan-1-amines to a wide range of polysubstituted bicyclo[3.1.1]heptan-1-amines through a photochemical, formal (4 + 2)-cycloaddition of an intermediate imine diradical. To our knowledge, this is the first reported method to convert the bicyclo[1.1.1]pentane skeleton to the bicyclo[3.1.1]heptane skeleton. Hydrolysis of the imine products gives complex, sp³-rich primary amine building blocks.

Pyrrolidine in Drug Discovery: A Versatile Scaffold for Novel Biologically Active Compounds

The five-membered pyrrolidine ring is one of the nitrogen heterocycles used widely by medicinal chemists to obtain compounds for the treatment of human diseases. The great interest in this saturated scaffold is enhanced by (1) the possibility to efficiently explore the pharmacophore space due to sp3-hybridization, (2) the contribution to the stereochemistry of the molecule, (3) and the increased three-dimensional (3D) coverage due to the non-planarity of the ring-a phenomenon called "pseudorotation". In this review, we report bioactive molecules with target selectivity characterized by the pyrrolidine ring and its derivatives, including pyrrolizines, pyrrolidine-2-one, pyrrolidine-2,5-diones and prolinol described in the literature from 2015 to date. After a comparison of the physicochemical parameters of pyrrolidine with the parent aromatic pyrrole and cyclopentane, we investigate the influence of steric factors on biological activity, also describing the structure-activity relationship (SAR) of the studied compounds. To aid the reader's approach to reading the manuscript, we have planned the review on the basis of the synthetic strategies used: (1) ring construction from different cyclic or acyclic precursors, reporting the synthesis and the reaction conditions, or (2) functionalization of preformed pyrrolidine rings, e.g., proline derivatives. Since one of the most significant features of the pyrrolidine ring is the stereogenicity of carbons, we highlight how the different stereoisomers and the spatial orientation of substituents can lead to a different biological profile of drug candidates, due to the different binding mode to enantioselective proteins. We believe that this work can guide medicinal chemists to the best approach in the design of new pyrrolidine compounds with different biological profiles.

Limonin as a Starting Point for the Construction of Compounds with High Scaffold Diversity

Structurally complex natural products have been a fruitful source for the discovery and development of new drugs. In an effort to construct a compound collection populated by architecturally complex members with unique scaffolds, we have used the natural product limonin as a starting point. Limonin is an abundant triterpenoid natural product and, through alteration of its heptacyclic core ring system using short synthetic sequences, a collection of 98 compounds was created, including multiple members with novel ring systems. The reactions leveraged in the construction of these compounds include novel ring cleavage, rearrangements, and cyclizations, and this work is highlighted by the discovery of a novel B-ring cleavage reaction, a unique B/C-ring rearrangement, an atypical D-ring cyclization, among others. Computational analysis shows that 52 different scaffolds/ring systems were produced during the course of this work, of which 36 are unprecedented. Phenotypic screening and structure-activity relationships identified compounds with activity against a panel of cancer cell lines.

Natural-Like Spirocyclic Δα,β -Butenolides Obtained from Diazo Homophthalimides

α-Diazo homophotalimides were reacted with various propiolic acids on Rh₂ (esp)₂ catalysis. The resulting propiolate esters were transformed into novel, heterocyclic Δ^α,β -spirobutenolides in good to excellent product yields. The approach represents a fundamentally novel entry into natural-like Δ^α,β -spirobutenolides present in many biologically active natural products as well as fully synthetic compounds endowed with diverse biological activities. The Δ^α,β -spirobutenolides thus obtained were shown to inhibit thioredoxin reductase, a selenocysteine enzyme target for cancer. Moreover, for the best compound in the series (TrxR IC₅₀ 1.49±0.08 μM), by using MALDI-TOF mass-spectrometry it was shown that it selectively binds selenocysteine in the presence of a 10-fold excess of cysteine. This validates the new compound as a promising lead for anticancer therapy development.

Biflavonoid as potential 3-chymotrypsin-like protease (3CLpro) inhibitor of SARS-Coronavirus

3CL protease is one of the key proteins expressed by SARS-Coronavirus-2 cell, the potential to be targeted in the discovery of antivirus during this COVID-19 pandemic. This protein regulates the proteolysis of viral polypeptide essential in forming RNA virus. 3CL protease (3CLpro) was commonly targeted in the previous SARS-Coronavirus including bat and MERS, hence, by blocking this protein activity, the coronavirus should be eradicated. This study aims to review the potency of biflavonoid as the SARS-Coronavirus-2 3CLpro inhibitor. The review was initiated by describing the chemical structure of biflavonoid and followed by listing its natural source. Instead, the synthetic pathway of biflavonoid was also elaborated. The 3CLpro structure and its function were also illustrated followed by the list of its 3D-crystal structure available in a protein data bank. Lastly, the pharmacophores of biflavonoid have been identified as a protease inhibitor, was also discussed. This review hopefully will help researchers to obtain packed information about biflavonoid which could lead to the study in designing and discovering a novel SARS-Coronavirus-2 drug by targetting the 3CLpro enzyme.

Escape from planarity in fragment-based drug discovery: A physicochemical and 3D property analysis of synthetic 3D fragment libraries

Fragment-based drug discovery (FBDD) has grown into a well-established approach in the pursuit of new therapeutics. Key to the success of FBDD is the low molecular complexity of the initial hits and this has resulted in fragment libraries that mainly contain compounds with a two-dimensional (2D) shape. In an effort to increase the chemical diversity and explore the impact of increased molecular complexity on the hit rate of fragment library screening, several academic and industrial groups have designed and synthesised novel fragments with a three-dimensional (3D) shape. This review provides an overview of 25 synthetic 3D fragment libraries from the recent literature. We calculate and compare physicochemical properties and descriptors that are typically used to measure molecular three-dimensionality such as fraction sp³ (Fsp³), plane of best fit (PBF) scores and principal moment of inertia (PMI) plots. Although the libraries vary widely in structure and properties, some key common features can be identified which may have utility in designing the next generation of 3D fragment libraries.

Opportunities for Tapping into Three-Dimensional Chemical Space through a Quaternary Carbon

A quaternary carbon bears four other carbon substituents or combination of four non-hydrogen substituents at four vertices of a tetrahedron. The spirocyclic quaternary carbon positioned at the center of a bioactive molecule offers conformational rigidity, which in turn reduces the penalty for conformational entropy. The quaternary carbon is a predominant feature of natural product structures and has been associated with more effective and selective binding to target proteins compared to planar compounds with a high sp² count. The presence of a quaternary carbon stereocenter allows the exploration of novel chemical space to obtain new molecules with enhanced three-dimensionality. These characteristics, coupled to an increasing awareness to develop sp³-rich molecules, boosted utility of quaternary carbon stereocenters in bioactive compounds. It is hoped that this Perspective will inspire the chemist to utilize quaternary carbon stereocenters to enhance potency, selectivity, and other drug-like properties.

Fsp3: A new parameter for drug-likeness

The drug-likeness of a compound is a key factor during the initial phases of drug discovery. It can be defined as the similarity between compounds and drugs. Here, we collate research related to the fraction of sp³ carbon atoms (Fsp³), including related high-throughput screening (HTS) cases, structural modifications based on Fsp³, and strategies to improve it. We also introduce new synthetic methods for spirocyclic scaffolds. It is likely that the reasonable rigidity of spirocyclic scaffolds will provide a new generation of drug candidates.

Tandem Copper-Catalyzed Regioselective N-Arylation-Aza-Michael Addition: Synthesis of Tetracyclic 5H-Benzothiazolo[3,2-a]quinazoline Derivatives

A copper-catalyzed tandem process integrating regioselective N-arylation, followed by aza-Michael addition, is disclosed using 2-aminobenzothiazoles and ortho-halo cinnamic acid congeners. This process generated diverse tetracyclic 5H-benzothiazolo[3,2-a]quinazoline derivatives in moderate to good yields. The present tandem reaction appears to proceed through concomitant ring opening of 2-aminobenzothiazole and S-arylation to give the ortho-cyanamide-substituted diaryl thioether intermediate. The thus generated intermediate likely undergoes an unprecedented Truce-Smiles-type rearrangement involving S- to N-aryl migration, followed by reformation of the thiazole ring and intramolecular aza-Michael addition to furnish the title products.

Identification of Gibberellic Acid Derivatives That Deregulate Cholesterol Metabolism in Prostate Cancer Cells

The naturally occurring pentacyclic diterpenoid gibberellic acid (1) was used in the generation of a drug-like amide library using parallel-solution-phase synthesis. Prior to the synthesis, a virtual library was generated and prioritized based on drug-like physicochemical parameters such as log P, hydrogen bond donor/acceptor counts, and molecular weight. The structures of the synthesized analogues (2-13) were elucidated following analysis of the NMR, MS, UV, and IR data. Compound 12 afforded crystalline material, and its structure was confirmed by X-ray crystallographic analysis. All compounds were evaluated in vitro for cytotoxicity and deregulation of lipid metabolism in LNCaP prostate cancer cells. While no cytotoxic activity was identified at the concentrations tested, synthesized analogues 3, 5, 7, 10, and 11 substantially reduced cellular uptake of free cholesterol in prostate cancer cells, suggesting a novel role of gibberellic acid derivatives in deregulating cholesterol metabolism.

Potential New H1N1 Neuraminidase Inhibitors from Ferulic Acid and Vanillin: Molecular Modelling, Synthesis and in Vitro Assay

We report the computational and experimental efforts in the design and synthesis of novel neuraminidase (NA) inhibitors from ferulic acid and vanillin. Two proposed ferulic acid analogues, MY7 and MY8 were predicted to inhibit H1N1 NA using molecular docking. From these two analogues, we designed, synthesised and evaluated the biological activities of a series of ferulic acid and vanillin derivatives. The enzymatic H1N1 NA inhibition assay showed MY21 (a vanillin derivative) has the lowest IC50 of 50 μM. In contrast, the virus inhibition assay showed MY15, a ferulic acid derivative has the best activity with the EC50 of ~0.95 μM. Modelling studies further suggest that these predicted activities might be due to the interactions with conserved and essential residues of NA with ΔGbind values comparable to those of oseltamivir and zanamivir, the two commercial NA inhibitors.

Compound high-quality criteria: a new vision to guide the development of drugs, current situation

For several decades, the pharmaceutical industry has suffered due to major issues such as reductions of the number of FDA approved drugs and biologics. Several analyses have been highlighted that the 'druglikeness' is one of the strategies to improve succeed rates of screening such as, for instance, high-throughput screening (HTS), and then hits (as starting point), leads and clinical candidates. It is clear that the improvement of compound quality accelerates the drug discovery projects. The monitoring of several indices to avoid 'molecular obesity' (ADMET problems) of final drugs from good-quality 'low-fat' starting points represents today a powerful strategy of optimization process. The development of the new guides to find drugs highlighting attempts at improving the attrition rate from hits to final medicines by focusing on how to improve the druggability of hits, leads and drugs during the drug discovery process represents a key approach to design next better generation of medicines.

The use of isolated natural products as scaffolds for the generation of chemically diverse screening libraries for drug discovery

This Highlight examines the use of isolated natural products as scaffolds in the semi-synthesis of drug discovery libraries, and the potential of this rarely used method to contribute to successful natural product library generation strategies.

Capturing nature's diversity

Natural products are universally recognized to contribute valuable chemical diversity to the design of molecular screening libraries. The analysis undertaken in this work, provides a foundation for the generation of fragment screening libraries that capture the diverse range of molecular recognition building blocks embedded within natural products. Physicochemical properties were used to select fragment-sized natural products from a database of known natural products (Dictionary of Natural Products). PCA analysis was used to illustrate the positioning of the fragment subset within the property space of the non-fragment sized natural products in the dataset. Structural diversity was analysed by three distinct methods: atom function analysis, using pharmacophore fingerprints, atom type analysis, using radial fingerprints, and scaffold analysis. Small pharmacophore triplets, representing the range of chemical features present in natural products that are capable of engaging in molecular interactions with small, contiguous areas of protein binding surfaces, were analysed. We demonstrate that fragment-sized natural products capture more than half of the small pharmacophore triplet diversity observed in non fragment-sized natural product datasets. Atom type analysis using radial fingerprints was represented by a self-organizing map. We examined the structural diversity of non-flat fragment-sized natural product scaffolds, rich in sp3 configured centres. From these results we demonstrate that 2-ring fragment-sized natural products effectively balance the opposing characteristics of minimal complexity and broad structural diversity when compared to the larger, more complex fragment-like natural products. These naturally-derived fragments could be used as the starting point for the generation of a highly diverse library with the scope for further medicinal chemistry elaboration due to their minimal structural complexity. This study highlights the possibility to capture a high proportion of the individual molecular interaction motifs embedded within natural products using a fragment screening library spanning 422 structural clusters and comprised of approximately 2800 natural products.