Lowering Lipophilicity by Adding Carbon: AzaSpiroHeptanes, a logD Lowering Twist

Reactivity and Selectivity of Azaspirocycles in Radical C-H Functionalization

Investigations of saturated spirocycles toward selective C-H functionalization reactions are scarce, despite their potential applications. In this work, we uncovered fundamental reactivity and selectivity differences between saturated heterocycles and their spirocyclic analogues using a model radical C-H xanthylation coupled with computational analysis. Ultimately, this study sheds light on the fundamental, understudied radical reactivity of spirocycles, thereby allowing for a pronounced chemical tunability that will prove to be advantageous in the expansion of their chemical space and applications in medicinal chemistry.

Bicyclo[m.n.k]alkane Building Blocks as Promising Benzene and Cycloalkane Isosteres: Multigram Synthesis, Physicochemical and Structural Characterization

Electrophilic double bond functionalization - intramolecular enolate alkylation sequence was used to obtain a series of bridged and fused bicyclo[m.n.k]alkane derivatives (i. e., bicyclo[4.1.1]octanes, bicyclo[2.2.1]heptanes, bicyclo[3.2.1]octanes, bicyclo[3.1.0]hexanes, and bicyclo[4.2.0]heptanes). The scope and limitations of the method were established, and applicability to the multigram synthesis of target bicyclic compounds was illustrated. Using the developed protocols, over 50 mono- and bifunctional building blocks relevant to medicinal chemistry were prepared. The synthesized compounds are promising isosteres of benzene and cycloalkane rings, which is confirmed by their physicochemical and structural characterization (pKa , LogP, and exit vector parameters (EVP)). "Rules of thumb" for the upcoming isosteric replacement studies were proposed.

Identification and Optimization of Small Molecule Pyrazolopyrimidine TLR7 Agonists for Applications in Immuno-oncology

Small molecule toll-like receptor (TLR) 7 agonists have gathered considerable interest as promising therapeutic agents for applications in cancer immunotherapy. Herein, we describe the development and optimization of a series of novel TLR7 agonists through systematic structure-activity relationship studies focusing on modification of the phenylpiperidine side chain. Additional refinement of ADME properties culminated in the discovery of compound 14, which displayed nanomolar reporter assay activity and favorable drug-like properties. Compound 14 demonstrated excellent in vivo pharmacokinetic/pharmacodynamic profiles and synergistic antitumor activity when administered in combination with aPD1 antibody, suggesting opportunities of employing 14 in immuno-oncology therapies with immune checkpoint blockade agents.

M. Subbaiah M, Kumar BV, Subramani L, Wang B, Li YX, Sivaprakasam P, Critton D, Mulligan D, Sandhu B, Xie C, Ramakrishnan R, Nagar J, Dudhgaonkar S, Oderinde MS, Murtaza A, Schieven GL, Mathur A, Gavai AV, Vite G, Gangwar S. Discovery of Novel TLR7 Agonists as Systemic Agent for Combination With aPD1 for Use in Immuno-oncology

We have designed and developed novel and selective TLR7 agonists that exhibited potent receptor activity in a cell-based reporter assay. In vitro, these agonists significantly induced secretion of cytokines IL-6, IL-1β, IL-10, TNFa, IFNa, and IP-10 in human and mouse whole blood. Pharmacokinetic and pharmacodynamic studies in mice showed a significant secretion of IFNα and TNFα cytokines. When combined with aPD1 in a CT-26 tumor model, the lead compound showed strong synergistic antitumor activity with complete tumor regression in 8/10 mice dosed using the intravenous route. Structure-activity relationship studies enabled by structure-based designs of TLR7 agonists are disclosed.

Scalable Diastereoselective Electrosynthesis of Spiro[benzofuran-2,2'-furan]-3-ones

Spirobenzofuran scaffolds, because of their three-dimensional structure, are incorporated into several valuable natural products and drug candidate molecules. Herein, with the assistance of electrosynthesis, we introduce a novel electrochemical approach for achieving spirobenzofurans in a user-friendly and operationally simple undivided cell setup under constant current. This metal-catalyst-free electrochemical procedure afforded spiro[benzofuran-2,2'-furan]-3-ones with high diastereoselectivity. Compatibility with gram-scale synthesis along with the convenient accessibility of reaction instruments and starting materials collectively raised the importance of this protocol compared to previous challenging methods. Furthermore, mechanistic cognizance of this reaction is obtained by the investigation of the cyclic voltammetry spectra of reactants.

1-Azaspiro[3.3]heptane as a Bioisostere of Piperidine

1-Azaspiro[3.3]heptanes were synthesized, characterized, and validated biologically as bioisosteres of piperidine. The key synthesis step was thermal [2+2] cycloaddition between endocyclic alkenes and the Graf isocyanate, ClO2 S-NCO, to give spirocyclic β-lactams. Reduction of the β-lactam ring with alane produced 1-azaspiro[3.3]heptanes. Incorporation of this core into the anesthetic drug bupivacaine instead of the piperidine fragment resulted in a new patent-free analogue with high activity.

Electrochemical synthesis of spirocyclic morpholines and tetrahydrofurans via an oxidative dearomatisation strategy

Simple and scalable electrochemical oxidation of the electron-rich benzene ring followed by intramolecular capture of reactive cation-radical intermediates opens access to spirocyclic morpholines and tetrahydrofurans. The obtained molecules can be readily modified to value-added building blocks.

Visible-Light-Mediated Intermolecular [2 + 2]-Cycloaddition Reaction of 3-Alkylideneindolin-2-one with Alkenes via Triplet Energy Transfer for the Synthesis of 3-Spirocyclobutyl Oxindoles

[2 + 2]-Cycloaddition is the most straightforward approach to the construction of cyclobutanes. In this paper, the intermolecular [2 + 2]-cycloaddition reaction of 3-alkylideneindolin-2-ones with alkenes was achieved. This reaction can be used in the synthesis of 3-spirocyclobutyl oxindoles, polycyclic oxindoles, and late stage modification of some drug molecules.

Silver(I)-Catalyzed Synthesis of Cuneanes from Cubanes and their Investigation as Isosteres

Bridged or caged polycyclic hydrocarbons have rigid structures that project substituents into precise regions of 3D space, making them attractive as linking groups in materials science and as building blocks for medicinal chemistry. The efficient synthesis of new or underexplored classes of such compounds is, therefore, an important objective. Herein, we describe the silver(I)-catalyzed rearrangement of 1,4-disubstituted cubanes to cuneanes, which are strained hydrocarbons that have not received much attention since they were first described in 1970. The synthesis of 2,6-disubstituted or 1,3-disubstituted cuneanes can be achieved with high regioselectivities, with the regioselectivity being dependent on the electronic character of the cubane substituents. A preliminary assessment of cuneanes as scaffolds for medicinal chemistry suggests cuneanes could serve as isosteric replacements of trans-1,4-disubstituted cyclohexanes and 1,3-disubstituted benzenes. An analogue of the anticancer drug sonidegib was synthesized, in which the 1,2,3-trisubstituted benzene was replaced with a 1,3-disubstituted cuneane.

Unexplored Facet of Pincer Ligands: Super-Reductant Behavior Applied to Transition-Metal-Free Catalysis

Pincer ligands are well-established supporting ancillaries to afford robust coordination to metals across the periodic table. Despite their widespread use in developing homogeneous catalysts, the redox noninnocence of the ligand backbone is less utilized in steering catalytic transformations. This report showcases a trianionic, symmetric NNN-pincer to drive C-C cross-coupling reactions and heterocycle formation via C-H functionalization, without any coordination to transition metals. The starting substrates are aryl chlorides that can tease the limit of a catalyst's ability to promote a reductive cleavage at a much demanding potential of -2.90 V vs SCE. The reducing power of the simple trianionic ligand backbone has been tremendously amplified by shining visible light on it. The catalyst's success relies on its easy access to the one-electron oxidized iminosemiquinonate form that has been thoroughly characterized by X-band electron paramagnetic resonance spectroscopy through spectroelectrochemical experiments. The moderately long-lived excited-state lifetime (10.2 ns) and such a super-reductive ability dependent on the one-electron redox shuttle between the bisamido and iminosemiquinonato forms make this catalysis effective.

Visible-light-induced organophotocatalytic and singlet oxygen-initiated domino construction of 1,4-dihydropyridines, C-3 functionalized spiro[indoline-3,4'-pyridines] and C-11 functionalized spiro[indeno-[1,2-b]quinoxaline-11,4'-pyridines]

A highly efficient pot, atom, and step economical method for the construction of pharmacologically potent structurally functionalized 1,4-dihydropyridines, quaternary centered C-3 functionalized spiro[indoline-3,4'-pyridines], and C-11 functionalized spiro[indeno[1,2-b]quinoxaline-11,4'-pyridines] via rose bengal photoredox catalysis under blue LED irradiation in an aqueous medium at room temperature has been developed. The products were isolated in excellent yields within a short reaction time for a variety of functional groups under transition metal- and ligand-free energy-efficient conditions in a green solvent system with high reaction mass efficiency and process mass intensity, which are the key advantages of the current work.

Replacing the oxidation-sensitive triaminoaryl chemotype of problematic KV 7 channel openers: Exploration of a nicotinamide scaffold

K_V 7 channel openers have proven their therapeutic value in the treatment of pain as well as epilepsy and, moreover, they hold the potential to expand into additional indications with unmet medical needs. However, the clinically validated but meanwhile discontinued K_V 7 channel openers flupirtine and retigabine bear an oxidation-sensitive triaminoraryl scaffold, which is suspected of causing adverse drug reactions via the formation of quinoid oxidation products. Here, we report the design and synthesis of nicotinamide analogs and related compounds that remediate the liability in the chemical structure of flupirtine and retigabine. Optimization of a nicotinamide lead structure yielded analogs with excellent K_V 7.2/3 opening activity, as evidenced by EC₅₀ values approaching the single-digit nanomolar range. On the other hand, weighted K_V 7.2/3 opening activity data including inactive compounds allowed for the establishment of structure-activity relationships and a plausible binding mode hypothesis verified by docking and molecular dynamics simulations.

Photoinduced Synthesis of Functionalized Oxacyclic Spirooxindoles Via Ring Expansion

A versatile photochemical ring-expansion protocol for the synthesis of oxacyclic spirooxindoles under catalyst-free conditions is described. The reaction is enabled by the use of unstrained O-containing heterocycles with 3-diazoindolin-2-ones under visible-light irradiation. Several synthetic advantages for this method are exhibited, including mild conditions, good functional group tolerance, operational simplicity, and scalability. Mechanistic studies indicate that the transformation may proceed through the formation of oxonium ylide intermediate followed by an ionic cyclization.

Applications of Isosteres of Piperazine in the Design of Biologically Active Compounds: Part 2

Applications of piperazine and homopiperazine in drug design are well-established, and these heterocycles have found use as both scaffolding and terminal elements and also as a means of introducing a water-solubilizing element into a molecule. In the accompanying review (10.1021/acs.jafc.2c00726), we summarized applications of piperazine and homopiperazine and their fused ring homologues in bioactive compound design along with illustrations of the use of 4-substituted piperidines and a sulfoximine-based mimetic. In this review, we discuss applications of pyrrolidine- and fused-pyrrolidine-based mimetics of piperazine and homopiperazine and illustrate derivatives of azetidine that include stretched and spirocyclic motifs, along with applications of a series of diaminocycloalkanes.

Applications of Isosteres of Piperazine in the Design of Biologically Active Compounds: Part 1

Piperazine and homopiperazine are well-studied heterocycles in drug design that have found gainful application as scaffolds and terminal elements and for enhancing the aqueous solubility of a molecule. The optimization of drug candidates that incorporate these heterocycles in an effort to refine potency, selectivity, and developability properties has stimulated the design and evaluation of a wide range of bioisosteres that can offer advantage. In this review, we summarize the design and application of bioisosteres of piperazine and homopiperazine that have almost exclusively been in the drug design arena. While there are ∼100 approved drugs that incorporate a piperazine ring, only a single marketed agricultural product is built on this heterocycle. As part of the review, we discuss some of the potential reasons underlying the relatively low level of importance of this heterocycle to the design of agrochemicals and highlight the potential opportunities for their use in contemporary research programs.

Turning the Other Cheek: Influence of the cis-Tetrafluorocyclohexyl Motif on Physicochemical and Metabolic Properties

The targeted introduction of substituents in order to tailor a molecule’s pharmacologic, physicochemical, and metabolic properties has long been of interest to medicinal chemists. The all-cis tetrafluorocyclohexyl motif—dubbed Janus face, due to its electrostatically polarized cyclohexyl ring—represents one such example where chemists might incorporate a metabolically stable, polar, lipocompatible motif. To better understand its potential utility, we have synthesized three series of matched molecular pairs (MMPs) where each MMP differs only in the cyclohexane unit, i.e., with a tetrafluorocyclohexyl or a standard cyclohexyl motif. With the introduction of the facially polarized all-cis tetrafluorocyclohexyl ring, the resulting compounds have significantly modified physicochemical properties (e.g., kinetic solubility, lipophilicity and permeability) and metabolic stabilities. These results further speak to the promise of this substituent as a tactic to improve the drug-like properties of molecules.

Identification and optimisation of a pyrimidopyridone series of IRAK4 inhibitors

In this article, we report the discovery of a series of pyrimidopyridones as inhibitors of IRAK4 kinase. From a previously disclosed 5-azaquinazoline series, we found that switching the pyridine ring for an N-substituted pyridone gave a novel hinge binding scaffold which retained potency against IRAK4. Importantly, introduction of the carbonyl established an internal hydrogen bond with the 4-NH, establishing a conformational lock and allowing truncation of the large basic substituent to a 1-methylcyclopyl group. Subsequent optimisation, facilitated by X-ray crystal structures, allowed identification of preferred substituents at both the pyridone core and pyrazole. Subsequent combinations of optimal groups allowed control of lipophilicity and identification of potent and selective inhibitors of IRAK4 with better in vitro permeability and lower clearance.

The N,N,O-Trisubstituted Hydroxylamine Isostere and Its Influence on Lipophilicity and Related Parameters

The influence of substitution of an N,N,O-trisubstituted hydroxylamine (-NR-OR'-) unit for a hydrocarbon (-CHR-CH2-), ether (-CHR-OR'-), or amine (-NR-CHR'-) moiety on lipophilicity and other ADME parameters is described. A matched molecular pair analysis was conducted across five series of compounds, which showed that the replacement of carbon-carbon bonds by N,N,O-trisubstituted hydroxylamines typically leads to a reduction in logP comparable to that achieved with a tertiary amine group. In contrast, the weakly basic N,N,O-trisubstituted hydroxylamines have greater logD 7.4 values than tertiary amines. It is also demonstrated that the N,N,O-trisubstituted hydroxylamine moiety can improve metabolic stability and reduce human plasma protein binding relative to the corresponding hydrocarbon and ether units. Coupled with recent synthetic methods for hydroxylamine assembly by N-O bond formation, these results provide support for the re-evaluation of the N,N,O-trisubstituted hydroxylamine moiety in small-molecule optimization schemes in medicinal chemistry.

A stereochemical journey around spirocyclic glutamic acid analogs

A practical divergent synthetic approach is reported for the library of regio- and stereoisomers of glutamic acid analogs built on the spiro[3.3]heptane scaffold. Formation of the spirocyclic scaffold was achieved starting from a common precursor - an O-silylated 2-(hydroxymethyl)cyclobutanone derivative. Its olefination required using the titanium-based Tebbe protocol since the standard Wittig reaction did not work with this particular substrate. The construction of the second cyclobutane ring of the spirocyclic system was achieved through either subsequent dichloroketene addition or Meinwald oxirane rearrangement as the key synthetic steps, depending on the substitution patterns in the target compounds (1,6- or 1,5-, respectively). Further modified Strecker reaction of the resulting racemic spirocyclic ketones with the Ellman's sulfinamide as a chiral auxiliary had low to moderate diastereoselectivity; nevertheless, all stereoisomers were isolated in pure form via chromatographic separation, and their absolute configuration was confirmed by X-ray crystallography. Members of the library were tested for the inhibitory activity against H. pylori glutamate racemase.

6-Hydroxymethyl Indolizidin-2-one Amino Acid Synthesis, Conformational Analysis, and Biomedical Application as Dipeptide Surrogates in Prostaglandin-F2α Modulators

6-Hydroxymethyl indolizidin-2-one amino acids were synthesized in 10 steps from l-serine by intramolecular ring opening of a symmetrical epoxide and lactam formation. X-ray analyses indicated the bicycles replicated ideal peptide type II' β-turn central dihedral angle geometry. Inside a prostaglandin-F_2α receptor modulator, the 6-hydroxymethyl analogue retained inhibitory activity on myometrial contractility.

Target-Based Evaluation of "Drug-Like" Properties and Ligand Efficiencies

Physicochemical descriptors commonly used to define "drug-likeness" and ligand efficiency measures are assessed for their ability to differentiate marketed drugs from compounds reported to bind to their efficacious target or targets. Using ChEMBL version 26, a data set of 643 drugs acting on 271 targets was assembled, comprising 1104 drug-target pairs having ≥100 published compounds per target. Taking into account changes in their physicochemical properties over time, drugs are analyzed according to their target class, therapy area, and route of administration. Recent drugs, approved in 2010-2020, display no overall differences in molecular weight, lipophilicity, hydrogen bonding, or polar surface area from their target comparator compounds. Drugs are differentiated from target comparators by higher potency, ligand efficiency (LE), lipophilic ligand efficiency (LLE), and lower carboaromaticity. Overall, 96% of drugs have LE or LLE values, or both, greater than the median values of their target comparator compounds.

Stereoselective synthesis and applications of spirocyclic oxindoles

This review summaries recent synthetic developments towards spirocyclic oxindoles and applications as valuable medicinal and synthetic targets.

Spirocyclic Scaffolds in Medicinal Chemistry

Spirocyclic scaffolds are incorporated in various approved drugs and drug candidates. The increasing interest in less planar bioactive compounds has given rise to the development of synthetic methodologies for the preparation of spirocyclic scaffolds. In this Perspective, we summarize the diverse synthetic routes to obtain spirocyclic systems. The impact of spirocycles on potency and selectivity, including the aspect of stereochemistry, is discussed. Furthermore, we examine the changes in physicochemical properties as well as in in vitro and in vivo ADME using selected studies that compare spirocyclic compounds to their nonspirocyclic counterparts. In conclusion, the value of spirocyclic scaffolds in medicinal chemistry is discussed.

Improving metabolic stability and removing aldehyde oxidase liability in a 5-azaquinazoline series of IRAK4 inhibitors

In this article, we report our efforts towards improving in vitro human clearance in a series of 5-azaquinazolines through a series of C4 truncations and C2 expansions. Extensive DMPK studies enabled us to tackle high Aldehyde Oxidase (AO) metabolism and unexpected discrepancies in human hepatocyte and liver microsomal intrinsic clearance. Our efforts culminated with the discovery of 5-azaquinazoline 35, which also displayed exquisite selectivity for IRAK4, and showed synergistic in vitro activity against MyD88/CD79 double mutant ABC-DLBCL in combination with the covalent BTK inhibitor acalabrutinib.

Synthesis of (R) and (S)-3-Chloro-5-(3-methylmorpholino)-4H-1,2,6-thiadiazin-4-ones

Reaction of 3,5-dichloro-4H-1,2,6-thiadiazin-4-one with (R) and (S)-3-methylmorpholines (2 equiv), in THF, at ca. 20 °C gave (R) and (S)-3-chloro-5-(3-methylmorpholino)-4H-1,2,6-thiadiazin-4-ones in 95 and 97% yields, respectively. The new compounds were fully characterized.