Revealing Atropisomer Axial Chirality in Drug Discovery

Stereocontrol in Conformationally Stable C(sp2)─C(sp3) Atropisomers

We report a two-step sequence for the enantioselective construction of a rare family of stable C(sp2)─C(sp3) atropisomers featuring two additional stereogenic centers. The process begins with an organocatalyzed dihydrobenzofurannulation that establishes and controls the stereochemistry of two carbon centers, followed by a highly diastereoselective functionalization that significantly enhances the barrier to diastereomerization of the C(sp2)─C(sp3) bond, effectively locking and stabilizing its configuration.

Regioselective Oxyamination of Biaryls Using Nitroarenes

Biaryl frameworks are pivotal in natural products, pharmaceuticals, agrochemicals, and materials, with the 2'-amino-2'-hydroxy-1,1'-biaryl motif being especially valuable for catalysis and bioactivity. However, synthesizing these non-C2-symmetric biaryls efficiently and regioselectively remains challenging due to limitations in current methods, such as prefunctionalization and structural constraints. Herein, we report a regioselective oxyamination of cyclometalated biaryl lanthanum reagents using nitroarenes. This lanthanum-based approach uniquely utilizes the oxophilicity and nucleophilicity of organolanthanum intermediates, enabling dual incorporation of oxygen and nitrogen into biaryl skeletons. A proposed 8-membered metallacycle intermediate avoids undesired nitrosoarene formation, delivering 2'-amino-2'-hydroxy-1,1'-biaryls with high efficiency. This one-pot, step-economical and transition-metal-free method achieves exceptional regioselectivity and a broad substrate scope, addressing longstanding challenges in biaryl functionalization and providing significant implications for catalysis, drug development, and materials science.

Rhodium(III)-Catalyzed Redox-Neutral [4 + 2] Annulation of 3,5-Diaryloxadiazoles with Alkynes: A Dual C-H Activation Strategy for Constructing C-N Atropisomers

A rhodium(III)-catalyzed dual-ring formation via cascade C-H activation/[4 + 2] annulation of 3,5-diaryoxadiazoles with alkynes was developed. This strategy has been demonstrated with a variety of 3,5-diaryloxadiazoles and alkynes, and it has been successfully scaled up to gram-scale synthesis, highlighting its potential significance in the direct construction of C-N atropisomers. Furthermore, the cleavage of the N-O bond is essential for the formation of the bicyclic structure in the absence of an external oxidant. Mechanistic studies revealed that cleavage of the C-H bond at the 3-phenyl group of oxadiazole was likely a rate-determining step in this reaction.

Organocatalytic atroposelective de novo construction of monoaxially and 1,4-diaxially chiral fused uracils with potential antitumor activity

Atropisomers bearing multiple stereogenic axes are of increasing relevance to materials science, pharmaceuticals, and catalysis. However, the catalytic enantioselective construction of these atropisomers in a single step remains synthetically challenging. We herein report the first NHC-organocatalytic enantioselective synthesis of a new class of monoaxially and 1,4-diaxially chiral fused uracil scaffolds. Preliminary studies on the antitumor activity of selected compounds demonstrated that this new class of axially chiral uracil derivatives may have potential applications in the discovery of new lead compounds in medicinal chemistry.

Beyond Barriers, Big Crystallization Hurdles: Atropisomerism in Beyond Rule of Five Compounds Explored by Computational and NMR Studies

Stereochemical purity, stability, and selection of a suitable solid-state form are pivotal factors in pharmaceutical development, particularly for complex beyond Rule of 5 (bRo5) compounds. In this study, we explore the intricate interplay between atropisomerism and crystallization using two model bRo5 compounds, namely, ACBI1 and BI201335, both violating three of four Lipinski's rules. One of the tool compounds exhibits Class 2 atropisomeric behavior, and the other is devoid of it. A diverse array of crystallization methods, including solution-phase crystallization, cocrystallization, and salt formation, were applied, revealing the critical role of atropisomerism-induced stereochemistry in polymorphism and nucleation outcomes. In silico torsion profile calculations and NMR studies were employed to elucidate the rotational energy barriers and confirm the presence or absence of atropisomerism. This comprehensive analysis highlights the significance of understanding stereochemical phenomena such as atropisomerism in designing and developing bRo5 compounds. By integrating advanced analytical techniques and crystallization strategies, this work provides novel insights into tailoring pharmaceutical properties for next-generation therapeutics.

Organocatalytic Atroposelective Cross-Coupling of 2-Naphthols with Diaryliodonium Salts

Due to their modularity and conciseness, atroposelective cross-coupling is one of the most attractive approaches for synthesizing axially chiral binaphthyl molecules. While transition metal-catalyzed cross-couplings provide reliable synthetic strategies, alternative methods that accommodate a broader range of substrates without their pre-functionalization are highly beneficial. Here, we demonstrate that using the bifunctional organocatalyst (DHQD)2PHAL enables atroposelective cross-coupling of 2-naphthols and diaryliodonium salts with high efficiency, and yields (up to 72%) and excellent enantioselectivity (up to >99% enantiomeric excess). Further transformations of the products highlight the versatility of other binaphthyl compounds while maintaining their axial chirality.

Sulfur-Controlled Modulation of Peptoid Atropisomeric Foldamers

We incorporated the hetero atoms (O/S) at the ortho-position to investigate the steric influence on controlling the rotational barrier around the C-N chiral axis and to elucidate the chiral attributes of sulfur-containing N-aryl peptoids. This study reports the simultaneous installation of a C-N chiral axis and the integration of sulfur-containing stereogenic elements in peptoid atropisomeric foldamers. By leveraging multiple chiral elements in peptoids, we demonstrated subtle structural variations, particularly by varying the sulfur oxidation states, that can lead to significant differences in the rotational energy barrier, as determined by dynamic HPLC. Additionally, we employed single-crystal X-ray crystallography to elucidate local conformational ordering and computational studies to identify noncovalent interactions in this class of atropisomers. Through these combined approaches, we explored sulfur-controlled modulation of N-aryl peptoid atropisomeric foldamers.

Discovery of Nirmatrelvir (PF-07321332): A Potent, Orally Active Inhibitor of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2) Main Protease

In early 2020, severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) infections leading to COVID-19 disease reached a global level leading to the World Health Organization (WHO) declaration of a pandemic. Scientists around the globe rapidly responded to try and discover novel therapeutics and repurpose extant drugs to treat the disease. This work describes the preclinical discovery efforts that led to the invention of PF-07321332 (nirmatrelvir, 14), a potent and orally active inhibitor of the SARS CoV-2 main protease (Mpro) enzyme. At the outset we focused on modifying PF-00835231 (1) discovered in 2004 as a potent inhibitor of the SARS CoV-1 Mpro with poor systemic exposure. Our effort was focused on modifying 1 with the goal of engineering in oral bioavailability by design, while maintaining cellular potency and low metabolic clearance. Modifications of 1 ultimately led to the invention of nirmatrelvir 14, the Mpro inhibitor component in PAXLOVID.

Simultaneous Construction of Axial and Central Stereogenicity by Cobalt-Catalyzed Stereoconvergent Reductive Coupling of Heterobiaryl Triflates and Aldehydes

Catalytic stereoconvergent coupling of racemic heterobiaryl triflates and aldehydes promoted by a readily available chiral cobalt complex is presented. Such processes represent an unprecedented reaction pathway for cobalt catalysis that enable simultaneous construction of axial and central stereogenicity through diastereo- and enantioselective dynamic kinetic transformations and introduction of a chiral fragment onto the heterobiaryl cores without the requirement of preforming stoichiometric amounts of organometallic reagents, affording densely functionalized secondary alcohols in up to 96 % yield, >98 : 2 dr and >99.5:0.5 er. Preliminary investigations on the application of the products demonstrate their potential for serving as a new class of chiral catalysts and ligands. Mechanistic studies suggest that a dynamic kinetic stereoselective process induced by chiral cobalt catalysis is involved.

Asymmetric Intramolecular Hydroamination to Construct Diverse N-N/C-N Indole Atropisomers via Cooperative Pd(0) and Chiral Phosphoric Acid Catalysis

Here we present an enantioselective intramolecular hydroamination reaction of o-aminophenyl-1,3-enynes via cooperative catalysis of Pd(0) and chiral phosphoric acid. This approach enables the efficient construction of N-N/C-N axially stereogenic indoles with broad skeletal diversity and high levels of enantioselectivity in a completely atom-economic manner. Mechanistic studies indicate that a protonation of the alkyne moiety via Pd(0) π-Lewis base activation is favored, and the chiral phosphate counteranion plays a crucial role in controlling the atroposelectivity in the ring-closure step.

A Helically-Twisted Stereodynamic Probe for Chiroptical Sensing of Chiral Amines through Point-to-Helical Chirality Transmission

Chiral amines and amino alcohols form an important category of molecules employed in the designing of new drugs and catalyst. Herein, we present a helically-twisted stereodynamic dialdehyde probe 1 for the determining of absolute configuration, and enantiomeric excess of chiral amine and amino alcohols. Probe 1 is based on the pyridine-2,6-dicarboxamide (PDC) core and undergoes rapid interconversion between the P- and M- conformers. However, upon imine formation with chiral amines, probe 1 gets locked it in a single conformer majorly. This induces a strong CD signal in addition to changes in the UV-vis and fluorescence signals. The CD spectral change allowed for quantitative enantiomeric excess determination of chiral amines. Circular polarized luminescence (CPL) spectra having the glum of 1×10-3 was obtained upon imine formation between probe 1 and diamine 2. Single crystal X-ray diffraction studies (SCXRD) confirmed the twisted conformation in 1@(R)-4 and 1@(S)-4, stabilized by intramolecular hydrogen bonding between bound imine nitrogen and proximate amide group.

Rhodium-Catalyzed Atroposelective Synthesis of Axially Chiral 1-Aryl Isoquinolines via De Novo Isoquinoline Formation

Axially chiral heterobiaryl moieties serve as core skeletons for bioactive molecules, chiral ligands, and organocatalysts. Enantioselective de novo formation of the heteroaromatic ring is one of the most straightforward approaches to access enantioenriched heterobiaryls. Herein, an enantioselective de novo construction of isoquinolines by rhodium-catalyzed C─H activation/annulation of aromatic imines with alkynes is disclosed. This approach is operationally simple, allowing for rapid access to a variety of axially chiral 1-aryl isoquinolines in excellent yields and enantioselectivity (up to 98% yield and 99:1 er). The synthetic application of the current method was demonstrated by functional group transformations and suitability for millimolar-scale reactions. Detailed experimental and theoretical studies revealed the turnover-limiting step and provided insight into the origin of the enantioselectivity for this reaction.

Discovery of Elironrasib (RMC-6291), a Potent and Orally Bioavailable, RAS(ON) G12C-Selective, Covalent Tricomplex Inhibitor for the Treatment of Patients with RAS G12C-Addicted Cancers

The discovery of elironrasib (RMC-6291) represents a significant breakthrough in targeting the previously deemed undruggable GTP-bound, active KRASG12C. To target the active state of RAS (RAS(ON)) directly, we have employed an innovative tri-complex inhibitor (TCI) modality involving formation of a complex with an inhibitor, the intracellular chaperone protein CypA, and the target protein KRASG12C in its GTP-bound form. The resulting tri-complex inhibits oncogenic signaling, inducing tumor regressions across various preclinical models of KRASG12C mutant human cancers. Here we report structure-guided medicinal chemistry efforts that led to the discovery of elironrasib, a potent, orally bioavailable, RAS(ON) G12C-selective, covalent, tri-complex inhibitor. The investigational agent elironrasib is currently undergoing phase 1 clinical trials (NCT05462717, NCT06128551, NCT06162221), with preliminary data indicating clinical activity in patients who had progressed on first-generation inactive state-selective KRASG12C inhibitors.

Stereoselective synthesis of atropisomeric amides enabled by intramolecular acyl transfer

C-N atropisomeric amides are important compounds in medicinal chemistry and agrochemistry. Atropselective methods for their synthesis are therefore important. In this study, a novel strategy to make C-N atropisomeric amides based on intramolecular acyl transfer via a tethered Lewis basic pyridine or tertiary amine group is reported. The reactions operate under kinetic control and in most cases are highly atropselective, with the products isolable as pure, single diastereoisomers following chromatography. The kinetically favored atropisomer can also be isomerised into the alternative thermodynamically favored atropisomer upon heating. The kinetic and thermodynamic outcomes are supported by computational studies, while additional mechanistic studies support operation via initial fast acylation of the Lewis basic group, followed by rate-determining acyl transfer, which also enables control over the atropisomer formed.

Atropisomerism of diflunisal unveiled by rotational spectroscopy and quantum chemical calculations

The most stable conformer of laser-ablated diflunisal has been isolated in a supersonic expansion and experimentally detected through high-resolution chirped-pulse rotational spectroscopy. State-of-the-art chemical calculations allowed to understand the nature of the strong stabilization of the detected conformer and its atropisomer among a total of sixteen theoretically predicted conformers and confirmed the presence of a resonance assisted hydrogen bond (RAHB) between the hydroxyl hydrogen atom and the carbonyl oxygen atom of the carboxylic acid group. The comparison of the experimental data from this work and the information found in the literature about the molecule in condensed phases corroborates the existence of these two atropisomers and is contextualized within the complexation arrangement of diflunisal with relevant proteins.

Coordination-induced axial chirality controls the metal-centred configuration in a stereogenic-at-iron catalyst

A new approach is introduced to control the metal-centred configuration of stereogenic-at-iron catalysts by utilizing axial ligand chirality, which becomes locked upon metal coordination. This strategy is applied to an iron catalyst containing two chelating N-(2-pyridyl)-substituted triazol-5-ylidene mesoionic carbenes (MICs) resulting in a helical topology with a stereogenic iron centre.

Conformational Analysis of Swallowtail Motifs in Porphyrins

Aqueous solubilization of porphyrins, often accomplished with appended polar aryl groups, can also be achieved with symmetrically branched alkyl (i.e., swallowtail) groups terminated with polar moieties. Here, carboxylic acids are employed as termini (versus prior phosphono- or phosphoester termini) in designs of trans-AB-porphyrins bearing a single swallowtail group (A) or trans-A2-porphyrins bearing two swallowtail groups. Variable-temperature 1H NMR studies (-60 to 97 °C) revealed that the 4-heptanedioic acid group at the meso-position of the free base porphyrin rotates with rate constant 5 s-1 (310 K) and Arrhenius energy barrier Ea = 11.5 kcal/mol, whereas an isopropyl group undergoes rotation ∼1000-times faster (k = 5770 s-1). The interconversion is sufficiently fast that conformational diastereomers, as when two such swallowtail groups are present in a trans-A2-porphyrin, would not be isolable at room temperature (Class I atropisomers). DFT calculations (4 porphyrins containing the isopropyl or 4-heptanedioic acid groups) showed that the lowest energy conformer contains the swallowtail C-H unit in the plane of the porphyrin. The presence of one or two 4-heptanedioic acid moieties imparted solubility of the porphyrin in phosphate-buffered saline (PBS). The results suggest applications in the life sciences where compact, aqueous-soluble porphyrins are desired.

Recent advances in organocatalytic atroposelective reactions

Axial chirality is present in a variety of naturally occurring compounds, and is becoming increasingly relevant also in medicine. Many axially chiral compounds are important as catalysts in asymmetric catalysis or have chiroptical properties. This review overviews recent progress in the synthesis of axially chiral compounds via asymmetric organocatalysis. Atroposelective organocatalytic reactions are discussed according to the dominant catalyst activation mode. For covalent organocatalysis, the typical enamine and iminium modes are presented, followed by N-heterocyclic carbene-catalyzed reactions. The bulk of the review is devoted to non-covalent activation, where chiral Brønsted acids feature as the most prolific catalytic structure. The last part of the article discusses hydrogen-bond-donating catalysts and other catalyst motifs such as phase-transfer catalysts.

Organocatalytic Atroposelective Synthesis of Axially Chiral Indolyl Ketosulfoxonium Ylides

Despite recent advancements in the catalytic generation of axial chirality, reports on non-biaryl atropisomers remain limited because of the stringent steric requirements necessary to establish effective rotational brakes. Herein, we present a novel class of monoaryl atropisomers, indolyl ketosulfoxonium ylides, and describe an organocatalytic protocol for their synthesis. We discovered that a chiral phosphoric acid (CPA) serves as an effective catalyst for the highly enantioselective iodination of ortho-aminophenylethynyl sulfoxonium ylides. Under the optimized reaction conditions, a strong preference for the intended iodination process over the competing protonation was observed. Subsequently, intramolecular amide cyclization enabled the formation of sterically congested indole fragments. Furthermore, the synthetic utility of the products was demonstrated by showcasing versatile transformations into other chiral scaffolds with complete retention of optical purity.

A New Dawn for Targeted Cancer Therapy: Small Molecule Covalent Binding Inhibitor Targeting K-Ras (G12C)

K-Ras is a frequently mutated oncogene in human malignancies, and the development of inhibitors targeting various oncogenic K-Ras mutant proteins is a major challenge in targeted cancer therapy, especially K-Ras(G12C) is the most common mutant, which occurs in pancreatic ductal adenocarcinoma (PDAC), non-small cell lung cancer (NSCLC), colorectal cancer (CRC) and other highly prevalent malignancies. In recent years, significant progress has been made in developing small molecule covalent inhibitors targeting K-Ras(G12C), thanks to the production of nucleophilic cysteine by the G12C mutant, breaking the "spell" that K-Ras protein cannot be used as a drug target. With the successful launch of sotorasib and adagrasib, the development of small molecule inhibitors targeting various K-Ras mutants has continued to gain momentum. In recent years, with the popularization of highly sensitive surface plasmon resonance (SPR) technology, fragment-based drug design strategies have shown great potential in the development of small molecule inhibitors targeting K-Ras(G12C), but with the increasing number of clinically reported acquired drug resistance, addressing inhibitor resistance has gradually become the focus of this field, indirectly indicating that such small molecule inhibitors still the potential for the development of these small molecule inhibitors are also indirectly indicated. This paper traces the development of small molecule covalent inhibitors targeting K-Ras(G12C), highlighting and analyzing the structural evolution and optimization process of each series of inhibitors and the previous inhibitor design methods and strategies, as well as their common problems and general solutions, in order to provide inspiration and help to the subsequent researchers.

Atroposelective synthesis of axially chiral imidazo[1,2-a]pyridines via asymmetric multicomponent reaction

Imidazo[1,2-a]pyridines are privileged heterocycles with diverse applications in medicinal chemistry; however, the catalytic asymmetric synthesis of these heterocyclic structures remains underexplored. Herein, we present an efficient and modular approach for the atroposelective synthesis of axially chiral imidazo[1,2-a]pyridines via an asymmetric multicomponent reaction. By utilizing a chiral phosphoric acid catalyst, the Groebke-Blackburn-Bienaymé reaction involving various 6-aryl-2-aminopyridines, aldehydes, and isocyanides gave access to a wide range of imidazo[1,2-a]pyridine atropoisomers with high to excellent yields and enantioselectivities. Extensive control experiments underscored the pivotal role of the remote hydrogen bonding donor on the substrates in achieving high stereoselectivity for these reactions. The versatile derivatizations of these atropisomeric products, especially their role as an analog of NOBINs and their facile conversion into unique 6,6-spirocyclic products, further emphasize the merits of this methodology.

Catalyst-Substrate Pairings for Carbocyclic and Heterocyclic Systems in Atroposelective Quinazolinone Synthesis

Asymmetric catalytic reaction development depends critically on the matching of an appropriate catalytic scaffold with a substrate of interest. In many cases, a catalyst will be discovered to be quite selective for a given substrate, and that same catalyst is then evaluated for its scope with respect to alterations of the substrate. In the context of a catalytic atroposelective cyclocondensation, we discovered that a chiral phosphoric acid catalyst (CPA), (R)-TCYP, mediated these processes with up to 98:2 enantiomeric ratio (er) and in 95% yield. Yet, when the same reaction was attempted in the presence of a basic nitrogen heteroatom within the substrate, enantioselectivity was significantly reduced (73:27 er). In these instances, a different catalyst scaffold based on phosphothreonine (pThr), while ineffective for the carbocyclic substrate (53:47 er), was found to be quite selective (90:10 er) for its pyridyl analog. Mechanistic studies exploring this divergence in reactivity unveiled that the 8-carbocyclic substrate (using (R)-TCYP) displayed a positive nonlinear effect (NLE), whereas the 8-heterocyclic substrate (using a pThr-based catalyst) displayed no NLE at all. The mechanistic distinctions between these two scenarios suggest significant differences in the nature of the noncovalent interactions that operate to deliver high enantioselectivity.

Novel non-peptide uracil-derived human gonadotropin-releasing hormone receptor antagonists

Gonadotropin-releasing hormone (GnRH) is the main regulator of the reproductive system, acting on gonadotropic cells by binding to the GnRH1 receptor (GnRH1R). Traditionally, therapies targeting this receptor have relied on peptide modulators, which required subcutaneous or intramuscular injections. Due to the limitations of the parenteral administrations, there is a growing interest in developing oral small molecule modulators of GnRH1R as more convenient therapeutic alternatives. In this study, we examined the potential of chemically modifying elagolix, the first approved non-peptide, orally active GnRH1R antagonist, to increase its atropisomeric properties by introducing new moieties. We designed and synthesized the thio-uracil (1) and cytosine (2) derivatives of elagolix, both demonstrating GnRH1R antagonistic activities, with EC50 values of 39 and 110 nM, respectively. The atropisomers of 1 and 2 were efficiently separated using silica gel chromatography, and extensive NMR investigation, supported by Density Functional Theory (DFT) calculations, allowed us to define their conformations and rotational barriers. Docking and Molecular Dynamics (MD) studies revealed that 1 and 2 bind to GnRH1R with ΔG values comparable to elagolix, but through distinct binding modes. These results highlight the potential of non-peptide modulators to effectively modulate GnRH1R activity and pave the way for developing novel modulators.

Ligand-Controlled Regiodivergent Ring Expansion of Benzosilacyclobutenes with Alkynes en Route to Axially Chiral Silacyclohexenyl Arenes

A ligand-controlled regiodivergent and enantioselective ring expansion of benzosilacyclobutenes with internal naphthyl alkynes has been achieved by adjusting the ligand cavity size. The ligand (S)-8H-binaphthyl phosphoramidite, featuring small methyl groups on its arms, provides a spacious cavity that favors sterically demanding Si-Csp3 ring expansion, predominantly yielding axially chiral (S)-1-silacyclohexenyl arenes. In contrast, the ligand (R)-spiro phosphoramidite, with bulky t-Bu groups on its arms, offers a compact cavity that facilitates less sterically demanding Si-Csp2 ring expansion, leading primarily to axially chiral (S)-2-silacyclohexenyl arenes. Density functional theory calculations delineate distinct mechanistic pathways for each ring expansion route and elucidate their regio- and enantioselectivity.

Mechanism and origin of enantioselectivity for organocatalyzed asymmetric heteroannulation of alkynes in the construction of axially chiral C2-arylquinoline

Axially chiral C2-arylquinoline has been successfully constructed via asymmetric heteroannulation of alkynes catalyzed by chiral phosphoric acid with high yield and high enantioselectivity. Inspired by this intriguing work, theoretical calculations have been carried out, and the detailed reaction mechanism has been elaborated, in which the whole reaction can be divided into steps including hydrogen transfer, C-N bonding, annulation reaction and the final dehydration processes. The initial hydrogen-transfer reaction has two possible pathways, while the subsequent C-N bonding process has eight possible pathways. Then, after the annulation reaction and the final dehydration processes, the major product and byproduct were formed. QTAIM and IGMH analyses were used to illustrate the role of weak intermolecular interactions in the catalytic process, and the distortion/interaction and EDA analyses provided a deeper understanding of the origin of enantioselectivity. The calculated results are consistent with the experimental results. This work would provide valuable insights into asymmetric reactions catalyzed by chiral phosphoric acid.

Lenacapavir Exhibits Atropisomerism-Mechanistic Pharmacokinetics and Disposition Studies of Lenacapavir Reveal Intestinal Excretion as a Major Clearance Pathway

Lenacapavir (LEN), a long-acting injectable, is the first approved human immunodeficiency virus type 1 capsid inhibitor and one of a few Food and Drug Administration-approved drugs that exhibit atropisomerism. LEN exists as a mixture of two class 2 atropisomers that interconvert at a fast rate (half-life < 2 hours) with a ratio that is stable over time and unaffected by enzymes or binding to proteins in plasma. LEN exhibits low systemic clearance (CL) in nonclinical species and humans; however, in all species, the observed CL was higher than the in vitro predicted CL. The volume of distribution was moderate in nonclinical species and consistent with the tissue distribution observed by whole-body autoradiography in rats. LEN does not distribute to brain, consistent with being a P-glycoprotein (P-gp) substrate. Mechanistic drug disposition studies with [14C]LEN in intravenously dosed bile duct-cannulated rats and dogs showed a substantial amount of unchanged LEN (31%-60% of dose) excreted in feces, indicating that intestinal excretion (IE) was a major clearance pathway for LEN in both species. Coadministration of oral elacridar, a P-gp inhibitor, in rats decreased CL and IE of LEN. Renal excretion was < 1% of dose in both species. In plasma, almost all radioactivity was unchanged LEN. Low levels of metabolites in excreta included LEN conjugates with glutathione, pentose, and glucuronic acid, which were consistent with metabolites formed in vitro in Hμrel hepatocyte cocultures and those observed in human. Our studies highlight the importance of IE for efflux substrates that are highly metabolically stable compounds with slow elimination rates. SIGNIFICANCE STATEMENT: LEN is a long-acting injectable that exists as conformationally stable atropisomers. Due to an atropisomeric interconversion rate that significantly exceeds the in vivo elimination rate, the atropisomer ratio of LEN remains constant in circulation. The disposition of LEN highlights that intestinal excretion has a substantial part in the elimination of compounds that are metabolically highly stable and efflux transporter substrates.

A stereodivergent multicomponent approach for the synthesis of C-N atropisomeric peptide analogues

A four-component Ugi reaction is described for the stereoselective synthesis of novel C-N atropisomeric peptide analogues. Using this approach, a combination of simple, readily available starting materials (ortho-substituted anilines, aldehydes, carboxylic acids and isocyanides) could be combined to access complex products possessing both central and axial chirality in up to 92% yield and >95 : 5 d.r. Variation of the reaction temperature enabled the development of stereodivergent reactions capable of selectively targeting either diastereoisomer of a desired product from a single set of starting materials with high levels of stereocontrol. Detailed experimental and computational studies have been performed to probe the reaction mechanism and stereochemical outcome of these reactions. Preliminary studies show that novel atropisomeric scaffolds prepared using this method display inhibitory activity against M. tuberculosis with a significant difference in activity observed between different atropisomers.

NMR spectroscopy can help accelerate antiviral drug discovery programs

Small molecule drugs have an important role to play in combating viral infections, and biophysics support has been central for contributing to the discovery and design of direct acting antivirals. Perhaps one of the most successful biophysical tools for this purpose is NMR spectroscopy when utilized strategically and pragmatically within team workflows and timelines. This report describes some clear examples of how NMR applications contributed to the design of antivirals when combined with medicinal chemistry, biochemistry, X-ray crystallography and computational chemistry. Overall, these multidisciplinary approaches allowed teams to reveal and expose compound physical properties from which design ideas were spawned and tested to achieve the desired successes. Examples are discussed for the discovery of antivirals that target HCV, HIV and SARS-CoV-2.

Secofumitremorgins C and D, a pair of atropisomers from saltern-derived fungus Aspergillus fumigatus GXIMD00544

A pair of atropisomers secofumitremorgins C (1a) and D (1b), together with fifteen known alkaloids (2-16), were isolated from a saltern-derived fungus Aspergillus fumigatus GXIMD00544. The structures of atropisomers 1a and 1b were elucidated by the detailed spectroscopic data, chemical reaction and quantum chemical calculations. Compounds 1 and 8 displayed antifungal spore germination effects against plant pathogenic fungus associated with sugarcane Fusarium sp. with inhibitory rates of 53% and 77% at the concentration of 100 µM, repectively. Atropisomers 1 also exhibited antifouling potential against Balanus amphitrite larval settlement with an inhibitory rate of 96% at the concentration of 100 µM.

Bioactive atropisomers: Unraveling design strategies and synthetic routes for drug discovery

Atropisomerism, an expression of axial chirality caused by limited bond rotation, is a prominent aspect within the field of medicinal chemistry. It has been shown that atropisomers of a wide range of compounds, including established FDA-approved drugs and experimental molecules, display markedly different biological activities. The time-dependent reversal of chirality in atropisomers poses complexity and obstacles in the process of drug discovery and development. Nonetheless, recent progress in understanding atropisomerism and enhanced characterization methods have greatly assisted medicinal chemists in the effective development of atropisomeric drug molecules. This article provides a comprehensive review of their special design thoughts, synthetic routes, and biological activities, serving as a reference for the synthesis and biological evaluation of bioactive atropisomers in the future.

Atropisomeric 1-phenylbenzimidazoles affecting microtubule organization: influence of axial chirality

Benzimidazoles are frequently used in medicinal chemistry. Their anticancer effect is among the most prominent biological activities exhibited by this scaffold. Although numerous benzimidazole derivatives have been synthesized, possible atropisomerism of ortho-substituted 1-phenylbenzimidazoles has been largely overlooked. The aim of this research was to synthesize a small library of novel atropisomeric benzimidazole derivatives and explore their biological activity in various cancer and normal human cell lines. The new unique structural motif provides an interesting 3D architecture with axial chirality, which further contributes to molecular complexity and specificity. Racemates and their separated atropisomers arrested the cell cycle, caused apoptosis, and affected microtubule organization in cancer cells in vitro at different intensities. Moreover, this phenomenon was also verified by the inhibition of endothelial cell migration. These results showed that (+)-atropisomers, especially 5n, exhibit a stronger effect and show promise as agents for cancer therapy.

Asymmetric Synthesis of an Atropisomeric β-Carboline via Regioselective Intermolecular Rh(I)-Catalyzed [2 + 2 + 2] Cyclotrimerization

The rational design of atropisomeric small molecules is becoming increasingly common in chemical synthesis as a result of the unique advantages this property provides in drug discovery, asymmetric catalysis, and chiroptical activity. In this study, we designed a synthesis of a configurationally stable β-carboline in six steps. Our synthesis made use of an innovative Grignard addition/elimination reaction that formed an yne-ynamide precursor that then reacted with ethyl cyanoformate in a rhodium(I)-catalyzed [2+2+2] cyclotrimerization reaction to give the atropisomeric β-carboline in excellent yield, good enantioselectivity, and excellent regioselectivity. Extensive optimization of this transformation is described. Racemization kinetics experiments were also conducted on the individual atropisomers and their absolute configurations were determined by circular dichroism.

Quantum chemical package Jaguar: A survey of recent developments and unique features

This paper is dedicated to the quantum chemical package Jaguar, which is commercial software developed and distributed by Schrödinger, Inc. We discuss Jaguar's scientific features that are relevant to chemical research as well as describe those aspects of the program that are pertinent to the user interface, the organization of the computer code, and its maintenance and testing. Among the scientific topics that feature prominently in this paper are the quantum chemical methods grounded in the pseudospectral approach. A number of multistep workflows dependent on Jaguar are covered: prediction of protonation equilibria in aqueous solutions (particularly calculations of tautomeric stability and pKa), reactivity predictions based on automated transition state search, assembly of Boltzmann-averaged spectra such as vibrational and electronic circular dichroism, as well as nuclear magnetic resonance. Discussed also are quantum chemical calculations that are oriented toward materials science applications, in particular, prediction of properties of optoelectronic materials and organic semiconductors, and molecular catalyst design. The topic of treatment of conformations inevitably comes up in real world research projects and is considered as part of all the workflows mentioned above. In addition, we examine the role of machine learning methods in quantum chemical calculations performed by Jaguar, from auxiliary functions that return the approximate calculation runtime in a user interface, to prediction of actual molecular properties. The current work is second in a series of reviews of Jaguar, the first having been published more than ten years ago. Thus, this paper serves as a rare milestone on the path that is being traversed by Jaguar's development in more than thirty years of its existence.

Porphyrin Atropisomerism as a Molecular Engineering Tool in Medicinal Chemistry, Molecular Recognition, Supramolecular Assembly, and Catalysis

Porphyrin atropisomerism, which arises from restricted σ-bond rotation between the macrocycle and a sufficiently bulky substituent, was identified in 1969 by Gottwald and Ullman in 5,10,15,20-tetrakis(o-hydroxyphenyl)porphyrins. Henceforth, an entirely new field has emerged utilizing this transformative tool. This review strives to explain the consequences of atropisomerism in porphyrins, the methods which have been developed for their separation and analysis and present the diverse array of applications. Porphyrins alone possess intriguing properties and a structure which can be easily decorated and molded for a specific function. Therefore, atropisomerism serves as a transformative tool, making it possible to obtain even a specific molecular shape. Atropisomerism has been thoroughly exploited in catalysis and molecular recognition yet presents both challenges and opportunities in medicinal chemistry.

Enantioselective Synthesis of Heteroatom-Linked Non-Biaryl Atropisomers

Atropisomers hold significant fascination, not only for their prevalence in natural compounds but also for their biological importance and wide-ranging applications as chiral materials, ligands, and organocatalysts. While biaryl and heterobiaryl atropisomers are commonly studied, the enantioselective synthesis of less abundant heteroatom-linked non-biaryl atropisomers presents a formidable challenge in modern organic synthesis. Unlike classical atropisomers, these molecules allow rotation around two bonds, resulting in low barriers to enantiomerization through concerted bond rotations. In recent years the discovery of new configurationally stable rare non-biaryl scaffolds such as aryl amines, aryl ethers and aryl sulfones as well as innovative methodologies to control their configuration have been disclosed in the literature and constitute the topic of this minireview.

Impact of atropisomerism on a non-steroidal glucocorticoid receptor agonist

To investigate atropisomers of non-steroidal glucocorticoid receptor modulator GSK866, a virtual library of substituted benzoic acid analogues was enumerated. Compounds from this library were subjected to a torsion angle scan using Spartan'20 to calculate the torsion rotation energy barrier which identified compounds predicted to be stable as atropisomers. After synthesis of the library, analysis showed that compounds 13 and 14 existed as stable atropisomers 13a, 13b, 14a and 14b, in agreement with the earlier calculations. Screening in a glucocorticoid receptor cellular assay showed that one compound from each atropisomer pair was significantly more potent than the other. Docking in a public structure of the glucocorticoid receptor (PBD code 3E7C) enabled the stereochemistry of the two most potent compounds 13a and 14b to be assigned as (R a) and (S a), respectively.

Discovery of BI-9508, a Brain-Penetrant GPR88-Receptor-Agonist Tool Compound for In Vivo Mouse Studies

Decreased activity and expression of the G-protein coupled receptor GPR88 is linked to many behavior-linked neurological disorders. Published preclinical GPR88 allosteric agonists all have in vivo pharmacokinetic properties that preclude their progression to the clinic, including high lipophilicity and poor brain penetration. Here, we describe our attempts to improve GPR88 agonists' drug-like properties and our analysis of the trade-offs required to successfully target GPR88's allosteric pocket. We discovered two new GPR88 agonists: One that reduced morphine-induced locomotor activity in a murine proof-of-concept study, and the atropoisomeric BI-9508, which is a brain penetrant and has improved pharmacokinetic properties and dosing that recommend it for future in vivo studies in rodents. BI-9508 still suffers from high lipophilicity, and research on this series was halted. Because of its utility as a tool compound, we now offer researchers access to BI-9508 and a negative control free of charge via Boehringer Ingelheim's open innovation portal opnMe.com.

Evolution in the asymmetric synthesis of biaryl ethers and related atropisomers

Axially chiral biaryl ethers and related compounds hold valuable potential in natural products, medicinal chemistry, and catalysis; however, their asymmetric syntheses have always been overlooked compared to other biaryl/hetero-biaryl atropisomers. Unlike the later class molecules bearing a single chiral axis, the former category possesses a unique type of atropisomerism bearing two potential axes. Due to their great importance in diverse research domains, catalytic atropselective biaryl ether synthesis has recently witnessed an upsurge. This highlight article provides an elaborated view on the developments of catalytic synthetic methods that have been explored to achieve dual axial chirality in biaryl ethers and related scaffolds.

Nickel-Catalyzed Chemoselective Carbomagnesiation for Atroposelective Ring-Opening Difunctionalization

There is a pressing need for methods that can connect enantioenriched organic compounds with readily accessible building blocks via asymmetric functionalization of unreactive chemical bonds in organic synthesis and medicinal chemistry. Herein, the asymmetric chemoselective cleavage of two unactivated C(Ar)-O bonds in the same molecule is disclosed for the first time through an unusual nickel-catalyzed carbomagnesiation. This reaction facilitates the evolution of a novel atroposelective ring-opening difunctionalization. Utilizing readily available dibenzo bicyclic substrates, diverse valuable axially chiral biaryls are furnished with high efficiencies. Synthetic elaborations showcase the application potential of this method. The features of this method include good atom-economy, multiple roles of the nucleophile, and a simple catalytic system that enables the precise magnesiation of an α-C(Ar)-O bond and arylation of a β-C(Ar)-O bond.

Atroposelective catalysis

Atropisomeric compounds-stereoisomers that arise from the restricted rotation about a single bond-have attracted widespread attention in recent years due to their immense potential for applications in a variety of fields, including medicinal chemistry, catalysis and molecular nanoscience. This increased interest led to the invention of new molecular motors, the incorporation of atropisomers into drug discovery programmes and a wide range of novel atroposelective reactions, including those that simultaneously control multiple stereogenic axes. A diverse set of synthetic methodologies, which can be grouped into desymmetrizations, (dynamic) kinetic resolutions, cross-coupling reactions and de novo ring formations, is available for the catalyst-controlled stereoselective synthesis of various atropisomer classes. In this Review, we generalize the concepts for the catalyst-controlled stereoselective synthesis of atropisomers within these categories with an emphasis on recent advancements and underdeveloped atropisomeric scaffolds beyond stereogenic C(sp2)-C(sp2) axes. We also discuss more complex systems with multiple stereogenic axes or higher-order stereogenicity.

Natural anti-neuroinflammatory inhibitors in vitro and in vivo from Aglaia odorata

Fifty compounds including seven undescribed (1, 13, 18-20, 30, 31) and forty-three known (2-12, 14-17, 21-29, 32-50) ones were isolated from the extract of the twigs and leaves of Aglaia odorata with anti-neuroinflammatory activities. Their structures were determined by a combination of spectral analysis and calculated spectra (ECD and NMR). Among them, compounds 13-25 were found to possess tertiary amide bonds, with compounds 16, 17, and 19-21 existing detectable cis/trans mixtures in 1H NMR spectrum measured in CDCl3. Specifically, the analysis of the cis-trans isomerization equilibrium of tertiary amides in compounds 19-24 was conducted using NMR spectroscopy and quantum chemical calculations. Bioactivity evaluation showed that the cyclopenta[b]benzofuran derivatives (2-6, 8, 10, 12) could inhibit nitric oxide production at the nanomolar concentration (IC50 values ranging from 2 to 100 nM) in lipopolysaccharide-induced BV-2 cells, which were 413-20670 times greater than that of the positive drug (minocycline, IC50 = 41.34 μM). The cyclopenta[bc]benzopyran derivatives (13-16), diterpenoids (30-35), lignan (40), and flavonoids (45, 47, 49, 50) also demonstrated significant inhibitory activities with IC50 values ranging from 1.74 to 38.44 μM. Furthermore, the in vivo anti-neuroinflammatory effect of rocaglaol (12) was evaluated via immunofluorescence, qRT-PCR, and western blot assays in the LPS-treated mice model. The results showed that rocaglaol (12) attenuated the activation of microglia and decreased the mRNA expression of iNOS, TNF-α, IL-1β, and IL-6 in the cortex and hippocampus of mice. The mechanistic study suggested that rocaglaol might inhibit the activation of the NF-κB signaling pathway to relieve the neuroinflammatory response.

Palladium-Catalyzed Atroposelective Suzuki-Miyaura Coupling to Construct Axially Chiral Tetra-Substituted α-Boryl Styrenes

Palladium-catalyzed Suzuki-Miyaura (SM) coupling is a valuable method for forming C─C bonds, including those between aryl moieties. However, achieving atroposelective synthesis of axially chiral styrenes via SM coupling remains challenging. In this study, a palladium-catalyzed atroposelective Suzuki-Miyaura coupling between gem-diborylalkenes and aryl halides is presented. Using the monophosphine ligand Me-BI-DIME (L2), a range of axially chiral tetra-substituted acyclic styrenes with high yields and excellent enantioselectivities are successfully synthesized. Control experiments reveal that the gem-diboryl group significantly influences the product enantioselectivities and the coupling prefers to occur at sites with lower steric hindrance. Additionally, the alkenyl boronate group in the products proves versatile, allowing for various transformations while maintaining high optical purities.

Novel phenanthrene/bibenzyl trimers from the tubers of Bletilla striata attenuate neuroinflammation via inhibition of NF-κB signaling pathway

Five novel (9,10-dihydro) phenanthrene and bibenzyl trimers, as well as two previously identified biphenanthrenes and bibenzyls, were isolated from the tubers of Bletilla striata. Their structures were elucidated through comprehensive analyses of NMR and HRESIMS spectroscopic data. The absolute configurations of these compounds were determined by calculating rotational energy barriers and comparison of experimental and calculated ECD curves. Compounds 5b and 6 exhibited inhibitory effects on LPS-induced NO production in BV-2 cells, with IC50 values of 12.59 ± 0.40 and 15.59 ± 0.83 μmol·L-1, respectively. A mechanistic study suggested that these compounds may attenuate neuroinflammation by reducing the activation of the AKT/IκB/NF-κB signaling pathway. Additionally, compounds 3a, 6, and 7 demonstrated significant PTP1B inhibitory activities, with IC50 values of 1.52 ± 0.34, 1.39 ± 0.11, and 1.78 ± 0.01 μmol·L-1, respectively. Further investigation revealed that compound 3a might inhibit LPS-induced PTP1B overexpression and NF-κB activation, thereby mitigating the neuroinflammatory response in BV-2 cells.

Conformation Analysis and Stereodynamics of Symmetrically ortho-Disubstituted Carvacrol Derivatives

The design and synthesis of analogs of natural products can be a valuable source of medicinal preparations for the pharmaceutical industry. In the present study, the structural elucidation of eleven derivatives of 2,4-dihalogeno substituted synthetic analogues of the natural compound carvacrol was carried out by means of NMR experiments, and of another thirteen by DFT calculations. By selective NOE experiments and the irradiation of CH signals of the isopropyl group, individual conformers were assigned as syn and anti. By comparing GIAO/B3LYP/6-311++G(d,p)-calculated and experimentally measured vicinal 3JCH spin-spin constants, this assignment was confirmed. An unusual relationship is reported for proton-carbon vicinal couplings: 3JCH (180°) < 3JCH (0°). The conformational mobility of carvacrols was studied by 2D EXSY spectra. The application of homonuclear decoupling technique (HOBS) to these spectra simplifies the spectra, improves resolution without reducing the sensitivity, and allows a systematic examination of the rotational barrier of all compounds via their CH signals of the isopropyl group in a wider temperature interval. The rate constants of the isopropyl rotation between syn and anti conformers were determined and the corresponding energy barriers (14-17 kcal/mol) were calculated. DFT calculations of the energy barriers in carvacrol derivatives allowed the determination of the steric origin of the restricted isopropyl rotation. The barrier height depends on the size of the 2- and 4-position substituents, and is independent of the derivatization of the OH group.

Investigating the diastereoselective synthesis of a macrocycle under Curtin-Hammett control

This work sheds new light on the stereoselective synthesis of chiral macrocycles containing twisted aromatic units, valuable π-conjugated materials for recognition, sensing, and optoelectronics. For the first time, we use the Curtin-Hammett principle to investigate a chiral macrocyclisation reaction, revealing the potential for supramolecular π-π interactions to direct the outcome of a dynamic kinetic resolution, favouring the opposite macrocyclic product to that expected under reversible, thermodynamically controlled conditions. Specifically, a dynamic, racemic perylene diimide dye (1 : 1 P : M) is strapped with an enantiopure (S)-1,1'-bi-2-naphthol group (P-BINOL) to form two diastereomeric macrocyclic products, the homochiral macrocycle (PP) and the heterochiral species (PM). We find there is notable selectivity for the PM macrocycle (dr = 4 : 1), which is rationalised by kinetic templation from intramolecular aromatic non-covalent interactions between the P-BINOL π-donor and the M-PDI π-acceptor during the macrocyclisation reaction.

Synthesis, structure and stereodynamics of atropisomeric N-chloroamides

Atropisomeric N-chloroamides were efficiently accessed by electrophilic halogenation of ortho-substituted secondary anilides. The stereodynamics of atropisomerism in these novel scaffolds was interrogated by detailed experimental and computational studies, revealing that racemization is correlated with amide isomerization. The stereoelectronic nature of the amide was shown to significantly influence racemization rates, with potentially important implications for other C-N atropisomeric scaffolds.

Deracemization of Atropisomeric Biaryls Enabled by Copper Catalysis

Atropisomeric biaryls have found crucial applications in versatile chiral catalysts as well as in ligands for transition metals. Herein, we have developed an efficient crystallization-induced deracemization (CID) method to access chiral biaryls from their racemates with a chiral ammonium salt under copper catalysis including BINOL, NOBIN, and BINAM derivatives. After being significantly accelerated by its bidentate diamine ligand, the copper catalyst exhibits high efficiency and selectivity in racemizing biaryl skeletons, and the cocrystal complex would be enantioselectively formed together with chiral ammonium salt, which on acid-quenching would directly deliver chiral biaryl without further chromatographic purification. This CID process is easily scalable, and the chiral ammonium salt was nicely recoverable. Ligand effect studies showed that bulky alkyl substitution was an indispensable element to ensure efficient racemization, which probably proceeds via a radical-cation intermediate and further allows axial rotation by forming a delocalized radical.

Identification of amentoflavone as a potent SARS-CoV-2 Mpro inhibitor: a combination of computational studies and in vitro biological evaluation

Small-molecule inhibitors of SARS-CoV-2 Mpro that block the active site pocket of the viral main protease have been considered potential therapeutics for the development of drugs against SARS-CoV-2. Here, we report the identification of amentoflavone (a biflavonoid) through docking-based virtual screening of a library comprised of 231 compounds consisting of flavonoids and isoflavonoids. The docking results were further substantiated through extensive analysis of the data obtained from all-atom 150 ns MD simulation. End-state effective free energy calculations using MM-PBSA calculations further suggested that (Ra)-amentoflavone (C3'-C8''-atropisomer) may show a greater binding affinity towards the Mpro than (Sa)-amentoflavone. In vitro cytotoxicity assay established that amentoflavone showed a high CC50 value indicating much lower toxicity. Further, potent inhibition of the Mpro by amentoflavone was established by studying the effect on HEK293T cells treated with SARS-CoV-2 Mpro expressing plasmid.Communicated by Ramaswamy H. Sarma.

First atroposelective Chan-Lam coupling for the synthesis of C-N linked biaryls

The first atroposelective Chan-Lam coupling for the synthesis of C-N axial enantiomers is reported with good yields and ee. MnO2 additive is crucial for the success of the coupling. The longstanding problem of the lack of enantioselective synthesis to make chiral C-N linked atropisomers is solved.

Rhodium(I)-Catalyzed Asymmetric Hydroarylative Cyclization of 1,6-Diynes to Access Atropisomerically Labile Chiral Dienes

Axially chiral open-chained olefins are an underexplored class of atropisomers, whose enantioselective synthesis represents a daunting challenge due to their relatively low racemization barrier. We herein report rhodium(I)-catalyzed hydroarylative cyclization of 1,6-diynes with three distinct classes of arenes, enabling highly enantioselective synthesis of a broad range of axially chiral 1,3-dienes that are conformationally labile (ΔG≠ (rac)=26.6-28.0 kcal/mol). The coupling reactions in each category proceeded with excellent enantioselectivity, regioselectivity, and Z/E selectivity under mild reaction conditions. Computational studies of the coupling of quinoline N-oxide system reveal that the reaction proceeds via initial oxidative cyclization of the 1,6-diyne to give a rhodacyclic intermediate, followed by σ-bond metathesis between the arene C-H bond and the Rh-C(vinyl) bond, with subsequent C-C reductive elimination being enantio-determining and turnover-limiting. The DFT-established mechanism is consistent with the experimental studies. The coupled products of quinoline N-oxides undergo facile visible light-induced intramolecular oxygen-atom transfer, affording chiral epoxides with complete axial-to-central chirality transfer.