Stereochemical Aspects Research Articles

Unraveling Stereochemical Structure-Activity Relationships of Sesquiterpene Lactones for Inhibitory Effects on STAT3 Activation.

Sesquiterpene lactones, a class of natural compounds abundant in the Asteraceae family, have gained attention owing to their diverse biological activities, and particularly their anti-proliferative effects on human cancer cells. In this study, we systematically investigated the structure-activity relationship of ten sesquiterpene lactones with the aim of elucidating the structural determinants for the STAT3 inhibition governing their anti-proliferative effects. Our findings revealed a significant correlation between the STAT3 inhibitory activity and the anti-proliferative effects of sesquiterpene lactones in MDA-MB-231 breast cancer cell lines. Among the compounds tested, alantolactone and isoalantolactone emerged as the most potent STAT3 inhibitors, highlighting their potential as candidates for anticancer drug development. Through protein-ligand docking studies, we revealed the structural basis of STAT3 inhibition by sesquiterpene lactones, emphasizing the critical role of hydrogen-bonding interactions with key residues, including Arg609, Ser611, Glu612, and Ser613, in the SH2 domain of STAT3. Furthermore, our conformational analysis revealed the decisive role of the torsion angle within the geometry-optimized structures of sesquiterpene lactones in their STAT3 inhibitory activity (R=0.80, p<0.01). These findings not only provide preclinical evidence for sesquiterpene lactones as promising phytomedicines against diseases associated with abnormal STAT3 activation, but also highlight the importance of stereochemical aspects in their activity.

N-Benzyl piperidine Fragment in Drug Discovery.

The N-benzyl piperidine (N-BP) structural motif is commonly employed in drug discovery due to its structural flexibility and three-dimensional nature. Medicinal chemists frequently utilize the N-BP motif as a versatile tool to fine-tune both efficacy and physicochemical properties in drug development. It provides crucial cation-π interactions with the target protein and also serves as a platform for optimizing stereochemical aspects of potency and toxicity. This motif is found in numerous approved drugs and clinical/preclinical candidates. This review focuses on the applications of the N-BP motif in drug discovery campaigns, emphasizing its role in imparting medicinally relevant properties. The review also provides an overview of approved drugs, the clinical and preclinical pipeline, and discusses its utility for specific therapeutic targets and indications, along with potential challenges.

Fagopyrins from Buckwheat Flowers: Structural and Stereochemical Characterization Through Combined NMR/CD Spectroscopy and Theoretical Calculations.

Fagopyrins are phenantroperylenequinones present in the flowers of Fagopyrum esculentum (buckwheat) endowed with photodynamic activity. It has been reported that fagopyrin extracts actually contain a complex mixture of closely related compounds, differing only on the nature of the perylenequinone substituents. We report our systematic and detailed study on the chemical composition of fagopyrin extracts by a combination of preparative and analytical techniques. The combined use of 1H-NMR and CD spectroscopy was found to be particularly suited to fully characterize all stereochemical aspects of the extracted fagopyrins. For the first time nine isomers have been structurally characterized and their stereochemistry fully elucidated. The presence of two different heterocyclic ring substituents, two stereogenic centers and the inherent axial chirality of the aromatic system provides a complex stereochemical relationships among isomers, thus giving account of the high level of molecular multiplicity found in the extract.

Stereochemical Aspects of the C-Glycosylation of Pyranosides and Furanosides

AbstractThe stereoselective synthesis of α- and β-C-glycosides is one of the most challenging areas of research in the field of glycoside chemistry. In this review, we summarize the various methods available for stereocontrolled glycosylation and also discuss the predictive models available to explain the stereochemical outcome of six- and five-membered-ring oxocarbenium ions with allyltrimethylsilane nucleophile under Lewis acid conditions.1 Introduction2 Stereochemical Aspects during Glycoside Bond Formation in Pyranosides2.1 Lewis Acid Mediated Nucleophilic Addition to Six-Membered-Ring Oxocarbenium Ions2.2 Arylalane Addition to Anhydroglucose2.3 Glucal Epoxide Method2.4 Glycosyl Leaving Group Substitution Method2.5 Glycosylation via Transition-Metal-Mediated Cross-Coupling3 Stereochemical Aspects during Glycoside Bond Formation in Furanosides­3.1 Lewis Acid Mediated Nucleophilic Addition to Five-Membered-Ring Oxocarbenium Ions4 Summary and Conclusion

Natural-Product-Inspired Discovery of Trimethoxyphenyl-1,2,4-triazolosulfonamides as Potent Tubulin Polymerization Inhibitors.

An approach of natural product-inspired strategy and incorporation of an NP-privileged motif has been investigated for the discovery of new tubulin polymerization inhibitors. Two series, N-Arylsulfonyl-3-arylamino-5-amino-1,2,4-triazole derivatives, and their isomers were considered. The compounds were synthesized by construction of the N-aryl-1,2,4-triazole-3,5-diamine motif and sulfonylation. Although the chemo- and regioselectivity in sulfonylation were challenging due to multiple ring-tautomerizable-NH and exocyclic NH2 functionalities present in the molecular motifs, the developed synthetic method enabled the preparation of designed molecular skeletons with biologically important motifs. The approach also led to explore interesting molecular regio- and stereochemical aspects valuable for activity. The X-ray crystallography study indicated that the hydrogen bonding between the arylamine-NH and the arylsulfonyl-"O" unit and appropriate molecular-functionality topology allowed the cis-locking of two aryls, which is important for tubulin-binding and antiproliferative properties. All synthesized compounds majorly showed characteristic antiproliferative effects in breast cancer cells (MCF-7), and four compounds exhibited potent antiproliferative activity. One compound potently bound to tubulin at the colchicine site and inhibited tubulin polymerization in vitro. The compound significantly depolymerized microtubules in MCF-7 cells, arrested the cells at the G2/M phase, and induced cell death. This study represents the importance of the design strategy in medicinal chemistry and the molecular structural features relevant to anticancer anti-tubulin properties. The explored molecules have the potential for further development.

A time trend of urinary 4-methylbenzylidene camphor metabolites in young adults from Germany

4-methylbenzylidene camphor (4-MBC) is used as a UV-B filter in cosmetics. Two oxidized metabolites of 4-MBC – 3-(4-carboxybenzylidene)camphor (cx-MBC) and 3-(4-carboxybenzylidene)-6-hydroxycamphor (cx-MBC-OH) – were analyzed in 250 24-h urine samples from young adults in Germany. The samples were from the German Environmental Specimen Bank (ESB) and represented exposure in the years 1995, 2005, 2010, 2015 and 2019.A UHPLC-MS/MS method enabled the sensitive determination of both metabolites, with limits of quantification at 0.15 μg L−1 (cx-MBC) and 0.30 μg L−1 (cx-MBC-OH), respectively. A temporal trend of the internal exposure to 4-MBC was clearly noticeable. The metabolite cx-MBC was frequently quantifiable at the beginning of the period: in 70% of the samples in 1995, and 56% in 2005. After 2005, urinary concentrations and detection rates of cx-MBC dropped to reach very low levels. In 2015 and 2019, the detection rate was only 2% and 0%, respectively. A similar trend was observed for cx-MBC-OH, though overall, this metabolite was detected less often and at lower concentration levels than cx-MBC. Nowadays, measurable levels of urinary 4-MBC metabolites are an extremely rare occurrence in Germany. These trends are consistent with the history of 4-MBC use by the cosmetic industry. The highest measured individual concentration of 16.20 μg L−1 (in a sample of the year 2005) was still more than 30 times below the health-based guidance value (HBM-I).An investigation of the ratios between both metabolites uncovered several features of the 4-MBC metabolism which have been essentially overlooked until now. In particular, stereochemical aspects should be explored in future studies.As urine was collected in autumn/winter in Northwestern Germany, the 4-MBC metabolites measured probably do not arise from sunscreen products in a narrow sense. They rather may reveal the use of other skin care products containing 4-MBC for UV protection as an added feature.

DFT Studies on the Molecular Structure, Regioisomerism, Ground and Excited state Charge Transfer Properties of Spiro‐heterocycles

AbstractThe electronic structure, stereochemical aspects and charge transfer properties of the spiro compound (5S,8S) spiro‐{6‐phenyl‐1‐aza‐3‐oxa‐7‐thia‐bicyclo[3,3,0]‐octene‐8,3’(2’H)‐indol}‐2’‐one (spiro bicyclo adduct) synthesized using the multi‐component reaction via 1,3‐dipolar cycloaddition of isatin and thioproline with the dipolarophile phenylacetylene have been studied. The two lowest energy regio‐isomers of the spiro heterocycle formed from the stereospecific dipolar reaction have been analysed along with the electron‐withdrawing and releasing substituents using DFT method at the CAM‐B3LYP/6‐311++G(d,p) level of theory. The atomic charges and the stabilization energy due to the intramolecular charge delocalization process calculated using the natural orbitals at the different molecular sites reveal the different donor‐acceptor interactions occurring in the system. The intramolecular electronic transitions (specifically n to π* and π to π*) is found to occur from the localized donor end component to the acceptor end components in the multi‐component system. The hole produced by the ionization of the entities is found to migrate from the thioproline component to the phenyl acetylene part in a time scale of around 4 fs. The electron‐withdrawing and donating substituents on the spirobicyclo adduct have been proven to tune the excited and ground state charge transfer properties uniquely. The results can shed light on how multi‐component reactions can be directed to produce spiro adducts with versatile applications.

Polymyxin Stereochemistry and Its Role in Antibacterial Activity and Outer Membrane Disruption.

With increasing rates of resistance toward commonly used antibiotics, especially among Gram-negative bacteria, there is renewed interested in polymyxins. Polymyxins are lipopeptide antibiotics with potent anti-Gram-negative activity and are generally believed to target lipid A, the lipopolysaccharide (LPS) anchor found in the outer membrane of Gram-negative bacteria. To characterize the stereochemical aspects of their mechanism(s) of action, we synthesized the full enantiomers of polymyxin B and the polymyxin B nonapeptide (PMBN). Both compounds were compared with the natural compounds in biological and biophysical assays, revealing strongly reduced antibacterial activity for the enantiomeric species. The enantiomeric compounds also exhibit reduced LPS binding, lower outer membrane (OM) permeabilization, and loss of synergetic potential. These findings provide new insights into the stereochemical requirements underlying the mechanisms of action of polymyxin B and PMBN.

Antiproliferative Activity of (-)-Isopulegol-based 1,3-Oxazine, 1,3-Thiazine and 2,4-Diaminopyrimidine Derivatives.

A series of novel heterocyclic structures, namely 1,3‐oxazines, 1,3‐thiazines and 2,4‐diaminopyrimidines, were designed and synthesised. The bioassay tests demonstrated that, among these analogues, 2,4‐diaminopyridine derivatives showed significant antiproliferative activity against different human cancer cell lines (A2780, SiHa, HeLa, MCF‐7 and MDA‐MB‐231). Pyrimidines substituted with N 2‐(p‐trifluoromethyl)aniline, in particular, displayed a potent inhibitory effect on the growth of cancer cells. Structure–activity relationships were also studied from the aspects of stereochemistry on the aminodiol moiety as well as exploring the effects of substituents on the pyrimidine scaffold.

Regio- and Diastereoselective Carbometalation Reaction of Cyclopropenes.

ConspectusThe various facets of the chemistry of cyclopropane derivatives, the smallest carbocycle, are amazingly diverse and continue to fascinate theoreticians, synthetic or structural chemists having interest in fundamental physical, medicinal chemistry, and natural product synthesis. The challenges generated by this intriguing cyclic arrangement of only three tetravalent carbons represent a wide area of the chemical spectrum. From fundamental aspects of bonding through the synthesis of highly strained molecules, the understanding of the mode of action in biological systems to the selective cleavage into acyclic substrates makes the chemistry of these small rings fascinating. Therefore, efficient routes to prepare differently polysubstituted cyclopropanes have always been of a primordial importance. In the past decade, we and others have expanded the scope of the carbometalation reaction of cyclopropenes as a broad and general method to the formation of stereodefined cyclopropane derivatives. Although cyclopropenes, with their even higher strain energy, easily undergo addition reactions of organometallic reagents, their carbometalation reactions generate new regio-, diastereo-, and enantioselectivity issues that needed to be addressed. These various stereochemical aspects accompanied our research from its origins to today, and we are proposing in this Account, a didactic overview of the different ways by which cyclopropenes can lead to the formation of polysubstituted cyclopropanes or open-products possessing several stereogenic centers as a single regio- and diastereomer.We initially launched our research campaign on the chemistry of these strained three-membered rings by the regio- and diastereoselective copper-catalyzed carbomagnesiation of enantiomerically enriched cyclopropenyl carbinols. The directing alcohol governed both the regio- and diastereoselectivity of the addition and also served as a good leaving group as it undergoes a selective 1,2-elimination reaction to provide enantioenriched alkylidenecyclopropanes in excellent yields and enantiomeric excesses. Then, we turned our attention to the regio- and stereoselective synthesis of stereodefined tri- and tetrasubstituted cyclopropanes through the diastereoselective addition to sp2- monosubstituted cyclopropenyl ester derivatives. With the aim to further expand this concept to the formation of penta- and hexa-substituted cyclopropanes as single isomer, we had first to design the preparation of the required 1,2-disubstituted cyclopropenes that would control the regioselective addition of the organometallic derivatives. The synthesis of penta- and hexa-substituted cyclopropanes was then reported for the first time as a single regio- and diastereomer. It should be noted that the in situ formed cyclopropyl-metal intermediate is configurationally stable and can be subsequently functionalized with pure retention of the configuration by addition of electrophiles. Then, the enantioselective-catalyzed carbometalation reaction of achiral cyclopropenes allowed the synthesis of several new classes of cyclopropane derivatives in high enantiomeric ratios. Finally, by combining the regio- and diastereoselective carbometalation reaction of a cyclopropene with a subsequent reaction of the resulting cyclopropylmetal species, a selective carbon–carbon bond cleavage was observed to lead to the preparation of acyclic substrates possessing several stereocenters including a quaternary carbon stereogenic center. Our original vision of using strain within an embedded double bond in a three-membered ring has provided new routes to the stereoselective synthesis of polysubstituted cyclopropanes and has been extremely successful, as it represents a current new tool for the synthesis of persubstituted cyclopropanes as a single diastereomer.

Switching on Cytotoxicity of Water-Soluble Diiron Organometallics by UV Irradiation.

The diiron compounds [Fe2Cp2(CO)2(μ-CO)(μ-CSEt)]CF3SO3, [1]CF3SO3, K[Fe2Cp2(CO)3(CNCH2CO2)], K[2], [Fe2Cp2(CO)2(μ-CO)(μ-CNMe2)]NO3, [3]NO3, [Fe2Cp2(CO)2(PTA){μ-CNMe(Xyl)}]CF3SO3, [4]CF3SO3, and [Fe2Cp2(CO)(μ-CO){μ-η:1η3-C(4-C6H4CO2H)CHCNMe2}]CF3SO3, [5]CF3SO3, containing a bridging carbyne, isocyanoacetate, or vinyliminium ligand, were investigated for their photoinduced cytotoxicity. Specifically, the novel water-soluble compounds K[2], [3]NO3, and [4]CF3SO3 were synthesized and characterized by elemental analysis and IR and multinuclear NMR spectroscopy. Stereochemical aspects concerning [4]CF3SO3 were elucidated by 1H NOESY NMR and single-crystal X-ray diffraction. Cell proliferation studies on human skin cancer (A431) and nontumoral embryonic kidney (HEK293) cells, with and without a 10-min exposure to low-power UV light (350 nm), highlighted the performance of the aminocarbyne [3]NO3, nicknamed NIRAC (Nitrate-Iron-Aminocarbyne), which is substantially nontoxic in the dark but shows a marked photoinduced cytotoxicity. Spectroscopic (IR, UV-vis, NMR) measurements and the myoglobin assay indicated that the release of one carbon monoxide ligand represents the first step of the photoactivation process of NIRAC, followed by an extensive disassembly of the organometallic scaffold.

Catalytic reductive ring opening of epoxides enabled by zirconocene and photoredox catalysis

Catalytic reductive ring opening of epoxides enabled by zirconocene and photoredox catalysis

Allosteric modulation of dopamine D2L receptor in complex with Gi1 and Gi2 proteins: the effect of subtle structural and stereochemical ligand modifications

BackgroundAllosteric modulation of G protein-coupled receptors (GPCRs) is nowadays one of the hot topics in drug discovery. In particular, allosteric modulators of D2 receptor have been proposed as potential modern therapeutics to treat schizophrenia and Parkinson’s disease.MethodsTo address some subtle structural and stereochemical aspects of allosteric modulation of D2 receptor, we performed extensive in silico studies of both enantiomers of two compounds (compound 1 and compound 2), and one of them (compound 2) was synthesized as a racemate in-house and studied in vitro.ResultsOur molecular dynamics simulations confirmed literature reports that the R enantiomer of compound 1 is a positive allosteric modulator of the D2L receptor, while its S enantiomer is a negative allosteric modulator. Moreover, based on the principal component analysis (PCA), we hypothesized that both enantiomers of compound 2 behave as silent allosteric modulators, in line with our in vitro studies. PCA calculations suggest that the most pronounced modulator-induced receptor rearrangements occur at the transmembrane helix 7 (TM7). In particular, TM7 bending at the conserved P7.50 and G7.42 was observed. The latter resides next to the Y7.43, which is a significant part of the orthosteric binding site. Moreover, the W7.40 conformation seems to be affected by the presence of the positive allosteric modulator.ConclusionsOur work reveals that allosteric modulation of the D2L receptor can be affected by subtle ligand modifications. A change in configuration of a chiral carbon and/or minor structural modulator modifications are solely responsible for the functional outcome of the allosteric modulator.Graphical abstract

On the Question of Stepwise [4+2] Cycloaddition Reactions and Their Stereochemical Aspects

Even at the end of the twentieth century, the view of the one-step [4+2] cycloaddition (Diels-Alder) reaction mechanism was widely accepted as the only possible one, regardless of the nature of the reaction components. Much has changed in the way these reactions are perceived since then. In particular, multi-step mechanisms with zwitterionic or diradical intermediates have been proposed for a number of processes. This review provided a critical analysis of such cases.

Transition‐Metal‐Free Synthesis of 1‐Indanone Skeleton: A Brief Update

AbstractTransition‐metal‐free carbon‐carbon bond forming reactions have drawn great interest because they are operationally simple, cost‐effective and environmentally benign. However, the construction of indanone core under metal‐free condition has been long‐standing challenges to organic chemists. In this article, recent advances (2015–2021) in transition‐metal‐free strategies towards 1‐indanone skeletons are reviewed and they are classified as acid‐catalyzed, base‐catalyzed, organocatalytic and catalyst‐free methods. In most cases, mechanisms for the transformations and stereochemical aspects of the product formation have been demonstrated.

A comprehensive review of chemistry and pharmacological aspects of natural cyanobacterial azoline-based circular and linear oligopeptides

The cyanobacterial oligopeptides are recognized for being highly selective, efficacious and relatively safer compounds with diverse bioactivities. Azoline-based natural compounds consist of heterocycles which are reduced analogues of five-membered heterocyclic azoles. Among other varieties of azoline-based natural compounds, the heteropeptides bearing oxazoline or thiazoline heterocycles possess intrinsic structural properties with captivating pharmacological profiles, representing excellent templates for the design of novel therapeutics. The specificity of heteropeptides has been translated into prominent safety, tolerability, and efficacy profiles in humans. These peptidic congeners serve as ideal intermediary between small molecules and biopharmaceuticals based on their typically low production complexity compared to the protein-based biopharmaceuticals. The distinct bioproperties and unique structures render these heteropeptides one of the most promising lead compounds for drug discovery. The high degree of chemical diversity in cyanobacterial secondary metabolites may constitute a prolific source of new entities leading to the development of new pharmaceuticals. This review focuses on the azoline-based natural oligopeptides with emphasis on distinctive structural features, stereochemical aspects, biological activities, structure activity relationship, synthetic and biosynthetic aspects as well as mode of action of cyanobacteria-derived peptides.

Photoredox Reaction of Naphthoquinone C‐Glycoside Revisited: Insight into Stereochemical Aspect

AbstractInsights into the naphthoquinone photoredox reactions have been gained from the reactions of a C‐glycosyl naphthoquinone. The retentiveness comes from the balance of the lifetime of intermediary zwitterionic species relative to the conformational change to bring about the stereo‐mutating C−C bond rotation.

Stereochemical aspects in the synthesis of novel N-(purin-6-yl)dipeptides as potential antimycobacterial agents.

The synthesis of purine conjugates with natural amino acids is one of the promising directions in search for novel therapeutic agents, including antimycobacterial agents. The purpose of this study was to synthesize N-(purin-6-yl)dipeptides containing the terminal fragment of (S)-glutamic acid. To obtain the target compounds, two synthetic routes were tested. The first of them is based on coupling of N-(purin-6-yl)-(S)-amino acids to dimethyl (S)-glutamate in the presence of carbodiimide coupling agent followed by the removal of ester groups. However, it turned out that this coupling process was accompanied by racemization of the chiral center of N-(purin-6-yl)-α-amino acids and in all cases led to mixtures of (S,S)- and (R,S)-diastereomers (6:4). Individual (S,S)-diastereomers were obtained using an alternative approach based on the nucleophilic substitution of chlorine in 6-chloropurine or 2-amino-6-chloropurine with corresponding dipeptides as nucleophiles. The enantiomeric purity of the target compounds was confirmed by chiral HPLC. To test the assumption that racemization of the chiral center of N-(purin-6-yl)-α-amino acids occurs with the participation of nitrogen atoms of the imidazole ring via the stage of formation of a chirally labile intermediate, we obtained such structural analogs of N-(purin-6-yl)-(S)-alanine as N-(9-benzylpurin-6-yl)-(S)-alanine and N-(7-deazapurin-6-yl)-(S)-alanine. It was found that coupling of these compounds to dimethyl (S)-glutamate was also accompanied by racemization. This indicates that the imidazole fragment does not play a crucial role in this process. When testing the antimycobacterial activity of some of the obtained compounds, conjugates with moderate activity against the laboratory Mycobacterium tuberculosis H37Rv strain (MIC 3.1–6.25 μg/mL) were identified.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00726-021-02958-0.

Mechanisms of Chiral Transfer in Optically Active Dopant – Nematic Liquid Crystal Systems

Induction of helical mesophases by incorporating chiral dopants into the nematics matrix is the promising modern trends in the chemistry of liquid crystals. This process is associated with a unique phenomenon - an amplification of chirality in liquid-crystalline phases, which ensures the detection of enantiomers by their chiral induction, much more sensitive than other methods. The relevance of this approach is due to the need to create perspective electro-optical devices operating with ultra-low control voltages based on twist effects, chromatographic stationary phases with high chiral selectivity, flexible magnets, photo-sensitive nanostructures, and other smart LC materials. The successful solution of these problems is impossible without experimental research and theoretical comprehension of the mechanisms of third level chiral transfer optically active dopant – nematic liquid crystal. In the last decade, a large number of works have appeared on the solution of these problems. This review is devoted to a generalization of the experimental results and a theoretical description of the transfer of molecular chirality to orientationally ordered systems with the participation of both chiral molecular substituents with an asymmetric carbon atom and planar or quasi-planar fragments chirally distorted relative to each other. The stereochemical aspects of induction associated with the structural correspondences of the dopant and nematic liquid crystal, as well as the main classes of optically active additives, are discussed. Application of metal complexes, both Werner and macroheterocyclic, are presented. Special attention is paid to the results of the mechanisms study of chiral transfer due to various intermolecular interactions: hydrogen bonding, axial coordination, and the formation of inclusion compounds. The high efficiency of induction of spiral mesophases has been demonstrated with a combination of different self-assembly mechanisms in liquid crystal - chiral additive systems.

Molecular docking and dynamics simulation study of telomerase inhibitors as potential anti-cancer agents

Normal cells’ genomic identity is protected by telomeres and sometimes chromosomal instability was observed due to shortening of telomerase because of successive cell divisions. Reports indicate that telomerase length is crucial in determining telomerase activity which in turn leads to cancer initiation. It is reported that telomere length regulation has been identified as a plausible strategy for cancer diagnostics and treatment. In the present MS, we explored the telomerase inhibitory activity of catechin analogues and it’s oligomers using computational methods. The structural properties of different ligands discussed in the MS were computed using density functional theory. Conformational effect of different chromene subunit such as 2R, 3R conformations were explored using computational methods. The stereochemical contributions to receptor binding such as intra ligand π-interactions of these ligands were also investigated. We herein propose that these stereochemical aspects of catechins and their oligomers as the most vital factor deciding the effective binding with the N-terminal domain of telomerase which is an efficient strategy in cancer therapy.