Organic Stereochemistry. Part 8

This review terminates our general presentation of the principles of stereochemistry with special reference to the biomedicinal sciences. Here, we discuss and illustrate the principles of prostereoisomerism, and apply these to product and substrate? product stereoselectivity in drug metabolism. The review begins with an overview of the concept of prostereoisomerism, discussing such aspects as homotopic, enantiotopic, and diastereotopic groups and faces. The main part of this review is dedicated to drug and xenobiotic metabolism. Here, the concept of prostereoisomerism proves particularly helpful to avoid confusing metabolic reactions in which an existing stereogenic element (e.g., a stereogenic center) influences the course of the reaction (substrate stereoselectivity), with metabolic reactions which create a stereogenic element (almost always a stereogenic center; product stereoselectivity). Specifically, examples of product stereoselectivity will be taken from functionalization reactions (so‐called phase‐I reactions) and conjugation (so‐called phase‐II reactions). Cases where stereoisomeric substrates show distinct product stereoselectivities (substrate? product stereoselectivity) will also be presented.     

Organic Stereochemistry. Part 5

This review continues a general presentation of the principles of stereochemistry with special reference to the medicinal sciences. Here, we discuss and illustrate molecular and clinical phenomena of stereoselectivity in pharmacological effects, namely activity differences between stereoisomers, principally enantiomers. The review begins with didactic models of chiral recognition, with a main focus on the early model of Easson and Stedman. There follows a Molecular Modeling (MM) and Molecular Dynamics (MD) depiction of the differential interaction of the enantiomers of hyoscyamine with cholinergic muscarinic receptors. The next section is devoted to various rationalizations in stereoselective pharmacological activity, e.g., the influence of optical purity on enantioselectivity, Pfeiffer's rule, and eudismic analysis. The review ends with selected examples taken from various fields of preclinical and clinical pharmacology, of differences between stereoisomers in terms of drug absorption, distribution, and excretion. The influence of conformational factor in molecular pharmacology will be discussed in Part 6, while stereoselective aspects of xenobiotic metabolism will be reviewed in Parts 7 and 8.     

StereoPHIP: Stereoselective Parahydrogen-Induced Polarization

Parahydrogen-induced polarization (PHIP) followed by polarization transfer to ¹³C is a rapidly developing technique for the generation of ¹³C-hyperpolarized substrates. Chirality plays an essential role in living systems and differential metabolism of enantiomeric pairs of metabolic substrates is well documented. Inspired by asymmetric hydrogenation, here we report stereoPHIP, which involves the addition of parahydrogen to a prochiral substrate with a chiral catalyst followed by polarization transfer to ¹³C spins. We demonstrate that parahydrogen could be rapidly added to the prochiral precursor to both enantiomers of lactic acid (D and L), with both the (R,R) and (S,S) enantiomers of a chiral rhodium(I) catalyst to afford highly ¹³C-hyperpolarized (over 20 %) L- and D-lactate ester derivatives, respectively, with excellent stereoselectivity. We also show that the hyperpolarized ¹H signal decays obtained with the (R,R) and (S,S) catalysts were markedly different. StereoPHIP expands the scope of conventional PHIP to the production of ¹³C hyperpolarized chiral substrates with high stereoselectivity.     

Total Synthesis of (18S)‐ and (18R)‐Homolargazole by Rhodium‐Catalyzed Hydrocarboxylation

Homolargazole derivatives, in which the macrocycle of natural largazole is extended by one methylene group, were prepared by the recently developed rhodium‐catalyzed hydrocarboxylation reaction onto allenes. This strategy gives access to both the (18S)‐ and (18R)‐stereoisomers in high stereoselectivity under ligand control.     

Graphs to chemical structures 3. General theorems with the use of different sets of sphericity indices for combinatorial enumeration of nonrigid stereoisomers

The extended sphericity indices of k-cycles, which were defined in Part 2 of this series (S. Fujita, Theor Chem Acc, Online: http://www.springerlink.com/index/10.1007/s00214-004-0606-z) according to the enantiospheric, homospheric, or hemispheric nature of each k-cycle, are further extended to prove more general theorems for enumerating nonrigid stereoisomers with rotatable ligands. One of the extended points is the use of different sets of sphericity indices to treat one or more orbits contained in skeletons and ligands. Another is to take account of chirality in proligands and sub-proligands, the latter of which are introduced to consider further inner structures of ligands. Two theorems for enumerating nonrigid stereoisomers are proved by adopting two schemes of their derivation, i.e., the scheme ``positions of a skeleton ⇐ proligands ⇐ ligands (positions of a ligand ⇐ sub-proligands)' and the scheme ``(positions of a skeleton ⇐ proligands ⇐ ligands (positions of a ligand)) ⇐ sub-proligands'. The theorems are applied to the stereoisomerism of trihydroxyglutaric acids. Thereby, it is demonstrated where Pólya's theorem and other previous methods are deficient, when applied to the enumeration of stereoisomers.     

Organic Stereochemistry. Part 4

This Part 4 continues a general presentation of the principles of stereochemistry with special reference to medicinal compounds and their interactions with biological systems. Here, we discuss and illustrate two major aspects of conformational isomerism, namely a) the concept of torsional isomerism about single bonds, and b) the intertwined conformational and configurational aspects of the stereochemistry of cyclic systems. The review begins with a brief reminder of the history and thermodynamics of conformational isomerism, and goes on to explain and illustrate the conventions and graphical representations used for conformers. Examples are then examined, beginning with ethane, the simplest one, and building up to more complex cases, documenting the attractive or repulsive role of substituents. A similar approach is applied when dealing with cyclic systems, although here the presentation necessarily takes into account configurational aspects specific to cyclic systems. The pharmacological implications of the concepts discussed here will be presented in Part 6.     

Pheromone synthesis: Part CVII? - synthesis of 2,6-dimethyloctyl formate, a potent mimic of the aggregation pheromone of the flour beetles

A mixture of the four stereoisomers of 2.6-dimethyloctyl formate was synthesized, and found to be a potent mimic of (4R,8R)-4,8-dimethyldecanal, the aggregation pheromone of the flour beetles,Tribolium castaneum andTribolium confusum. For Part CVI, see Mori K and Puapoomchareon P 1988Liebigs Ann. Chem. 175     

Improving the Cβ Stereoselectivity of l-Threonine Aldolase for the Synthesis of l-threo-4-Methylsulfonylphenylserine by Modulating the Substrate-Binding Pocket To Control the Orientation of the Substrate Entrance

l -Threonine aldolase from Actinocorallia herbida (AhLTA) is an ideal catalyst for producing l -threo-4-methylsulfonylphenylserine [(2S,3R)- 1 b ], a key chiral precursor for florfenicol and thiamphenicol. The moderate C_β stereoselectivity is the main obstacle to the industrial application of AhLTA. To address this issue, a combinatorial active-site saturation test (CAST) together with sequence conservatism analysis was applied to engineer the AhLTA toward improved C_β stereoselectivity. The optical mutant Y314R could asymmetrically synthesize l -threo-4-methylsulfonylphenylserine with 81 % diastereomeric excess (de), which is 23 % higher than wild-type AhLTA. Molecular dynamic (MD) simulations revealed that the mechanism for the improvement in C_β stereoselectivity of Y314R is due to the acylamino group of residues Arg314 controlling the orientation of substrate 4-methylsulfonyl benzaldehyde ( 1 a ) in the active pocket by directed interaction with the methylsulfonyl group; this leads to asymmetric synthesis of l -threo-4-methylsulfonylphenylserine. The success in this study demonstrates that direct control of substrates in an active pocket is an attract strategy to address the C_β stereoselectivity problem of LTA and contribute to the industrial application of LTA.     

Studies of a proposed mechanism for the reaction between 2H-pyran-2-ones and organomagnesium compounds

Part of the reaction between 2H-pyran-2-ones and organomagnesium compounds has been investigated by means of MNDO and ab initio calculations. Criteria for the mechanism of reaction are provided by the stereoselectivity observed and calculations are consistent with this stereoselectivity. Conformations of the reaction intermediates are given.     

Organic Stereochemistry. Part 6

Following the previous Part on the mechanisms of chiral recognition in pharmacology, the road was open to cover one aspect of stereoselectivity that had been evoked in Part 5 but not discussed explicitly, namely the pharmacological significance of the conformational behavior of active molecules. There, we saw how ligands and binding sites adapt to each other, but these results were not related explicitly to the conformational behavior of the ligand. The focus of the present Part is to use a few well‐known drugs, examine their conformational behavior, compare the 3D geometry of probable conformers with rigid analogs acting at the same receptor, and reflect on the concept of ‘active conformation’.     

Cyclopropenes and methylenecyclopropanes in 1,3-dipolar cycloaddition reactions

The review considers the main results of the cycloaddition reactions involving cyclopropenes and methylenecyclopropanes, the compounds bearing strained three-membered rings and, respectively, endo- and exocyclic double bonds. The main attention is focused on the reactions of these compounds with 1,3-dipoles (nitrones, azomethine imines, azomethine ylides, carbonyl ylides, etc.), which gave complex heterocyclic systems with high regio- and stereoselectivity.

     

Stereoselective Chiral Molecular Carbon Imides Featuring 12-Fold [5]helicenes Around Four Cores**

Despite the great progress in research on molecular carbons containing multiple helicenes around one core, realizing the stereoselectivity of carbons containing multiple helicenes around more cores is still a great challenge. Herein, molecular carbon C₂₀₄ featuring 12-fold [5]helicenes around four cores was successfully constructed by using nine perylene diimide (PDI) units, and exhibits good solubility and stability. Despite 256 possible stereoisomers caused by the 12-fold [5]helicenes, we only obtained one pair of enantiomers with D₃ symmetry. There are four possible pairs of enantiomers with D₃ symmetry, namely 7A, 7B, 7C and 7D. Theoretical and experimental results verify that the obtained structure belongs to 7C, which has the lowest energy. The enantiomers can also be separated by chiral HPLC. These results suggest that choosing PDIs as building blocks can not only improve the solubility and stability but also realize the stereoselectivity and chirality of molecular carbons.     

Substrate‐Dependent Stereospecificity of Tyl‐KR1: An Isolated Polyketide Synthase Ketoreductase Domain from Streptomyces fradiae

The stereospecificity of an enzymatic reaction depends on the way in which a substrate and its enantiomer bind to the active site. These binding modes cannot be easily predicted. We have studied the stereospecificity and stereoselectivity of the ketoreductase domain Tyl‐KR1 of the tylactone polyketide synthase from Streptomyces fradiae by analysing the stereochemical outcome of the reduction of five different keto ester substrates. The absolute configuration of the Tyl‐KR1 reduction products was determined by using vibrational circular dichroism (VCD) spectroscopy combined with quantum chemical calculations. The conversion of only one of the tested substrates, 2‐methyl‐3‐oxovaleric acid N‐acetylcysteamine thioester, afforded the expected anti‐(2R,3R) configuration of the α‐methyl‐β‐hydroxyl ester product, representing the stereochemistry observed for the physiological polyketide product tylactone. For all other substrates, which were modified with respect to the type of ester and/or the chain length (C₄ instead of C₅), the opposite configuration (anti‐(2S,3S)) was obtained with significant enantio‐ and diastereoselectivity. Inversion of both stereocentres suggests completely different binding modes invoked by only minor modifications of the substrate structure.     

Inside Cover: Structural and Mechanistic Studies on Substrate and Stereoselectivity of the Indole Monooxygenase VpIndA1: New Avenues for Biocatalytic Epoxidations and Sulfoxidations (Angew. Chem. Int. Ed. 17/2023)

Flavoprotein monooxygenases are a versatile group of enzymes for biocatalytic transformations. Among these, group E monooxygenases (GEMs) catalyze enantioselective epoxidation and sulfoxidation reactions. Here, we describe the crystal structure of an indole monooxygenase from the bacterium Variovorax paradoxus EPS, a GEM designated as VpIndA1. Complex structures with substrates reveal productive binding modes that, in conjunction with force-field calculations and rapid mixing kinetics, reveal the structural basis of substrate and stereoselectivity. Structure-based redesign of the substrate cavity yielded variants with new substrate selectivity (for sulfoxidation of benzyl phenyl sulfide) or with greatly enhanced stereoselectivity (from 35.1 % to 99.8 % ee for production of (1S,2R)-indene oxide). This first determination of the substrate binding mode of GEMs combined with structure-function relationships opens the door for structure-based design of these powerful biocatalysts.     

Antibacterial effect of butyryl alkannin from Arnebia euchroma against vancomycin-resistant pathogens of Enterococcus faecalis causing urinary tract infections

This study was carried out to investigate the biomedicinal potential of a bioactive marker component, butyryl alkannin, isolated from n-hexane root extract of Arnebia euchroma against various vancomycin-resistant Enterococcus (VRE) isolates of Enterococcus faecalis causing urinary tract infections. As a result, butyryl alkannin showed significant antibacterial activity against multidrug-resistant E. faecalis pathogens of VRE as minimum inhibitory concentration values which were found in the range of 3.13 to 6.26 μg ml^? 1. The findings of this study justify biological and biomedicinal potential of butyryl alkannin compound as confirmed by its higher and significant antibacterial efficacy against VRE isolates of E. faecalis as compared to standard antibiotic vancomycin.     

Graphs to chemical structures 5. Combinatorial enumeration of centroidal and bicentroidal three-dimensional trees as stereochemical models of alkanes

Three-dimensional trees (3D-trees), which are defined as a 3D version of trees, are enumerated by Fujita’s proligand method formulated in Part 1 to Part 3 of this series (Fujita in Theor Chem Acc 113:73–79, 113:80–86, 2005; 115:37–53, 2006). Such 3D-trees are classified into centroidal and bicentroidal 3D-trees, which correspond to respective promolecules having proligands as substituents. In order to enumerate such centroidal and bicentroidal 3D-trees, cycle indices with chirality fittingness (CI-CFs) are formulated as being composed of three kinds of sphericity indices, i.e., a _d for homospheric cycles, c _d for enantiospheric cycles, and b _d for hemispheric cycles. The CI–CFs are capable of giving itemized results with respect to chiral and achiral 3D-trees so that they are applied to derive functional equations (a(x), c(x ²), and b(x)). The generating functions of planted 3D-trees, which are formulated and calculated elsewhere, are introduced into such functional equations. Thereby, the numbers of 3D-trees or equivalently those of alkanes as stereoisomers are calculated and collected up to a carbon content of 20 in a tabular form. Now, the enumeration problem initiated by a mathematician Cayley (Philos Mag 47(4):444–446, 1874) has been solved in such a systematic and integrated manner as satisfying both mathematical and chemical requirements.     

Analysis of Methylcitric Acid by Enantioselective Multidimensional Gas Chromatography-Mass Spectrometry

Methylcitric acid (2-hydroxybutane-1,2,3-tricarboxylic acid–MCA) is a structural analogue of citric acid, but due to an additional methyl group it is a chiral molecule with two stereogenic centers and thus four stereoisomers are conceivable. MCA occurs naturally as prominent metabolite in body fluids of patients with inherited metabolic diseases such as propionic acidemia, methylmalonic aciduria, or holocarboxylase synthetase deficiency. Therefore methylcitric acid is considered to be an important diagnostic marker for these diseases. MCA is most likely produced from accumulated propionyl-CoA in these diseases by the enzyme si-citrate synthase from the citric acid cycle; however, there are other enzymes known which could catalyze the same reaction with different stereoselectivity, such as re-citrate synthase or the more specific enzyme methylcitrate synthase, found in microorganisms. Almost all methods dealing with MCA in the literature are non-enantioselective. For that reason there is no information about occurrence of MCA enantiomers in healthy people, patients with propionic acidemia, methylmalonic aciduria, or holocarboxylase synthetase deficiency and about value of enantiomeric distribution for diagnosis and long-term treatment. The enantioselective analysis of MCA as corresponding trimethyl ester was achieved by enantioselective multidimensional gas chromatography coupled with mass spectrometry using heptakis-(2,3-di-O-methyl-6-O-tert-butyl-dimethylsilyl)-β-cyclodextrin as chiral stationary phase. The described method allows a reliable screening of MCA in complex matrices like urine without time consuming sample preparation and with mass selective detection. During this investigation urine samples from various patients and healthy controls were analyzed. As concluded, MCA is a good diagnostic marker and can be easily measured by the method presented. Only the two stereoisomers (2S,3R) and (2S,3S) were detectable in patients and healthy controls. The varying ratios of these stereoisomers cannot presently be correlated with the health status of patients, although there are some indications that this might be possible. However, the quantitative levels of MCA, determined as the ratio of MCA absolute peak area divided by 1,000 to the creatinine contents of urine samples in this investigation, showed a dependence on the state of health and MCA would thus also be a possible marker for long-term treatment. Such a substance is of major interest nowadays since there are different studies searching for such a long-term marker in propionic acidemia or methylmalonic aciduria.     

Photocycloadditions of 2-(trimethylsilyloxy)-1,3-butadiene to 2-cycloalkenones. Access to the basic pentalenolactone skeleton

The [2 + 2] Photocycloaddition of 2-(trimethylsilyloxy)-1,3-butadiene to a number of 2-cycloalkenones proved to be quite a general reaction leading to good yields of the cycloadducts (Table). This finding is surprising since dienes, in general, are better known as quenchers of enone triplets rather than as photochemical reactants. Both the high substrate concentrations, which can be employed in these cycloadditions, and the remarkable regio and stereoselectivity of the processes qualify them as valuable for syntheses. In a first application, the photoproducts 1a, b were transformed in three steps into a viable precursor 4 of the pentalenolactone-G and -H antibiotics.     

Analytical and semipreparative chiral separation of cis‐itraconazole on cellulose stationary phases by high‐performance liquid chromatography

cis‐Itraconazole is a chiral antifungal drug administered as a racemate. The knowledge of properties of individual cis‐itraconazole stereoisomers is vital information for medicine and biosciences as different stereoisomers of cis‐itraconazole may possess different affinity to certain biological pathways in the human body. For this purpose, either chiral synthesis of enantiomers or chiral separation of racemate can be used. This paper presents a two‐step high‐performance liquid chromatography approach for the semipreparative isolation of four stereoisomers (two enantiomeric pairs) of itraconazole using polysaccharide stationary phases and volatile organic mobile phases without additives in isocratic mode. The approach used involves the separation of the racemate into three fractions (i.e. two pure stereoisomers and one mixed fraction containing the remaining two stereoisomers) in the first run and consequent separation of the collected mixed fraction in the second one. For this purpose, combination of cellulose tris‐(4‐methylbenzoate) and cellulose tris‐(3,5‐dimehylphenylcarbamate) columns with complementary selectivity for cis‐itraconazole provided full separation of all four stereoisomers (with purity of each isomer > 97%). The stereoisomers were collected, their optical rotation determined and their identity confirmed based on the results of a previously published study. Pure separated stereoisomers are subjected to further biological studies.     

Single-Point Mutant Inverts the Stereoselectivity of a Carbonyl Reductase toward β-Ketoesters with Enhanced Activity

Enzyme stereoselectivity control is still a major challenge. To gain insight into the molecular basis of enzyme stereo-recognition and expand the source of antiPrelog carbonyl reductase toward β-ketoesters, rational enzyme design aiming at stereoselectivity inversion was performed. The designed variant Q139G switched the enzyme stereoselectivity toward β-ketoesters from Prelog to antiPrelog, providing corresponding alcohols in high enantiomeric purity (89.1–99.1 % ee). More importantly, the well-known trade-off between stereoselectivity and activity was not found. Q139G exhibited higher catalytic activity than the wildtype enzyme, the enhancement of the catalytic efficiency (k_cat/K_m) varied from 1.1- to 27.1-fold. Interestingly, the mutant Q139G did not lead to reversed stereoselectivity toward aromatic ketones. Analysis of enzyme–substrate complexes showed that the structural flexibility of β-ketoesters and a newly formed cave together facilitated the formation of the antiPrelog-preferred conformation. In contrast, the relatively large and rigid structure of the aromatic ketones prevents them from forming the antiPrelog-preferred conformation.