Fusing 2D and 3D molecular graphs as unambiguous molecular descriptors for conformational and chiral stereoisomers.

The rapid progress of machine learning (ML) in predicting molecular properties enables high-precision predictions being routinely achieved. However, many ML models, such as conventional molecular graph, cannot differentiate stereoisomers of certain types, particularly conformational and chiral ones that share the same bonding connectivity but differ in spatial arrangement. Here, we designed a hybrid molecular graph network, Chemical Feature Fusion Network (CFFN), to address the issue by integrating planar and stereo information of molecules in an interweaved fashion. The three-dimensional (3D, i.e., stereo) modality guarantees precision and completeness by providing unabridged information, while the two-dimensional (2D, i.e., planar) modality brings in chemical intuitions as prior knowledge for guidance. The zipper-like arrangement of 2D and 3D information processing promotes cooperativity between them, and their synergy is the key to our model's success. Experiments on various molecules or conformational datasets including a special newly created chiral molecule dataset comprised of various configurations and conformations demonstrate the superior performance of CFFN. The advantage of CFFN is even more significant in datasets made of small samples. Ablation experiments confirm that fusing 2D and 3D molecular graphs as unambiguous molecular descriptors can not only effectively distinguish molecules and their conformations, but also achieve more accurate and robust prediction of quantum chemical properties.

Evaluation of GC-MS for identification and characterization of pneumococcal serotype 24A, 24B, and 24F capsular polysaccharide.

Analysis of pneumococcal polysaccharides (PnPs) has been an arduous task, especially in similar serotypes. Pneumococci invades the host immune response by modulating capsule structure with small genetic changes making them indistinguishable from similar serotypes by conventional modes of analysis. The new serotype 24F causing invasive pneumococcal-resistant infection is an analytical challenge for its analysis as related serotypes 24A and 24B Ps share a common backbone. The difference in the branched chain which contains arabinitol and ribitol in 24F and 24B respectively are stereoisomers making their identification even more challenging. The composition analysis by GC-MS revealed distinct peaks for arabinitol in 24F and 24A Ps and ribitol in Pn 24B serotype polysaccharide. The mass spectral analysis confirmed their identification along with a heterologous cross-reactivity which confirmed anti-Pn-24F mAb reactive to Pn 24B than Pn 24A. The quantitative analysis of pneumococcal 24A, 24B and 24F using GC-MS showed sensitive analysis over the concentration range 3.125-200 µg/mL with regression coefficient >0.99 making ideal modality for the characterization, identification, and quantitation of pneumococcal 24A, 24B and 24F similar serotypes.

Study of the stereospecificity in the biotransformation of the four isomers of loxoprofen sodium in rats by chiral HPLC.

Loxoprofen sodium is a chiral drug with two chiral centers. In our previous work, we found that the elimination of its four isomers showed stereospecificity in rats, while how the stereospecific behavior occurred in vivo was unclear. To clarify this issue, each single isomer of loxoprofen sodium was prepared by a chiral semi-preparative high-performance liquid chromatography (HPLC) and then administered to rats. By analysis of each isomer in rat plasma utilizing an analytical chiral HPLC, it was discovered that the chiral inversion occurred only to its (2R)-isomers, one from (1'S,2R)- to (1'S,2S)-isomer and the other from (1'R,2R)- to (1'R,2S)-isomer. The reduction of α-substituted cyclopentanone occurred only to its (1'R)-isomers, with (1'R,2R)-isomer reduced to (2'S,1'R,2R)-trans-alcohol and (1'R,2S)- to (2'S,1'R,2S)-trans-alcohol. Interestingly, both the inversion and the reduction reaction occurred to its (1'R,2R)-isomer due to the special stereo-structure with both (2R)- and (1'R)-configuration, and conversely, neither of them occurred to its (1'S,2S)-isomer, which caused the significantly different elimination rate in vivo. These new findings were meaningful for evaluation of the safety and efficacy of chiral drugs.

Phenothiazine Derivatives: The Importance of Stereoisomerism in the Tolerance and Efficacy of Antimicrobials.

Stereoisomers are molecules that are identical in atomic constitution and bonding. The biological properties may, however, differ significantly between two enantiomers (individual stereoisomers). JBC 1847, a phenothiazine derivative with strong antimicrobial activity against Gram-positive bacteria, exists in two enantiomers, S and R. Under standard chemical synthesis (S)-and (R)-JBC 1847 will be present in 50/50 amount (racemic). In this study, we have investigated the antimicrobial activity, the in vivo tolerance and therapeutic efficacy of purified (S)-JBC 1847. Compared to JBC 1847 racemic, the antimicrobial activity of (S)-JBC 1847 in vitro was in the same range or slightly increased, while the maximum tolerable concentration in vivo was five times higher for (S)-JBC 1847 (5 mg/kg versus 20 mg/kg bodyweight). Furthermore, the in vivo efficacy of (S)-JBC 1847 in a mouse peritonitis MRSA model was comparable to the activity of vancomycin. In conclusion, the antimicrobial activity and tolerance of a medical stereoisomeric compound may be significantly different using purified enantiomers compared with the racemic state. Supplementary Information: The online version contains supplementary material available at 10.1007/s12088-024-01309-3.

A rapid intracellular enrichment of alkylating payload is essential for melphalan flufenamide potency and mechanism of action.

Despite decades of development of treatments and the successful application of targeted therapies for multiple myeloma, clinical challenges remain for patients with relapsed/refractory disease. A drug designed for efficient delivery of an alkylating payload into tumor cells that yields a favorable therapeutic window can be an attractive choice. Herein we describe melphalan flufenamide (melflufen), a drug with a peptide carrier component conjugated to an alkylating payload, and its cellular metabolism. We further underline the fundamental role of enzymatic hydrolysis in the rapid and robust accumulation of alkylating metabolites in cancer cells and their importance for downstream effects. The formed alkylating metabolites were shown to cause DNA damage, both on purified DNA and on chromatin in cells, with both nuclear and mitochondrial DNA affected in the latter. Furthermore, the rapid intracellular enrichment of alkylating metabolites is shown to be essential for the rapid kinetics of the downstream intracellular effects such as DNA damage signaling and induction of apoptosis. To evaluate the importance of enzymatic hydrolysis for melflufen's efficacy, all four stereoisomers of the compound were studied in a systematic approach and shown to have a different pattern of metabolism. In comparison with melflufen, stereoisomers lacking intracellular accumulation of alkylating payloads showed cytotoxic activity only at significantly higher concentration, slower DNA damage kinetics, and different mechanisms of action to reach cellular apoptosis.

Tetraphenylethene-Based cis/trans Isomers for Targeted Fluorescence Sensing and Biomedical Applications.

Molecular probes which can be modulated, functionalized and used to visualize the processes are highly desirable for understanding and manipulating biological systems. Geometric cis and trans isomers of tetraphenylethene (TPE) emerge as attractive candidates to fulfill these tasks thanks to the unique aggregation-induced emission properties, tailorable structures, and responsiveness to external stimuli. This minireview focuses on cis and trans isomers of TPE derivatives that are functionalized with molecular recognition units for fluorescence detection, bioimaging and cancer therapy. The effects of molecular geometry on fluorescence property, target binding ability and biological activity are summarized. The feasibility to in vitro and in vivo switch molecular configuration and thus bio-activity is discussed. Finally, the future development and challenges are discussed in view of TPE-based stereoisomers for targeted sensing and imaging-guided modulation of biological processes.

Natural Vitamin E Supplementation during Pregnancy in Rats Increases RRR-α-Tocopherol Stereoisomer Proportion and Enhances Fetal Antioxidant Capacity, Compared to Synthetic Vitamin E Administration.

INTRODUCTION: Low dietary intake of vitamin E is a global public health issue. RRR-α-tocopherol (RRR-αT) is the only naturally occurring vitamin E stereoisomer, but the equimolecular mixture of all eight stereoisomers, synthetic vitamin E (S-αT), is commonly consumed. The objective of this study was to evaluate bioavailability and antioxidant activity of RRR-αT versus S-αT, in both mother and fetus, after maternal supplementation during pregnancy. METHODS: Female rats (7 weeks of age) received a modified AIN-93G diet supplemented with 75 IU/kg of RRR-αT (NVE, n = 20) or S-αT (SVE, n = 17). At delivery, the levels of αT, stereoisomer distribution, and antioxidant capacity were analyzed in maternal and fetal plasma. RESULTS: NVE administration significantly increased the proportion of RRR-αT stereoisomer in maternal and fetal plasma. The percentage of RRR-αT increased from 32.76% to 88.33% in maternal plasma, and 35.25% to 97.94% in fetal plasma, in the NVE group compared to SVE. Fetal plasma from the NVE group was found to have higher total antioxidant capacity compared to SVE. Lastly, fetal plasma RRR-αT stereoisomer percentage was positively associated with expression levels of scavenger receptor class B type 1 (SR-B1) in the placenta. CONCLUSIONS: Both natural and synthetic sources of vitamin E showed similar bioavailability. Still, NVE supplementation increased the proportion of RRR-αT and promoted higher antioxidant activity in fetal plasma at birth. Placental SR-B1 might be involved in the stereoselective transfer of RRR-αT stereoisomer across the placenta and may improve αT bioactivity in the fetus.

Structure, Optical and Magnetic Properties of Two Isomeric 2-Bromomethylpyridine Cu(II) Complexes [Cu(C6H9NBr)2(NO3)2] with Very Different Binding Motives.

Two isomeric 2-bromomethylpyridine Cu(II) complexes [Cu(C6H9NBr)2(NO3)2] with 2-bromo-5-methylpyridine (L1) and 2-bromo-4-methylpyridine (L2) were synthesized as air-stable blue materials in good yields. The crystal structures were different with [Cu(L1)2(NO3)2] (CuL1) crystallizing in the monoclinic space group P21/c, while the 4-methyl derivative CuL2 was solved and refined in triclinic P1¯. The orientation of the Br substituents in the molecular structure (anti (CuL1) vs. syn (CuL2) conformations) and the geometry around Cu(II) in an overall 4 + 2 distorted coordination was very different with two secondary (axially elongated) Cu-O bonds on each side of the CuN2O2 basal plane in CuL1 or both on one side in CuL2. The two Br substituents in CuL2 come quite close to the Cu(II) centers and to each other (Br⋯Br ~3.7 Å). Regardless of these differences, the thermal behavior (TG/DTA) of both materials is very similar with decomposition starting at around 160 °C and CuO as the final product. In contrast to this, FT-IR and Raman frequencies are markedly different for the two isomers and the UV-vis absorption spectra in solution show marked differences in the π-π* absorptions at 263 (CuL2) or 270 (CuL1) nm and in the ligand-to-metal charge transfer bands at around 320 nm which are pronounced for CuL1 with the higher symmetry at the Cu(II) center, but very weak for CuL2. The T-dependent susceptibility measurements also show very similar results (µeff = 1.98 µB for CuL1 and 2.00 µB for CuL2 and very small Curie-Weiss constants of about -1. The EPR spectra of both complexes show axial symmetry, very similar averaged g values of 2.123 and 2.125, respectively, and no hyper-fine splitting.

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.

Iridium-Catalyzed Chemo-, Diastereo-, and Enantioselective Allyl-Allyl Coupling: Accessing All Four Stereoisomers of (E)-1-Boryl-Substituted 1,5-Dienes by Chirality Pairing.

Here, we report a highly chemo-, diastereo-, and enantioselective allyl-allyl coupling between branched allyl alcohols and α-silyl-substituted allylboronate esters, catalyzed by a chiral iridium complex. The α-silyl-substituted allylboronate esters can be chemoselectively coupled with allyl electrophiles, affording a diverse set of enantioenriched (E)-1-boryl-substituted 1,5-dienes in good yields, with excellent stereoselectivity. By permuting the chiral iridium catalysts and the substrates, we efficiently and selectively obtained all four stereoisomers bearing two consecutive chiral centers. Mechanistic studies via density functional theory calculations revealed the origins of the diastereo- and chemoselectivities, indicating the pivotal roles of the steric interaction, the ß-silicon effect, and a rapid desilylation process. Additional synthetic modifications for preparing a variety of enantioenriched compounds containing contiguous chiral centers are also included.

Improving the accuracy of 31P NMR chemical shift calculations by use of scaling methods.

Calculation of 31P NMR chemical shifts for a series of tri- and tetracoordinate phosphorus compounds using several basis sets and density functional theory (DFT) functionals gave a modest fit to experimental chemical shifts, but an excellent linear fit when plotted against the experimental values. The resultant scaling methods were then applied to a variety of "large" compounds previously selected by Latypov et al. and a set of stereoisomeric and unusual compounds selected here. No one method was best for all structural types. For compounds that contain P-P bonds and P-C multiple bonds, the Latypov et al. method using the PBE0 functional was best (mean absolute deviation/root mean square deviation (MAD/RMSD) = 6.9/8.5 ppm and 6.6/8.2 ppm, respectively), but for the full set of compounds gave higher deviations (MAD/RMSD = 8.2/12.3 ppm), and failed by over 60 ppm for a three-membered phosphorus heterocycle. Use of the M06-2X functional for both the structural optimization and NMR chemical shift calculation was best overall for the compounds without P-C multiple bonds (MAD/RMSD = 5.4/7.1 ppm), but failed by 30-49 ppm for compounds having any P-C multiple-bond character. Failures of these magnitudes have not been reported previously for these widely used functionals. These failures were then used to screen a variety of recommended functionals, leading to better overall methods for calculation of these chemical shifts: optimization with the M06-2X functional and NMR calculation with the PBE0 or ωB97x-D functionals gave values for MAD/RMSD = 6.9/8.5 ppm and 6.8/9.1 ppm, respectively, over an experimental chemical shift range of -181 to 356 ppm. Due to the unexplained failures observed, we recommend use of more than one method when looking at novel structures.

Integrating ion mobility into comprehensive multidimensional metabolomics workflows: critical considerations.

BACKGROUND: Ion mobility (IM) separation capabilities are now widely available to researchers through several commercial vendors and are now being adopted into many metabolomics workflows. The added peak capacity that ion mobility offers with minimal compromise to other analytical figures-of-merit has provided real benefits to sensitivity and structural selectivity and have allowed more specific metabolite annotations to be assigned in untargeted workflows. One of the greatest promises of contemporary IM-enabled instrumentation is the capability of operating multiple analytical dimensions inline with minimal sample volumes, which has the potential to address many grand challenges currently faced in the omics fields. However, comprehensive operation of multidimensional mass spectrometry comes with its own inherent challenges that, beyond operational complexity, may not be immediately obvious to practitioners of these techniques. AIM OF REVIEW: In this review, we outline the strengths and considerations for incorporating IM analysis in metabolomics workflows and provide a critical but forward-looking perspective on the contemporary challenges and prospects associated with interpreting IM data into chemical knowledge. KEY SCIENTIFIC CONCEPTS OF REVIEW: We outline a strategy for unifying IM-derived collision cross section (CCS) measurements obtained from different IM techniques and discuss the emerging field of high resolution ion mobility (HRIM) that is poised to address many of the contemporary challenges associated with ion mobility metabolomics. Whereas the LC step limits the throughput of comprehensive LC-IM-MS, the higher peak capacity of HRIM can allow fast LC gradients or rapid sample cleanup via solid-phase extraction (SPE) to be utilized, significantly improving the sample throughput.

Elucidating the structure and functions of Resolvin D6 isomers on nerve regeneration with a distinctive trigeminal transcriptome.

Innervation sustains cornea integrity. Pigment epithelium-derived factor (PEDF) plus docosahexaenoic acid (DHA) regenerated damaged nerves by stimulating the synthesis of a new stereoisomer of Resolvin D6 (RvD6si). Here, we resolved the structure of this lipid isolated from mouse tears after injured corneas were treated with PEDF + DHA. RvD6si synthesis was inhibited by fluvoxamine, a cytochrome P450 inhibitor, but not by 15- or 5-LOX inhibitors, suggesting that the 4- and 17-hydroxy of DHA have an RR- or SR-configuration. The two compounds were chemically synthesized. Using chiral phase HPLC, four peaks of RvD6si1-4 from tears were resolved. The RR-RvD6 standard eluted as a single peak with RvD61 while pure SR-RvD6 eluted with RvD63 . The addition of these pure mediators prompted a trigeminal ganglion transcriptome response in injured corneas and showed that RR-RvD6 was the more potent, increasing cornea sensitivity and nerve regeneration. RR-RvD6 stimulates Rictor and hepatocyte growth factor (hgf) genes specifically as upstream regulators and a gene network involved in axon growth and suppression of neuropathic pain, indicating a novel function of this lipid mediator to maintain cornea integrity and homeostasis after injury.

Development and validation of a novel stability-indicating reverse phase HPLC method for the determination of sacubitril-valsartan premix stereoisomers: Cellulose tris(4-methyl benzoate) stationary phase.

A new stability indicating reverse phase HPLC method has been developed and validated as per International Conference on Harmonization guidelines for the determination of sacubitril-valsartan premix stereoisomers, namely, (2R)-valsartan, (2S,4S)-sacubitril, (2R,4S)-sacubitril, and (2R,4R)-sacubitril. Primarily, stability indicating separation study was done on reverse phase LC conditions; it was described by peak homogeneity of sacubitril-valsartan and its stereoisomers. Cellulose tris(4-methylbenzoate) packing column Chiralcel OJ-RH(150 mm × 4.6 mm), 5 µm provided better resolution than those of amylose based stationary phase's. Resolution between two arbitrary adjacent analyte was found to be more than 2.0 with 0.1% trifluoroacetic acid in water as mobile phase-A and mobile phase-B consisting of acetonitrile, methanol, and trifluoroacetic acid (90:10:0.1, v/v/v). Gradient elution was performed at a flow rate of 1.0 ml/min, column temperature 20°C, injection volume 10 µl, UV detection at 254 nm and run time was 52 min. The detector response linearity of stereoisomers found to be linear (R2  ≥ 0.9998), limit of detection (0.290 µg/ml, 0.122 µg/ml, 0.123 µg/ml, and 0.124 µg/ml), and limit of quantification (0.878 µg/ml, 0.370 µg/ml, 0.373 µg/ml, and 0.375 µg/ml), respectively. Percentage recovery was found to be 98-105. Finally, the proposed method is user friendly and can be used in bulk drugs analysis.

Application of Feature-Based Molecular Networking for Comparative Metabolomics and Targeted Isolation of Stereoisomers from Algicolous Fungi.

Seaweed endophytic (algicolous) fungi are talented producers of bioactive natural products. We have previously isolated two strains of the endophytic fungus, Pyrenochaetopsis sp. FVE-001 and FVE-087, from the thalli of the brown alga Fucus vesiculosus. Initial chemical studies yielded four new decalinoylspirotetramic acid derivatives with antimelanoma activity, namely pyrenosetins A-C (1-3) from Pyrenochaetopsis sp. strain FVE-001, and pyrenosetin D (4) from strain FVE-087. In this study, we applied a comparative metabolomics study employing HRMS/MS based feature-based molecular networking (FB MN) on both Pyrenochaetopsis strains. A higher chemical capacity in production of decalin derivatives was observed in Pyrenochaetopsis sp. FVE-087. Notably, several decalins showed different retention times despite the same MS data and MS/MS fragmentation pattern with the previously isolated pyrenosetins, indicating they may be their stereoisomers. FB MN-based targeted isolation studies coupled with antimelanoma activity testing on the strain FVE-087 afforded two new stereoisomers, pyrenosetins E (5) and F (6). Extensive NMR spectroscopy including DFT computational studies, HR-ESIMS, and Mosher's ester method were used in the structure elucidation of compounds 5 and 6. The 3'R,5'R stereochemistry determined for compound 6 was identical to that previously reported for pyrenosetin C (3), whose stereochemistry was revised as 3'S,5'R in this study. Pyrenosetin E (5) inhibited the growth of human malignant melanoma cells (A-375) with an IC50 value of 40.9 µM, while 6 was inactive. This study points out significant variations in the chemical repertoire of two closely related fungal strains and the versatility of FB MN in identification and targeted isolation of stereoisomers. It also confirms that the little-known fungal genus Pyrenochaetopsis is a prolific source of complex decalinoylspirotetramic acid derivatives.

3-keto-DON, but Not 3-epi-DON, Retains the in Planta Toxicological Potential after the Enzymatic Biotransformation of Deoxynivalenol.

Deoxynivalenol (DON) is a secondary fungal metabolite that is associated with many adverse toxicological effects in agriculture as well as human/animal nutrition. Bioremediation efforts in recent years have led to the discovery of numerous bacterial isolates that can transform DON to less toxic derivatives. Both 3-keto-DON and 3-epi-DON were recently shown to exhibit reduced toxicity, compared to DON, when tested using different cell lines and mammalian models. In the current study, the toxicological assessment of 3-keto-DON and 3-epi-DON using in planta models surprisingly revealed that 3-keto-DON, but not 3-epi-DON, retained its toxicity to a large extent in both duckweeds (Lemna minor L.) and common wheat (Triticum aestivum L.) model systems. RNA-Seq analysis revealed that the exposure of L. minor to 3-keto-DON and DON resulted in substantial transcriptomic changes and similar gene expression profiles, whereas 3-epi-DON did not. These novel findings are pivotal for understanding the environmental burden of the above metabolites as well as informing the development of future transgenic plant applications. Collectively, they emphasize the fundamental need to assess both plant and animal models when evaluating metabolites/host interactions.

A Cheminformatics Study Regarding the Human Health Risks Assessment of the Stereoisomers of Difenoconazole.

Difenoconazole is a chemical entity containing two chiral centers and having four stereoisomers: (2R,4R)-, (2R,4S)-, (2S,4R)- and (2S,4S)-difenoconazole, the marketed product containing a mixture of these isomers. Residues of difenoconazole have been identified in many agricultural products and drinking water. A computational approach has been used to evaluate the toxicological effects of the difenoconazole stereoisomers on humans. It integrates predictions of absorption, distribution, metabolism, excretion and toxicity (ADMET) profiles, prediction of metabolism sites, and assessment of the interactions of the difenoconazole stereoisomers with human cytochromes, nuclear receptors and plasma proteins by molecular docking. Several toxicological effects have been identified for all the difenoconazole stereoisomers: high plasma protein binding, inhibition of cytochromes, possible hepatotoxicity, neurotoxicity, mutagenicity, skin sensitization potential, moderate potential to produce endocrine disrupting effects. There were small differences in the predicted probabilities of producing various biological effects between the distinct stereoisomers of difenoconazole. Furthermore, there were significant differences between the interacting energies of the difenoconazole stereoisomers with plasma proteins and human cytochromes, the spectra of the hydrogen bonds and aromatic donor-acceptor interactions being quite distinct. Some distinguishing results have been obtained for the (2S,4S)-difenoconazole: it registered the highest value for clearance, exposed reasonable probabilities to produce cardiotoxicity and carcinogenicity and negatively affected numerous nuclear receptors.

(+)-Catechin Stereoisomer and Gallate Induce Oxidative Stress in Rat Aorta.

The goal of the work was to study changes in the activity of the angiotensin-converting enzyme (ACE) and production of reactive oxygen species (ROS) in the aorta of rats after the intraperitoneal injection of stereoisomers of catechin and gallate. The activity of ACE in the aorta sections was determined by measuring the hydrolysis of hippuryl-l-histidyl-l-leucine. The production of ROS in the aorta sections was estimated from the oxidation of dichlorodihydrofluorescein. The time and dose dependences of the effect of catechin stereoisomers and gallate on ACE activity and ROS production in the aorta were studied. It was shown that (+)-catechin and gallate increased the ACE activity and ROS production, and (-)-catechin and (-)-epicatechin did not influence these parameters. The doses of (+)-catechin and gallate that increased the ACE activity to a half-maximal value (AD50) were 0.04 and 0.03 µg/kg, respectively. Fucoidin, a blocker of leukocyte adhesion to the endothelium, reduced the ACE activity to the control level in the aortas of (+)-catechin-treated rats.

In Vitro and In Silico Studies of Human Tyrosyl-DNA Phosphodiesterase 1 (Tdp1) Inhibition by Stereoisomeric Forms of Lipophilic Nucleosides: The Role of Carbohydrate Stereochemistry in Ligand-Enzyme Interactions.

Inhibition of human DNA repair enzyme tyrosyl-DNA phosphodiesterase 1 (Tdp1) by different chiral lipophilic nucleoside derivatives was studied. New Tdp1 inhibitors were found in the series of the studied compounds with IC50 = 2.7-6.7 µM. It was shown that D-lipophilic nucleoside derivatives manifested higher inhibition activity than their L-analogs, and configuration of the carbohydrate moiety can influence the mechanism of Tdp1 inhibition.

Directing Multivalent Aptamer-Receptor Binding on the Cell Surface with Programmable Atom-Like Nanoparticles.

Multivalent interactions of biomolecules play pivotal roles in physiological and pathological settings. Whereas the directionality of the interactions is crucial, the state-of-the-art synthetic multivalent ligand-receptor systems generally lack programmable approaches for orthogonal directionality. Here, we report the design of programmable atom-like nanoparticles (aptPANs) to direct multivalent aptamer-receptor binding on the cell interface. The positions of the aptamer motifs can be prescribed on tetrahedral DNA frameworks to realize atom-like orthogonal valence and direction, enabling the construction of multivalent molecules with fixed aptamer copy numbers but different directionality. These directional-yet-flexible aptPAN molecules exhibit the adaptability to the receptor distribution on cell surfaces. We demonstrate the high-affinity tumor cell binding with a linear aptPAN oligomer (≈13-fold improved compared to free aptamers), which leads to ≈50 % suppression of cell growth.