Exploring the impact of alignment media on RDC analysis of phosphorus-containing compounds: a molecular docking approach.

Residual dipolar couplings (RDCs) are employed in NMR analysis when conventional methods, such as J-couplings and nuclear Overhauser effects (NOEs) fail. Low-energy (optimized) conformers are often used as input structures in RDC analysis programs. However, these low-energy structures do not necessarily resemble conformations found in anisotropic environments due to interactions with the alignment medium, especially if the analyte molecules are flexible. Considering interactions with alignment media in RDC analysis, we developed and evaluated a molecular docking-based approach to generate more accurate conformer ensembles for compounds in the presence of the poly-γ-benzyl-L-glutamate alignment medium. We designed chiral phosphorus-containing compounds that enabled us to utilize 31P NMR parameters for the stereochemical analysis. Using P3D/PALES software to evaluate diastereomer discrimination, we found that our conformer ensembles outperform moderately the standard, low-energy conformers in RDC analysis. To further improve our results, we (i) averaged the experimental values of the molecular docking-based conformers by applying the Boltzmann distribution and (ii) optimized the structures through normal mode relaxation, thereby enhancing the Pearson correlation factor R and even diastereomer discrimination in some cases. Nevertheless, we presume that significant differences between J-couplings in isotropic and in anisotropic environments may preclude RDC measurements for flexible molecules. Therefore, generating conformer ensembles based on molecular docking enhances RDC analysis for mildly flexible systems while flexible molecules may require applying more advanced approaches, in particular approaches including dynamical effects.

Extending molecular dynamics with dipolar NMR tensors as constraints to chiral phosphorus compounds.

Molecular dynamics with orientational constraints (MDOC) simulations use NMR parameters as tensorial constraints in the stereochemical analysis of small molecules. 13C-31P Residual dipolar couplings-aided MDOC simulations of small phosphorus molecules determined the relative configurations of rigid molecules after including 3JH-H-couplings as additional constraints. However, flexible molecules remain a problem.

Development of an Albumin-Polymer Bioconjugate via Covalent Conjugation and Supramolecular Interactions.

Preexisting serum albumin-polymer bioconjugates have been formed either through covalent conjugation or supramolecular interactions. However, the viability of producing a bioconjugate where both covalent conjugation and supramolecular interactions have been adopted is yet to be explored. In this work, the noncovalent interaction of two polymers bearing fatty acid-based end-functionalities were compared and the superior binder was carried forward for testing with serum albumin that possessed a polymer conjugated to its Cys34 residue. The studies demonstrated that an albumin-polymer bioconjugate equipped with polymers via both covalent and supramolecular interactions can be successfully achieved.

Unsymmetrical benzothiazole-based dithienylethene photoswitches.

Herein, we investigate the structure-property relationships in a new series of benzothiazole based unsymmetrical hexafluorocyclopentene dithienylethenes (DTEs) and compare the results with the known facts for symmetric diarylethenes (DAEs). We reveal high photocyclization efficiency resulting from a significant shift of ground state equilibrium to the antiparallel conformation and a barrierless excited state pathway to conical intersection, which remains unperturbed even in polar solvents for most of the prepared DTEs. Furthermore, we uncover that the rate of back thermal cycloreversion correlates clearly more with the central C-C bond-length in the transition state than with the central C-C bond-length in the ground state of the cyclic form. Finally, our detailed vibrational spectral analysis of studied DTEs points out significant changes in Raman and infrared spectra during photoswitching cycles which pave the way for a non-destructive readout of stored information.

Can third-party observers detect attraction in others based on subtle nonverbal cues?

In a series of three studies, we examined whether third-party observers can detect attraction in others based on subtle nonverbal cues. We employed video segments of dates collected from a speed-dating experiment, in which daters went on a brief (approx. 4 min) blind-date and indicated whether they would like to go on another date with their brief interaction partner or not. We asked participants to view these stimuli and indicate whether or not each couple member is attracted to their partner. Our results show that participants could not reliably detect attraction, and this ability was not influenced by the age of the observer, video segment location (beginning or middle of the date), video duration, or general emotion recognition capacity. Contrary to previous research findings, our findings suggest that third-party observers cannot reliably detect attraction in others. However, there was one exception: Recognition rose above chance level when the daters were both interested in their partners compared to when they were not interested. Supplementary Information: The online version contains supplementary material available at 10.1007/s12144-022-02927-0.

Phosphate-Based Self-Immolative Linkers for Tuneable Double Cargo Release.

Phosphorus-based self-immolative (SI) linkers offer a wide range of applications, such as smart materials and drug-delivery systems. Phosphorus SI linkers are ideal candidates for double-cargo delivery platforms because they have a higher valency than carbon. A series of substituted phosphate linkers was designed for releasing two phenolic cargos through SI followed by chemical hydrolysis. Suitable modifications of the lactate spacer increased the cargo release rate significantly, from 1 day to 2 hours or 5 minutes, as shown for linkers containing p-fluoro phenol. In turn, double cargo linkers bearing p-methyl phenol released their cargo more slowly (4 days, 4 hours, and 15 minutes) than their p-fluoro analogues. The α-hydroxyisobutyrate linker released both cargos in 25 minutes. Our study expands the current portfolio of SI constructs by providing a double cargo delivery option, which is crucial to develop universal SI platforms.

Phosphate-Based Self-Immolative Linkers for Tuneable Double Cargo Release.

Invited for the cover of this issue are Eliska Procházková, Ondrej Baszczynski, and colleagues at IOCB (Prague) and Charles University (Prague). The image depicts phosphorus-based, double-cargo, self-immolative linkers capable of releasing both cargos sequentially after activation by light. Read the full text of the article at 10.1002/chem.202101805.

NMR Structure Elucidation of Naphthoquinones from Quambalaria cyanescens.

Naphthoquinones isolated from Quambalaria cyanescens (quambalarines) are natural pigments possessing significant cytotoxic and antimicrobial properties. Determining the structure of naphthoquinone compounds is important for the understanding of their biological activities and the informed synthesis of related analogues. Identifying quambalarines is challenging, because they contain a hydroxylated naphthoquinone scaffold and have limited solubility. Here, we report a detailed structural study of quambalarine derivatives, which form strong intramolecular hydrogen bonds (IMHBs) that enable the formation of several tautomers; these tautomers may complicate structural investigation due to their fast interconversion. To investigate tautomeric equilibria and identify new quambalarines, we complemented the experimental NMR spectroscopy data with density functional theory (DFT) calculations.

Pupil mimicry promotes trust through the theory-of-mind network.

The human eye can provide powerful insights into the emotions and intentions of others; however, how pupillary changes influence observers' behavior remains largely unknown. The present fMRI-pupillometry study revealed that when the pupils of interacting partners synchronously dilate, trust is promoted, which suggests that pupil mimicry affiliates people. Here we provide evidence that pupil mimicry modulates trust decisions through the activation of the theory-of-mind network (precuneus, temporo-parietal junction, superior temporal sulcus, and medial prefrontal cortex). This network was recruited during pupil-dilation mimicry compared with interactions without mimicry or compared with pupil-constriction mimicry. Furthermore, the level of theory-of-mind engagement was proportional to individual's susceptibility to pupil-dilation mimicry. These data reveal a fundamental mechanism by which an individual's pupils trigger neurophysiological responses within an observer: when interacting partners synchronously dilate their pupils, humans come to feel reflections of the inner states of others, which fosters trust formation.

Phosphate-Based Self-Immolative Linkers for the Delivery of Amine-Containing Drugs.

Amine-containing drugs often show poor pharmacological properties, but these disadvantages can be overcome by using a prodrug approach involving self-immolative linkers. Accordingly, we designed l-lactate linkers as ideal candidates for amine delivery. Furthermore, we designed linkers bearing two different cargos (aniline and phenol) for preferential amine cargo release within 15 min. Since the linkers carrying secondary amine cargo showed high stability at physiological pH, we used our strategy to prepare phosphate-based prodrugs of the antibiotic Ciprofloxacin. Therefore, our study will facilitate the rational design of new and more effective drug delivery systems for amine-containing drugs.

Optimization of norbornyl-based carbocyclic nucleoside analogs as cyclin-dependent kinase 2 inhibitors.

We report on the discovery of norbornyl moiety as a novel structural motif for cyclin-dependent kinase 2 (CDK2) inhibitors which was identified by screening a carbocyclic nucleoside analogue library. Three micromolar hits were expanded by the use of medicinal chemistry methods into a series of 16 novel compounds. They had prevailingly micromolar activities against CDK2 and the best compound of the series attained IC50 of 190 nM. The binding modes were explored in molecular details by modeling and docking. Quantum mechanics-based scoring was used to rationalize the affinities. In conclusion, the discovered 9-hydroxymethylnorbornyl moiety was shown by joint experimental-theoretical efforts to be able to serve as a novel substituent for CDK2 inhibitors. This finding opens door to the exploration of chemical space towards more effective derivatives targeting this important class of protein kinases.

Could 5'-N and S ProTide analogues work as prodrugs of antiviral agents?

The nucleoside/nucleotide derived antiviral agents have been the most important components of antiviral therapy used in clinics. Recently, the focus of the medicinal chemists within this exciting research field has been affected mainly by the lack of effective therapies for the Hepatitis C virus (HCV) infection and several other "neglected" diseases caused by viruses such as Zika or Dengue. 2'-Methyl modified nucleosides and their monophosphate prodrugs (ProTides) have revolutionized the therapies for HCV in the last few years and, according to the latest research efforts, have also brought a promise for treatment of diseases caused by other members of Flaviviridae family. Here, we report on the design and synthesis of 5'-N and S modified ProTides derived from 2'-methyladenosine. We studied potential applicability of these derivatives as prodrugs of this archetypal antiviral compound.

Polysubstituted 5-Phenylazopyrimidines: Extremely Fast Non-ionic Photochromic Oscillators.

Photochromic systems with an ultrahigh rate of thermal relaxation are highly desirable for the development of new efficient photochromic oscillators. Based on DFT calculations, we designed a series of 5-phenylazopyrimidines with strong push-pull character in silico and observed very low energy barriers for the thermal (Z)-to-(E) isomerization. The structure of the (Z)-isomer of the slowest isomerizing derivative in the series was confirmed by NMR analysis with in situ irradiation at low temperature. The substituents can tune the lifetime of thermal back isomerization from hundreds of microseconds to several nanoseconds (8 orders of magnitude). The photoswitching parameters were extracted from transient absorption techniques and a dominant rotation mechanism of the (Z)-to-(E) thermal fading was proposed based on DFT calculations.

Reactive cyclic intermediates in the ProTide prodrugs activation: trapping the elusive pentavalent phosphorane.

Nucleotide prodrugs (ProTides) based on phosphate or phosphonate compounds are potent and successfully marketed antiviral drugs. Although their biological properties are well explored, experimental evidence on the mechanism of their activation pathway is still missing. In this study, we synthesized two ProTide analogues, which can be activated by UV light. Using 31P and 13C NMR spectroscopy with in situ irradiation, we followed the ProTide activation pathway in various solvents, and we detected the first proposed intermediate and the monoamidate product. Furthermore, we used mass spectrometry (MS) coupled with infrared spectroscopy in the gas phase to detect and to characterize the elusive cyclic pentavalent phosphorane and cyclic acyl phosphoramidate intermediates. Our combined NMR and MS data provided the first experimental evidence of the cyclic intermediates in the activation pathway of ProTide prodrugs.

In-group defense, out-group aggression, and coordination failures in intergroup conflict.

Intergroup conflict persists when and because individuals make costly contributions to their group's fighting capacity, but how groups organize contributions into effective collective action remains poorly understood. Here we distinguish between contributions aimed at subordinating out-groups (out-group aggression) from those aimed at defending the in-group against possible out-group aggression (in-group defense). We conducted two experiments in which three-person aggressor groups confronted three-person defender groups in a multiround contest game (n = 276; 92 aggressor-defender contests). Individuals received an endowment from which they could contribute to their group's fighting capacity. Contributions were always wasted, but when the aggressor group's fighting capacity exceeded that of the defender group, the aggressor group acquired the defender group's remaining resources (otherwise, individuals on both sides were left with the remainders of their endowment). In-group defense appeared stronger and better coordinated than out-group aggression, and defender groups survived roughly 70% of the attacks. This low success rate for aggressor groups mirrored that of group-hunting predators such as wolves and chimpanzees (n = 1,382 cases), hostile takeovers in industry (n = 1,637 cases), and interstate conflicts (n = 2,586). Furthermore, whereas peer punishment increased out-group aggression more than in-group defense without affecting success rates (Exp. 1), sequential (vs. simultaneous) decision-making increased coordination of collective action for out-group aggression, doubling the aggressor's success rate (Exp. 2). The relatively high success rate of in-group defense suggests evolutionary and cultural pressures may have favored capacities for cooperation and coordination when the group goal is to defend, rather than to expand, dominate, and exploit.

Photoswitchable Intramolecular Hydrogen Bonds in 5-Phenylazopyrimidines Revealed By In Situ Irradiation NMR Spectroscopy.

NMR spectroscopy with in situ irradiation uncovered unique photoswitchable intramolecular hydrogen bonds (IMHBs) in 5-phenylazopyrimidines with two hydrogen bond donors. These compounds form two stable rotamers, each with one IMHB, and the rotamer ratio changes reversibly upon UV or visible light irradiation. Strong substituent dependence of photoinduced structural changes was observed; using suitable substituents, orthogonal photoswitching can be achieved. For example, whereas UV irradiation caused switching between the two rotamers of the trans isomer of a compound with electron-donating methoxy substituent, visible light enabled to obtain the cis photoisomer. No cis isomer was detected for compounds with electro-neutral or electron-accepting substituents, but photoswitching between the two trans isomers was observed. On the other hand, compounds without hydrogen-bond donors or with one donor only formed stable cis isomers. A mechanism of the photoswitching was proposed by DFT computations.

Photoswitching Behavior of 5-Phenylazopyrimidines: In Situ Irradiation NMR and Optical Spectroscopy Combined with Theoretical Methods.

The photoswitching behavior of 5-phenylazopyrimidines was investigated by optical methods and NMR spectroscopy with in situ irradiation sustained by mathematical modeling and DFT calculations. Irradiation of various compounds with electron-donating groups on the pyrimidine ring and substituents with electron-withdrawing as well as electron-donating substituent in the para-position of the phenyl ring were examined. All compounds could be successfully converted to the cis isomer; this isomerization and the subsequent thermal fading were studied. Switching cycles can be repeated without signs of photodegradation for most of the compounds, which makes them adept to molecular photoswitches. Interestingly, the chloro and cyano derivatives can be switched without UV light, which makes them vis(π → π*)-vis(n → π*) photoswitches. Surprisingly equal trans-to- cis photoisomerization quantum yields for π → π* and n → π* excitation indicate the blocking of the inversion pathway following π → π* excitation. In contrast to that, DFT computations suggest the inversion mechanism for the reverse thermal cis-to- trans isomerization of 5-phenylazopyrimidines.

Synthesis of tRNA analogues containing a terminal ribose locked in the South conformation to study tRNA-dependent enzymes.

We report here the synthetic route of two constrained dinucleotides and the determination of the sugar puckering by NMR analyses of the starting nucleosides. Enzymatic ligation to microhelix-RNAs provide access to tRNA analogues containing a 3' terminal A76 locked in South conformation. Biological evaluation of our tRNA analogues has been performed using amino-acyl tRNA-dependent transferase FemXWv, which mediates non-ribosomal incorporation of amino acids into the bacterial cell wall. We have shown that our tRNA analogues inhibited the aminoacyl transfer reaction catalyzed by FemXWv with IC50s of 10 and 8 µM. These results indicate that FemXWv displays a moderate preference for tRNAs containing a terminal A76 locked in the South conformation and that a South to North switch in the conformation of the terminal ribose might contribute to the release of the uncharged tRNAAla product of the aminoacyl transfer reaction catalyzed by FemXwv.

Influence of Intramolecular Charge Transfer and Nuclear Quantum Effects on Intramolecular Hydrogen Bonds in Azopyrimidines.

Intramolecular hydrogen bonds (IMHBs) in 5-azopyrimidines are investigated by NMR spectroscopy and DFT computations that involve nuclear quantum effects. A series of substituted 5-phenylazopyrimidines with one or two hydrogen bond donors able to form IMHBs with the azo group is prepared by azo coupling. The barrier of interconversion between two rotamers of the compounds with two possible IMHBs is determined by variable temperature NMR spectroscopy and it is demonstrated that the barrier is significantly affected by intramolecular charge transfer. Through-hydrogen-bond scalar coupling is investigated in 15N labeled compounds and the stability of the IMHBs is correlated with experimental NMR parameters and rationalized by path integral molecular dynamics simulations that involve nuclear quantum effects. Detailed information on the hydrogen bond geometry upon hydrogen-to-deuterium isotope exchange is obtained from a comparison of experimental and calculated NMR data.

Control of α/ß Anomer Formation by a 2',5' Bridge: Toward Nucleoside Derivatives Locked in the South Conformation.

We describe a novel stereoselective synthesis of nucleoside derivatives with the ribose ring locked in the South conformation by a bridge between C2' and C5'. Despite the intrinsic constraints of the bicyclic structure, we demonstrate that their synthesis can be achieved by ring closing metathesis of readily accessible precursors. The obtained ribose derivatives are, however, very poor substrates for further installation of the nucleobases, and even simple nucleophiles, such as azido or cyano anions, react with unexpected stereo- or regioselectivity under standard glycosylation conditions. Here we explain this behavior by employing density functional theory (DFT) computations and devise an alternative approach resulting in isomers with the desired orientation of the nucleobase.