Solid-state vibrational circular dichroism for pharmaceutical applications: Polymorphs and cocrystal of sofosbuvir

X-ray diffraction is a commonly used technique in the pharmaceutical industry for the determination of the atomic and molecular structure of crystals. However, it is costly, sometimes time-consuming, and it requires a considerable degree of expertise. Vibrational circular dichroism (VCD) spectroscopy resolves these limitations, while also exhibiting substantial sensitivity to subtle modifications in the conformation and molecular packaging in the solid state. This study showcases VCD's ability to differentiate between various crystal structures of the same molecule (polymorphs, cocrystals). We examined the most effective approach for producing high-quality spectra and unveiled the intricate link between structure and spectrum via quantum-chemical computations. We rigorously assessed, using alanine as a model compound, multiple experimental conditions on the resulting VCD spectra, with the aim of proposing an optimal and efficient procedure. The proposed approach, which yields reliable, reproducible, and artifact-free results with maximal signal-to-noise ratio, was then validated using a set comprising of three amino acids (serine, alanine, tyrosine), one hydroxy acid (tartaric acid), and a monosaccharide (ribose) to mimic active pharmaceutical components. Finally, the optimized approach was applied to distinguish three polymorphs of the antiviral drug sofosbuvir and its cocrystal with piperazine. Our results indicate that solid-state VCD is a prompt, cost-effective, and easy-to-use technique to identify crystal structures, demonstrating potential for application in pharmaceuticals. We also adapted the cluster and transfer approach to calculate the spectral properties of molecules in a periodic crystal environment. Our findings demonstrate that this approach reliably produces solid-state VCD spectra of model compounds. Although for large molecules with many atoms per unit cell, such as sofosbuvir, this approach has to be simplified and provides only a qualitative match, spectral calculations, and energy analysis helped us to decipher the observed differences in the experimental spectra of sofosbuvir.

Contact lenses as a potential vehicle of Candida transmission

PURPOSE

Contact lenses can be contaminated with various microorganisms, including pathogenic yeasts of the genus Candida, which are known for their ability to adhere to abiotic surfaces, including plastic materials used for various medical purposes. Microbial contamination of the lenses can lead to infection of the wearer's eyes. The purpose of this study was to simulate the contamination of contact lenses with C. albicans and C. parapsilosis, analyze the interaction of the microorganisms with the lens material, and optimize the protocol for PCR-based analysis of the microbial agents responsible for lens contamination.

METHODS

Hilafilcon lenses were exposed to C. albicans and C. parapsilosis cultures, washed, and examined for their ability to further spread the contamination. Scanning electron microscopy was used to analyze the attachment of yeast cells to the lenses. Infrared spectroscopy was used to examine the potential changes in the lens material due to Candida contamination. The protocol for DNA isolation from contaminated lenses was established to enable PCR analysis of microbes attached to the lenses.

RESULTS

Hilafilcon lenses contaminated with Candida were able to spread the contamination even after washing with saline or with a commercial cleaning solution. In the present experimental settings, the yeasts did not grow into the lenses but began to form biofilms on the surface. However, the ability of the lenses to retain water was altered. The PCR-based protocol could be used to help identify the type of contamination of contact lenses.

CONCLUSION

Once contaminated with Candida albicans or Candida parapsilosis, Hilafilcon contact lenses are difficult to clean. Yeasts began to form biofilms on lens surfaces.

Stereocontrolled Synthesis of Chiral Helicene-Indenido ansa- and Half-Sandwich Metal Complexes and Their Use in Catalysis

Despite recent tremendous progress in the synthesis of nonplanar chiral aromatics, and helicenes in particular, their conversion to half-sandwich or sandwich transition metal complexes still lags behind, although they represent an attractive family of modular and underexplored chiral architectures with a potential catalytic use. In this work, starting from various chiral helicene-indene proligands, we prepared the enantio- and diastereopure oxa[6]- and oxa[7]helicene-indenido half-sandwich RhI and RhIII complexes and oxa[7]helicene-bisindenido ansa-metallocene FeII complex. To document their use, oxahelicene-indenido half-sandwich RhIII complexes were employed as chiral catalysts in enantioselective C-H arylation of benzo[h]quinolines with 1-diazonaphthoquinones to afford a series of axially chiral biaryls in mostly good to high yields and in up to 96 : 4 er. Thus, we developed stereocontrolled synthesis of chiral helicene-indenido ansa- and half-sandwich metal complexes, successfully demonstrated the first use of such helicene Cp-related metal complexes in enantioselective catalysis, and described an unusual sequence of efficient central-to-helical-to-planar-to-axial chirality transfer.

Foldamers controlled by functional triamino acids: structural investigation of α/γ-hybrid oligopeptides

Peptide-like foldamers controlled by normal amide backbone hydrogen bonding have been extensively studied, and their folding patterns largely rely on configurational and conformational constraints induced by the steric properties of backbone substituents at appropriate positions. In contrast, opportunities to influence peptide secondary structure by functional groups forming individual hydrogen bond networks have not received much attention. Here, peptide-like foldamers consisting of alternating α,β,γ-triamino acids 3-amino-4-(aminomethyl)-2-methylpyrrolidine-3-carboxylate (AAMP) and natural amino acids glycine and alanine are reported, which were obtained by solution phase peptide synthesis. They form ordered secondary structures, which are dominated by a three-dimensional bridged triazaspiranoid-like hydrogen bond network involving the non-backbone amino groups, the backbone amide hydrogen bonds, and the relative configuration of the α,β,γ-triamino and α-amino acid building blocks. This additional stabilization leads to folding in both nonpolar organic as well as in aqueous environments. The three-dimensional arrangement of the individual foldamers is supported by X-ray crystallography, NMR spectroscopy, chiroptical methods, and molecular dynamics simulations.

Stereoselective Reduction of Steroidal 4-Ene-3-ketones in the Presence of Biomass-Derived Ionic Liquids Leading to Biologically Important 5β-Steroids

The stereoselective reduction of the steroidal 4-ene-3-ketone moiety (enone) affords the 5β-steroid backbone that is a key structural element of biologically important neuroactive steroids. Neurosteroids have been currently studied as novel and potent central nervous system drug-like compounds for the treatment of, e.g., postpartum depression. As a green methodology, we studied the palladium-catalyzed hydrogenation of steroidal 4-ene-3-ketones in the presence of ionic liquids derived from natural carboxylic acids. The hydrogenation proceeds with improved 5β-selectivity in the presence of tetrabutylammonium carboxylates as additives compared to the exclusive use of an organic solvent. Under optimal conditions, using tetrabutylammonium d-mandelate, the reduction of testosterone led to 5β-dihydrotestosterone in high yield and stereoselectivity and no byproduct formation was observed. Moreover, the catalyst could be recycled. The presence of additional substituents on the steroid backbone showed a significant effect on the 5β-selectivity.

What are the minimal folding seeds in proteins? Experimental and theoretical assessment of secondary structure propensities of small peptide fragments

Certain peptide sequences, some of them as short as amino acid triplets, are significantly overpopulated in specific secondary structure motifs in folded protein structures. For example, 74% of the EAM triplet is found in α-helices, and only 3% occurs in the extended parts of proteins (typically β-sheets). In contrast, other triplets (such as VIV and IYI) appear almost exclusively in extended parts (79% and 69%, respectively). In order to determine whether such preferences are structurally encoded in a particular peptide fragment or appear only at the level of a complex protein structure, NMR, VCD, and ECD experiments were carried out on selected tripeptides: EAM (denoted as pro-'α-helical' in proteins), KAM(α), ALA(α), DIC(α), EKF(α), IYI(pro-β-sheet or more generally, pro-extended), and VIV(β), and the reference α-helical CATWEAMEKCK undecapeptide. The experimental data were in very good agreement with extensive quantum mechanical conformational sampling. Altogether, we clearly showed that the pro-helical vs. pro-extended propensities start to emerge already at the level of tripeptides and can be fully developed at longer sequences. We postulate that certain short peptide sequences can be considered minimal "folding seeds". Admittedly, the inherent secondary structure propensity can be overruled by the large intramolecular interaction energies within the folded and compact protein structures. Still, the correlation of experimental and computational data presented herein suggests that the secondary structure propensity should be considered as one of the key factors that may lead to understanding the underlying physico-chemical principles of protein structure and folding from the first principles.

Superanionic DNA: enzymatic synthesis of hypermodified DNA bearing four different anionic substituents at all four nucleobases

We designed and synthesized a set of four 2'-deoxyribonucleoside 5'-O-triphosphates (dNTPs) derived from 5-substituted pyrimidines and 7-substituted 7-deazapurines bearing anionic substituents (carboxylate, sulfonate, phosphonate, and phosphate). The anion-linked dNTPs were used for enzymatic synthesis of modified and hypermodified DNA using KOD XL DNA polymerase containing one, two, three, or four modified nucleotides. The polymerase was able to synthesize even long sequences of >100 modified nucleotides in a row by primer extension (PEX). We also successfully combined two anionic and two hydrophobic dNTPs bearing phenyl and indole moieties. In PCR, the combinations of one or two modified dNTPs gave exponential amplification, while most of the combinations of three or four modified dNTPs gave only linear amplification in asymmetric PCR. The hypermodified ONs were successfully re-PCRed and sequenced by Sanger sequencing. Biophysical studies including hybridization, denaturation, CD spectroscopy and molecular modelling and dynamics suggest that the presence of anionic modifications in one strand decreases the stability of duplexes while still preserving the B-DNA conformation, whilst the DNA hypermodified in both strands adopts a different secondary structure.

Discovery of a Druggable, Cryptic Pocket in SARS-CoV-2 nsp16 Using Allosteric Inhibitors

A collaborative, open-science team undertook discovery of novel small molecule inhibitors of the SARS-CoV-2 nsp16-nsp10 2'-O-methyltransferase using a high throughput screening approach with the potential to reveal new inhibition strategies. This screen yielded compound 5a, a ligand possessing an electron-deficient double bond, as an inhibitor of SARS-CoV-2 nsp16 activity. Surprisingly, X-ray crystal structures revealed that 5a covalently binds within a previously unrecognized cryptic pocket near the S-adenosylmethionine binding cleft in a manner that prevents occupation by S-adenosylmethionine. Using a multidisciplinary approach, we examined the mechanism of binding of compound 5a to the nsp16 cryptic pocket and developed 5a derivatives that inhibited nsp16 activity and murine hepatitis virus replication in rat lung epithelial cells but proved cytotoxic to cell lines canonically used to examine SARS-CoV-2 infection. Our study reveals the druggability of this newly discovered SARS-CoV-2 nsp16 cryptic pocket, provides novel tool compounds to explore the site, and suggests a new approach for discovery of nsp16 inhibition-based pan-coronavirus therapeutics through structure-guided drug design.

Phenyl-Substituted Cibalackrot Derivatives: Synthesis, Structure, and Solution Photophysics

Three symmetrically and three unsymmetrically substituted cibalackrot (7,14-diphenyldiindolo[3,2,1-de:3',2',1'-ij][1,5]naphthyridine-6,13-dione, 1) dyes carrying two derivatized phenyl rings have been synthesized as candidates for molecular electronics and especially for singlet fission, a process of interest for solar energy conversion. Solution measurements provided singlet and triplet excitation energies and fluorescence yields and lifetimes; conformational properties were analyzed computationally. The molecular properties are close to ideal for singlet fission. However, crystal structures, obtained by single-crystal X-ray diffraction (XRD), are rather similar to those of the polymorphs of solid 1, in which the formation of a charge-separated state followed by intersystem crossing, complemented with excimer formation, outcompetes singlet fission. Results of calculations by the approximate SIMPLE method suggest which ones among the solid derivatives are the best candidates for singlet fission, but it appears difficult to change the crystal packing in a desirable direction. We also describe the preparation of three specifically deuteriated versions of 1, expected to help sort out the mechanism of fast intersystem crossing in its charge-separated state.

Helical Bilayer Nanographenes: Impact of the Helicene Length on the Structural, Electrochemical, Photophysical, and Chiroptical Properties

Helical bilayer nanographenes (HBNGs) are chiral π-extended aromatic compounds consisting of two π-π stacked hexabenzocoronenes (HBCs) joined by a helicene, thus resembling van der Waals layered 2D materials. Herein, we compare [9]HBNG, [10]HBNG, and [11]HBNG helical bilayers endowed with [9], [10], and [11]helicenes embedded in their structure, respectively. Interestingly, the helicene length defines the overlapping degree between the two HBCs (number of benzene rings involved in π-π interactions between the two layers), being 26, 14, and 10 benzene rings, respectively, according to the X-ray analysis. Unexpectedly, the electrochemical study shows that the lesser π-extended system [9]HBNG shows the strongest electron donor character, in part by interlayer exchange resonance, and more red-shifted values of emission. Furthermore, [9]HBNG also shows exceptional chiroptical properties with the biggest values of g_abs and g_lum (3.6 × 10^-2) when compared to [10]HBNG and [11]HBNG owing to the fine alignment in the configuration of [9]HBNG between its electric and magnetic dipole transition moments. Furthermore, spectroelectrochemical studies as well as the fluorescence spectroscopy support the aforementioned experimental findings, thus confirming the strong impact of the helicene length on the properties of this new family of bilayer nanographenes.

Helicene-based π-conjugated macrocycles: their synthesis, properties, chirality and self-assembly into molecular stripes on a graphite surface

Fully aromatic helicenes are attractive building blocks for the construction of inherently chiral π-conjugated macrocyclic nanocarbons. These hitherto rare molecular architectures are envisaged to exhibit remarkable (chir)optical properties, self-assembly, charge/spin transport, induced ring current or a fascinating Möbius topology. Here the synthesis of helically chiral macrocycles that combine angular dibenzo[5]helicene units as corners and linear trans-stilbene-4,4'-diyl linkers as edges is reported. By subjecting a racemic or enantiopure divinyl derivative of dibenzo[5]helicene to olefin metathesis, which was catalysed by a 2nd generation Piers catalyst under kinetic control, a π-conjugated helicene cyclic trimer (33%) and a tetramer (22%) were obtained, which were separated by GPC. Combining racemic/asymmetric synthesis with the resolution of enantiomers/diastereomers by SFC/HPLC on a chiral column, both homochiral (+)-(M,M,M)/(-)-(P,P,P) and heterochiral (+)-(M,M,P)/(-)-(M,P,P) stereoisomers of the helicene cyclic trimer could be obtained in an enantio- and diastereomerically enriched form. The complete energy profile of their interconversion was compiled on the basis of kinetic measurements and numerical solution of the proposed kinetic model. In equilibrium, the heterochiral diastereomer predominates over the homochiral one (ca. 75 : 25 at 76 °C). π-Conjugation along a large, twisted circuit in the helicene cyclic trimer is rather disrupted, stabilising this formally antiaromatic molecule. Using an optimised PeakForce mode of ambient AFM, the self-assembly of otherwise highly mobile stereoisomers of the helicene cyclic trimer on the HOPG surface could be studied. Irrespective of the stereochemistry, strong preferences for the edge-to-edge interaction of these macrocycles were found to form very long parallel 1D molecular stripes in ordered 2D nanocrystals, a result also supported by molecular dynamics simulations. Six trityl groups, initially introduced to the macrocycle to enhance solubility, serve as a key "molecular Velcro" system in the self-assembly of macrocycles to maximise their mutual van der Waals interactions.

31P NMR parameters may facilitate the stereochemical analysis of phosphorus-containing compounds

Conventional Nuclear Magnetic Resonance (NMR) analysis relies on H-H/C-H interactions. However, these interactions are sometimes insufficient for an accurate and precise NMR analysis. In this study, we show that ³¹P NMR parameters can provide critical structural insights into the stereochemistry of phosphorus-containing compounds. For this purpose, we prepared a set of model phosphorus-based proline derivatives, separated diastereoisomers, and determined their absolute configuration by single-crystal X-ray diffraction. After supplementing these results by electronic circular dichroism (ECD) spectroscopy, we combined experimental data and DFT calculations from our model compounds to perform a detailed conformational analysis, thereby determining their relative configuration. Overall, our findings establish an experimental paradigm for combining ³¹P NMR spectroscopy with other optical methods to facilitate the stereochemical analysis of phosphorus-containing compounds.

In vitro evolution reveals non-cationic protein-RNA interaction mediated by metal ions

RNA–peptide/protein interactions have been of utmost importance to life since its earliest forms, reaching even before the last universal common ancestor (LUCA). However, the ancient molecular mechanisms behind this key biological interaction remain enigmatic because extant RNA–protein interactions rely heavily on positively charged and aromatic amino acids that were absent (or heavily under-represented) in the early pre-LUCA evolutionary period. Here, an RNA-binding variant of the ribosomal uL11 C-terminal domain was selected from an approximately 10¹⁰ library of partially randomized sequences, all composed of ten prebiotically plausible canonical amino acids. The selected variant binds to the cognate RNA with a similar overall affinity although it is less structured in the unbound form than the wild-type protein domain. The variant complex association and dissociation are both slower than for the wild-type, implying different mechanistic processes involved. The profile of the wild-type and mutant complex stabilities along with molecular dynamics simulations uncovers qualitative differences in the interaction modes. In the absence of positively charged and aromatic residues, the mutant uL11 domain uses ion bridging (K⁺/Mg²⁺) interactions between the RNA sugar-phosphate backbone and glutamic acid residues as an alternative source of stabilization. This study presents experimental support to provide a new perspective on how early protein–RNA interactions evolved, where the lack of aromatic/basic residues may have been compensated by acidic residues plus metal ions.

Push–pull amino-nitro helicenes: synthesis, (chir)optical properties and self-assembly into thin films

A series of regioisomeric push–pull amino-nitro [6]helicenes and a related [7]helicene derivative were prepared and their racemates resolved into enantiomers.

Rhodium-Catalyzed Enantioselective Synthesis of Highly Fluorescent and CPL-Active Dispiroindeno[2,1-c]fluorenes

The enantioselective synthesis of chiral [7]-helical dispirodihydro[2,1-c]indenofluorenes (DSF-IFs) was achieved for the first time in good yields with high er values (er up to 99 : 1). The crucial step of the whole reaction sequence was the enantioselective intramolecular [2+2+2] cycloaddition of tethered triynediols to indenofluorenediols, which was catalyzed by a Rh/SEGPHOS® complex. Further transformations led to the corresponding DSF-IFs. The prepared helically chiral DSF-IFs combine circularly polarized luminescence (CPL) activity (g_lum =∼10^-3 ) with exceptionally high fluorescence quantum yields (up to Φ_lum =0.97).

Enzyme catalysis prior to aromatic residues: Reverse engineering of a dephospho-CoA kinase

The wide variety of protein structures and functions results from the diverse properties of the 20 canonical amino acids. The generally accepted hypothesis is that early protein evolution was associated with enrichment of a primordial alphabet, thereby enabling increased protein catalytic efficiencies and functional diversification. Aromatic amino acids were likely among the last additions to genetic code. The main objective of this study was to test whether enzyme catalysis can occur without the aromatic residues (aromatics) by studying the structure and function of dephospho-CoA kinase (DPCK) following aromatic residue depletion. We designed two variants of a putative DPCK from Aquifex aeolicus by substituting (a) Tyr, Phe and Trp or (b) all aromatics (including His). Their structural characterization indicates that substituting the aromatics does not markedly alter their secondary structures but does significantly loosen their side chain packing and increase their sizes. Both variants still possess ATPase activity, although with 150-300 times lower efficiency in comparison with the wild-type phosphotransferase activity. The transfer of the phosphate group to the dephospho-CoA substrate becomes heavily uncoupled and only the His-containing variant is still able to perform the phosphotransferase reaction. These data support the hypothesis that proteins in the early stages of life could support catalytic activities, albeit with low efficiencies. An observed significant contraction upon ligand binding is likely important for appropriate organization of the active site. Formation of firm hydrophobic cores, which enable the assembly of stably structured active sites, is suggested to provide a selective advantage for adding the aromatic residues.

Rapid Self-Healing and Thixotropic Organogelation of Amphiphilic Oleanolic Acid-Spermine Conjugates

Natural and abundant plant triterpenoids are attractive starting materials for the synthesis of conformationally rigid and chiral building blocks for functional soft materials. Here, we report the rational design of three oleanolic acid-triazole-spermine conjugates, containing either one or two spermine units in the target molecules, using the Cu(I)-catalyzed Huisgen 1,3-dipolar cycloaddition reaction. The resulting amphiphile-like molecules 2 and 3, bearing just one spermine unit in the respective molecules, self-assemble into highly entangled fibrous networks leading to gelation at a concentration as low as 0.5% in alcoholic solvents. Using step-strain rheological measurements, we show rapid self-recovery (up to 96% of the initial storage modulus) and sol ⇔ gel transition under several cycles. Interestingly, rheological flow curves reveal the thixotropic behavior of the gels. To the best of our knowledge, this kind of behavior was not shown in the literature before, neither for a triterpenoid nor for its derivatives. Conjugate 4, having a bolaamphiphile-like structure, was found to be a nongelator. Our results indicate that the position and number of spermine units alter the gelation properties, gel strength, and their self-assembly behavior. Preliminary cytotoxicity studies of the target compounds 2-4 in four human cancer cell lines suggest that the position and number of spermine units affect the biological activity. Our results also encourage exploring other triterpenoids and their derivatives as sustainable, renewable, and biologically active building blocks for multifunctional soft organic nanomaterials.

Enzymatic synthesis of hypermodified DNA polymers for sequence-specific display of four different hydrophobic groups

A set of modified 2'-deoxyribonucleoside triphosphates (dNTPs) bearing a linear or branched alkane, indole or phenyl group linked through ethynyl or alkyl spacer were synthesized and used as substrates for polymerase synthesis of hypermodified DNA by primer extension (PEX). Using the alkyl-linked dNTPs, the polymerase synthesized up to 22-mer fully modified oligonucleotide (ON), whereas using the ethynyl-linked dNTPs, the enzyme was able to synthesize even long sequences of >100 modified nucleotides in a row. In PCR, the combinations of all four modified dNTPs showed only linear amplification. Asymmetric PCR or PEX with separation or digestion of the template strand can be used for synthesis of hypermodified single-stranded ONs, which are monodispersed polymers displaying four different substituents on DNA backbone in sequence-specific manner. The fully modified ONs hybridized with complementary strands and modified DNA duplexes were found to exist in B-type conformation (B- or C-DNA) according to CD spectral analysis. The modified DNA can be replicated with high fidelity to natural DNA through PCR and sequenced. Therefore, this approach has a promising potential in generation and selection of hypermodified aptamers and other functional polymers.

Characterization and in vitro assembly of tick-borne encephalitis virus C protein

Tick-borne encephalitis virus (TBEV), a member of flaviviruses, represents a serious health threat by causing human encephalitis mainly in central and eastern Europe, Russia, and northeastern Asia. As no specific therapy is available, there is an urgent need to understand all steps of the TBEV replication cycle at the molecular level. One of the critical events is the packaging of flaviviral genomic RNA by TBEV C protein to form a nucleocapsid. We purified recombinant TBEV C protein and used a combination of physical-chemical approaches, such as size-exclusion chromatography, circular dichroism, NMR spectroscopies, and transmission electron microscopy, to analyze its structural stability and its ability to dimerize/oligomerize. We compared the ability of TBEV C protein to assemble in vitro into a nucleocapsid-like structure with that of dengue C protein.

Synthesis of Racemic, Diastereopure, and Enantiopure Carba- or Oxa[5]-, [6]-, [7]-, and -[19]helicene (Di)thiol Derivatives

A series of carba- or oxa[5]-, [6]-, [7]-, and -[19]helicene (di)thiols was prepared. The Miyazaki-Newman-Kwart rearrangement of (dimethylcarbamothioyl)oxy (oxa)helicenes in a flow reactor or nucleophilic substitution of dichloro (oxa)helicenes with alkanethiolates were used in the sulfanylation step. Despite the high temperatures employed in this key step, no conformational scrambling was observed during the asymmetric synthesis of the diastereo- and enantiopure oxahelicenes. Single-molecule conductivity of the longest oxa[19]helicene dithiol derivative was studied by the scanning tunneling microscopy break-junction method.