An Atlas of the base inter-RNA stacks involved in bacterial translation

Nucleobase-specific noncovalent interactions play a crucial role in translation. Herein, we provide a comprehensive analysis of the stacks between different RNA components in the crystal structures of the bacterial ribosome caught at different translation stages. Analysis of tRNA||rRNA stacks reveals distinct behaviour; both the A-and E-site tRNAs exhibit unique stacking patterns with 23S rRNA bases, while P-site tRNAs stack with 16S rRNA bases. Furthermore, E-site stacks exhibit diverse face orientations and ring topologies-rare for inter-chain RNA interactions-with higher average interaction energies than A or P-site stacks. This suggests that stacking may be essential for stabilizing tRNA progression through the E-site. Additionally, mRNA||rRNA stacks reveal other geometries, which depend on the tRNA binding site, whereas 16S rRNA||23S rRNA stacks highlight the importance of specific bases in maintaining the integrity of the translational complex by linking the two rRNAs. Furthermore, tRNA||mRNA stacks exhibit distinct geometries and energetics at the E-site, indicating their significance during tRNA translocation and elimination. Overall, both A and E-sites display a more diverse distribution of inter-RNA stacks compared to the P-site. Stacking interactions in the active ribosome are not simply accidental byproducts of biochemistry but are likely invoked to compensate and support the integrity and dynamics of translation.

Synthesis, biological evaluation, and molecular docking study of xanthene-linked thiosemicarbazones as cholinesterase inhibitors

This study delineates the design and synthesis of a series of xanthene-based thiosemicarbazones that show low μM inhibition of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), crucial enzymes associated with, among others, Alzheimer's Disease (AD) pathology. Despite FDA-approved AChE inhibitors being frontline treatments for AD, there remains a need for agents exhibiting improved efficacy and selectivity. Our synthesized series demonstrate meaningful inhibition against AChE (IC50 ranging from 4.2 to 62 μM). These compounds exhibit comparatively lower potency against BChE (IC50 values between 64 and 315 μM), showcasing a pronounced AChE selectivity compared to physostigmine. The selectivity index for the compounds between the two targets does vary between 0.02 and 0.75 highlighting that even minor structural differences can have drastic effects on protein interactions. Molecular docking insights further substantiated these observations, revealing the importance of the xanthene scaffold for AChE-binding and the aryl R2 moiety for BChE interactions. Notably, some compounds demonstrated dual enzyme targeting, emphasizing their interactions could be exploited for developing monotherapies against cholinesterase-associated neurodegenerative afflictions like AD. Collectively, these findings suggest that xanthene-based thiosemicarbazones are a promising and highly accessible scaffold that deserve further investigative exploration in the cholinesterase inhibitor therapeutic landscape.Communicated by Ramaswamy H. Sarma.

Improvement of electrolytes for aluminum ion batteries: A molecular dynamics study

The aluminum ion battery (AIB) is a promising technology, but there is a lack of understanding of the desired nature of the batteries' electrolytes. The ionic charge carriers in these batteries are not simply Al3+ ions but the anionic AlCl4- and Al2Cl7-, which form in the electrolyte. Using computational analysis, this study illustrates the effect of mole ratios and organic solvents to improve the AIB electrolytes. To this end, molecular dynamics simulations were conducted on varying ratios forming acidic, neutral, and basic mixtures of the AlCl3 salt with 1-ethyl-3-methylimidazolium chloride (EMImCl) ionic liquid (IL) and an organic solvent electrolyte [dichloromethane (DCM) or toluene]. The data obtained from diffusion calculations indicates that the solvents could improve the transport properties. Both DCM and toluene lead to higher diffusion coefficients, and higher conductivity. Detailed calculations demonstrated solvents can effectively improve the formation of AlCl3⋯Cl (AlCl4-) and AlCl4-···AlCl4- (Al2Cl7-) especially in acidic mixtures. The densities, around 1.25 g/cm3 for electrolyte mixtures of AlCl3-EMImCl, were consistent with experiment. These results, in agreement with experimental findings, strongly suggest that DCM in acidic media with AlCl3 and EMImCl might provide a promising basis for battery development.

Biallelic Mutations in P4HTM Cause Syndromic Obesity

We previously demonstrated that 50% of children with obesity from consanguineous families from Pakistan carry pathogenic variants in known monogenic obesity genes. Here, we have discovered a novel monogenetic recessive form of severe childhood obesity using an in-house computational staged approach. The analysis included whole-exome sequencing data of 366 children with severe obesity, 1,000 individuals of the Pakistan Risk of Myocardial Infarction Study (PROMIS) study, and 200,000 participants of the UK Biobank to prioritize genes harboring rare homozygous variants with putative effect on human obesity. We identified five rare or novel homozygous missense mutations predicted deleterious in five consanguineous families in P4HTM encoding prolyl 4-hydroxylase transmembrane (P4H-TM). We further found two additional homozygous missense mutations in children with severe obesity of Indian and Moroccan origin. Molecular dynamics simulation suggested that these mutations destabilized the active conformation of the substrate binding domain. Most carriers also presented with hypotonia, cognitive impairment, and/or developmental delay. Three of the five probands died of pneumonia during the first 2 years of the follow-up. P4HTM deficiency is a novel form of syndromic obesity, affecting 1.5% of our children with obesity associated with high mortality. P4H-TM is a hypoxia-inducible factor that is necessary for survival and adaptation under oxygen deprivation, but the role of this pathway in energy homeostasis and obesity pathophysiology remains to be elucidated.

Rational Design, Synthesis, and Characterization of a Solid Δ9-Tetrahydrocannabinol Nanoformulation Suitable for "Microdosing" Applications

Background: This article highlights the formulation of a solid Δ9-tetrahydrocannabinol (THC)-loaded ingestible prepared from pure THC distillate. Methods: A THC-containing ethanol-assisted cannabinoid nanoemulsion (EACNE) was created using a solvent displacement technique. Subsequently, the EACNE was converted to a solid powdery material while still retaining its THC potency, a format uniquely suited for "microdosing" applications. Results: EACNE had an average lipid droplet size of ∼190 nm, with a polydispersity index of 0.15, and an average droplet ζ potential of -49±10 mV. The nanoemulsion (NE) was colloidally stable for at least 6 weeks, with no meaningful change in cannabinoid potency over the experimental period, as determined by high-performance liquid chromatography analysis. The EACNE remained stable when subjected to physical stresses such as heat, freeze/thaw cycles, carbonation, dilution to beverage concentrations, high sucrose concentrations, and a pH range between 5 and 8. The microencapsulated EACNE demonstrated limited free-flowing behavior but was freely redispersible in water without any visible phase separation. Conclusions: We report the design, creation, and characterization of a THC NE generated without the use of specialized equipment, such as a microfluidizer or a high-pressure homogenizer. This emulsion could readily be converted to a water-redispersible powder. This embodiment is particularly suited for THC "microdosing," a practice that might decouple the health benefits of THC from its psychotropic effects.

Structural Mapping of the Base Stacks Containing Post-transcriptionally Modified Bases in RNA

Post-transcriptionally modified bases play vital roles in many biochemical processes involving RNA. Analysis of the non-covalent interactions associated with these bases in RNA is crucial for providing a more complete understanding of the RNA structure and function; however, the characterization of these interactions remains understudied. To address this limitation, we present a comprehensive analysis of base stacks involving all crystallographic occurrences of the most biologically relevant modified bases in a large dataset of high-resolution RNA crystal structures. This is accompanied by a geometrical classification of the stacking contacts using our established tools. Coupled with quantum chemical calculations and an analysis of the specific structural context of these stacks, this provides a map of the stacking conformations available to modified bases in RNA. Overall, our analysis is expected to facilitate structural research on altered RNA bases.

Occurrence and classification of T-shaped interactions between nucleobases in RNA structures

Understanding the frequency and structural context of discrete noncovalent interactions between nucleotides is of pivotal significance in establishing the rules that govern RNA structure and dynamics. Although T-shaped contacts (i.e., perpendicular stacking contacts) between aromatic amino acids and nucleobases at the nucleic acid-protein interface have recently garnered attention, the analogous contacts within the nucleic acid structures have not been discussed. In this work, we have developed an automated method for identifying and unambiguously classifying T-shaped interactions between nucleobases. Using this method, we identified a total of 3261 instances of T-shaped (perpendicular stacking) contacts between two nucleobases in an array of RNA structures from an up-to-date dataset of <= 3.5 Å resolution crystal structures deposited in the Protein Data Bank.

Dock-able linear and homodetic di, tri, tetra and pentapeptide library from canonical amino acids: SARS-CoV-2 Mpro as a case study

Peptide-based therapeutics are increasingly pushing to the forefront of biomedicine with their promise of high specificity and low toxicity. Although noncanonical residues can always be used, employing only the natural 20 residues restricts the chemical space to a finite dimension allowing for comprehensive in silico screening. Towards this goal, the dataset comprising all possible di-, tri-, and tetra-peptide combinations of the canonical residues has been previously reported. However, with increasing computational power, the comprehensive set of pentapeptides is now also feasible for screening as the comprehensive set of cyclic peptides comprising four or five residues. Here, we provide both the complete and prefiltered libraries of all di-, tri-, tetra-, and penta-peptide sequences from 20 canonical amino acids and their homodetic (N-to-C-terminal) cyclic homologues. The FASTA, simplified molecular-input line-entry system (SMILES), and structure-data file (SDF)-three dimension (3D) libraries can be readily used for screening against protein targets. We also provide a simple method and tool for conducting identity-based filtering. Access to this dataset will accelerate small peptide screening workflows and encourage their use in drug discovery campaigns. As a case study, the developed library was screened against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease to identify potential small peptide inhibitors.

Repurposing host-guest chemistry to sequester virulence and eradicate biofilms in multidrug resistant Pseudomonas aeruginosa and Acinetobacter baumannii

The limited diversity in targets of available antibiotic therapies has put tremendous pressure on the treatment of bacterial pathogens, where numerous resistance mechanisms that counteract their function are becoming increasingly prevalent. Here, we utilize an unconventional anti-virulence screen of host-guest interacting macrocycles, and identify a water-soluble synthetic macrocycle, Pillar[5]arene, that is non-bactericidal/bacteriostatic and has a mechanism of action that involves binding to both homoserine lactones and lipopolysaccharides, key virulence factors in Gram-negative pathogens. Pillar[5]arene is active against Top Priority carbapenem- and third/fourth-generation cephalosporin-resistant Pseudomonas aeruginosa and Acinetobacter baumannii, suppressing toxins and biofilms and increasing the penetration and efficacy of standard-of-care antibiotics in combined administrations. The binding of homoserine lactones and lipopolysaccharides also sequesters their direct effects as toxins on eukaryotic membranes, neutralizing key tools that promote bacterial colonization and impede immune defenses, both in vitro and in vivo. Pillar[5]arene evades both existing antibiotic resistance mechanisms, as well as the build-up of rapid tolerance/resistance. The versatility of macrocyclic host-guest chemistry provides ample strategies for tailored targeting of virulence in a wide range of Gram-negative infectious diseases.

The "Nitrogen Effect": Complexation with Macrocycles Potentiates Fused Heterocycles to Form Halogen Bonds in Competitive Solvents

Weak intermolecular forces are typically very difficult to observe in highly competitive polar protic solvents as they are overwhelmed by the quantity of competing solvent. This is even more challenging for three-component ternary assemblies of pure organic compounds. In this work, we overcome these complications by leveraging the binding of fused aromatic N-heterocycles in an open resorcinarene cavity to template the formation of a three-component halogen-bonded ternary assembly in a protic polar solvent system.

"Breaking bud": the effect of direct chemical modifications of phytocannabinoids on their bioavailability, physiological effects, and therapeutic potential

Tetrahydrocannabinol (THC) and cannabidiol (CBD) are the two "major cannabinoids". However, their incorporation into clinical and nutraceutical preparations is challenging, owing to their limited bioavailability, low water solubility, and variable pharmacokinetic profiles. Understanding the organic chemistry of the major cannabinoids provides us with potential avenues to overcome these issues through derivatization. The resulting labile pro-drugs offer ready cannabinoid release in vivo, have augmented bioavailability, or demonstrate interesting pharmacological properties in their own right. This review identifies and discusses a subset of these advanced derivatization strategies for the major cannabinoids, where the starting material is the pure phytocannabinoid itself, and the final product either a cannabinoid pro-drug, or a novel pharmacoactive material.

Structural and Energetic Features of Base-Base Stacking Contacts in RNA

Nucleobase π-π stacking is one of the crucial organizing interactions within three-dimensional (3D) RNA architectures. Characterizing the structural variability of these contacts in RNA crystal structures will help delineate their subtleties and their role in determining function. This analysis of different stacking geometries found in RNA X-ray crystal structures is the largest such survey to date; coupled with quantum-mechanical calculations on typical representatives of each possible stacking arrangement, we determined the distribution of stacking interaction energies. A total of 1,735,481 stacking contacts, spanning 359 of the 384 theoretically possible distinct stacking geometries, were identified. Our analysis reveals preferential occurrences of specific consecutive stacking arrangements in certain regions of RNA architectures. Quantum chemical calculations suggest that 88 of the 359 contacts possess intrinsically stable stacking geometries, whereas the remaining stacks require the RNA backbone or surrounding macromolecular environment to force their formation and maintain their stability. Our systematic analysis of π-π stacks in RNA highlights trends in the occurrence and localization of these noncovalent interactions and may help better understand the structural intricacies of functional RNA-based molecular architectures.

Guanidinium–amino acid hydrogen-bonding interactions in protein crystal structures: implications for guanidinium-induced protein denaturation

Structural analysis of guanidinium–amino acid interaction pairs in protein crystal structures is coupled with an effective scheme for classifying the optimized pairs, to gain understanding of the guanidinium:protein hydrogen bonding modes.

Divalent Benzimidazolium-Based Axles for Self-Reporting Pseudorotaxanes

Mono- and (bis)benzimidazoliums were evaluated both experimentally and computationally for their potential as pseudopolyrotaxane axle building blocks. Their aggregation and photophysical behavior, along with their potential to form a [2]pseudorotaxane with dibenzyl-24-crown-8, was studied through the synergistic application of 1D/2D and diffusion-ordered NMR spectroscopy, mass spectrometry, ultraviolet-visible and fluorescence spectroscopy, and time-dependent density functional theory. Their photophysical behavior was measured and modeled as a function of protonation state, solvent, and concentration. The axles show strong solvochromaticism and a very pronounced concentration-dependent optical profile, including self-quenching when a pseudorotaxane is formed. This axle with multiple recognition sites has the potential to form pseudorotaxanes with tunable optical behavior.

The discovery of Zika virus NS2B-NS3 inhibitors with antiviral activity via an integrated virtual screening approach

With expanding recent outbreaks and a lack of treatment options, the Zika virus (ZIKV) poses a severe health concern. The availability of ZIKV NS2B-NS3 co-crystallized structures paved the way for rational drug discovery. A computer-aided structure-based approach was used to screen a diverse library of compounds against ZIKV NS2B-NS3 protease. The top hits were selected based on various binding free energy calculations followed by per-residue decomposition analysis. The selected hits were then evaluated for their biological potential with ZIKV protease inhibition assay and antiviral activity. Among 26 selected compounds, 8 compounds showed promising activity against ZIKV protease with a percentage inhibition of greater than 25 and 3 compounds displayed ∼50% at 10 µM, which indicates an enrichment rate of approximately 36% (threshold IC₅₀ < 10 µM) in the ZIKV-NS2B-NS3 protease inhibition assay. Of these, only one compound (23) produced whole-cell anti-ZIKV activity, and the binding mode of 23 was extensively analyzed through long-run molecular dynamics simulations. The current study provides a promising starting point for the further development of novel compounds against ZIKV.

Giving Preparative Thin-Layer Chromatography Some Tender ­Loving Care

Preparative thin-layer chromatography (prepTLC) is a commonly used method of purification suitable for small-scale reactions. However, descriptions of the preferred methodology to load, run, and recover samples from prepTLC are non-standard and varied, making it part of the ‘hidden curriculum’ of laboratory techniques. In this article we report on the simple, cost-effective methods we use to load and collect samples from a plate, which enhance the convenience, speed, and precision of this technique.

Naphthalene-functionalized resorcinarene as selective, fluorescent self-quenching sensor for kynurenic acid

Naphthalene-functionalized resorcinarene selectively binds kynurenic acid in the presence of excess tryptophan in aqueous media, highlighting the potential of functionalized resorcinarenes as sensory recognition elements for biomolecular analytes.

A revised synthesis of 6-alkoxy-2-aminopurines with late-stage convergence allowing for increased molecular complexity

This streamlined synthesis allows the alcohol at the 6-position of 6-alkoxy-2-arylaminopurines to be used only in moderate excess, rather than as solvent, opening up the possibility of accessing more complicated molecules.

Reaction of Alkynyl- and Alkenyltrifluoroborates with Propargyldicobalt Cations: Alkynylation, Alkenylation, and Cyclopropanation Product Pathways

The Lewis acid-mediated Nicholas reactions of propargyl acetate-Co₂(CO)₆ complexes with a series of potassium alkynyltrifluoroborates and potassium alkenyltrifluoroborates are described. Alkynyltrifluoroborates directly alkynylate the intermediate propargyldicobalt cations. In contrast, alkenyltrifluoroborates proceed through one of the three modes of dominant reactivity: C-2-substituted alkenyltrifluorobrates directly alkenylate, predominantly with the retention of stereochemistry. C-1-substituted alkenyltrifluoroborates alkenylate at C-2. Potassium vinyltrifluoroborate incorporates a cyclopropane at the site propargyl to alkynedicobalt. Computational analysis of these systems explains the differential modes of reactivity of alkenyltrifluoroborates and outlines the probable mechanisms for the formation of each product.

Fragment-based in silico design of SARS-CoV-2 main protease inhibitors

3CLpro is essential for SARS-CoV-2 replication and infection; its inhibition using small molecules is a potential therapeutic strategy. In this study, a comprehensive crystallography-guided fragment-based drug discovery approach was employed to design new inhibitors for SARS-CoV-2 3CLpro. All small molecules co-crystallized with SARS-CoV-2 3CLpro with structures deposited in the Protein Data Bank were used as inputs. Fragments sitting in the binding pocket (87) were grouped into eight geographical types. They were interactively coupled using various synthetically reasonable linkers to generate larger molecules with divalent binding modes taking advantage of two different fragments' interactions. In total, 1,251 compounds were proposed, and 7,158 stereoisomers were screened using Glide (standard precision and extra precision), AutoDock Vina, and Prime MMGBSA. The top 22 hits having conformations approaching the linear combination of their constituent fragments were selected for MD simulation on Desmond. MD simulation suggested 15 of these did adopt conformations very close to their constituent pieces with far higher binding affinity than either constituent domain alone. These structures could provide a starting point for the further design of SARS-CoV-2 3CLpro inhibitors with improved binding, and structures are provided.

Synthesis, characterization and stress-testing of a robust quillaja saponin stabilized oil-in-water phytocannabinoid nanoemulsion

BACKGROUND

This study describes the design, optimization, and stress-testing of a novel phytocannabinoid nanoemulsion generated using high-pressure homogenization. [Formula: see text], a plant-derived commercial emulsifier containing quillaja saponin, was used to stabilize the lipid phase droplets in water. Stress-testing was performed on this nanoemulsion in order to evaluate its chemical and colloidal stability under the influence of different environmental factors, encompassing both physical and chemical stressors.

METHODS

Extensive optimization studies were conducted to arrive at an ideal nanoemulsion formulation. A coarse emulsion containing 16.6 wt% CBD-enriched cannabis distillate and 83.4 wt% carrier (soybean) oil dispersed in 10 wt% [Formula: see text] (1.5 wt% quillaja saponin) solution after 10 homogenization cycles at a pressure of 30,000 psi produced a stable nanoemulsion. This nanoemulsion was then subjected to the stress studies.

RESULTS

The optimized nanoemulsion had an average droplet diameter of ca. 120 nm and average droplet surface ζ potentials of ca. -30 mV. It was imaged and characterized by a variety of protocols. It proved to be stable to droplet agglomeration and phase separation upon storage under ambient conditions for 6 weeks, as well as under a variety of physical stressors such as heat, cold, dilution, and carbonation. pH values ≤2 and moderately high salt concentrations (> 100 mM), however, destabilized the nanoemulsion, eventually leading to phase separation. Cannabis potency, determined by HPLC, was detrimentally affected by any changes in the nanoemulsion phase stability.

CONCLUSIONS

Quillaja saponin stabilized cannabidiol(CBD)-enriched nanoemulsions are stable, robust systems even at low emulsifier concentrations, and are therefore significant from both a scientific as well as a commercial perspective.

Synergistic broad-spectrum antibacterial activity of Hypoxis hemerocallidea-derived silver nanoparticles and streptomycin against respiratory pathobionts

Respiratory tract infections arise due to the introduction of microbes into the airway, disrupting the normal, healthy, complex interdependent microbiome. The selective disruption of this community can be either beneficial or dangerous. Nanoparticles are a potential tool for modifying this population. Coated silver nanoparticles (AgNPs) were synthesized using ethanolic extracts of Hypoxis hemerocallidea (EEHH), a Southern African plant used extensively in traditional medicine and the source of many bioactive secondary metabolites. The room temperature reaction between silver nitrate and EEHH forms largely spherical AgNPs with an average diameter of 6-20 nm. These nanoparticles show similar levels of antibacterial activity as the broad-spectrum antibiotic streptomycin against Bacillus cereus, Streptococcus pneumonia, Escherichia coli, Pseudomonas aeuroginosa, and Moraxella catarrhalis. However, the AgNPs synergistically increase the antibacterial activity of streptomycin when they are applied in combination (30-52%). AgNPs are reiterated to be promising dual-function antibiotics, synergistically enhancing activity while also acting as delivery agents for small molecules.

New isolate from Salvinia molesta with antioxidant and urease inhibitory activity

Urease plays a significant role in the pathogenesis of urolithiasis pyelonephritis, urinary catheter encrustation, hepatic coma, hepatic encephalopathy, and peptic acid duodenal ulcers. Salvinia molesta was explored to identify new bioactive compounds with particular emphasis on urease inhibitors. The aqueous methanol extract was fractionated using solvents of increasing polarity. A series of column chromatography and later HPLC were performed on butanol extract. The structures of the resulting pure compounds were resolved using NMR (1D and 2D), infrared, and mass spectroscopy. The novel isolate was evaluated for antioxidant activity (using DPPH, superoxide anion radical scavenging, oxidative burst, and Fe⁺² chelation assays), anti-glycation behavior, anticancer activity, carbonic anhydrase inhibition, phosphodiesterase inhibition, and urease inhibition. One new glucopyranose derivative 6'-O-(3,4-dihydroxybenzoyl)-4'-O-(4-hydroxybenzoyl)-α/β-D-glucopyranoside (1) and four known glycosides were identified. Glycoside 1 demonstrated promising antioxidant potential with IC₅₀ values of 48.2 ± 0.3, 60.3 ± 0.6, and 42.1 ± 1.8 μM against DPPH, superoxide radical, and oxidative burst, respectively. Its IC₅₀ in the Jack bean urease inhibition assay was 99.1 ± 0.8 μM. The mechanism-based kinetic studies presented that compound 1 is a mixed-type inhibitor of urease with a K_i value of 91.8 ± 0.1 μM. Finally, molecular dynamic simulations exploring the binding mode of compound 1 with urease provided quantitative agreement between estimated binding free energies and the experimental results. The studies corroborate the use of compound 1 as a lead for QSAR studies as an antioxidant and urease inhibitor. Moreover, it needs to be further evaluated through the animal model, that is, in vivo or tissue culture-based ex-vivo studies, to establish their therapeutic potential against oxidative stress phosphodiesterase-II and urease-induced pathologies.

The biosynthesis of the cannabinoids

Abstract

Cannabis has been integral to Eurasian civilization for millennia, but a century of prohibition has limited investigation. With spreading legalization, science is pivoting to study the pharmacopeia of the cannabinoids, and a thorough understanding of their biosynthesis is required to engineer strains with specific cannabinoid profiles. This review surveys the biosynthesis and biochemistry of cannabinoids. The pathways and the enzymes’ mechanisms of action are discussed as is the non-enzymatic decarboxylation of the cannabinoic acids. There are still many gaps in our knowledge about the biosynthesis of the cannabinoids, especially for the minor components, and this review highlights the tools and approaches that will be applied to generate an improved understanding and consequent access to these potentially biomedically-relevant materials.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s42238-021-00062-4.

Not-So-Innocent Anions Determine the Mechanism of Cationic Alkylators

Alkylating reagents based on thioimidazolium ionic liquids were synthesized and the influence of the anion on the alkylation reaction mechanism explored in detail using both experimental and computational methods. Thioimidazolium cations transfer alkyl substituents to nucleophiles, however the reaction rate was highly dependent on anion identity, demonstrating that the anion is not innocent in the mechanism. Detailed analysis of the computationally-derived potential energy surfaces associated with possible mechanisms indicated that this dependence arises from a combination of anion induced electronic, steric and coordinating effects, with highly nucleophilic anions catalyzing a 2-step process while highly non-nucleophilic, delocalized anions favor a 1-step reaction. This work also confirms the presence of ion-pairs and aggregates in solution thus supporting anion-induced control over the reaction rate and mechanism. These findings provide new insight into an old reaction allowing for better design of cationic alkylators in synthesis, gene expression, polymer science, and protein chemistry applications.

Extensive Crystallographic Fragment-Based Approach to Design SARS CoV2 3CLpro Main Protease Inhibitors and Related Metadata.. [DOI: 10.26434/chemrxiv.13550246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

<p>3CLpro is a vital protein for the SARS-CoV-2 replications and its inhibition using small molecules is a <i>bona fide</i> approach used to develop new drugs against the virus. In this study, a comprehensive crystallography-guided fragment-based drug discovery approach was employed to design new inhibitors for SARS-CoV-2 3CLpro. Protein Data Bank was explored to find small molecules cocrystallized with SARS-CoV-2 3CLpro. The fragments sitting in the binding pocket (87) were interactively coupled using various linkers with the intention to get molecules having the same orientation as those of the constituting fragments. In total, 1251 couples were prepared and converted to maximum possible stereoisomers using LigPrep for screening using Glide (standard precision and extra precision), AutoDock Vina, and Prime MMGBSA. Top 22 hits having conformations similar to their cocrystallized fragments were selected for MD simulation on Desmond. MD simulation suggested that 15 hits had conformations very close to their constituting fragments. Results indicated that these hits were computationally reliable and could be considered for further development. This suggests that the study could provide a benchmark starting point for the further design of SARS-CoV-2 3CLpro inhibitors with improved binding (data provided). <br></p>

Extensive Crystallographic Fragment-Based Approach to Design SARS CoV2 3CLpro Main Protease Inhibitors and Related Metadata.. [DOI: 10.26434/chemrxiv.13550246.v1]

3CLpro is a vital protein for the SARS-CoV-2 replications and its inhibition using small molecules is a bona fide approach used to develop new drugs against the virus. In this study, a comprehensive crystallography-guided fragment-based drug discovery approach was employed to design new inhibitors for SARS-CoV-2 3CLpro. Protein Data Bank was explored to find small molecules cocrystallized with SARS-CoV-2 3CLpro. The fragments sitting in the binding pocket (87) were interactively coupled using various linkers with the intention to get molecules having the same orientation as those of the constituting fragments. In total, 1251 couples were prepared and converted to maximum possible stereoisomers using LigPrep for screening using Glide (standard precision and extra precision), AutoDock Vina, and Prime MMGBSA. Top 22 hits having conformations similar to their cocrystallized fragments were selected for MD simulation on Desmond. MD simulation suggested that 15 hits had conformations very close to their constituting fragments. Results indicated that these hits were computationally reliable and could be considered for further development. This suggests that the study could provide a benchmark starting point for the further design of SARS-CoV-2 3CLpro inhibitors with improved binding (data provided).

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Efficient and reproducible synthesis of an Fmoc-protected Tn antigen

Glycoconjugate ready for solid-phase-peptide synthesis is scalably accessible using a palladium-mediated glycosylation.

Detecting Mercury (II) and Thiocyanate Using "Turn-on" Fluorescence of Graphene Quantum Dots

In this work, 1.8 nm graphene quantum dots (GQDs), exhibiting bright blue fluorescence, were prepared using a bottom-up synthesis from citric acid. The fluorescence of the GQDs could be almost completely quenched (about 96%) by adding Hg²⁺. Quenching was far less efficient with other similar heavy metals, Tl⁺, Pb²⁺ and Bi³⁺. Fluorescence could be near quantitatively restored through the introduction of thiocyanate. This "turn-on" fluorescence can thus be used to detect both or either environmental and physiological contaminants mercury and thiocyanate and could prove useful for the development of simple point-of-care diagnostics in the future. Graphical Abstract.

Cannabinoids and Cannabinoid Receptors: The Story so Far

Like most modern molecular biology and natural product chemistry, understanding cannabinoid pharmacology centers around molecular interactions, in this case, between the cannabinoids and their putative targets, the G-protein coupled receptors (GPCRs) cannabinoid receptor 1 (CB₁) and cannabinoid receptor 2 (CB₂). Understanding the complex structure and interplay between the partners in this molecular dance is required to understand the mechanism of action of synthetic, endogenous, and phytochemical cannabinoids. This review, with 91 references, surveys our understanding of the structural biology of the cannabinoids and their target receptors including both a critical comparison of the extant crystal structures and the computationally derived homology models, as well as an in-depth discussion about the binding modes of the major cannabinoids. The aim is to assist in situating structural biochemists, synthetic chemists, and molecular biologists who are new to the field of cannabis research.

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Cannabinoid research has greatly expanded

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Structural biology and computational chemistry jointly provide mechanistic insight

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Structural data are being generated at an exponentially increasing rate

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Phytocannabinoid targeting of other GPCR receptors deserves investigation

Bringing a Molecular Plus One: Synergistic Binding Creates Guest-Mediated Three-Component Complexes

C_ethyl-2-methylresorcinarene (A), pyridine (B), and a set of 10 carboxylic acids (Cn) associate to form A·B·Cn ternary assemblies with 1:1:1 stoichiometry, representing a useful class of ternary systems where the guest mediates complex formation between the host and a third component. Although individually weak in solution, the combined strength of the multiple noncovalent interactions organizes the complexes even in a highly hydrogen-bond competing methanol solution, as explored by both experimental and computational methods. The interactions between A·B and Cn are dependent on the pK_a values of carboxylic acids. The weak interactions between A and C further reinforce the interactions between A and B, demonstrating positive cooperativity. Our results reveal that the two-component system such as that formed by A and B can form the basis for the development of specific sensors for the molecular recognition of carboxylic acids.

Synthesis, physical characterization, and antifungal and antibacterial activities of oleic acid capped nanomagnetite and cobalt-doped nanomagnetite

Nanoparticles, 10–14 nm, consisting of either Fe3O4 or Co0.2Fe2.8O4 stabilized with oleic acid, were prepared using solution combustion. Their structural and magnetic properties were examined using X-ray diffractometry, scanning electron microscopy, vibrating sample magnetometry, and Fourier-transform infrared spectroscopy. The properties of both sets of materials are similar, except that the cobalt-doped particles are considerably less magnetic. The in vitro inhibitory activities of the nanoparticles were assessed against pathogenic bacteria Shigella dysenteriae, Klebsiella pneumoniae, Acinetobacter baumannii, Streptococcus pyogenes, and pathogenic fungi and molds Candida albicans, Fusarium oxysporum, and Aspergillus fumigatus. The magnetite nanoparticles were moderately effective against all tested pathogens, but the activity of the cobalt-doped nanoparticles was significantly lower, possibly due to an interruption of the Fenton reaction at the bacterial membrane. This work suggests that potentially doping magnetite with stronger metal oxidants may instead enhance their antimicrobial effects.

Differential Expression of Glucose Transporters and Hexokinases in Prostate Cancer with a Neuroendocrine Gene Signature: A Mechanistic Perspective for 18F-FDG Imaging of PSMA-Suppressed Tumors

Although the incidence of de novo neuroendocrine prostate cancer (PC) is rare, recent data suggest that low expression of prostate-specific membrane antigen (PSMA) is associated with a spectrum of neuroendocrine hallmarks and androgen receptor (AR) suppression in PC. Previous clinical reports indicate that PCs with a phenotype similar to neuroendocrine tumors can be more amenable to imaging by ¹⁸F-FDG than by PSMA-targeting radioligands. In this study, we evaluated the association between neuroendocrine gene signature and ¹⁸F-FDG uptake-associated genes including glucose transporters (GLUTs) and hexokinases, with the goal of providing a genomic signature to explain the reported ¹⁸F-FDG avidity of PSMA-suppressed tumors. Methods: Data-mining approaches, cell lines, and patient-derived xenograft models were used to study the levels of 14 members of the SLC2A family (encoding GLUT proteins), 4 members of the hexokinase family (genes HK1-HK3 and GCK), and PSMA (FOLH1 gene) after AR inhibition and in correlation with neuroendocrine hallmarks. Also, we characterize a neuroendocrine-like PC (NELPC) subset among a cohort of primary and metastatic PC samples with no neuroendocrine histopathology. We measured glucose uptake in a neuroendocrine-induced in vitro model and a zebrafish model by nonradioactive imaging of glucose uptake using a fluorescent glucose bioprobe, GB2-Cy3. Results: This work demonstrated that a neuroendocrine gene signature associates with differential expression of genes encoding GLUT and hexokinase proteins. In NELPC, elevated expression of GCK (encoding glucokinase protein) and decreased expression of SLC2A12 correlated with earlier biochemical recurrence. In tumors treated with AR inhibitors, high expression of GCK and low expression of SLC2A12 correlated with neuroendocrine histopathology and PSMA gene suppression. GLUT12 suppression and upregulation of glucokinase were observed in neuroendocrine-induced PC cell lines and patient-derived xenograft models. A higher glucose uptake was confirmed in low-PSMA tumors using a GB2-Cy3 probe in a zebrafish model. Conclusion: A neuroendocrine gene signature in neuroendocrine PC and NELPC associates with a distinct transcriptional profile of GLUTs and hexokinases. PSMA suppression correlates with GLUT12 suppression and glucokinase upregulation. Alteration of ¹⁸F-FDG uptake-associated genes correlated positively with higher glucose uptake in AR- and PSMA-suppressed tumors. Zebrafish xenograft tumor models are an accurate and efficient preclinical method for monitoring nonradioactive glucose uptake.

Neuro- and hepatic toxicological profile of (S)-2,4-diaminobutanoic acid in embryonic, adolescent and adult zebrafish

(S)-2,4-Diaminobutanoic acid (DABA) is a noncanonical amino acid often co-produced by cyanobacteria along with β-N-methylamino-l-alanine (BMAA) in algal blooms. Although BMAA is a well-established neurotoxin, the toxicity of DABA remains unclear. As part of our development of biocompatible materials, we wish to make use of DABA as both a building block and as the end-product of enzymatically induced depolymerization; however, if it is toxic at very low concentrations, this would not be possible. We examined the toxicity of DABA using both in vivo embryonic and adult zebrafish models. At higher sublethal concentrations (700 μm), the fish demonstrated early signs of cardiotoxicity. Adolescent zebrafish were able to tolerate a higher concentration. Post-mortem histological analysis of juvenile zebrafish showed no liver or brain abnormalities associated with hepato- or neurotoxicity. Combined, these results show that DABA exhibits no overt toxicity at concentrations (100-300 μm) within an order of magnitude of those envisioned for its application. This study further highlights the low cost and ease of using zebrafish as an early-stage toxicological screening tool.

Adsorption of bovine serum albumin (BSA) by bare magnetite nanoparticles with surface oxidative impurities that prevent aggregation

Bare, uncoated magnetite nanoparticles, synthesized using an electrochemical surfactant-free synthesis, have highly oxidized surfaces that prevent aggregation. These particles have demonstrated highly intriguing biological activity showing extremely potent antibiotic activity against both gram-positive and gram-negative bacteria with little toxicity to rats. This difference in activity could be ascribed to the nature of the protein corona. The kinetics and thermodynamics of the binding of bovine serum albumin (BSA), used as a model serum protein, to these magnetite nanoparticles were analyzed. There is no significant change in particle diameter by dynamic light scattering following adsorption, indicating corona formation does not induce aggregation. The maximum adsorption capacity of the particles was determined to be 300 mg of BSA per gram of magnetite. The particles are able to adsorb 90% of the BSA at protein concentrations as high as 500 mg/L. The adsorption is best described using a pseudo second order model and a Langmuir Type III isotherm model. Thermodynamic analysis showed that the process is entropically driven and is spontaneous at all tested temperatures and conditions. However, it appears to be a weak to moderate physical adsorption. This moderate binding affinity could indicate the differential biological activity of these particles towards bacteria and mammalian cells and further support the contention that these are potentially useful new tools for targeting antibiotic-resistant bacteria.

Halogen bonding and host-guest chemistry between N-alkylammonium resorcinarene halides, diiodoperfluorobutane and neutral guests

Single crystal X-ray structures of halogen-bonded assemblies formed between host N-hexylammonium resorcinarene bromide (1) or N-cyclohexylammonium resorcinarene chloride (2), and 1,4-diiodooctafluorobutane and accompanying small solvent guests (methanol, acetonitrile and water) are presented. The guests’ inclusion affects the geometry of the cavity of the receptors 1 and 2, while the divalent halogen bond donor 1,4-diiodooctafluorobutane determines the overall nature of the halogen bond assembly. The crystal lattice of 1 contains two structurally different dimeric assemblies A and B, formally resulting in the mixture of a capsular dimer and a dimeric pseudo-capsule. ¹H and ¹⁹F NMR analyses supports the existence of these halogen-bonded complexes and enhanced guest inclusion in solution.

Computational, experimental details, and biological raw data accompanying the publication: "The synthesis and characterization of a nanomagnetite with potent antibacterial activity and low mammalian toxicity"

This data file includes experimental details on how to make uncoated iron oxide nanoparticles using a green electrochemical method. It provides the raw data on the antibacterial activity of one of these formulations, and the full computational data and methodology used to generate that data, of several different magnetite clusters of specific spin multiplicities for 4, 5, 7 and 9 iron atom magnetite clusters. This data will assist other researchers wishing to replicate or expand on these results for the investigation and use of nanomagnetite for antibacterial applications.

Recent advances in the application of carbohydrates as renewable feedstocks for the synthesis of nitrogen-containing compounds

Carbohydrates, in the form of chitin, chitosan and cellulose, are one of the most available, renewable, and sustainable chemical feedstocks. Their conversion to biofuels, fine chemicals, and industrially-relevant monomers is becoming increasingly viable and promising as innovation decreases the price of this technology, and climate change and the price of fossil fuels increases the social and economic costs of using traditional feedstocks. In recent years, carbohydrates have been increasingly used as sources for nitrogen-containing fine chemicals. This chapter, with 86 references, provides a brief overview of the conversion of carbohydrate biomass to the standard hydrocarbon and oxygen-containing derivatives, and then provides a survey of recent progress in converting the biopolymers, and the derived mono and di-saccharides, into nitrogen-containing molecules with a special focus on N-heterocycle synthesis for medicinal applications.