Molecular structure, NBO analysis of the hydrogen-bonded interactions, spectroscopic (FT-IR, FT-Raman), drug likeness and molecular docking of the novel anti COVID-2 molecule (2E)-N-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide (Dimer) - quantum chemical approach.

Prospective antiviral molecule (2E)-N-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide has been probed using Fourier transform infrared (FTIR), FT-Raman and quantum chemical computations. The geometry equilibrium and natural bond orbital analysis have been carried out with density functional theory employing Becke, 3-parameter, Lee-Yang-Parr method with the 6-311G++(d,p) basis set. The vibrational assignments pertaining to different modes of vibrations have been augmented by normal coordinate analysis, force constant and potential energy distributions. Drug likeness and oral activity have been carried out based on Lipinski's rule of five. The inhibiting potency of 2(2E)-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide has been investigated by docking simulation against SARS-CoV-2 protein. The optimized geometry shows a planar structure between the chromone and the side chain. Differences in the geometries due to the substitution of the electronegative atom and intermolecular contacts due to the chromone and hydrazinecarbothioamide were analyzed. NBO analysis confirms the presence of two strong stable hydrogen bonded NH⋯O intermolecular interactions and two weak hydrogen bonded CH⋯O interactions. The red shift in NH stretching frequency exposed from IR substantiates the formation of NH⋯O intermolecular hydrogen bond and the blue shift in CH stretching frequency substantiates the formation of CH⋯O intermolecular hydrogen bond. Drug likeness, absorption, distribution, metabolism, excretion and toxicity property gives an idea about the pharmacokinetic properties of the title molecule. The binding energy of the nonbonding interaction with Histidine 41 and Cysteine 145, present a clear view that 2(2E)-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide can irreversibly interact with SARS-CoV-2 protease.

An Unexpected Split-Merge Pathway in the Assembly of the Symmetric Nonribosomal Peptide Antibiotic Closthioamide.

Closthioamide (CTA) is a symmetric nonribosomal peptide (NRP) comprised of two diaminopropane-linked polythioamidated monomers. CTA is biosynthesized by Ruminiclostridium cellulolyticum via an atypical NRP synthetase (NRPS)-independent biosynthetic pathway. Although the logic for monomer assembly was recently elucidated, the strategy for the biosynthesis and incorporation of the diamine linker remained a mystery. By means of genome editing, synthesis, and in vitro biochemical assays, we demonstrate that the final steps in CTA maturation proceed through a surprising split-merge pathway involving the dual use of a thiotemplated intermediate. This pathway includes the first examples of an aldo-keto reductase catalyzing the reductive release of a thiotemplated product, and of a transthioamidating transglutaminase. In addition to clarifying the remaining steps in CTA assembly, our data shed light on largely unexplored pathways for NRPS-independent peptide biosynthesis.

Unambiguous Detection of Elevated Levels of Hypochlorous Acid in Double Transgenic AD Mouse Brain.

Alzheimer's disease (AD) is one of the most prevalent forms of dementia. The current diagnosis methods based on the behavior and cognitive decline or imaging of core biomarkers, namely, amyloid-ß (Aß) plaques and neurofibrillary tangles (NFTs), in the brain offer poor to moderate success. Detection and imaging of biomarkers that cause additional traits of pathophysiological aberrations in the brain are invaluable to monitor early disease onset and progression of AD pathology. The pathological hallmark of AD is associated with generation of excessive reactive oxygen species (ROS) in the brain, which aggravate oxidative stress and inflammation. ROS production involves elevated levels of hypochlorous acid (HOCl) and can serve as one of the potential biomarkers for the diagnosis of AD. We report the design, synthesis, and characterization of switchable coumarin-morpholine (CM) conjugates as off-on fluorescence probes for the specific detection of HOCl produced and proximally localized with amyloid plaques. The nonfluorescent thioamide probe CM2 undergoes regioselective transformation to fluorescent amide probe CM1 in the presence of HOCl (∼90-fold fluorescence enhancement and 0.32 quantum yield) with high selectivity and sensitivity (detection limit: 0.17 µM). The excellent cellular uptake and blood-brain barrier (BBB) crossing ability of CM2 allowed unambiguous and differential detection, imaging, and quantification of HOCl in cellular milieu and in the wild type (WT) and AD mouse brains. This study demonstrates the elevated level of HOCl in the AD mouse brain and the potential to expand the repertoire of biomarkers for the diagnosis of AD.

Development and validation of a colorimetric method for the quantitative analysis of thioamide derivatives.

Thioamides (Thm) have diverse biological activities. This work presents the development and validation of simple, rapid and accurate spectrophotometric method for the analysis of Thm derivatives in pure form and in plasma. This spectrophotometric method has not been used before for determination of Thm. A review of the literature revealed that the monitoring of S- group assay is based on the reaction with DTNB according to the Ellman method to form a yellow complex which absorbs at 412 nm. To assay the thioamides according to this method it is necessary to make the basic medium have S- to react with the DTNB. Experimental conditions affecting the color development were studied and optimized. The proposed spectrophotometric procedures were effectively validated with respect to linearity, ranges, precision, accuracy, specificity, robustness, detection and quantification limits. Calibration curves of the formed colored product with DTNB showed good linear relationships over the concentration ranges (0, 50, 100, 500, 1000, 1500 mg/L). The proposed method was successfully applied to the assay of Thm monitoring with good accuracy. The principal advantages of the proposed method were rapidity and suitability for the routine quality control assay of the drug alone and in monitoring form without interference.

Semi-synthesis of thioamide containing proteins.

Our laboratory has shown that the thioamide, a single atom O-to-S substitution, can be a versatile fluorescence quenching probe that is minimally-perturbing when placed at many locations in a protein sequence. In order to make these and other thioamide experiments applicable to full-sized proteins, we have developed methods for incorporating thioamides by generating thiopeptide fragments through solid phase synthesis and ligating them to protein fragments expressed in E. coli. To install donor fluorophores, we have adapted unnatural amino acid mutagenesis methods, including the generation of new tRNA synthetases for the incorporation of small, intrinsically fluorescent amino acids. We have used a combination of these two methods, as well as chemoenzymatic protein modification, to efficiently install sidechain and backbone modifications to generate proteins labeled with fluorophore/thioamide pairs.

Direct recognition and quantification by voltammetry of thiol/thioamide mixes in seawater.

Thiols and thioamides form part of the pool of reduced sulfur substances (RSS) that modify the health of aquatic ecosystems acting as radical scavengers and heavy metal ligands. Their concentrations could be easily determined in seawater by cathodic stripping voltammetry (CSV) were it not be for the coalescence of their responses in a single peak. Here, we modified the traditional CSV method of RSS analysis to allow individual recognition and quantification in thiol/thioamide mixes. Glutathione, cysteine, thiourea and thioacetamide in UV digested seawater were repeatedly analyzed shifting the deposition potential (E(dep)) in the range +0.07 to -0.4V at high resolution. The representation of peak height (i(p)) and peak potential (E(p)) vs E(dep) resulted in different and distinctive profiles for each substance that allowed the selection of adequate E(dep) ranges for their separate quantification. Copper saturation modified thiol profiles and cancelled the response of thioamides. The vs E(dep) profiles explained the nature of the different thiols and thioamides present in the sample and permitted their individual quantification with excellent accuracy. The utility of the method was put to test with seawater modified with natural unknown RSS from pore waters and Posidonia oceanica exudates. Although both samples gave similar CSV signals, the vs E(dep) profiles unveiled completely different electrochemical behaviors incompatible with a similar nature. Based on those profiles we hypothesized that pore waters released a glutathione/thiourea mix and that one or several unidentified RSS formed part of P. oceanica exudates. The analytical scheme proposed here opens a new door to the use of direct voltammetry in the qualitative and quantitative determination of RSS in natural waters.

Identification and control of metal-chelating chromatographic artifacts in the analysis of a malonohydrazide derivative drug compound.

Two unusual chromatographic artifact peaks were detected in the HPLC analysis for content of a malonohydrazide derivative drug and drug-related impurities. The artifacts were identified as the copper(II) chelating complexes with the drug compound and one of the process impurities. Our investigations suggested that built-up of Cu(2+) contamination in the HPLC system was the primary source for formation of the chelating artifacts. A rinse procedure using diluted EDTA solution was developed, and demonstrated to effectively purge trace level of heavy metals including Cu(2+) from the system, and therefore inhibited the formation of both chelates. Furthermore, the rinse was shown to introduce no detrimental impact on the response accuracy of the active drug compound and related impurities.

Vibrational characterization of the tertiary amide and thioamide group.

Force field calculations and vibrational spectra of (CH(3))(2)NCOCON(CH(3))(2) (TMO), (CH(3))(2)NCOCSN(CH(3))(2) (TMMTO) and (CH(3))(2)NCSCSN(CH(3))(2) (TMDTO) are discussed. The amide and thioamide fundamentals and those of other simple tertiary amides are compared. A characteristic pattern in infrared and Raman is proposed.

[Studies of thioamides and their derivatives. VIII. Products of decomposition of quaternary salts of 1-[alpha-alkylthio-p-dimethyl- amino)benzylidene]piperidine and 1-[alpha-alkylthio-(p-trialkyl- ammonio)benzylidene]piperidine]. / Badania w dziedzinie tioamidów i ich pochodnych. VIII. Produkty rozkladu czwartorzedowych soli 1-[alpha-alkilotio-(p-dimetyloamino)benzylideno]piperydyniowych I 1-[alpha-alkilotio-(p-trialkiloamonio)benzylideno]piperydyniowych.

Products of decomposition of eight quaternary salts, derivatives of 1-[alpha-alkylthio-(p-dimethylamino)benzylidene]-piperidinium, in water, ethanol, pyridine and glacial acetic acid were investigated. IR and UV spectra of the obtained decomposition products were measured, and the compounds were tested for cytostatic activity.