Preparation and Diels-Alder chemistry of 4-vinylimidazoles

Various 4-vinylimidazole derivatives have been prepared from the corresponding 4-iodoimidazoles or from urocanic acid. Several methods for the elaboration of these vinylimidazoles and their Diels-Alder reactions are reported. All of the vinylimidazoles prepared in the course of this study react with N-phenylmaleimide quite readily with mild thermal activation providing a single cycloadduct, in most cases the initial, nonaromatic adduct. With more electron rich substrates, there is a tendency for these initial cycloadducts to undergo aromatization, ene reaction, and oxidation although this can be circumvented to a large extent by the choice of reaction conditions. Limited reactions were observed with other dienophiles, providing the expected cycloadducts in most cases, although an abnormal adduct was obtained in one case with dimethyl acetylene dicarboxylate. These substrates also participate in regioselective Diels-Alder reactions with monoactivated dienophiles, but require fairly forcing conditions, thus only providing the aromatized cycloadducts in modest yields. An investigation of substituent effects at the 2-position of the imidazole moiety was undertaken, in which electron-donating and weakly electron-withdrawing substituents are tolerated. In addition, several substrates with terminally substituted vinyl moieties have been investigated.     

Application of a validated stability-indicating densitometric thin-layer chromatographic method to stress degradation studies on moxifloxacin

A simple, sensitive, selective, precise and stability-indicating high-performance thin-layer chromatographic (HPTLC) method for densitometric determination of moxifloxacin both as a bulk drug and from pharmaceutical formulation was developed and validated as per the International Conference on Harmonization (ICH) guidelines. The method employed TLC aluminium plates pre-coated with silica gel 60F-254 as the stationary phase and the mobile phase consisted of n-propanol-ethanol-6 M ammonia solution (4:1:2, v/v/v). Densitometric analysis of moxifloxacin was carried out in the absorbance mode at 298 nm. Compact spots for moxifloxacin were found at R_f value of 0.58 ± 0.02. The linear regression analysis data for the calibration plots showed good linear relationship with r = 0.9925 in the working concentration range of 100-800 ng spot⁻¹. The method was validated for precision, accuracy, ruggedness, robustness, specificity, recovery, limit of detection (LOD) and limit of quantitation (LOQ). The LOD and LOQ were 3.90 and 11.83 ng spot⁻¹, respectively. Drug was subjected to acid and alkali hydrolysis, oxidation, dry heat, wet heat treatment and photodegradation. All the peaks of degradation products were well resolved from the standard drug with significantly different R_f values. Statistical analysis proves that the developed HPTLC method is reproducible and selective. As the method could effectively separate the drug from its degradation products, it can be employed as stability-indicating one. Moreover, the proposed HPTLC method was utilized to investigate the kinetics of the acidic and alkaline degradation processes at different temperatures. Arrhenius plot was constructed and apparent pseudo-first-order rate constant, half-life and activation energy were calculated. In addition the pH-rate profile for degradation of moxifloxacin in constant ionic strength buffer solutions within the pH range 1.2-10.8 was studied.     

Confined Water in Amyloid‐Competent Oligomers of the Prion Protein

Conformational switching of the prion protein into the abnormal form involves the formation of (obligatory) molten‐oligomers that mature into ordered amyloid fibrils. The role of water in directing the course of amyloid formation remains poorly understood. Here, we show that the mobility of the water molecules within the on‐pathway oligomers is highly retarded. The water relaxation time within the oligomers was estimated to be ≈1 ns which is about three orders of magnitude slower than the bulk water and resembles the characteristics of (trapped) nano‐confined water. We propose that the coalescence of these obligatory oligomers containing trapped water is entropically favored because of the release of ordered water molecules in the bulk milieu and results in the sequestration of favorable inter‐chain amyloid contacts via nucleated conformational conversion. The dynamic role of water in protein aggregation will have much broader implications in a variety of protein misfolding diseases.     

Identification of γ-AApeptides with potent and broad-spectrum antimicrobial activity

We report the identification of a new class of antimicrobial peptidomimetics-γ-AApeptides with potent and broad-spectrum activity, including clinically-relevant strains that are unresponsive to most antibiotics. They are also not prone to select for drug-resistance.     

A Novel Synthesis of Bisbenzyl Ketones by DCC Induced Condensation of Phenylacetic Acid

1,3-Dicyclohexylcarbodiimide (DCC) has been found to effect condensation of two molecules of phenylacetic acids in the presence of dimethylaminopyridine leading to the formation of bisbenzyl ketones.

CDRI communication No. 5670     

TANGO: A high through-put conformation generation and semiempirical method-based optimization tool for ligand molecules

Lead optimization is one of the crucial steps in the drug discovery pipeline. After identifying the lead molecule and obtaining its 2D geometry, understanding the best conformation it would attain in 3D still remains one of the most challenging steps in drug discovery. There have been multiple methods and algorithms that are directed toward achieving best conformation for the lead molecules. TANGO focuses on conformation generation and its optimization using semiempirical energy calculations. The conformation generation is based on torsion angle rotation of the exocyclic bonds. The energy calculations are performed using MOPAC. The unique feature of this tool lies in the implementation of Message Passing Interface (MPI) for conformation generation and semiempirical-based optimization. A well-defined architecture handling the input and output generation has been used. The master and slave approach to handle operations involved in torsion angle rotation and energy calculations has helped in load balancing the process of conformation generation. The benchmarking results suggest that TANGO scales significantly well across eight nodes with each node utilizing 16 cores. This tool may prove to very useful in high throughput generation of semiempirically optimized small molecule conformations. The use of semiempirical methods for optimization generates a conformational ensemble thereby helping to obtain stable and alternate stable conformers for a given ligand molecule. © 2018 Wiley Periodicals, Inc.     

Monte Carlo analysis of the internal structure of light scattering particles with slit-scan illumination

An algorithm based upon a Monte Carlo procedure for calculating the scattering and absorption by a host particle containing a distribution of particulate inclusions is described. The host particle is sufficiently large so that ray optics can be applied. The inclusions are too small for ray optics but sufficiently large so that the full boundary-value formalism must be used. A major consideration is to determine whether the internal structure is better resolved when slit-scan illumination is utilized rather than plane wave illumination. The algorithm is tested for a layered sphere for which the boundary value solution is available.     

Automated Antibody De Novo Sequencing and Its Utility in Biopharmaceutical Discovery

Applications of antibody de novo sequencing in the biopharmaceutical industry range from the discovery of new antibody drug candidates to identifying reagents for research and determining the primary structure of innovator products for biosimilar development. When murine, phage display, or patient-derived monoclonal antibodies against a target of interest are available, but the cDNA or the original cell line is not, de novo protein sequencing is required to humanize and recombinantly express these antibodies, followed by in vitro and in vivo testing for functional validation. Availability of fully automated software tools for monoclonal antibody de novo sequencing enables efficient and routine analysis. Here, we present a novel method to automatically de novo sequence antibodies using mass spectrometry and the Supernovo software. The robustness of the algorithm is demonstrated through a series of stress tests.

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