Pharmaceutical Compounds
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2021 ◽  
Author(s):  
Jessica E. Burch ◽  
Austin G. Smith ◽  
Seb Caille ◽  
Shawn D. Walker ◽  
Ryan Wurz ◽  
...  

The application of microcrystal electron diffraction (microED) to a variety of pharmaceutical compounds is reported. The examples and work detailed showcase the utility of microED as a routine technique for the rapid collection, analysis, and generation of structural data on a number of pharmaceutically relevant compounds, requiring minimal sample preparation and often without the need for time-consuming vitrification and cryo transfer processes. The development of a scripted data processing workflow allowed for simultaneous collection and processing of electron diffraction data, further expediting structural analysis of fifteen compounds.


2021 ◽  
pp. 1-11
Author(s):  
Narjes Hajali ◽  
Afshin Taghva Manesh ◽  
Ahmad Seif

Formations of bimolecular barbituric acid (BA) complexes through hydrogen-bonding (HB) interactions were investigated in this work. BA has been known as a starting compound of pharmaceutical compounds developments, in which the molecular and atomic features of parent BA in homo-paring with another BA molecule were investigated here. The models were optimized to reach the stabilized structures and their properties were evaluated at the molecular and atomic scales. Density functional theory (DFT) calculations were performed to provide required information for achieving the goal of this work. Six dimer models were obtained finally according to examining all possible starting dimers configurations for involving in optimization calculations. N-H . . . O and C-H . . . O interactions were also involved in dimers formations besides participation of the X-center of parent BA in interaction. Molecular and atomic scales features were evaluated for characterizing the dimers formations. As a consequence, several configurations of BA dimers were obtained showing the importance of performing such structural analyses for developing further compounds from BA.


2021 ◽  
Author(s):  
Anda Trifan ◽  
Defne Gorgun ◽  
Zongyi Li ◽  
Alexander Brace ◽  
Maxim Zvyagin ◽  
...  

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) replication transcription complex (RTC) is a multi-domain protein responsible for replicating and transcribing the viral mRNA inside a human cell. Attacking RTC function with pharmaceutical compounds is a pathway to treating COVID-19. Conventional tools, e.g., cryo-electron microscopy and all-atom molecular dynamics (AAMD), do not provide sufficiently high resolution or timescale to capture important dynamics of this molecular machine. Consequently, we develop an innovative workflow that bridges the gap between these resolutions, using mesoscale fluctuating finite element analysis (FFEA) continuum simulations and a hierarchy of AI-methods that continually learn and infer features for maintaining consistency between AAMD and FFEA simulations. We leverage a multi-site distributed workflow manager to orchestrate AI, FFEA, and AAMD jobs, providing optimal resource utilization across HPC centers. Our study provides unprecedented access to study the SARS-CoV-2 RTC machinery, while providing general capability for AI-enabled multi-resolution simulations at scale.


Toxics ◽  
2021 ◽  
Vol 9 (10) ◽  
pp. 257
Author(s):  
Joana P. Fernandes ◽  
C. Marisa R. Almeida ◽  
Maria A. Salgado ◽  
Maria F. Carvalho ◽  
Ana P. Mucha

Various contaminants of emerging concern (CECs) have been detected in different ecosystems, posing a threat to living organisms and the environment. Pharmaceuticals are among the many CECs that enter the environment through different pathways, with wastewater treatment plants being the main input of these pollutants. Several technologies for the removal of these pollutants have been developed through the years, but there is still a lack of sustainable technologies suitable for being applied in natural environments. In this regard, solutions based on natural biological processes are attractive for the recovery of contaminated environments. Bioremediation is one of these natural-based solutions and takes advantage of the capacity of microorganisms to degrade different organic pollutants. Degradation of pollutants by native microorganisms is already known to be an important detoxification mechanism that is involved in natural attenuation processes that occur in the environment. Thus, bioremediation technologies based on the selection of natural degrading bacteria seem to be a promising clean-up technology suitable for application in natural environments. In this review, an overview of the occurrence and fate of pharmaceuticals is carried out, in which bioremediation tools are explored for the removal of these pollutants from impacted environments.


2021 ◽  
Author(s):  
Erik Svensson Grape ◽  
Victoria Rooth ◽  
Mathias Nero ◽  
Tom Willhammar ◽  
A. Ken Inge

Structure determination of pharmaceutical compounds is invaluable for drug development but is challenging for those that form as small crystals with defects. Bismuth subsalicylate (BSS), among the most commercially significant bismuth compounds, is an active ingredient in over-the-counter medications such as Pepto-Bismol, used to treat dyspepsia and H. pylori infections. Despite its century-long history, the structure has remained unknown. Three-dimensional electron diffraction and hierarchical clustering analysis were applied on select data from ordered crystals, revealing a layered structure. In other less ordered crystals, high-resolution scanning transmission electron microscopy revealed variations in the stacking of layers. Together, these modern electron crystallography techniques provide a new toolbox for structure determination of active pharmaceutical ingredients and drug discovery, demonstrated by this study of BSS.


2021 ◽  
pp. 100009
Author(s):  
Ziqing Lin ◽  
Hua-Chia Tai ◽  
Emanuele Petruzzella ◽  
Feili Tang ◽  
Yun K. Ye ◽  
...  

2021 ◽  
Author(s):  
Matthew Bahr ◽  
Aakankschit Nandkeolyar ◽  
John Kenna ◽  
Luigi DaVia ◽  
Neysa Nevins ◽  
...  

The goal of the SAMPL (Statistical Assessment of the Modeling of Proteins and Ligands) challenge is to improve the accuracy of current computational models to estimate free energy of binding, deprotonation, distribution and other associated physical properties that are useful for the design of new pharmaceutical products. New experimental datasets of physicochemical properties provide opportunities for prospective evaluation of computational prediction methods. Here, aqueous pKa and a range of bi-phasic logD values for a variety of pharmaceutical compounds were determined through a streamlined automated process to be utilized in the SAMPL8 physical property challenge. The goal of this paper is to provide an in-depth review of the experimental methods utilized to create a comprehensive data set for the blind prediction challenge. The significance of this work involves the use of high throughput experimentation equipment and instrumentation to produce acid dissociation constants for twenty-three drug molecules, as well as distribution coefficients for eleven of those molecules.


Chemosensors ◽  
2021 ◽  
Vol 9 (10) ◽  
pp. 273
Author(s):  
Cristian Gómez-Canela ◽  
Sílvia Edo ◽  
Natalia Rodríguez ◽  
Gemma Gotor ◽  
Sílvia Lacorte

Wastewaters are considered one of the main sources of pollution in the aquatic environment as release a large number of contaminants every day. Emerging contaminants such as pharmaceuticals have special interest due to the high levels of consumption by the global population, their bioactive properties and because actual directives do not include the monitoring of pharmaceuticals. Moreover, it is well-known that pharmaceuticals can be degraded to metabolites or transformation products (TPs), which could be more toxic than the parental compound. In this study, we have developed an analytical method based on solid-phase extraction (SPE) and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) to determine 76 highly consumed pharmaceuticals, including metabolites and TPs in wastewater effluents. In the 10 wastewaters analysed, the mean concentrations were in the µg L−1 levels, being mycophenolic acid, levodopa, ibuprofen, 4-aminoantypirine, losartan, amylmetacresol, amoxicillin, fluticasone, tramadol, budesonide, chlorpheniramine and diclofenac the pharmaceuticals with the highest concentrations. This study provides a comprehensive optimization on the MS conditions to determine pharmaceutical compounds and their metabolites and provides a spectral characterization to be used for the identification of these compounds in water.


2021 ◽  
Vol 300 ◽  
pp. 113569
Author(s):  
Simranjeet Singh ◽  
Vijay Kumar ◽  
Amith G. Anil ◽  
Dhriti Kapoor ◽  
Sutripto Khasnabis ◽  
...  

Nanomaterials ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 2368
Author(s):  
Nikola Slepičková Slepičková Kasálková ◽  
Petr Slepička ◽  
Václav Švorčík

The versatility of the arrangement of C atoms with the formation of different allotropes and phases has led to the discovery of several new structures with unique properties. Carbon nanomaterials are currently very attractive nanomaterials due to their unique physical, chemical, and biological properties. One of these is the development of superconductivity, for example, in graphite intercalated superconductors, single-walled carbon nanotubes, B-doped diamond, etc. Not only various forms of carbon materials but also carbon-related materials have aroused extraordinary theoretical and experimental interest. Hybrid carbon materials are good candidates for high current densities at low applied electric fields due to their negative electron affinity. The right combination of two different nanostructures, CNF or carbon nanotubes and nanoparticles, has led to some very interesting sensors with applications in electrochemical biosensors, biomolecules, and pharmaceutical compounds. Carbon materials have a number of unique properties. In order to increase their potential application and applicability in different industries and under different conditions, they are often combined with other types of material (most often polymers or metals). The resulting composite materials have significantly improved properties.


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