A computational predicting of possible inhibitors of the main SARS-CoV-2 protease found in Algerian herbal medicines

COVID-19 is a zoonotic viral disease caused by the SARS-CoV-2 virus. Its abrupt outbreak has caused a tremendous challenge to public health systems due to the rapid spread of the virus. In this sense, a great deal of work has been focused on finding substances from herbal plants to be used against this virus. In order to investigate the molecular interactions between natural metabolites from Algerian herbal plants and the SARS-CoV-2 protease Mpro, computational docking and molecular dynamics were used, also the drug likeness degree and in silico ADMET prediction were carried out in this study. warfarin and catalponol preferentially binds to a pocket of the SARS-Cov-2 Mpro active site that is made up of residues His 41 to Glu 166 and Leu 27 to His 163 with a relatively low binding energy of -7.1 and -6.6 kcal/mol respectively. Dynamic molecular assay further established that only warfarin managed to stay in the active site. The results suggest that warfarin may be an interesting candidate for development as a medical treatment of COVID-19 and more research is proposed, without disregarding its toxicity which deserves to be well studied.

El COVID-19 es una enfermedad zoonótica causada por el virus SARS-CoV-2. Su abrupto brote en años recientes ha supuesto un tremendo desafío para los sistemas de salud pública, como resultado de la rápida propagación del virus. En tal sentido, muchos trabajos se han centrado en encontrar sustancias de origen vegetal, para ser utilizadas contra este virus. Se realizaron estudios de acoplamiento computacional y dinámica molecular para investigar las interacciones moleculares entre los metabolitos secundarios de las plantas herbales argelinas con la Proteasa Mpro del SARS-CoV-2, también se realizaron estudios de semejanza con drogas mediante ADMET computacional. La warfarina y el catalponol se unen preferentemente al sitio activo SARS-Cov-2 Mpro que se compone de residuos His 41 a Glu 166 y Leu 27 a His 163 con una energía de enlace relativamente baja, -7,1 y -6,6 kcal/mol respectivamente. Los ensayos de dinámica molecular establecieron además que sólo la warfarina logró permanecer en el sitio activo. Estos resultados sugieren que la warfarina puede ser un candidato interesante para el desarrollo como tratamiento médico de COVID-19 e instan a realizar más investigaciones, sin dejar de lado estudios de toxicidad respectivos.

A COVID-19 é uma doença zoonótica causada pelo vírus SARS-CoV-2, cujo surto abrupto nos últimos anos representou um tremendo desafio para os sistemas de saúde pública devido à rápida disseminação do vírus. Nesse sentido, muitos trabalhos têm se concentrado em encontrar substâncias de origem vegetal, para serem utilizadas contra esse vírus. Estudos de ancoragem computacional e dinâmica molecular foram conduzidos para investigar as interações moleculares entre metabólitos secundários de ervas argelinas com o SARS-CoV-2 Protease Mpro, estudos de similaridade de drogas também foram conduzidos usando ADMET in silico. A varfarina e o catalponol ligam-se preferencialmente ao sítio ativo SARS-Cov-2 Mpro que é composto pelos resíduos His 41 a Glu 166 e Leu 27 a His 163 com uma energia de ligação relativamente baixa, -7,1 e -6,6 kcal/mol, respectivamente. Ensaios de dinâmica molecular estabeleceram ainda que apenas a varfarina conseguiu permanecer no sítio ativo. Esses resultados sugerem que a varfarina pode ser um candidato interessante para desenvolvimento como tratamento médico para COVID-19 e exigem mais pesquisas, incluindo os respectivos estudos de toxicidade.

Pyrene Scaffold as Real-Time Fluorescent Turn-on Chemosensor for Selective Detection of Trace-Level Al(III) and Its Aggregation-Induced Emission Enhancement.

A pyrene based fluorescent probe, 3-methoxy-2-((pyren-2yl-imino)methyl)phenol (HL), was synthesized via simple one-pot reaction from inexpensive reagents. It exhibited high sensitivity and selectivity toward Al(3+) over other relevant metal ions and also displayed novel aggregation-induced emission enhancement (AIEE) characteristics in its aggregate/solid state. When bound with Al(3+) in 1:1 mode, a significant fluorescence enhancement with a turn-on ratio of over ∼200-fold was triggered via chelation-enhanced fluorescence through sensor complex (Al-L) formation, and amusingly excess addition of Al(3+), dramatic enhancement of fluorescence intensity over manifold through aggregate formation was observed. The 1:1 stoichiometry of the sensor complex (Al-L) was calculated from Job's plot based on UV-vis absorption titration. In addition, the binding site of sensor complex (Al-L) was well-established from the (1)H NMR titrations and also supported by the fluorescence reversibility by adding Al(3+) and EDTA sequentially. Intriguingly, the AIEE properties of HL may improve its impact and studied in CH3CN-H2O mixtures at high water content. To gain insight into the AIEE mechanism of the HL, the size and growth process of particles in different volume percentage of water and acetonitrile mixture were studied using time-resolved photoluminescence, dynamic light scattering, optical microscope, and scanning electron microscope. The molecules of HL are aggregated into ordered one-dimensional rod-shaped microcrystals that show obvious optical waveguide effect.

Aggregation induced emission enhancement of 4,4'-bis(diethylamino)benzophenone with an exceptionally large blue shift and its potential use as glucose sensor.

Optical emission from a luminogen in solid state is generally red shifted with respect to its solution phase emission. However, in our present study, we report exceptionally large blue shifted enhanced emission from aggregated hydrosol of 4,4'-bis(diethylamino)benzophenone (BZP) compared to its solution phase emission in any good solvent. This exceptional blue emission from aggregated structure of BZP arises from its locally excited states with the concomitant suppression of twisted intramolecular charge transfer (TICT) motion. This is known as aggregation induced locally excited (AILE) state emission. A broad red shifted emission is also observed in case of larger aggregated structure of BZP and it originates from the excited intramolecular charge transfer (ICT) state of planar BZP. Morphology of the aggregated BZP is also studied by scanning electron microscopy and optical microscopy. This AILE emission of the luminogen is used for sensing glucose in aqueous solution at very low concentration. The quenching of AILE in presence of glucose has been explained due to hydrogen bonded complexation between glucose and BZP molecule present at the surface of the aggregated structure and is responsible for crystal softening, i.e. loosening of crystal packing.

Aggregation induced emission enhancement from Bathophenanthroline microstructures and its potential use as sensor of mercury ions in water.

Bathophenanthroline (BA) microstructures of various morphologies have been synthesized using a reprecipitation method. The morphologies of the particles are characterized using optical and scanning electron microscopy (SEM) methods. An aqueous dispersion of BA microstructures shows aggregation induced emission enhancement (AIEE) compared to BA in a good solvent, THF. This luminescent property of aggregated BA hydrosol is used for the selective detection of trace amounts of mercury ion (Hg(2+)) in water. It is observed that Hg(2+) ions can quench the photoluminescence (PL) intensity of BA aggregates even at very low concentrations, compared to other heavy metal ions e.g. nickel (Ni(2+)), manganese (Mn(2+)), cadmium (Cd(2+)), cobalt (Co(2+)), copper (Cu(2+)), ferrous (Fe(2+)) and zinc (Zn(2+)). This strong fluorescence quenching of aggregated BA in the presence of Hg(2+) ions has been explained as a complex interplay between the ground state complexation between BA and Hg(2+) ions and external heavy atom induced perturbation by Hg(2+) ions on the excited states of the fluorophore BA.

Computational nanochemistry study of the molecular structure and properties of ethambutol.

The M06 family of density functionals was employed to calculate the molecular structure and properties of the ethambutol molecule. Besides determination of molecular structures, UV-vis spectra were computed using TD-DFT in the presence of a solvent and the results compared with available experimental data. The chemical reactivity descriptors were calculated through conceptual DFT. The active sites for nucleophilic and electrophilic attacks have been chosen by relating them to Fukui function indices. A comparison between the descriptors calculated through vertical energy values and those arising from Koopmans' theorem approximation were performed in order to check the validity of the latter procedure.

Computational nanochemistry report on the oxicams--conceptual DFT indices and chemical reactivity.

A density functional theory study of eight oxicams was carried out in order to determine their global and local reactivities. These types of reactivities were measured by means of global and local reactivity descriptors coming from the conceptual density functional theory. Net electrophilicity as a global reactivity descriptor and local hypersoftness as a local reactivity descriptor were the used tools to distinguish reactivity and selectivity among these oxicams. Globally, isoxicam presents the highest electron donating capacity; meanwhile, the highest electron accepting capacity is exhibited by droxicam. Locally, two oxicams present neither nucleophilic nor electrophilic relevant reactivity in their peripheral pyridine ring, droxicam and tenoxicam, so that their more reactive zones are found on the respective fused rings. Oxicams have been divided into two subgroups in order to facilitate the local analysis of reactivity. One group is characterized because their most important condensed values for local hypersoftnes are well-separated: 4-meloxicam, lornoxicam, meloxicam, and normeloxicam. Meanwhile, the opposite situation is found in droxicam, isoxicam, piroxicam, and tenoxicam. As a whole, the nucleophilic characteristic noticeably predominates in these eight oxicams instead of an electrophilic behavior, thus meaning a greater tendency to donate electrons rather than withdrawing them; a consequence of this behavior implies a favorable interaction with a hypothetical receptor bearing one or more electron acceptor functional groups rather than electron donor functional groups; this would imply a maximization of this interaction from the covalent point of view.