Chemoinformatics

Polański, Jarosław

doi:10.1016/b978-044452701-1.00006-5

Cited by 14 publications

(6 citation statements)

References 102 publications

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“…Cheminformatics, or chemical informatics, merges computer and informational techniques to aid in understanding and manipulating chemical data, playing an integral role in drug discovery and therapeutics [117] .…”

Section: Application Of Nd Treatment Based On Cheminformaticsmentioning

confidence: 99%

Natural products in neuroprotective therapies: Experimental and cheminformatics approaches to manage neurological disorders

Rahman,

Hossain,

Rifat

et al. 2024

Appl. Chem. Eng.

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Neurological disorders (NDs) such as Alzheimer’s disease (AD), Parkinson’s disease (PD), epilepsy, despondency, and dementia have been evidenced as a rising concern among diverse geographical regions. Brain-related diseases are currently the main concern because they increase mortality and morbidity in the elderly. Regardless of the continual efforts by modern scientists to develop a promising pharmacological or surgical management, the outcome has not been satisfactory. Also, due to synthetic drugs’ associated side effects, scientists have taken the initiative to consider using natural compounds as an alternative. Hence, they obtain pretty effective results by using natural compounds. Natural ingredients are synthesized from a variety of plant and animal sources. These natural ingredients cure brain diseases through a variety of mechanisms. For effective medication advancement, the molecules must go through preliminary clinical systems that require some investment and significant speculation. In this situation, cheminformatics is fundamental in diminishing time and venture. Cheminformatics methods play a significant role in these issues, including 3-dimensional quantitative structure-activity relationship 3D-(QSAR), virtual screening, docking, molecular dynamic studies, and quantum chemical studies. The vital purpose of this study is to disclose different types of NDs and the neuroprotective effect of several natural products for experimental and cheminformatics-based therapy. Natural products like green tea, flavonoids, and ginseng are discussed as effective neuroprotective products. However, more investigation is expected to comprehend the better utilization of regular items in future exploratory and cheminformatics-based treatment for NDs.

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Section: Application Of Nd Treatment Based On Cheminformaticsmentioning

confidence: 99%

Natural products in neuroprotective therapies: Experimental and cheminformatics approaches to manage neurological disorders

Rahman,

Hossain,

Rifat

et al. 2024

Appl. Chem. Eng.

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“…The simulation of the motion is realized by the numerical solution of the classical Newtonian dynamic equations. 31 We used Gromacs v. 2020 to calculate the molecular dynamics (MD) simulation and the AMBER-99SB-ILDN force field. The topologies for the Amber force field were determined on the ACPYPE server (https://www.bio2byte.be/acpype/) for the best metabolite against mutates Mpro.…”

Section: Molecular Dynamics Simulation and Mm/gbsa Calculationmentioning

confidence: 99%

Identification of compounds from natural Peruvian sources as potential inhibitors of SARS-CoV-2 Mpro mutations by virtual screening and computational simulations

Barazorda Ccahuana,

Goyzueta Mamani,

Cárcamo Rodriguez

et al. 2023

Preprint

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The COVID-19 pandemic continues to be a public health problem worldwide. Several therapeutic targets of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been identified, whereas the main protease (Mpro) is necessary for virus replication. Since SARS-CoV-2 Mpro mutation rates are inherently high, searching for new inhibitors remains challenging. Herein, this work aimed to evaluate eighty-four natural compounds from Peruvian sources against different mutations on the Mpro target. Using computational technics, we applied virtual screening, all-atom molecular dynamics simulations, and binding free energy estimation by MM/GBSA methods. The virtual screening results helped us identify rutin as the top compound against different Mpro mutations. Likewise, the computational simulations demonstrated the high structural stability of the Mpro-rutin system. Our results demonstrated the antiviral capacity of compounds from Peruvian sources against SARS-CoV-2 Mpro and its mutations, which could significantly prevent and treat SARS-CoV-2 infection.

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“…The motion of the atoms is determined based on the classical Newtonian dynamic equation's numerical solution. MD not only provide the user with the predicted motion of atoms, but it also can provide thermodynamic data that can be used in further studies [3]. The first step and the most important one in MD is to define the interaction potential and ICNNFC 161-2 molecular topology for the system to be simulated.…”

Section: Introductionmentioning

confidence: 99%

Adsorption of Cations Using Graphene Oxide Loaded with Ionic Liquid: A Molecular Dynamic Simulation

Grira¹,

ElGazar²,

Khalifeh³

et al. 2023

World Congress on Recent Advances in Nanotechnology

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Sea water desalination is the process of separating salts from water to produce potable water. It is a very important process for countries that lack fresh water sources such as UAE. Many techniques are used in this process, but the most common one is the reverse osmosis (RO) process, which uses semipermeable membranes. Although this technique is widely used, it has a major drawback which is membrane fouling. Membrane fouling is caused due to inorganic salt deposition. This problem decreases the efficiency of the process and increases the costs. To solve the problem of inorganic salts fouling on the water filtration/desalination membranes, a proposed solution is to treat saltwater using a new adsorbent called GO-IL before sending it to the desalination process. GO-IL is an adsorbent made of graphene oxide nanosheets loaded with an ionic liquid called propylammonium nitrate. Treating saltwater using GO-IL aims to adsorb significant amounts of salts (e.g. Na + and Mg 2+ ) present in water before starting the desalination process. This pretreatment process reduces desalination membrane fouling, enhances the desalination process, and reduces cleaning and maintenance costs. The purpose of our work is to simulate the water pretreatment process using GO-IL on a molecular level scale using the computational power of Molecular Dynamics (MD) Simulations to test its efficiency.

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Chemoinformatics

Cited by 14 publications

References 102 publications

Natural products in neuroprotective therapies: Experimental and cheminformatics approaches to manage neurological disorders

Natural products in neuroprotective therapies: Experimental and cheminformatics approaches to manage neurological disorders

Identification of compounds from natural Peruvian sources as potential inhibitors of SARS-CoV-2 Mpro mutations by virtual screening and computational simulations

Adsorption of Cations Using Graphene Oxide Loaded with Ionic Liquid: A Molecular Dynamic Simulation

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