scholarly journals The computational screening of inhibitor for black fungus and white fungus by D-glucofuranose derivatives using in silico and SAR study

2021 ◽  
pp. 1-18
Author(s):  
Ajoy Kumer ◽  
Unesco Chakma ◽  
Mohammed M. Matin ◽  
Shopnil Akash ◽  
Debashis Howlader ◽  
...  
Keyword(s):  
In Silico ◽  
Computational Screening ◽  
Sar Study

scholarly journals Antimalarial phytochemicals as inhibitors against COVID-19 ACE2 receptor: Computational screening

2021 ◽  
Vol 13 (2) ◽  
pp. 10835
Author(s):  
Ouided BENSLAMA ◽  
Nedjwa MANSOURI ◽  
Rabah ARHAB
Keyword(s):  
Hydrogen Bond ◽  
In Silico ◽  
Pharmacophore Model ◽  
In Silico Analysis ◽  
Active Site Residues ◽  
Hydrophobic Region ◽  
Hydrogen Bond Acceptor ◽  
Computational Screening ◽  
Docking Approach ◽  
Therapeutic Molecules

Quinine, artemisinin, febrifugine, brusatol, chaparrin tehranolide, glaucarubin, sergeoliden, and yingzhaosu A, nine antimalarial phytochemicals, were the focus of an in-silico analysis aimed at discovering new therapeutic molecules against COVID-19 infection. The screening of these molecules included a molecular docking approach within the Angiotensin-converting enzyme-2 (ACE2) receptor. In addition, drug-likeness, ADMET analysis and pharmacophore mapping have been performed. The result of the docking process was based on the energy binding values as well as the number and type of interactions established with the receptor active site residues, which were compared with those of co-crystallized ligand and chloroquine. Febrifugine showed the most interesting energetic and interactive activities that were closer to the reference molecule and better than those of chloroquine. Whereas artemisinin has produced results that are the closest to those of chloroquine. Similarly, drug-likeness and ADMET analysis have shown that febrifugine and artemisinin check most of the filters and pharmacokinetic properties required for the choice of an effective therapeutic molecule. A pharmacophore model was designed on the basis of a training set consisting of the most relevant molecules; it has one metal ligator cum hydrophobic region cum hydrogen bond acceptor, one hydrogen bond acceptor cum metal ligator and one hydrophobic aromatic ring. This model is proposed to be used for the in-silico discovery of new therapeutic molecules against coronavirus.

scholarly journals COCONUT online: Collection of Open Natural Products database

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Maria Sorokina ◽  
Peter Merseburger ◽  
Kohulan Rajan ◽  
Mehmet Aziz Yirik ◽  
Christoph Steinbeck
Keyword(s):  
Natural Products ◽  
Small Molecules ◽  
In Silico ◽  
Web Interface ◽  
Computational Screening ◽  
Online Resource ◽  
The World ◽  
Potential Applications ◽  
Living Organisms ◽  
Application Fields

AbstractNatural products (NPs) are small molecules produced by living organisms with potential applications in pharmacology and other industries as many of them are bioactive. This potential raised great interest in NP research around the world and in different application fields, therefore, over the years a multiplication of generalistic and thematic NP databases has been observed. However, there is, at this moment, no online resource regrouping all known NPs in just one place, which would greatly simplify NPs research and allow computational screening and other in silico applications. In this manuscript we present the online version of the COlleCtion of Open Natural prodUcTs (COCONUT): an aggregated dataset of elucidated and predicted NPs collected from open sources and a web interface to browse, search and easily and quickly download NPs. COCONUT web is freely available at https://coconut.naturalproducts.net.

scholarly journals In silico Study of Potential Non-oxime Reactivator for Sarin-inhibited Human Acetylcholinesterase

2021 ◽  
Vol 29 (3) ◽  
Author(s):  
Rauda A. Mohamed ◽  
Keat Khim Ong ◽  
Norhana Abdul Halim ◽  
Noor Azilah Mohd Kasim ◽  
Siti Aminah Mohd Noor ◽  
...  
Keyword(s):  
Binding Energy ◽  
In Silico ◽  
Docking Study ◽  
Dynamics Simulation ◽  
Nucleophilic Attack ◽  
Organophosphate Poisoning ◽  
Nipecotic Acid ◽  
Computational Screening ◽  
The Stability ◽  
New Compounds

The search for new compounds other than oxime as potential reactivator that is effective upon organophosphate poisoning treatments is desired. The less efficacy of oxime treatment has been the core factor. Fourteen compounds have been screened via in silico approach for their potential as sarin-inhibited human acetylcholinesterase poisoning antidotes. The selection of the compounds to be synthesized based on this computational screening, reduces the time and cost needed. To perform the docking study of sarin-inhibited acetylcholinesterase and reactivator-sarin inhibited acetylcholinesterase complexations, a bioinformatics tool was used. Estimation of the nucleophilic attack distance and binding energy of fourteen potential compounds with sarin inhibited acetylcholinesterase complexes to determine their antidote capacities was carried out using Autodock. A commercially available antidote, 2-PAM was used for the comparison. The best docked-pose was further examined with molecular dynamics simulation. Apart from being lipophilic, a compound with a carboxylic acid, (R)-Boc-nipecotic acid is shown to exhibit 6.29 kcal/mol binding energy with 8.778 Å distance of nucleophilic attack. The stability and flexibility of the sarin-inhibited acetylcholinesterase, complexed with (R)-Boc-nipecotic acid suggests this compound should be tested experimentally as a new, promising antidote for sarin-inhibited acetylcholinesterase poisoning.

In-silico screening of 2,3-diphenylquinozaline derivatives as C-met kinase inhibitors

2017 ◽  
Vol 4 (3) ◽  
pp. 41-45
Author(s):  
Nehla Yahcoob ◽  
Baskar Lakshmanan ◽  
Jyothi Achuthanandhan ◽  
Vijayakumar Balakrishnan
Keyword(s):  
Binding Energy ◽  
Tyrosine Kinase ◽  
In Silico ◽  
Kinase Inhibitors ◽  
Therapeutic Potential ◽  
Biological Activities ◽  
Wide Spectrum ◽  
Binding Interaction ◽  
In Silico Screening ◽  
Sar Study

Quinoxaline, an important class of heterocylic compounds drawn greater attention due to their wide spectrum of biological activities. They are considered as an important chemical scaffold for anticancer drug design  due to their potential inhibitory activity against  C-met tyrosine kinase. C-met kinase inhibitors  are a class of small molecules that having therapeutic potential in  the treatment of various types of cancers. The present study aims to focus on the chemistry of quinoxaline derivatives, their potential activities against C-met tyrosine kinase, and in-silico screening of designed compounds. A series of twelve compounds were designed and docked against C-met tyrosine kinase for their binding energy. All compounds were found to be interacting  well with the protein. Compound NQ1 was found to have good binding energy showing an estimated Ki value of  1.1μm.  SAR  study indicated the presence of an electron withdrawing substitution on  benzilidine  phenyl ring of quinoxaline greatly improves its binding interaction with the protein.

scholarly journals Piperazine-substituted derivatives of favipiravir for Nipah virus inhibition: What do in silico studies unravel?

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Raju Lipin ◽  
Anantha Krishnan Dhanabalan ◽  
Krishnasamy Gunasekaran ◽  
Rajadurai Vijay Solomon
Keyword(s):  
In Silico ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Nipah Virus ◽  
New Drugs ◽  
Structure Property ◽  
Binding Ability ◽  
Computational Screening ◽  
In Silico Studies

AbstractFavipiravir is found to show excellent in-vitro inhibition activity against Nipah virus. To explore the structure–property relationship of Favipiravir, in silico designing of a series of piperazine substituted Favipiravir derivatives are attempted and computational screening has been done to evaluate its bimolecular interactions with Nipah virus. The geometrical features of all the molecules have been addressed from Density Functional Theory calculations. Chemical reactivity descriptor analysis was carried out to understand various reactivity parameters. The drug-likeness properties were estimated by a detailed ADMET study. The binding ability and the mode of binding of these derivatives into the Nipah virus are obtained from molecular docking studies. Our calculations show greater binding ability for the designed inhibitors compared to that of the experimentally reported molecule. Overall, the present work proves to offers new insights and guidelines for synthetic chemists to develop new drugs using piperazine substituted Favipiravir in the treatment of Nipah virus.

scholarly journals Coconut Online: Collection of Open Natural Products Database

2020 ◽  
Author(s):  
Maria Sorokina ◽  
Peter Merseburger ◽  
Kohulan Rajan ◽  
Mehmet Aziz Yirik ◽  
Christoph Steinbeck
Keyword(s):  
Natural Products ◽  
Small Molecules ◽  
In Silico ◽  
Web Interface ◽  
Computational Screening ◽  
Online Resource ◽  
Potential Applications ◽  
Living Organisms

Abstract Natural products (NPs) are small molecules produced by living organisms with potential applications in pharmacology and other industries for their high bioactivities. Over the years a multiplication of thematic NP databases has been observed. However, there is no online resource regrouping all known NPs in just one place, which would greatly simplify NP research and allow computational screening and other in silico applications. Here we present the COlleCtion of Open Natural prodUcTs (COCONUT): an aggregated dataset of NPs available in different open sources and a subsequent web interface to browse, search and easily and quickly download NPs. COCONUT web is freely available at https://coconut.naturalproducts.net.

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