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Patra SG, Mondal H, Chattaraj PK. Variation in Electrophilicity on Electronic Excitation. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4359] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Himangshu Mondal
- Department of Chemistry Indian Institute of Technology Kharagpur India
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2
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Basak HK, Saha S, Ghosh J, Paswan U, Karmakar S, Pal A, Chatterjee A. Sequence Analysis, Structure Prediction of Receptor Proteins and In Silico
Study of Potential Inhibitors for Management of Life Threatening
COVID-19. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180818666210804141613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Treatment of the Covid-19 pandemic caused by the highly contagious and
pathogenic SARS-CoV-2 is a global menace. Day by day, this pandemic is getting worse. Doctors,
scientists and researchers across the world are urgently scrambling for a cure for novel corona virus
and continuously working at break neck speed to develop vaccines or drugs. But to date, there
are no specific drugs or vaccines available in the market to cope up with the virus.
Objective:
The present study helps us to elucidate 3D structures of SARS-CoV-2 proteins and also
to identify natural compounds as potential inhibitors against COVID-19.
Methods:
The 3D structures of the proteins were constructed using Modeller 9.16 modeling tool.
Modelled proteins were validated with PROCHECK by Ramachandran plot analysis. In this study,
a small library of natural compounds (fifty compounds) was docked to the hACE2 binding site of
the modelled surface glycoprotein of SARS-CoV-2 using AutoDock Vina to repurpose these inhibitors
against SARS-CoV-2. Conceptual density functional theory calculations of the best eight
compounds had been performed by Gaussian-09. Geometry optimizations for these molecules were
done at M06-2X/ def2-TZVP level of theory. ADME parameters, pharmacokinetic properties and
drug likeness of the compounds were analyzed using swissADME website.
Results:
In this study, we analysed the sequences of surface glycoprotein, nucleocapsid phosphoprotein
and envelope protein obtained from different parts of the globe. We modelled all the different
sequences of surface glycoprotein and envelop protein in order to derive 3D structure of a molecular
target, which is essential for the development of therapeutics. Different electronic properties
of the inhibitors have been calculated using DFT through M06-2X functional with def2-TZVP
basis set. Docking result at the hACE2 binding site of all modelled surface glycoproteins of SARSCoV-
2 showed that all the eight inhibitors (actinomycin D, avellanin C, ichangin, kanglemycin A,
obacunone, ursolic acid, ansamiotocin P-3 and isomitomycin A) studied here were many folds
better compared to hydroxychloroquine which has been found to be effective to treat patients suffering
from COVID-19. All the inhibitors meet most of the criteria of drug likeness assessment.
Conclusion:
We expect that eight compounds (actinomycin D, avellanin C, ichangin, kanglemycin
A, obacunone, ursolic acid, ansamiotocin P-3 and isomitomycin A) can be used as potential inhibitors
against SARS-CoV-2.
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Affiliation(s)
- Hriday Kumar Basak
- In silico Chemical Laboratory, Department of Chemistry, Raiganj University, Raiganj, West Bengal, India
| | - Soumen Saha
- Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Joydeep Ghosh
- In silico Chemical Laboratory, Department of Chemistry, Raiganj University, Raiganj, West Bengal, India
| | - Uttam Paswan
- In silico Chemical Laboratory, Department of Chemistry, Raiganj University, Raiganj, West Bengal, India
| | - Sujoy Karmakar
- In silico Chemical Laboratory, Department of Chemistry, Raiganj University, Raiganj, West Bengal, India
| | - Ayon Pal
- Microbiology & Computational
Biology Laboratory, Department of Botany, Raiganj University, Raiganj, West Bengal, India
| | - Abhik Chatterjee
- In silico Chemical Laboratory, Department of Chemistry, Raiganj University, Raiganj, West Bengal, India
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Identification of new pyrazolyl piperidine molecules as factor Xa inhibitors: Design, synthesis, in silico, and biological evaluation. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Theoretical Study on the Structures, Spectral Properties, and Drugability of Xenicane-type Diterpenoids from Dictyota dichotoma. Chem Res Chin Univ 2021. [DOI: 10.1007/s40242-021-1296-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Microwave prompted solvent-free synthesis of new series of heterocyclic tagged 7-arylidene indanone hybrids and their computational, antifungal, antioxidant, and cytotoxicity study. Bioorg Chem 2021; 115:105259. [PMID: 34426144 DOI: 10.1016/j.bioorg.2021.105259] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 07/25/2021] [Accepted: 08/06/2021] [Indexed: 12/23/2022]
Abstract
In this study, we report the expeditious synthesis of ten new antifungal and antioxidant agents containing heterocyclic linked 7-arylidene indanone moiety. The solvent-free microwave technique, ample substrate scope, superfast synthesis, and very simple operation are noteworthy features of this protocol. Antifungal activities of the newly synthesized compounds were evaluated against four fungal strains namely Rhizophus oryzae, Mucor mucido, Aspergillus niger, and Candida albicans. Most of the compounds were shown strong inhibition of the investigated fungal agents. In vitro, antioxidant potential against DPPH and OH radicals affirmed that the synthesized compounds are good to excellent radicals scavenging agents. The cytotoxicity data of the synthesized compounds towards HL-60 cells uncovered that the synthesized compounds display very low to negligible cytotoxicity. The structural and quantum chemical parameters of the synthesized compounds were explored by employing density functional theory (DFT) at B3LYP functional using 6-311G(d,p) basis set. The compound 3a is discussed in detail for the theoretical and experimental correlation. Time-dependent density functional theory (TD-DFT) at CAM-B3LYP functional with 6-311G(d,p) basis set was used for the electronic absorption study in the gas phase and indichloromethane and benzene solvents. The UV-Visible absorption peaks and fundamental vibrational wavenumbers were computed and a good agreement between observed and theoretical results has been achieved. From the DFT and antifungal activity correlation, it has been found that the 7-heteroarylidene indanones with more stabilized LUMO energy levels display good antifungal potential.
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Carroll AR, Copp BR, Davis RA, Keyzers RA, Prinsep MR. Marine natural products. Nat Prod Rep 2021; 38:362-413. [PMID: 33570537 DOI: 10.1039/d0np00089b] [Citation(s) in RCA: 198] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This review covers the literature published in 2019 for marine natural products (MNPs), with 719 citations (701 for the period January to December 2019) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1490 in 440 papers for 2019), together with the relevant biological activities, source organisms and country of origin. Pertinent reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. Methods used to study marine fungi and their chemical diversity have also been discussed.
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Affiliation(s)
- Anthony R Carroll
- School of Environment and Science, Griffith University, Gold Coast, Australia. and Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Brent R Copp
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Rohan A Davis
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia and School of Enivironment and Science, Griffith University, Brisbane, Australia
| | - Robert A Keyzers
- Centre for Biodiscovery, School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Michèle R Prinsep
- Chemistry, School of Science, University of Waikato, Hamilton, New Zealand
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Babaei S, Niad M. Chemical reactivity descriptors as a tool of prediction in the synthesis of sandwich type polyoxometalate organic–inorganic hybrid compounds. Polyhedron 2020. [DOI: 10.1016/j.poly.2020.114710] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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