scholarly journals Chemical Reactivity Descriptors and Molecular Docking Studies of Octyl 6-O-hexanoyl-β-D-glucopyranosides

2021 ◽  
Vol 8 (2) ◽  
pp. 903-912
Author(s):  
Naimul Islam ◽  
Mohammad H.O. Roshid ◽  
Md. Lutfor Rahaman
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
Chemical Reactivity ◽  
Ester Group ◽  
Docking Studies ◽  
Urate Oxidase ◽  
Reactivity Descriptors ◽  
Main Protease ◽  
Chemical Reactivity Descriptors ◽  
Homo Lumo

The present study describes different chemical reactivity predictions of 6-O-hexanoylation of octyl β-D-glucopyranosides prepared from octyl β-D-glucopyranoside (OBG). Also, molecular docking of the OBGs was conducted against SARS-CoV-2 main protease (6LU7), urate oxidase (Aspergillus flavus; 1R51) and glucoamylase (Aspergillus niger; 1KUL). DFT optimization indicated that glucoside 1 and its ester derivatives 2-7 exist in 4C1 conformation with C1 symmetry. Interestingly, the addition of ester group(s) decreased the HOMO-LUMO gap (Δԑ) of glucosides indicating their good chemical reactivities, whereas the other chemical reactivity descriptors indicated their moderate reactive nature. This fact of moderate reactivity was confirmed by their molecular docking with 6LU7, 1R51 and 1KUL. All the esters showed a moderate binding affinity with these three proteins. More importantly, incorporation of the ester group(s) increased binding affinity with 6LU7 and 1R51, whereas decreased with 1KUL as compared to non-ester OBG 1.

scholarly journals Investigation of Some Antiviral N-Heterocycles as COVID 19 Drug: Molecular Docking and DFT Calculations

2020 ◽  
Vol 21 (11) ◽  
pp. 3922 ◽  
Author(s):  
Mohamed Hagar ◽  
Hoda A. Ahmed ◽  
Ghadah Aljohani ◽  
Omaima A. Alhaddad
Keyword(s):  
Dipole Moment ◽  
Molecular Docking ◽  
Dft Calculations ◽  
Binding Affinity ◽  
Electrostatic Potential ◽  
Density Functional ◽  
Molecular Electrostatic Potential ◽  
Hydrophobic Interactions ◽  
Chemical Reactivity ◽  
Main Protease

The novel coronavirus, COVID-19, caused by SARS-CoV-2, is a global health pandemic that started in December 2019. The effective drug target among coronaviruses is the main protease Mpro, because of its essential role in processing the polyproteins that are translated from the viral RNA. In this study, the bioactivity of some selected heterocyclic drugs named Favipiravir (1), Amodiaquine (2), 2′-Fluoro-2′-deoxycytidine (3), and Ribavirin (4) was evaluated as inhibitors and nucleotide analogues for COVID-19 using computational modeling strategies. The density functional theory (DFT) calculations were performed to estimate the thermal parameters, dipole moment, polarizability, and molecular electrostatic potential of the present drugs; additionally, Mulliken atomic charges of the drugs as well as the chemical reactivity descriptors were investigated. The nominated drugs were docked on SARS-CoV-2 main protease (PDB: 6LU7) to evaluate the binding affinity of these drugs. Besides, the computations data of DFT the docking simulation studies was predicted that the Amodiaquine (2) has the least binding energy (−7.77 Kcal/mol) and might serve as a good inhibitor to SARS-CoV-2 comparable with the approved medicines, hydroxychloroquine, and remdesivir which have binding affinity −6.06 and −4.96 Kcal/mol, respectively. The high binding affinity of 2 was attributed to the presence of three hydrogen bonds along with different hydrophobic interactions between the drug and the critical amino acids residues of the receptor. Finally, the estimated molecular electrostatic potential results by DFT were used to illustrate the molecular docking findings. The DFT calculations showed that drug 2 has the highest of lying HOMO, electrophilicity index, basicity, and dipole moment. All these parameters could share with different extent to significantly affect the binding affinity of these drugs with the active protein sites.

scholarly journals Molecular Docking Study on Several Benzoic Acid Derivatives against SARS-CoV-2

Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 5828
Author(s):  
Amalia Stefaniu ◽  
Lucia Pirvu ◽  
Bujor Albu ◽  
Lucia Pintilie
Keyword(s):  
Molecular Docking ◽  
Benzoic Acid ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Principal Component ◽  
Docking Study ◽  
Docking Studies ◽  
Molecular Docking Study ◽  
Alkyl Gallates ◽  
Main Protease

Several derivatives of benzoic acid and semisynthetic alkyl gallates were investigated by an in silico approach to evaluate their potential antiviral activity against SARS-CoV-2 main protease. Molecular docking studies were used to predict their binding affinity and interactions with amino acids residues from the active binding site of SARS-CoV-2 main protease, compared to boceprevir. Deep structural insights and quantum chemical reactivity analysis according to Koopmans’ theorem, as a result of density functional theory (DFT) computations, are reported. Additionally, drug-likeness assessment in terms of Lipinski’s and Weber’s rules for pharmaceutical candidates, is provided. The outcomes of docking and key molecular descriptors and properties were forward analyzed by the statistical approach of principal component analysis (PCA) to identify the degree of their correlation. The obtained results suggest two promising candidates for future drug development to fight against the coronavirus infection.

scholarly journals Potential Exploration of Recent FDA-Approved Anticancer Drugs Against Models of SARS-CoV-2’s Main Protease and Spike Glycoprotein: A Computational Study

2020 ◽  
Vol 11 (3) ◽  
pp. 10059-10073
Keyword(s):  
Anticancer Drugs ◽  
Computational Study ◽  
Chemical Reactivity ◽  
Dipole Moments ◽  
Amino Acid Residues ◽  
Spike Glycoprotein ◽  
Binding Ability ◽  
Reactivity Descriptors ◽  
Main Protease ◽  
Chemical Reactivity Descriptors

COVID-19 has become a worldwide risk to the healthcare system of practically every nation of the world, which originated from Wuhan, China. To date, no specific drugs are available to treat this disease. The exact source of the SARS-CoV-2 is yet unknown, although the early cases are associated with the Seafood market in Huanan, South China. This manuscript reports the in silico molecular modeling of recent FDA-approved anticancer drugs (Capmatinib, Pemigatinib, Selpercatinib, and Tucatinib) for their inhibitory action against COVID-19 targets. The selected anticancer drugs are docked on SARS-CoV-2 main protease (PDB ID: 6LU7) and SARS-CoV-2 spike glycoprotein (PDB ID: 6M0J) to ascertain the binding ability of these drugs. ADMET parameters of the drugs are assessed, and in addition, DFT calculations are done to investigate the pharmacokinetics, thermal parameters, dipole moments, and chemical reactivity descriptors. The docking energies (ΔG) and the interacting amino acid residues are discussed. Promising molecular docking conclusions have been accomplished, which demonstrated the potential of selected anticancer drugs for plausible drug development to fight COVID-19. Further optimizations with the drug may support the much-needed rapid response to mitigate the pandemic.

scholarly journals Β-SITOSTEROL: ISOLATION FROM MUNTINGIA CALABURA LINN BARK EXTRACT, STRUCTURAL ELUCIDATION AND MOLECULAR DOCKING STUDIES AS POTENTIAL INHIBITOR OF SARS-CoV-2 Mpro (COVID-19)

2020 ◽  
pp. 204-209
Author(s):  
RAKESH N CHAUDHARI ◽  
SHARUK L.KHAN ◽  
RAVINDRA S CHAUDHARY ◽  
SHIRISH P JAIN ◽  
FALAK A SIDDUQUI
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
Column Chromatography ◽  
Docking Studies ◽  
Bark Extract ◽  
Molecular Docking Studies ◽  
Ftir Characterization ◽  
Main Protease ◽  
Layer Chromatography ◽  
Muntingia Calabura

Objecive: A novel human coronavirus (HCoV), labelled as SARS-CoV-2 (COVID-19), causing pneumonia is spreading around the world. At present, there are no specific treatments for COVID-19. β-sitosterol is well known for its multiple biological actions. The aim of this research is to isolate and study binding affinity of β-sitosterol for SARS-CoV-2 (COVID-19) main protease (Mpro). Methods: Extraction and Column chromatography was performed to isolate the β-sitosterol from n-hexane extract of Muntingia calabura bark followed by thin layer chromatography (TLC), HPTLC, FTIR and UV-Visible Spectroscopy. The molecular docking studies were performed on SARS-CoV-2 Mpro to determine the binding affinity of the β-sitosterol by using PyRx Virtual Screening Tool. Results: In present study, preliminary phytochemical screening showed presence of carbohydrate, steroid, terpenoid and flavonoid compounds. Total 115 fractions were collected from column chromatography by using benzene as solvent by isocratic elution technique. HPTLC Fingerprinting analysis showed the presence of β-sitosterol under 366 nm. FTIR characterization was performed of the same fraction which clearly gives the absorption peaks which resembles to β-sitosterol structure. Conclusion: The overall study concludes this method can be considered as a standard method for isolation of β-sitosterol from Muntingia calabura bark. Favipiravir have less binding affinity i.e. -5.7 kcal/mol than β-sitosterol which has -6.9 kcal/mol. The no. of hydrogen bonds formed by the Favipiravir is much more i.e. 04 than β-sitosterol which formed only 01 hydrogen bond with SARS-CoV-2 Mpro.

scholarly journals Synthesis, characterization, investigation of biological activity, docking studies, and spectroscopic properties of hydrazone compounds containing different substituents

2019 ◽  
Vol 97 (4) ◽  
pp. 408-416
Author(s):  
Engin Yilmaz ◽  
Alaaddin Cukurovali
Keyword(s):  
Escherichia Coli ◽  
Staphylococcus Aureus ◽  
Molecular Docking ◽  
Electronic Absorption Spectra ◽  
Spectroscopic Properties ◽  
Docking Studies ◽  
Reactivity Descriptors ◽  
E Coli ◽  
Global Reactivity Descriptors ◽  
Homo Lumo

To assess electronic absorption spectra, molecular docking, and antibacterial activity, 12 new hydrazone compounds that have different substituents and in different positions were synthesized and characterized. HOMO–LUMO energies and theoretical electronic spectra of synthesized compounds were computed via Gaussian 09 software. Global reactivity descriptors were computed from HOMO–LUMO energies. In addition, 1JXA protein was used for molecular docking studies structure. Staphylococcus aureus ATCC 29213 and Enterococcus faecalis ATCC 29212 (as negative bacteria), Escherichia coli ATCC 25922, and Pseudomonas aeruginosa ATCC 27853 (as gram positive) was selected. Compound 3 was observed to be the most effective against propagations of E. Coli. Similarly, compounds 7 and 9 were found to be the most effective against the reproduction of P. aeroginosa. The most powerful compound against the growth of E. faecalis was ascertained to be compound 7.

Discovery of Some Antiviral Natural products to fight against Novel Corona Virus (SARS-CoV-2) using Insilico approach

2020 ◽  
Vol 23 ◽  
Author(s):  
Ashish Shah ◽  
Vaishali Patel ◽  
Bhumika Parmar
Keyword(s):  
Binding Affinity ◽  
Protein S ◽  
Docking Studies ◽  
Spike Protein ◽  
Enveloped Viruses ◽  
Bioactivity Prediction ◽  
Corona Virus ◽  
Main Protease ◽  
Antiviral Activities ◽  
Deadly Disease

Background: Novel Corona virus is a type of enveloped viruses with a single stranded RNA enclosing helical nucleocapsid. The envelope consists of spikes on the surface which are made up of proteins through which virus enters into human cells. Until now there is no specific drug or vaccine available to treat COVID-19 infection. In this scenario, reposting of drug or active molecules may provide rapid solution to fight against this deadly disease. Objective: We had selected 30 phytoconstituents from the different plants which are reported for antiviral activities against corona virus (CoVs) and performed insilico screening to find out phytoconstituents which have potency to inhibit specific target of novel corona virus. Methods: We had perform molecular docking studies on three different proteins of novel corona virus namely COVID-19 main protease (3CL pro), papain-like protease (PL pro) and spike protein (S) attached to ACE2 binding domain. The screening of the phytoconstituents on the basis of binding affinity compared to standard drugs. The validations of screened compounds were done using ADMET and bioactivity prediction. Results: We had screened five compounds biscoclaurine, norreticuline, amentoflavone, licoricidin and myricetin using insilico approach. All compounds found safe in insilico toxicity studies. Bioactivity prediction reviles that these all compounds may act through protease or enzyme inhibition. Results of compound biscoclaurine norreticuline were more interesting as this biscoclaurine had higher binding affinity for the target 3CLpro and PLpro targets and norreticuline had higher binding affinity for the target PLpro and Spike protein. Conclusion: Our study concludes that these compounds could be further explored rapidly as it may have potential to fight against COVID-19.

A New Series Of 1,3-Dimethylxanthine Based Adenosine A2a Receptor Antagonists As A Non-Dopaminergic Treatment Of Parkinson’s Disease

2020 ◽  
Vol 17 ◽  
Author(s):  
Suman Rohilla ◽  
Ranju Bansal ◽  
Puneet Chauhan ◽  
Sonja Kachler ◽  
Karl-Norbert Klotz
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Molecular Docking ◽  
Binding Affinity ◽  
Docking Studies ◽  
Binding Modes ◽  
Molecular Docking Studies ◽  
In Silico Docking ◽  
Adenosine A2a Receptor Antagonists ◽  
The Impact

Background: Adenosine receptors (AR) have emerged as competent and innovative nondopaminergic targets for the development of potential drug candidates and thus constitute an effective and safer treatment approach for Parkinson’s disease (PD). Xanthine derivatives are considered as potential candidates for the treatment Parkinson’s disease due to their potent A2A AR antagonistic properties. Objective: The objectives of the work are to study the impact of substituting N7-position of 8-m/pchloropropoxyphenylxanthine structure on in vitro binding affinity of compounds with various AR subtypes, in vivo antiparkinsonian activity and binding modes of newly synthesized xanthines with A2A AR in molecular docking studies. Methods: Several new 7-substituted 8-m/p-chloropropoxyphenylxanthine analogues have been prepared. Adenosine receptor binding assays were performed to study the binding interactions with various subtypes and perphenazine induced rat catatonia model was used for antiparkinsonian activity. Molecular docking studies were performed using Schrödinger molecular modeling interface. Results: 8-para-substituted xanthine 9b bearing an N7-propyl substituent displayed the highest affinity towards A2A AR (Ki = 0.75 µM) with moderate selectivity versus other AR subtypes. 7-Propargyl analogue 9d produced significantly longlasting antiparkinsonian effects and also produced potent and selective binding affinity towards A2A AR. In silico docking studies further highlighted the crucial structural components required to develop xanthine derived potential A2A AR ligands as antiparkinsonian agents. Conclusion: A new series of 7-substituted 8-m/p-chloropropoxyphenylxanthines having good affinity for A2A AR and potent antiparkinsonian activity has been developed.

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