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 Chemical Reactivity, Dipole Moment and First Hyperpolarizability of Aristolochic Acid I

2016 ◽  
Vol 21 (1) ◽  
pp. 1-9 ◽  
Author(s):  
Bhawani Datta Joshi
Keyword(s):  
Dipole Moment ◽  
Electrostatic Potential ◽  
Density Functional ◽  
Molecular Electrostatic Potential ◽  
Aristolochic Acid ◽  
Chemical Reactivity ◽  
Basis Set ◽  
Non Linear ◽  
Linear Optical ◽  
Aristolochic Acid I

Aristolochic acids (AAs) have been used in the treatment of oedema in  Chinese herb medicine  since  long  ago. In this paper, molecular electrostatic potential, chemical reactivity  and non linear optical properties  of  aristolochic  acid  I  (AA  I)  have  been  analyzed  using  density  functional  theory  employing  6-311++G(d,p)  basis set.  The chemical reactivity of the molecule has been explained with the help of chemical reactivity descriptors, molar refractivity and the molecular electrostatic potential surface (ESP).  The calculated dipole moment and first order hyperpolarizability show that the molecule possesses non-linear optical property.Journal of Institute of Science and TechnologyVolume 21, Issue 1, August 2016, page: 1-9

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 Spectroscopic Investigations, Computational Analysis and Molecular Docking to SAR-Cov-2 Targets Studies of 5,8-Quinolinedione Attached to Betulin Derivatives

Crystals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 76
Author(s):  
Monika Kadela-Tomanek ◽  
Maria Jastrzębska ◽  
Krzysztof Marciniec ◽  
Ewa Bębenek ◽  
Elwira Chrobak ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Electrostatic Potential ◽  
Density Functional ◽  
Molecular Electrostatic Potential ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Functional Theory ◽  
Drug Candidates ◽  
The Density Functional Theory ◽  
Ft Ir

The 5,8-quinolinedione-betulin hybrids were investigated using spectroscopic methods as well as a variety of quantum chemical calculations in order to characterize their molecular structure. We used FT-IR and NMR spectroscopy supplemented by the density functional theory (DFT) calculations, molecular electrostatic potential (MEP) and molecular orbital (HOMO, LUMO) analyses. The experimental and calculated FT-IR spectra showed a good correlation for all compounds. Analysis of carbonyl band showed that the compounds are the 7-mono substituted. The calculated 1H NMR and 13C NMR spectra of hybrids reproduced well the experimental ones. Identification of C-6 and C-7 carbon atoms of 5,8-quinolinedione revealed the position of betulin moiety at the C-7 of 5,8-quinolinedione. Molecular electrostatic potential maps of hybrids allowed to recognize the electrophilic and nucleophilic regions within the molecules. The molecular docking study was used to examine the interaction between the 5,8-quinolinedione-betulin hybrids and the SARS-CoV-2 protein, like: Mpro and PLpro. The obtained results showed that compounds with the highest Dock Score are good anti-SARS-CoV-2 potential drug candidates.

scholarly journals Spectroscopic and computational study of chromone derivatives with antitumor activity: detailed DFT, QTAIM and docking investigations

2021 ◽  
Vol 3 (2) ◽  
Author(s):  
Y. Sheena Mary ◽  
Y. Shyma Mary ◽  
K. S. Resmi ◽  
Ali Shokuhi Rad
Keyword(s):  
Electrostatic Potential ◽  
Density Functional ◽  
Molecular Electrostatic Potential ◽  
Energy Gap ◽  
Computational Study ◽  
Chemical Reactivity ◽  
Biological Activities ◽  
Docking Studies ◽  
Chromone Derivatives ◽  
Theoretical Investigations

AbstractTheoretical investigations of three pharmaceutically active chromone derivatives, (E)-3-((2,3,5,6-tetrafluorophenyl)hydrazono)methyl)-4H-chromen-4-one (TPC), (E)-3-((2-(2,4,6-trifluorophenyl)hydrazono)methyl)-4H-chromen-4-one (FHM) and(E)-3-((2-(perfluorophenyl)hydrazono)methyl)-4H-chromen-4-one (PFH) are reported. Molecular geometries, vibrational spectra, electronic properties and molecular electrostatic potential were investigated using density functional theory. Quantum theory of atoms in molecules (QTAIM) study shows that the maximum of ellipticity parameters in the existing bonds in TPC, FHM and PFH, attributes to the bonds involving in aromatic region points toward the π-bond interactions in the molecules. Based on energy gap (1.870, 1.649 and 1.590 eV) and electrophilicity index (20.233, 22.581 and 23.203 eV) values of TPC, FHM and PFH, we can conclude that all molecules have more biological activity. The molecular electrostatic potential maps were calculated to provide information on the chemical reactivity of the molecule and also to describe the intermolecular interactions. All these studies including docking studies, help a lot in determining the biological activities of chromone derivatives. Activities of chromone derivatives are compared with 5-fluorouracil and azathioprine (antitumor, antiproliferative standards) and were found to be higher than reference ones.

scholarly journals Investigation of Rosemary Active Ingredients as COVID-19 Inhibitors: Molecular Docking and DFT

2021 ◽  
Vol 9 (2) ◽  
Author(s):  
Talaat Habeeb
Keyword(s):  
Dipole Moment ◽  
Molecular Docking ◽  
Molecular Orbital ◽  
Active Ingredient ◽  
Density Functional ◽  
Energy Gap ◽  
Structural Complexity ◽  
Carnosic Acid ◽  
Main Protease ◽  
Docking Calculations

Rosemary is an important type of the natural Lamiaceae plant family with several medicinal properties, rendering it as a prospective inhibitor for the new SARS-CoV-2 virus. Its SARS-CoV-2 inhibition properties has not yet been reported. In this study the inhibition efficacy of rosemary against SARS-CoV-2 has been demonstrated using molecular docking along with systematic density-functional-theory (DFT) calculations. The estimated DFT data have shown that the dipole moment of rosemary active ingredient was in the range of 4.29-1.68 with the highest value attained by the carnosic acid. The high dipole moment for the carnosic acid may indicate its appropriate binding affinity pose within a specific virus target receptor. Moreover, the structural complexity for the carnosic acid gave rise to its highest calculated polarizability of 225.5 Bohr3 compared to the rest of the rosemary ingredients. Remarkably, the carnosic acid active ingredient has the least energy gap between the frontier orbitals (highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO)) of ~ 5.43 eV, with several hydrophilic sites for interactions, further enabling its binding with the virus receptors. Interestingly, and as anticipated from DFT results, molecular docking calculations showed that carnosic acid had the least binding energy (−6.9 kcal/mol) and, hence, can be regarded as a prospective inhibitor to SARS-CoV-2 main protease (Mpro). It binds to both Mpro catalytic dyads (Cys-145 and His-41) with hydrogen bond and π-interaction. This carnosic acid ligand binding quality was comparable to renowned SARS-CoV-2 drugs, hydroxychloroquine and favipiravir, having binding affinities of −6.1 and −5.1 kcal/mol, respectively.

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 Density Functional Theory and Molecular Docking Investigations of the Chemical and Antibacterial Activities for 1-(4-Hydroxyphenyl)-3-phenylprop-2-en-1-one

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3631
Author(s):  
Ahmed M. Deghady ◽  
Rageh K. Hussein ◽  
Abdulrahman G. Alhamzani ◽  
Abeer Mera
Keyword(s):  
Density Functional Theory ◽  
Antibacterial Activity ◽  
Molecular Docking ◽  
Carbonyl Group ◽  
Active Sites ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Basis Set ◽  
Molecular Docking Study ◽  
Functional Theory

The present investigation informs a descriptive study of 1-(4-Hydroxyphenyl) -3-phenylprop-2-en-1-one compound, by using density functional theory at B3LYP method with 6-311G** basis set. The oxygen atoms and π-system revealed a high chemical reactivity for the title compound as electron donor spots and active sites for an electrophilic attack. Quantum chemical parameters such as hardness (η), softness (S), electronegativity (χ), and electrophilicity (ω) were yielded as descriptors for the molecule’s chemical behavior. The optimized molecular structure was obtained, and the experimental data were matched with geometrical analysis values describing the molecule’s stable structure. The computed FT-IR and Raman vibrational frequencies were in good agreement with those observed experimentally. In a molecular docking study, the inhibitory potential of the studied molecule was evaluated against the penicillin-binding proteins of Staphylococcus aureus bacteria. The carbonyl group in the molecule was shown to play a significant role in antibacterial activity, four bonds were formed by the carbonyl group with the key protein of the bacteria (three favorable hydrogen bonds plus one van der Waals bond) out of six interactions. The strong antibacterial activity was also indicated by the calculated high binding energy (−7.40 kcal/mol).

scholarly journals Molecular Docking Senyawa Gingerol dan Zingiberol pada Tanaman Jahe sebagai Penanganan COVID-19

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Belinda D. P. M. Ratu ◽  
Widdhi Bodhi ◽  
Fona Budiarso ◽  
Billy J. Kepel ◽  
. Fatimawali ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
Amino Acid Residues ◽  
Autodock Vina ◽  
Discovery Studio ◽  
Main Protease ◽  
Docking Method ◽  
Pubmed Database ◽  
Almost All ◽  
The Impact

Abstract: COVID-19 is a new disease. Many people feel the impact of this disease. There is no definite cure for COVID-19, so many people use traditional medicine to ward off COVID-19, including ginger. This study aims to determine whether there is an interaction between compounds in ginger (gingerol and zingiberol) and the COVID-19’s main protease (6LU7). This study uses a molecular docking method using 4 main applications, namely Autodock Tools, Autodock Vina, Biovia Discovery Studio 2020, and Open Babel GUI. The samples used were gingerol and zingiberol compounds in ginger plants downloaded from Pubchem. The data used in this study used Mendeley, Clinical Key, and PubMed database. The study showed that almost all of the amino acid residues in the gingerol compound acted on the 6LU7 active site, whereas the zingiberol did not. The results of the binding affinity of ginger compounds, both gingerol and zingiberol, do not exceed the binding affinity of remdesivir, a drug that is widely researched as a COVID-19 handling drug. In conclusion, gingerol and zingiberol compounds in ginger can’t be considered as COVID-19’s treatment.Keywords: molecular docking, gingerol, zingiberol Abstrak: COVID-19 merupakan sebuah penyakit yang baru. Banyak masyarakat yang merasakan dampak dari penyakit ini. Belum ada pengobatan pasti untuk menyembuhkan COVID-19, sehingga banyak masyarakat yang menggunakan pengobatan tradisional untuk menangkal COVID-19, termasuk jahe. Penelitian ini bertujuan untuk mengetahui apakah ada interaksi antara senyawa pada jahe (gingerol dan zingiberol) dengan main protease COVID-19 (6LU7). Penelitian ini menggunakan metode molecular docking dengan menggunakan 4 aplikasi utama, yaitu Autodock Tools, Autodock Vina, Biovia Discovery Studio 2020, dan Open Babel GUI. Sampel yang digunakan yaitu senyawa gingerol dan zingiberol pada tanaman jahe yang diunduh di Pubchem. Data yang digunakan dalam penelitian ini menggunakan database Mendeley, Clinical Key, dan PubMed. Penelitian menunjukkan bahwa hampir semua residu asam amino pada senyawa gingerol bekerja pada sisi aktif 6LU7, sedangkan tidak demikian pada zingiberol. Hasil binding affinity senyawa jahe, baik gingerol maupun zingiberol tidak  melebihi binding affinity remdesivir, obat yang banyak diteliti sebagai obat penanganan COVID-19. Sebagai simpulan, senyawa gingerol dan zingiberol pada tanaman jahe tidak dapat dipertimbangkan sebagai penanganan COVID-19Kata Kunci: molecular docking, gingerol, zingiberol

scholarly journals Quantum Chemistry of Cocaine and its Isomers I: Energetics, Reactivity and Solvation

2021 ◽  
Vol 75 ◽  
Author(s):  
Safa Ben Amara ◽  
Thorsten Koslowski ◽  
Ali Zaidi
Keyword(s):  
Dipole Moment ◽  
Solvent Effect ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Theoretical Perspective ◽  
Solvent Polarity ◽  
Stable Conformation ◽  
Functional Theory ◽  
Implicit Solvents ◽  
The Rich

ABSTRACT We investigate the rich stereochemistry of cocaine and its diastereoisomers from a theoretical perspective using density functional theory. The relative stability of the eight considered isomers is discussed, and a comparison of the corresponding internal coordinates is given. Our results reveal that the S-pseudococaine isomer is the most stable conformation, whereas the natural occurring isomer (R-cocaine) lies higher in energy. The different isomers' chemical reactivity is discussed based on the calculation of the hardness, softness, electrophilicity and dipole moment. It was found that the dipole moment varies over a broad range from 0.65 to 4.60 D, whereas the other properties are slightly modified. The solvent effect on the energy stability of the cocaine isomers was studied by considering chloroform, dimethyl-sulfoxide (DMSO) and water as implicit solvents. Our calculations show that the different isomers' energy order and their energy gaps are slightly modified due to solvent effects. However, in all cases, the S-pseudococaine remains the most stable isomer. However, the dipole moment and the chemical reactivity of the cocaine isomers increase with the solvent polarity. Keywords: Cocaine isomers,DFT, stability, solvent effect, chemical reactivity.

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