Dalal . Harkati - Academia.edu (original) (raw)

Papers by Dalal . Harkati

Applied Sciences, 2022

Considerable data are available regarding the molecular genetics of the tobacco mosaic virus. The... more Considerable data are available regarding the molecular genetics of the tobacco mosaic virus. The disease caused by the tobacco mosaic virus is still out of control due to the lack of an efficient functional antagonist chemical molecule. Extensive research was carried out to try to find effective new anti-tobacco mosaic virus agents, however no study could find an effective agent which could completely inhibit the disease caused by the virus. In recent years, molecular docking, combined with molecular dynamics, which is considered to be one of the most important methods of drug discovery and design, were used to evaluate the type of binding between the ligand and its protein enzyme. The aim of the current work was to assess the in silico anti-tobacco mosaic virus activity for a selection of 41 new and 2 reference standard compounds. These compounds were chosen to examine their reactivity and binding efficiency with the tobacco mosaic virus coat protein (PDB ID: 2OM3). A comparison w...

License, which permits unrestricted use, distribution, and reproduction in any medium, provided t... more License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Conformational analysis of 18-ring membered macrolactones has been carried out using molecular mechanics calculations and molecular dynamics. A high conformational flexibility of macrolactones was obtained, and an important stereoselectivity was observed for the complexed macrolides. For 18d macrolactone, which was presented by a most favored conformer with 20.1% without complex, it was populated with 50.1 % in presence of Fe(CO)3. 1.

Journal of Computational and Theoretical Nanoscience, 2015

The major weather parameters like temperature, relative humidity, rainfall, wind speed and sunshi... more The major weather parameters like temperature, relative humidity, rainfall, wind speed and sunshine hour for a period of 43 years were collected and analyzed. This was done for crop planning and to develop an appropriate irrigation scheduling for different crops. The annual rainfall record indicated that in 40.47 per cent cases the normal rainfall (average ± 19%) was received in the study area, whereas, the per cent of below normal and above normal rainfall was found as 33.33 and 26.20 per cent, respectively. The highest PET was obtained in April and the lowest in December. The maximum net irrigation requirements for Rabi and Kharif season crops were found in February, March, April, June, September, October and November months. June to September months received the highest rainfall when the rainfall was received about 86 per cent of the total amount of annual rainfall. It appears that surplus rainfall (Rainfall>PET) during mid-June to August received and it can be harvested and use in high irrigation demand months.

Reviewer 1 (Dalal Harkati) | Reviewer 2 (Basil Saleh) | To read the reviews, click the links below.

In this study the Molecular geometry optimization, vibrational frequencies, energy gaps, net char... more In this study the Molecular geometry optimization, vibrational frequencies, energy gaps, net charges, dipole moments and heats of formation Hydantoin at the ground state, in present work, we have been calculated and performed by using the Molecular Mechanics, PM3, ab initio/HF and DFT/B3LYP methods basis set in order to obtain optimized geometrical parameters are in good agreement with experimental values. Comparison of the obtained fundamental vibrational frequencies of hydantoin result by DFT/B3LYP (6-311G++ (d, p)) method, are in a close agreement with the experimental data. Ab initio/HF with 6-31G basis set was used to investigate the effects of a variety of substituants (methyl ,dimethyl, trimethyl ,and chloride ,dichloride ,trichloride ) on the electronic properties of hydantoin derivatives. Detailed vibrational wave number shifts and vibrational mode analyses were reported.

Revue Roumaine de Chimie, 2019

The equilibrium geometries of 1,3,4-thiadiazole derivatives have been determined and analyzed at ... more The equilibrium geometries of 1,3,4-thiadiazole derivatives have been determined and analyzed at DFT level employing B3LYP/6-31G(d) basis set. The molecular electrostatic potential surface (MESP) that reveals centers of reactivity of the molecule and substitution effects of the molecular system have been studied using the HSAB principle (Hard Soft Acid and Base).Results such us, fundamental vibrational modes, 1 H NMR isotropic chemical shifts, frontier orbital energies (HOMO, LUMO), band gap energy, dipole moments, net charges are reported and discussed in terms of reactivity of 1,3,4-thiadiazole derivatives. The HOMO and LUMO analysis were used to elucidate information regarding charge transfer within the molecule. Isotropic chemical shifts were calculated using the Gauge-Independent Atomic Orbital (GIOAO) method. Finally, a comparison between the experimental data and the calculated results appeared a good agreement and show exceptional reactivity.

Journal of Molecular Structure, 2020

Abstract To establish a quantitative structure-activity relationship, 54 indazole derivatives wer... more Abstract To establish a quantitative structure-activity relationship, 54 indazole derivatives were analyzed by multiple linear regression MLR. The DFT-B3LYP method, with the basis set 6-311G, was performed to define the structure, chemical reactivity and properties of the compounds. This study was accompanied by molecular docking, global reactivity descriptors, absorption, distribution, metabolism and elimination (ADME) properties on a series of 21 compounds of selective estrogen receptor degraders (SERDs) that present the most active compounds from the dataset. The MLR regression equation displayed a good agreement between fitted and observed biological activities. A high average R2Boots greater than 0.5 indicates that the obtained model has good predictive power and robustness. In addition, an average value of R2pred (0.57) approximately equal to 0.6 may be taken as an indicator of good external predictability. The interactions between the most active compounds from the indazole series and ERα targets were explored through a molecular docking to elucidate the binding mode between the studied compounds and corresponding protein. Based on this study compounds 14, 43, 8 and 45 have no violated Lipinski’s rule of five and Veber’s rule, suggesting that these compounds would not have problems with oral bioavailability. Most of global reactivity results have an agreement with those obtained in this docking study.

SDRP Journal of Computational Chemistry & Molecular Modelling, 2018

We propose an original approach dedicated to QSAR modeling and clustering analysis based on a dat... more We propose an original approach dedicated to QSAR modeling and clustering analysis based on a dataset of 23 Benzothiazole derivatives as cytotoxic inhibitors. The choice of relevant molecular descriptors is a key step in QSAR modeling. In this work, model selection by exhaustive search is used to identify the best subset of molecular descriptors. Three distinct clusters have been identified using Kmeans clustering. Each cluster, groups a homogeneous class of molecules with respect their molecular descriptors. Silhouette analysis, used as cluster validation approach, proves that the molecules are very well clustered and there are no molecules placed in the wrong cluster. Moreover, the results emphasize that the molecular descriptors belonging to physico-chemical class appears to largely influence the cytotoxic activity of Benzothiazole derivatives. From this classification, all molecules with the trifluoromethyl group show a strong activity. The best cytotoxic activity was exhibited by compound containing two trifluoromethyl groups in ortho position. We suggested that this functional group is correlated to binding affinity. The PLS equations exhibit a good agreement between fitted and observed cytotoxic activities. According to the goodness of fit statistics, 67% and 80% of the variability in cytotoxic activity around its mean are explained. The Fstatistic test revealed the significance of both PLS regression equations. The values of bootstrapping correlation coefficient R 2 boots and leave-one-out cross-validation coefficient Q 2 Loo revealing that the resulting models have good predictive power and robustness. We concluded that the developed PLS equations can be successfully applied to predict the antiproliferative activity against breast cancer cells lines of Benzothiazole derivatives.

Reviews in Theoretical Science, 2016

Research Journal of Pharmaceutical, Biological and Chemical Sciences

Molecular geometry, vibrational frequencies, energy gaps, net charges, dipole moments and heats o... more Molecular geometry, vibrational frequencies, energy gaps, net charges, dipole moments and heats of indole formation at the ground state have been calculated by using the Molecular Mechanics, PM3, ab initio/HF and DFT/B3LYP methods. The optimized geometrical parameters are in good agreement with experimental values. Comparison of the obtained fundamental vibrational frequencies of Indole result by DFT/B3LYP (6-311G++(d,p)) method, are in a close agreement with the experimental data. Ab initio/HF with 6-31G basis set was used to investigate the effects of a variety of substituents (methyl, cyanide and dimethylamino) on the electronic properties of Indole derivatives.

Quantum Matter, 2016

ABSTRACT Molecular geometry and electronic structure of indole has been studied by Ab initio/HF a... more ABSTRACT Molecular geometry and electronic structure of indole has been studied by Ab initio/HF and DFT/B3LYP methods, with 6-311G++(dp) basis set have been depict and compared with experimental parameters. Density functional theory (DFT) method at the level of B3LYP with 6-311G++(d,p) basis set was used to investigate the effects of a variety of substituents (CH3, CN, F, OH, OCH3 and NH2) on the electronic and structural properties of indole. In this work, the calculated values, namely HOMO, LUMO, energy gaps, heat of formation, dipole moments and Mulliken charges of indole have been reported. The QSAR properties and Drug-like calculation on the basis of Lipinski rule of indole derivatives are reported and discussed as well.

ISRN Organic Chemistry, 2011

Conformational analysis of 18-ring membered macrolactones has been carried out using molecular me... more Conformational analysis of 18-ring membered macrolactones has been carried out using molecular mechanics calculations and molecular dynamics. A high conformational flexibility of macrolactones was obtained, and an important stereoselectivity was observed for the complexed macrolides. For 18d macrolactone, which was presented by a most favored conformer with 20.1% without complex, it was populated with 50.1% in presence of Fe(CO)3.

Environmental Toxicology and Pharmacology, 2013

In the current work, the relationship between the structure and activity of a series of novel thi... more In the current work, the relationship between the structure and activity of a series of novel thiazolidine-4carboxylic acid derivatives as potent influenza virus neuraminidase inhibitors was studied using docking, molecular dynamics (MD) simulations, and QSAR analysis. A 7,000 ps MD simulation in a cubic water box were employed to build 3D structure of the 2HU4 in a water environment. After reaching the equilibrium, the inhibitors were docked into the 2HU4 to realize the binding site of the enzyme. The docking analysis showed that the interaction of the inhibitors with residues Arg371, Arg430, Gly429, Ile427, Lys432, Pro431, Trp403, and Tyr347 plays an important role in the activities of the inhibitors. The docked configurations of the inhibitors with the lowest free energy were used to calculate the most feasible descriptors. The selected descriptors were related to the inhibitory activities using stepwise multiple linear regression, classification and regression trees, and least squares support vector regression techniques. The satisfactory results (R p 2 = 0.883, Q LOO 2 = 0.872, R L25%O 2 = 0.835, RMSE LOO = 0.310, and RMSE L25%O = 0.352) demonstrate that CART-LS-SVR models present the relationship between influenza virus neuraminidase inhibitors activity and molecular descriptors clearly. An energetic analysis based on MD calculations, revealed that the potency of the most active compound binding is governed by electrostatic and van der Waals contacts. The results provide a set of useful guidelines for the rational design of novel influenza virus neuraminidase inhibitors. Keywords Influenza virus neuraminidase Á Molecular docking Á Molecular dynamics simulation Á Thiazolidine-4-carboxylic acid derivatives Á Classification and regression trees Á Least squares support vector regression

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2020

Recently, a series of carbazole derivatives containing chalcone analogues (CDCAs) were synthetize... more Recently, a series of carbazole derivatives containing chalcone analogues (CDCAs) were synthetized as potent anticancer agents and apoptosis inducers. These compounds target the inhibition of topoisomerase II and present cytotoxic activities. After comparison to experiment, we validated the use of B3LYP, a density functional theory-based approach, to describe the structure and molecular properties of the carbazole subunit and CDCAs compounds of interest. Then, we derived relationships between the chemical descriptors and activity of these carbazole derivatives using multi-parameter optimization and quantitative structure activity relationships (QSAR) approaches. For the QSAR studies, we used multiple linear regression and artificial neural network statistical modelling. Our predicted activities are in good agreement with the experimental ones. We found that the most important parameter influencing the activity of the considered compounds is the octanol-water partition coefficient, highlighting the importance of flexibility as a key molecular parameter to favor cell membrane crossing and enhance the action of these CDCAs against topoisomerase II. Our results provide useful guidelines for designing new oral active CDCAs medicaments for cytotoxic inhibition.