Khedidja BENAROUS - Academia.edu (original) (raw)
Papers by Khedidja BENAROUS
Saudi pharmaceutical journal, May 1, 2024
Journal of Biomolecular Structure and Dynamics
Chemistry & biodiversity, Apr 11, 2024
Journal of Molecular Structure, Nov 1, 2023
Density functional theory calculations were performed with DFT method using both b3lyp/ 6-311++G(... more Density functional theory calculations were performed with DFT method using both b3lyp/ 6-311++G(d,p) and wb97xd/6-311++G(d,p) levels of theory to predict the molecular geometry, to evaluate the molecular electrostatic potential and frontier molecular orbitals of synthesized a new compound: caprolactam-glysine cluster (CL-Gly). Molecular docking study of the CL-Gly was carried out to clarify the interaction and the probable binding modes, between the title compound and DNA. The antibacterial activities of CL-Gly cluster against Gram-positive and Gramnegative bacteria was determined. In silico ADMET study was also performed for predicting pharmacokinetic and toxicity profile of the synthesized cluster which expressed good drug-like A c c e p t e d M a n u s c r i p t behavior and non-toxic nature. It was revealed that the compound has importance in drug discovery process.
Current Computer - Aided Drug Design, Jun 1, 2021
2019-nCoV is a novel coronavirus was isolated and identified in 2019 in Wuhan, China. On 17th Feb... more 2019-nCoV is a novel coronavirus was isolated and identified in 2019 in Wuhan, China. On 17th February and according to world health organization, a number of 71 429 confirmed cases worldwide, among them 2162 new cases recorded in the last 24 hours. There is no drug or vaccine for human and animal coronavirus. The inhibition of 3CL hydrolase enzyme provides a promising therapeutic principle for developing treatments against CoViD-19. The 3CLpro (Mpro) known for involving in counteracting the host innate immune response. This work presents the inhibitory effect of some natural compounds against 3CL hydrolase enzyme, and explain the main interactions in inhibitor-enzyme complex. Molecular docking study carried out using Autodock Vina. By screening several molecules, we identified three candidate agents that inhibit the main protease of coronavirus. Hispidin, lepidine E, and folic acid bound tightly in the enzyme, strong hydrogen bonds have been formed (1.69-1.80Å) with the active site residues. This study provides a possible therapeutic strategy for CoViD-19.
Bioorganic Chemistry, Jul 1, 2021
Alkaloids and phenols are potent inhibitors family for many enzymes used in many therapies. We ai... more Alkaloids and phenols are potent inhibitors family for many enzymes used in many therapies. We aim to evaluate in vitro and in silico, the inhibition effect of Hispidin, Harmaline, and Harmine as pure molecules to bovine milk xanthine oxidase (BXO), Molecular docking and SAR study with GOLD was done to explain the mechanism of action related to its inhibition, ADMET parameters were checked to confirm their pharmacokinetics (PK) using preADMET 2.0 server, we classified our inhibitors by applying five drug-likeness rules, the best-ranked inhibitors were chosen based on the approved ADMET properties, drug-likeness qualifications, and the best PLPchem score generated by GOLD. The in vitro results show important inhibition activity to BXO comparing to the control with an IC50 of 39.72 ± 3.60 µM, 51.00 ± 1.0 µM, and 48.52 ± 1.76 µM for Hispidin, Harmaline, and Harmine respectively. The in silico results show that Hispidin was the best inhibitor model with approved ADMET properties and qualification in all drug-likeness rules; Harmaline was saved second-best model to BXO with suitable ADMET properties and qualified in most drug-likeness rules. Eventually, Harmine was ranked third potent inhibitor model with acceptable ADMET properties, drug-likeness rules, and PLPchem score. The tested inhibitors could be significant in drug discovery, especially in treating gout disease; therefore, drug development, including clinical trials, should be done with promising results.
arXiv (Cornell University), Apr 19, 2020
2019-nCoV is a novel coronavirus was isolated and identified in 2019 in Wuhan, China. On 17th Feb... more 2019-nCoV is a novel coronavirus was isolated and identified in 2019 in Wuhan, China. On 17th February and according to world health organization, a number of 71 429 confirmed cases worldwide, among them 2162 new cases recorded in the last 24 hours. There is no drug or vaccine for human and animal coronavirus. The inhibition of 3CL hydrolase enzyme provides a promising therapeutic principle for developing treatments against CoViD-19. The 3CLpro (Mpro) known for involving in counteracting the host innate immune response. This work presents the inhibitory effect of some natural compounds against 3CL hydrolase enzyme, and explain the main interactions in inhibitor-enzyme complex. Molecular docking study carried out using Autodock Vina. By screening several molecules, we identified three candidate agents that inhibit the main protease of coronavirus. Hispidin, lepidine E, and folic acid bound tightly in the enzyme, strong hydrogen bonds have been formed (1.69-1.80Å) with the active site residues. This study provides a possible therapeutic strategy for CoViD-19.
Chemico-Biological Interactions, May 1, 2022
BACKGROUND Over-consumption of foods high in purines like seafood, red meat, and alcoholic bevera... more BACKGROUND Over-consumption of foods high in purines like seafood, red meat, and alcoholic beverages leads to hyperuricemia causing gout attacks. Xanthine oxidase was reported responsible for the overproduction of uric acid. MATERIAL AND METHODS We intend to test in silico and in vitro, the inhibition effect of four vitamins against bovine milk xanthine oxidase (BXO). We performed Molecular docking with GOLD v4.0, and the biological activity prediction with the PASS server. The best-selected vitamins were chosen based on their best PLPchem score. The BXO constant Km and Vmax were determined in vitro, and then the vitamins were tested for their inhibition effect to BXO. Furthermore, the inhibition constant Ki of each inhibitor were determined using Dixon method, the vitamins chosen were vitamin E, vitamin B9, vitamin D3, and vitamin C. RESULTS The in silico results show that the tested vitamins were the best inhibitors model with PLPchem scores up to 70 comparing to the control. The in vitro results show that BXO have a Km value of 163.55 μM with Vmax of 37 U, vitamins B9, E, C, and D3 were potent inhibitors to BXO with an IC50 of 34.10 ± 0.21, 36.68 ± 1.50, 39.01 ± 0.02, and 100.28 ± 0.33 μM, respectively comparing to the control (32.03 ± 0.73 μM). The kinetic study shows that all tested vitamins were Non-competitive inhibitors, the Ki values were 15 ± 1.76 μM, 29 ± 1.06 μM, 12 ± 1.41 μM, and 20 ± 0.71 μM, for respectively vitamins B9, E, C, and D3. CONCLUSION The obtained results promise an excellent strategy using vitamins to enhance immunity, treat hyperuricemia, and minimize the usual drug side effects.
Journal of Biomolecular Structure and Dynamics
Anti-Inflammatory & Anti-Allergy Agents in Medicinal Chemistry
Background: For the first time, the investigation of six anti-inflammatory drugs and six antihist... more Background: For the first time, the investigation of six anti-inflammatory drugs and six antihistaminic drugs for inhibitory activities against alpha-amylase has been evaluated using a new inhibition detection method in order to find new treatments for some diseases caused by α-amylase. Objective: The first part of this work was devoted to the evaluation of the inhibition activity of these drugs on salivary α-amylase in vitro. Then to study the nature of interactions and structure-activity relationship, using the Autodockvina program for molecular docking. Materials and Methods: The evaluation of the inhibitory activity of our drugs is achieved using a new method that has proved its sensitivity, quickness, and effectiveness. Results : The results of this study show that betamethasone and loratadine are potent α-amylase inhibitors with IC50 values 0.7mg/ml and 1.03 mg/ml, respectively compared to acarbose with IC50=5.6 μg/ml. Conclusion: The results showed that the loratadine and the...
Anti-Inflammatory & Anti-Allergy Agents in Medicinal Chemistry, 2021
Background: For the first time, the inhibitory effects on the human salivary alpha-amylase activi... more Background: For the first time, the inhibitory effects on the human salivary alpha-amylase activity of the anti-inflammatory drugs indomethacin, diclofenac sodium, ketoprofen, diclofenac potassium, diclofenac, triamcinolone acetonide, and the antihistamine drugs levocetirizine dihydrochloride, desloratadine, cycloheptadine hydrochloride, have been investigated to confirm the other properties of these drugs. Objective: This study aimed to determine the effect of nine known drugs on human salivary α-amylase in vitro and the nature of interactions with structure-activity relationship using molecular docking experiments. Methods: The inhibition of human salivary alpha amylase by the six anti-inflammatory and three antihistamine drugs has been carried out using the new method that has been proved in our previous work. Molecular docking has been achieved for the first time for these drugs using the Auto- Dock Vina program. Results: Cyproheptadine hydrochloride presented the highest inhibi...
Journal of Materials Research and Technology, 2020
Anti-Inflammatory & Anti-Allergy Agents in Medicinal Chemistry, 2018
Background: Inhibition activity of 8 synthetic molecules known as anti-allergy drugs on lipases h... more Background: Inhibition activity of 8 synthetic molecules known as anti-allergy drugs on lipases has been investigated. The enzymatic inhibition produced by these molecules is described here for the first time. Objective: The used anti-allergy drugs are: Loratidine, primalan, zyrtec, histagan, periactin, ketotifene, rifex and bilastine. Methods: Lipase inhibition is studied using the spectrophotometric method. Molecular docking has been achieved for the first time for these drugs using AutoDock Vina program to discuss the nature of interactions, structure-activity relationship and the mechanism of inhibition. Results: The biological evaluation of these molecules showed that most of these drugs are potent lipase inhibitors with competitive type inhibition. The best drug is loratidine with IC50=0.44mg/ml and Ki=0.86 mM and competitive type inhibition. Molecular docking studies of the studied molecules confirmed their competitive inhibitory type with their binding to the Catalytic Active Site (CAS) of lipases. Conclusion: Hence, these drugs could be used for obesity or candidiasis treatment taking advantage of the much-known details of their secondary effects as antiallergy drugs.
Journal of Biomolecular Structure and Dynamics
Current Computer - Aided Drug Design, Nov 4, 2022
Arab Journal of Basic and Applied Sciences
Cluster Computing
The fast spread of the COVID-19 over the world pressured scientists to find its cures. Especially... more The fast spread of the COVID-19 over the world pressured scientists to find its cures. Especially, with the disastrous results, it engendered from human life losses to long-term impacts on infected people's health and the huge financial losses. In addition to the massive efforts made by researchers and medicals on finding safe, smart, fast, and efficient methods to accurately make an early diagnosis of the COVID-19. Some researchers focused on finding drugs to treat the disease and its symptoms, others worked on creating effective vaccines, while several concentrated on finding inhibitors for the key enzymes of the virus, to reduce its spreading and reproduction inside the human body. These enzymes' inhibitors are usually found in aliments, plants, fungi, or even in some drugs. Since these inhibitors slow and halt the replication of the virus in the human body, they can help fight it at an early stage saving the patient from death risk. Moreover, if the human body's immune system gets rid of the virus at the early stage it can be spared from the disastrous sequels it may leave inside the patient's body. Our research aims to find aliments and plants that are rich in these inhibitors. In this paper, we developed a deep learning application that is trained with various aliments, plants, and drugs to detect if a component contains SARS-CoV-2 key inhibitor(s) intending to help them find more sources containing these inhibitors. The application is trained to identify various sources rich in thirteen coronavirus-2 key inhibitors. The sources are currently just aliments, plants, and seeds and the identification is done by their names.
Current Computer-Aided Drug Design
Background: Through this study, the Chemical composition realized by UHPLC-DAD-ESI-MSn allowed th... more Background: Through this study, the Chemical composition realized by UHPLC-DAD-ESI-MSn allowed the detection of different phenolic compounds groups from Pistacia atlantica Desf. leaves extracts. We studied the inhibition of main protease (CL3 Mpro) and RNA-dependent RNA polymerase (RdRp) of the SARS-CoV-2 by the identified molecules through molecular docking. Objective: The objective of this study is to identify compounds from Pistacia atlantica Desf. leaves extracts, which might have anti-viral effects. Methods: Chemical composition realized by UHPLC-DAD-ESI-MSn, the inhibition of main protease (CL3 Mpro) and RNA-dependent RNA polymerase (RdRp) of the SARS-CoV-2 is studied using molecular docking with Autodock Vina software. ADMET analysis was carried out. Results: The identified compounds are quinic acid, digallic acid, galloylquinic acid, gallic acid, trigallic acid, digalloylquinic acids, trigalloylquinic acids and methyl gallate; digallic and quinic acids are the best inhibitor...
South African Journal of Botany, 2022
Saudi pharmaceutical journal, May 1, 2024
Journal of Biomolecular Structure and Dynamics
Chemistry & biodiversity, Apr 11, 2024
Journal of Molecular Structure, Nov 1, 2023
Density functional theory calculations were performed with DFT method using both b3lyp/ 6-311++G(... more Density functional theory calculations were performed with DFT method using both b3lyp/ 6-311++G(d,p) and wb97xd/6-311++G(d,p) levels of theory to predict the molecular geometry, to evaluate the molecular electrostatic potential and frontier molecular orbitals of synthesized a new compound: caprolactam-glysine cluster (CL-Gly). Molecular docking study of the CL-Gly was carried out to clarify the interaction and the probable binding modes, between the title compound and DNA. The antibacterial activities of CL-Gly cluster against Gram-positive and Gramnegative bacteria was determined. In silico ADMET study was also performed for predicting pharmacokinetic and toxicity profile of the synthesized cluster which expressed good drug-like A c c e p t e d M a n u s c r i p t behavior and non-toxic nature. It was revealed that the compound has importance in drug discovery process.
Current Computer - Aided Drug Design, Jun 1, 2021
2019-nCoV is a novel coronavirus was isolated and identified in 2019 in Wuhan, China. On 17th Feb... more 2019-nCoV is a novel coronavirus was isolated and identified in 2019 in Wuhan, China. On 17th February and according to world health organization, a number of 71 429 confirmed cases worldwide, among them 2162 new cases recorded in the last 24 hours. There is no drug or vaccine for human and animal coronavirus. The inhibition of 3CL hydrolase enzyme provides a promising therapeutic principle for developing treatments against CoViD-19. The 3CLpro (Mpro) known for involving in counteracting the host innate immune response. This work presents the inhibitory effect of some natural compounds against 3CL hydrolase enzyme, and explain the main interactions in inhibitor-enzyme complex. Molecular docking study carried out using Autodock Vina. By screening several molecules, we identified three candidate agents that inhibit the main protease of coronavirus. Hispidin, lepidine E, and folic acid bound tightly in the enzyme, strong hydrogen bonds have been formed (1.69-1.80Å) with the active site residues. This study provides a possible therapeutic strategy for CoViD-19.
Bioorganic Chemistry, Jul 1, 2021
Alkaloids and phenols are potent inhibitors family for many enzymes used in many therapies. We ai... more Alkaloids and phenols are potent inhibitors family for many enzymes used in many therapies. We aim to evaluate in vitro and in silico, the inhibition effect of Hispidin, Harmaline, and Harmine as pure molecules to bovine milk xanthine oxidase (BXO), Molecular docking and SAR study with GOLD was done to explain the mechanism of action related to its inhibition, ADMET parameters were checked to confirm their pharmacokinetics (PK) using preADMET 2.0 server, we classified our inhibitors by applying five drug-likeness rules, the best-ranked inhibitors were chosen based on the approved ADMET properties, drug-likeness qualifications, and the best PLPchem score generated by GOLD. The in vitro results show important inhibition activity to BXO comparing to the control with an IC50 of 39.72 ± 3.60 µM, 51.00 ± 1.0 µM, and 48.52 ± 1.76 µM for Hispidin, Harmaline, and Harmine respectively. The in silico results show that Hispidin was the best inhibitor model with approved ADMET properties and qualification in all drug-likeness rules; Harmaline was saved second-best model to BXO with suitable ADMET properties and qualified in most drug-likeness rules. Eventually, Harmine was ranked third potent inhibitor model with acceptable ADMET properties, drug-likeness rules, and PLPchem score. The tested inhibitors could be significant in drug discovery, especially in treating gout disease; therefore, drug development, including clinical trials, should be done with promising results.
arXiv (Cornell University), Apr 19, 2020
2019-nCoV is a novel coronavirus was isolated and identified in 2019 in Wuhan, China. On 17th Feb... more 2019-nCoV is a novel coronavirus was isolated and identified in 2019 in Wuhan, China. On 17th February and according to world health organization, a number of 71 429 confirmed cases worldwide, among them 2162 new cases recorded in the last 24 hours. There is no drug or vaccine for human and animal coronavirus. The inhibition of 3CL hydrolase enzyme provides a promising therapeutic principle for developing treatments against CoViD-19. The 3CLpro (Mpro) known for involving in counteracting the host innate immune response. This work presents the inhibitory effect of some natural compounds against 3CL hydrolase enzyme, and explain the main interactions in inhibitor-enzyme complex. Molecular docking study carried out using Autodock Vina. By screening several molecules, we identified three candidate agents that inhibit the main protease of coronavirus. Hispidin, lepidine E, and folic acid bound tightly in the enzyme, strong hydrogen bonds have been formed (1.69-1.80Å) with the active site residues. This study provides a possible therapeutic strategy for CoViD-19.
Chemico-Biological Interactions, May 1, 2022
BACKGROUND Over-consumption of foods high in purines like seafood, red meat, and alcoholic bevera... more BACKGROUND Over-consumption of foods high in purines like seafood, red meat, and alcoholic beverages leads to hyperuricemia causing gout attacks. Xanthine oxidase was reported responsible for the overproduction of uric acid. MATERIAL AND METHODS We intend to test in silico and in vitro, the inhibition effect of four vitamins against bovine milk xanthine oxidase (BXO). We performed Molecular docking with GOLD v4.0, and the biological activity prediction with the PASS server. The best-selected vitamins were chosen based on their best PLPchem score. The BXO constant Km and Vmax were determined in vitro, and then the vitamins were tested for their inhibition effect to BXO. Furthermore, the inhibition constant Ki of each inhibitor were determined using Dixon method, the vitamins chosen were vitamin E, vitamin B9, vitamin D3, and vitamin C. RESULTS The in silico results show that the tested vitamins were the best inhibitors model with PLPchem scores up to 70 comparing to the control. The in vitro results show that BXO have a Km value of 163.55 μM with Vmax of 37 U, vitamins B9, E, C, and D3 were potent inhibitors to BXO with an IC50 of 34.10 ± 0.21, 36.68 ± 1.50, 39.01 ± 0.02, and 100.28 ± 0.33 μM, respectively comparing to the control (32.03 ± 0.73 μM). The kinetic study shows that all tested vitamins were Non-competitive inhibitors, the Ki values were 15 ± 1.76 μM, 29 ± 1.06 μM, 12 ± 1.41 μM, and 20 ± 0.71 μM, for respectively vitamins B9, E, C, and D3. CONCLUSION The obtained results promise an excellent strategy using vitamins to enhance immunity, treat hyperuricemia, and minimize the usual drug side effects.
Journal of Biomolecular Structure and Dynamics
Anti-Inflammatory & Anti-Allergy Agents in Medicinal Chemistry
Background: For the first time, the investigation of six anti-inflammatory drugs and six antihist... more Background: For the first time, the investigation of six anti-inflammatory drugs and six antihistaminic drugs for inhibitory activities against alpha-amylase has been evaluated using a new inhibition detection method in order to find new treatments for some diseases caused by α-amylase. Objective: The first part of this work was devoted to the evaluation of the inhibition activity of these drugs on salivary α-amylase in vitro. Then to study the nature of interactions and structure-activity relationship, using the Autodockvina program for molecular docking. Materials and Methods: The evaluation of the inhibitory activity of our drugs is achieved using a new method that has proved its sensitivity, quickness, and effectiveness. Results : The results of this study show that betamethasone and loratadine are potent α-amylase inhibitors with IC50 values 0.7mg/ml and 1.03 mg/ml, respectively compared to acarbose with IC50=5.6 μg/ml. Conclusion: The results showed that the loratadine and the...
Anti-Inflammatory & Anti-Allergy Agents in Medicinal Chemistry, 2021
Background: For the first time, the inhibitory effects on the human salivary alpha-amylase activi... more Background: For the first time, the inhibitory effects on the human salivary alpha-amylase activity of the anti-inflammatory drugs indomethacin, diclofenac sodium, ketoprofen, diclofenac potassium, diclofenac, triamcinolone acetonide, and the antihistamine drugs levocetirizine dihydrochloride, desloratadine, cycloheptadine hydrochloride, have been investigated to confirm the other properties of these drugs. Objective: This study aimed to determine the effect of nine known drugs on human salivary α-amylase in vitro and the nature of interactions with structure-activity relationship using molecular docking experiments. Methods: The inhibition of human salivary alpha amylase by the six anti-inflammatory and three antihistamine drugs has been carried out using the new method that has been proved in our previous work. Molecular docking has been achieved for the first time for these drugs using the Auto- Dock Vina program. Results: Cyproheptadine hydrochloride presented the highest inhibi...
Journal of Materials Research and Technology, 2020
Anti-Inflammatory & Anti-Allergy Agents in Medicinal Chemistry, 2018
Background: Inhibition activity of 8 synthetic molecules known as anti-allergy drugs on lipases h... more Background: Inhibition activity of 8 synthetic molecules known as anti-allergy drugs on lipases has been investigated. The enzymatic inhibition produced by these molecules is described here for the first time. Objective: The used anti-allergy drugs are: Loratidine, primalan, zyrtec, histagan, periactin, ketotifene, rifex and bilastine. Methods: Lipase inhibition is studied using the spectrophotometric method. Molecular docking has been achieved for the first time for these drugs using AutoDock Vina program to discuss the nature of interactions, structure-activity relationship and the mechanism of inhibition. Results: The biological evaluation of these molecules showed that most of these drugs are potent lipase inhibitors with competitive type inhibition. The best drug is loratidine with IC50=0.44mg/ml and Ki=0.86 mM and competitive type inhibition. Molecular docking studies of the studied molecules confirmed their competitive inhibitory type with their binding to the Catalytic Active Site (CAS) of lipases. Conclusion: Hence, these drugs could be used for obesity or candidiasis treatment taking advantage of the much-known details of their secondary effects as antiallergy drugs.
Journal of Biomolecular Structure and Dynamics
Current Computer - Aided Drug Design, Nov 4, 2022
Arab Journal of Basic and Applied Sciences
Cluster Computing
The fast spread of the COVID-19 over the world pressured scientists to find its cures. Especially... more The fast spread of the COVID-19 over the world pressured scientists to find its cures. Especially, with the disastrous results, it engendered from human life losses to long-term impacts on infected people's health and the huge financial losses. In addition to the massive efforts made by researchers and medicals on finding safe, smart, fast, and efficient methods to accurately make an early diagnosis of the COVID-19. Some researchers focused on finding drugs to treat the disease and its symptoms, others worked on creating effective vaccines, while several concentrated on finding inhibitors for the key enzymes of the virus, to reduce its spreading and reproduction inside the human body. These enzymes' inhibitors are usually found in aliments, plants, fungi, or even in some drugs. Since these inhibitors slow and halt the replication of the virus in the human body, they can help fight it at an early stage saving the patient from death risk. Moreover, if the human body's immune system gets rid of the virus at the early stage it can be spared from the disastrous sequels it may leave inside the patient's body. Our research aims to find aliments and plants that are rich in these inhibitors. In this paper, we developed a deep learning application that is trained with various aliments, plants, and drugs to detect if a component contains SARS-CoV-2 key inhibitor(s) intending to help them find more sources containing these inhibitors. The application is trained to identify various sources rich in thirteen coronavirus-2 key inhibitors. The sources are currently just aliments, plants, and seeds and the identification is done by their names.
Current Computer-Aided Drug Design
Background: Through this study, the Chemical composition realized by UHPLC-DAD-ESI-MSn allowed th... more Background: Through this study, the Chemical composition realized by UHPLC-DAD-ESI-MSn allowed the detection of different phenolic compounds groups from Pistacia atlantica Desf. leaves extracts. We studied the inhibition of main protease (CL3 Mpro) and RNA-dependent RNA polymerase (RdRp) of the SARS-CoV-2 by the identified molecules through molecular docking. Objective: The objective of this study is to identify compounds from Pistacia atlantica Desf. leaves extracts, which might have anti-viral effects. Methods: Chemical composition realized by UHPLC-DAD-ESI-MSn, the inhibition of main protease (CL3 Mpro) and RNA-dependent RNA polymerase (RdRp) of the SARS-CoV-2 is studied using molecular docking with Autodock Vina software. ADMET analysis was carried out. Results: The identified compounds are quinic acid, digallic acid, galloylquinic acid, gallic acid, trigallic acid, digalloylquinic acids, trigalloylquinic acids and methyl gallate; digallic and quinic acids are the best inhibitor...
South African Journal of Botany, 2022