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Zhang Y, Li C, Shu L, Teng YL, Dong BX. Research on the Construction of a Series of Transition Metal-Substituted Keggin-Type TMSPOMs@PCN-224 Composites through the Encapsulation Method and Their Electron Transfer Mechanism in CO 2RR. Inorg Chem 2024; 63:11592-11603. [PMID: 38861349 DOI: 10.1021/acs.inorgchem.4c00840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
In order to take advantage of the distinct reversible multielectron transfer properties of polyoxometalates (POMs) and increase the electron density at the active sites during the electrochemical reduction of CO2 (CO2RR), a range of transition metal-doped polyoxometalates (TMSPOMs) was entrapped within the porphyrin-based framework of PCN-224 via an encapsulation method, known as TMSPOMs@PCN-224 (TMSPOMs = [XW11O39MII(H2O)]n-, [XW11O40VIV]n-, M = CoII, MnII; X = Si, n = 6; X = P, n = 5). The central elements (Si, P) and the incorporated transition metals (VIV, CoII, and MnII) both play a role in adjusting the electronic structure and electron transfer during the CO2RR process. Remarkably, the composite material with cobalt substitution displayed significantly improved performance. Through fine-tuning the POM loading, the electrocatalytic activity was optimized, leading to an impressive Faradaic efficiency for CO production (FECO) of 89.9% for SiW11Co@PCN-224, a significant improvement compared to the 12.1% FECO of PCN-224. Furthermore, the electrochemical stability of this catalyst was demonstrated over 20 h. Comparative analyses involving six composite materials indicated a relationship between the negative charge of the polyanions and their ability to facilitate effective electron transfer, ultimately enhancing the catalyst's performance. Meanwhile, these findings were supported by density functional theory (DFT) calculations.
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Affiliation(s)
- Yan Zhang
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, Jiangsu, P. R. China
| | - Can Li
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, Jiangsu, P. R. China
| | - Lei Shu
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, Jiangsu, P. R. China
| | - Yun-Lei Teng
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, Jiangsu, P. R. China
| | - Bao-Xia Dong
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, Jiangsu, P. R. China
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Kawsar SMA, Munia NS, Saha S, Ozeki Y. In Silico Pharmacokinetics, Molecular Docking and Molecular Dynamics Simulation Studies of Nucleoside Analogs for Drug Discovery- A Mini Review. Mini Rev Med Chem 2024; 24:1070-1088. [PMID: 37957918 DOI: 10.2174/0113895575258033231024073521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 08/26/2023] [Accepted: 09/22/2023] [Indexed: 11/15/2023]
Abstract
Nucleoside analogs have been widely used as antiviral, antitumor, and antiparasitic agents due to their ability to inhibit nucleic acid synthesis. Adenosine, cytidine, guanosine, thymidine and uridine analogs such as didanosine, vidarabine, remdesivir, gemcitabine, lamivudine, acyclovir, abacavir, zidovusine, stavudine, and idoxuridine showed remarkable anticancer and antiviral activities. In our previously published articles, our main intention was to develop newer generation nucleoside analogs with acylation-induced modification of the hydroxyl group and showcase their biological potencies. In the process of developing nucleoside analogs, in silico studies play an important role and provide a scientific background for biological data. Molecular interactions between drugs and receptors followed by assessment of their stability in physiological environments, help to optimize the drug development process and minimize the burden of unwanted synthesis. Computational approaches, such as DFT, FMO, MEP, ADMET prediction, PASS prediction, POM analysis, molecular docking, and molecular dynamics simulation, are the most popular tools to culminate all preclinical study data and deliver a molecule with maximum bioactivity and minimum toxicity. Although clinical drug trials are crucial for providing dosage recommendations, they can only indirectly provide mechanistic information through researchers for pathological, physiological, and pharmacological determinants. As a result, in silico approaches are increasingly used in drug discovery and development to provide mechanistic information of clinical value. This article portrays the current status of these methods and highlights some remarkable contributions to the development of nucleoside analogs with optimized bioactivity.
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Affiliation(s)
- Sarkar M A Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Nasrin S Munia
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Supriyo Saha
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Premnagar, 248007, Dehradun, Uttarakhand, 248007, India
| | - Yasuhiro Ozeki
- School of Sciences, Yokohama City University, 22-2, Seto, Kanazawa-ku, Yokohama, 236-0027, Japan
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Rizi A, Sedik A, Acidi A, Rachedi KO, Ferkous H, Berredjem M, Delimi A, Abdennouri A, ALAM M, Ernst B, Benguerba Y. Sustainable and Green Corrosion Inhibition of Mild Steel: Insights from Electrochemical and Computational Approaches. ACS OMEGA 2023; 8:47224-47238. [PMID: 38107914 PMCID: PMC10720019 DOI: 10.1021/acsomega.3c06548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 12/19/2023]
Abstract
Natural and fragrant compounds, essential oils (EOs) extracted from plants through hydrodistillation, are gaining popularity as eco-friendly and sustainable agents to protect metals and alloys from corrosion in acidic environments. This research focused on extracting and characterizing an EO obtained from the Cuminum cyminum (CC) plant native to India. The study aimed to evaluate the inhibitory properties of this EO on mild steel in a 0.5 M HCl solution at different concentrations. Various analytical techniques, including potentiodynamic polarization curves, electrochemical impedance spectroscopy, optical microscopy, infrared spectroscopy, and proton magnetic resonance, were employed to assess the effectiveness of this EO extract. Our findings indicate that the Cuminum cyminum L (CCL) extract effectively reduces the corrosion of mild steel in hydrochloric acid with an inhibition efficiency ranging from 79.69 to 98.76%. The optimal inhibition concentration was 2 g/L of EO, and surface analysis confirmed the formation of a protective layer. Furthermore, our results suggest that the inhibitor binds to the metal surface through a charge-transfer process, creating a protective film. Finally, we utilized theoretical calculations and molecular dynamics simulations to elucidate the inhibition mechanism on both a global and local scale.
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Affiliation(s)
- Aicha Rizi
- Laboratory
of Applied Organic Chemistry LCOA, Synthesis of Biomolecules and Molecular
Modeling Group, Badji Mokhtar—Annaba
University, PO Box 12, Annaba 23000, Algeria
| | - Amel Sedik
- Scientific
and Technical Research Center in Physico-chemical Analysis (CRAPC), BP 384, Bou-Ismail industrial zone, RP 42004 Tipaza, Algeria
| | - Anissa Acidi
- Laboratory
of Applied Organic Chemistry LCOA, Synthesis of Biomolecules and Molecular
Modeling Group, Badji Mokhtar—Annaba
University, PO Box 12, Annaba 23000, Algeria
| | - Khadidja Otmane Rachedi
- Laboratory
of Applied Organic Chemistry LCOA, Synthesis of Biomolecules and Molecular
Modeling Group, Badji Mokhtar—Annaba
University, PO Box 12, Annaba 23000, Algeria
| | - Hana Ferkous
- Département
de Technologie, Université 20 août
1955 de Skikda, 21000 Skikda, Algeria
- Laboratoire
de Génie Mécanique et Matériaux, Faculté
de Technologie, Université de 20
Août 1955, Skikda 21000, Algeria
| | - Malika Berredjem
- Laboratory
of Applied Organic Chemistry LCOA, Synthesis of Biomolecules and Molecular
Modeling Group, Badji Mokhtar—Annaba
University, PO Box 12, Annaba 23000, Algeria
| | - Amel Delimi
- Département
de Technologie, Université 20 août
1955 de Skikda, 21000 Skikda, Algeria
- Laboratoire
de Génie Mécanique et Matériaux, Faculté
de Technologie, Université de 20
Août 1955, Skikda 21000, Algeria
| | - Amdjed Abdennouri
- Laboratoire
de Physico-Chimie des Surfaces et des Interfaces, Université 20 août 1955 de Skikda, BP 26, Route El Hadaik, 21000 Skikda, Algeria
| | - Manawwer ALAM
- Department
of Chemistry, College of Science, King Saud
University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | - Barbara Ernst
- Université
de Strasbourg, CNRS, IPHC UMR 7178, Laboratoire de Reconnaissance
et Procédés de Séparation Moléculaire
(RePSeM), ECPM 25 rue
Becquerel, F-67000 Strasbourg, France
| | - Yacine Benguerba
- Laboratoire
de Biopharmacie Et Pharmacotechnie (LPBT), Ferhat Abbas Setif 1 University, 19000 Setif, Algeria
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Kayes MR, Saha S, Alanazi MM, Ozeki Y, Pal D, Hadda TB, Legssyer A, Kawsar SM. Macromolecules: Synthesis, antimicrobial, POM analysis and computational approaches of some glucoside derivatives bearing acyl moieties. Saudi Pharm J 2023; 31:101804. [PMID: 37868643 PMCID: PMC10585311 DOI: 10.1016/j.jsps.2023.101804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 09/27/2023] [Indexed: 10/24/2023] Open
Abstract
Macromolecules i.e., carbohydrate derivatives are crucial to biochemical and medical research. Herein, we designed and synthesized eight methyl α-D-glucopyranoside (MGP) derivatives (2-8) in good yields following the regioselective direct acylation method. The structural configurations of the synthesized MGP derivatives were analyzed and verified using multiple physicochemical and spectroscopic techniques. Antimicrobial experiments revealed that almost all derivatives demonstrated noticeable antifungal and antibacterial efficacy. The synthesized derivatives showed minimum inhibitory concentration (MIC) values ranging from 0.75 µg/mL to 1.50 µg/mL and minimum bactericidal concentrations (MBCs) ranging from 8.00 µg/mL to 16.00 µg/mL. Compound 6 inhibited Ehrlich ascites carcinoma (EAC) cell proliferation by 10.36% with an IC50 of 2602.23 μg/mL in the MTT colorimetric assay. The obtained results were further rationalized by docking analysis of the synthesized derivatives against 4URO and 4XE3 receptors to explore the binding affinities and nonbonding interactions of MGP derivatives with target proteins. Compound 6 demonstrated the potential to bind with the target with the highest binding energy. In a stimulating environment, a molecular dynamics study showed that MGP derivatives have a stable conformation and binding pattern. The MGP derivatives were examined using POM (Petra/Osiris/Molinspiration) bioinformatics, and as a result, these derivatives showed good toxicity, bioavailability, and pharmacokinetics. Various antifungal/antiviral pharmacophore (Oδ-, O'δ-) sites were identified by using POM investigations, and compound 6 was further tested against other pathogenic fungi and viruses, such as Micron and Delta mutants of SARS-CoV-2.
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Affiliation(s)
- Mohammad R. Kayes
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh
| | - Supriyo Saha
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, Uttarakhand 248007, India
| | - Mohammed M. Alanazi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Yasuhiro Ozeki
- School of Sciences, Yokohama City University, 22-2, Seto, Kanazawa-Ku, Yokohama 236-0027, Japan
| | - Dilipkumar Pal
- Department of Pharmaceutical Sciences, Guru Ghasidas Vishwavidyalaya (A Central University), C.G, 495009 Bilaspur, India
| | - Taibi B. Hadda
- BBEH and LACE Laboratories of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, MB 524, 60000 Oujda, Morocco
| | - Abdelkhaleq Legssyer
- BBEH and LACE Laboratories of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, MB 524, 60000 Oujda, Morocco
| | - Sarkar M.A. Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh
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Suleiman M, Almalki FA, Ben Hadda T, Kawsar SMA, Chander S, Murugesan S, Bhat AR, Bogoyavlenskiy A, Jamalis J. Recent Progress in Synthesis, POM Analyses and SAR of Coumarin-Hybrids as Potential Anti-HIV Agents-A Mini Review. Pharmaceuticals (Basel) 2023; 16:1538. [PMID: 38004404 PMCID: PMC10675815 DOI: 10.3390/ph16111538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/18/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
The human immunodeficiency virus (HIV) is the primary cause of acquired immune deficiency syndrome (AIDS), one of the deadliest pandemic diseases. Various mechanisms and procedures have been pursued to synthesise several anti-HIV agents, but due to the severe side effects and multidrug resistance spawning from the treatment of HIV/AIDS using highly active retroviral therapy (HAART), it has become imperative to design and synthesise novel anti-HIV agents. Literature has shown that natural sources, particularly the plant kingdom, can release important metabolites that have several biological, mechanistic and structural representations similar to chemically synthesised compounds. Certainly, compounds from natural and ethnomedicinal sources have proven to be effective in the management of HIV/AIDS with low toxicity, fewer side effects and affordability. From plants, fungi and bacteria, coumarin can be obtained, which is a secondary metabolite and is well known for its actions in different stages of the HIV replication cycle: protease, integrase and reverse transcriptase (RT) inhibition, cell membrane fusion and viral host attachment. These, among other reasons, are why coumarin moieties will be the basis of a good building block for the development of potent anti-HIV agents. This review aims to outline the synthetic pathways, structure-activity relationship (SAR) and POM analyses of coumarin hybrids with anti-HIV activity, detailing articles published between 2000 and 2023.
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Affiliation(s)
- Mustapha Suleiman
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru 81310, Johor, Malaysia;
- Department of Chemistry, Sokoto State University, Birnin Kebbi Road, Sokoto 852101, Nigeria
| | - Faisal A. Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Mecca 21955, Saudi Arabia; (F.A.A.); (T.B.H.)
| | - Taibi Ben Hadda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Mecca 21955, Saudi Arabia; (F.A.A.); (T.B.H.)
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, MB 524, Oujda 60000, Morocco
| | - Sarkar M. A. Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, University of Chittagong, Chittagong 4331, Bangladesh;
| | - Subhash Chander
- Amity Institute of Phytochemistry & Phytomedicine, Amity University Uttar Pradesh, Noida 201313, India;
| | - Sankaranarayanan Murugesan
- Medicinal Chemistry Research Laboratory, Birla Institute of Technology & Science Pilani (BITS Pilani), Pilani Campus, Pilani 333031, India;
| | - Ajmal R. Bhat
- Department of Chemistry, R.T.M. Nagpur University, Nagpur 440033, India;
| | - Andrey Bogoyavlenskiy
- Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Joazaizulfazli Jamalis
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru 81310, Johor, Malaysia;
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Shafiq N, Shahzad N, Rida F, Ahmad Z, Nazir HA, Arshad U, Zareen G, Attiq N, Parveen S, Rashid M, Ali B. One-pot multicomponent synthesis of novel pyridine derivatives for antidiabetic and antiproliferative activities. Future Med Chem 2023; 15:1069-1089. [PMID: 37503685 DOI: 10.4155/fmc-2023-0132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023] Open
Abstract
Background: Due to the close relationship of diabetes with hypertension reported in various research, a set of pyridine derivatives with US FDA-approved drug cores were designed and integrated by artificial intelligence. Methods: Novel pyridines were designed and synthesized. Compounds MNS-1-MNS-4 were evaluated for their structure and were screened for their in vitro antidiabetic (α-amylase) activity and anticancer (HepG2) activity by methyl thiazolyl tetrazolium assay. Comparative 3D quantitative structure-activity relationship analysis and pharmacophore generation were carried out. Results: The study revealed MNS-1 and MNS-4 as good alternatives to acarbose as antidiabetic agents, and MNS-2 as a more viable, better alternative to doxorubicin in the methyl thiazolyl tetrazolium assay. Conclusion: This combination of studies identifies new and more active analogs of existing FDA-approved drugs for the treatment of diabetes.
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Affiliation(s)
- Nusrat Shafiq
- Synthetic & Natural Product Discovery Laboratory, Department of Chemistry, Government College Women's University Faisalabad, 38000, Pakistan
| | - Nabeel Shahzad
- Department of Chemistry, University of WAH, Wah Cantt, 44700, Pakistan
| | - Fatima Rida
- Synthetic & Natural Product Discovery Laboratory, Department of Chemistry, Government College Women's University Faisalabad, 38000, Pakistan
| | - Zaheer Ahmad
- Department of Chemistry, University of WAH, Wah Cantt, 44700, Pakistan
| | - Hafiza Ayesha Nazir
- Synthetic & Natural Product Discovery Laboratory, Department of Chemistry, Government College Women's University Faisalabad, 38000, Pakistan
| | - Uzma Arshad
- Synthetic & Natural Product Discovery Laboratory, Department of Chemistry, Government College Women's University Faisalabad, 38000, Pakistan
| | - Gul Zareen
- Synthetic & Natural Product Discovery Laboratory, Department of Chemistry, Government College Women's University Faisalabad, 38000, Pakistan
| | - Naila Attiq
- Synthetic & Natural Product Discovery Laboratory, Department of Chemistry, Government College Women's University Faisalabad, 38000, Pakistan
| | - Shagufta Parveen
- Synthetic & Natural Product Discovery Laboratory, Department of Chemistry, Government College Women's University Faisalabad, 38000, Pakistan
| | - Maryam Rashid
- Synthetic & Natural Product Discovery Laboratory, Department of Chemistry, Government College Women's University Faisalabad, 38000, Pakistan
| | - Basharat Ali
- Department of Chemistry, Khawaja Fareed University of Engineering & Information Technology, Rahim Yar Khan, Punjab, 64200, Pakistan
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Hosen MA, Qais FA, Chtita S, Rahman IA, Almehdi AM, Ali F, Almalki FA, Hadda TB, Laaroussi H, Kawsar SMA. In silico and POM analysis for potential antimicrobial agents of thymidine analogs by using molecular docking, molecular dynamics and ADMET profiling. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023; 42:877-918. [PMID: 37235455 DOI: 10.1080/15257770.2023.2215839] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 04/19/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023]
Abstract
Nucleoside analogs are an important, well-established class of clinically useful medicinal agents that exhibit potent antimicrobial activity. Thus, we designed to explore the synthesis and spectral characterization of 5'-O-(myristoyl)thymidine esters (2-6) for in vitro antimicrobial, molecular docking, molecular dynamics, SAR, and POM analyses. An unimolar myristoylation of thymidine under controlled conditions furnished the 5'-O-(myristoyl)thymidine and it was further converted into four 3'-O-(acyl)-5'-O-(myristoyl)thymidine analogs. The chemical structures of the synthesized analogs were ascertained by analyzing their physicochemical, elemental, and spectroscopic data. In vitro antimicrobial tests along with PASS, prediction indicated expectant antibacterial functionality of these thymidine esters compared to the antifungal activities. In support of this observation, their molecular docking studies have been performed against lanosterol 14α-demethylase (CYP51A1) and Aspergillus flavus (1R51) and significant binding affinities and non-bonding interactions were observed. The stability of the protein-ligand complexes was monitored by a 100 ns MD simulation and found the stable conformation and binding mode in a stimulating environment of thymidine esters. Pharmacokinetic predictions were studied to assess their ADMET properties and showed promising results in silico. SAR investigation indicated that acyl chains, lauroyl (C-12) and myristoyl (C-14), combined with deoxyribose, were most effective against the tested bacterial and fungal pathogens. The POM analyses provide the structural features responsible for their combined antibacterial/antifungal activity and provide guidelines for further modifications, with the aim of improving each activity and selectivity of designed drugs targeting potentially drug-resistant microorganisms. It also opens avenues for the development of newer antimicrobial agents targeting bacterial and fungal pathogens.
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Affiliation(s)
- Mohammed A Hosen
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
| | - Faizan A Qais
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Samir Chtita
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Ibrahim A Rahman
- Department of Chemistry, University of Sharjah, Sharjah, United Arab Emirates
| | - Ahmed M Almehdi
- Department of Chemistry, University of Sharjah, Sharjah, United Arab Emirates
| | - Ferdausi Ali
- Department of Microbiology, Faculty of Biological Science, University of Chittagong, Chittagong, Bangladesh
| | - Faisal A Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Taibi B Hadda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, Oujda, Morocco
| | - Hamid Laaroussi
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, Oujda, Morocco
| | - Sarkar M A Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
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Bogoyavlenskiy A, Alexyuk M, Alexyuk P, Berezin V, Almalki FA, Ben Hadda T, Alqahtani AM, Ahmed SA, Dall'Acqua S, Jamalis J. Computer Analysis of the Inhibition of ACE2 by Flavonoids and Identification of Their Potential Antiviral Pharmacophore Site. Molecules 2023; 28:molecules28093766. [PMID: 37175179 PMCID: PMC10179817 DOI: 10.3390/molecules28093766] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 04/25/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
In the present study, we investigated the antiviral activities of 17 flavonoids as natural products. These derivatives were evaluated for their in vitro antiviral activities against HIV and SARS-CoV-2. Their antiviral activity was evaluated for the first time based on POM (Petra/Osiris/Molispiration) theory and docking analysis. POM calculation was used to analyze the atomic charge and geometric characteristics. The side effects, drug similarities, and drug scores were also assumed for the stable structure of each compound. These results correlated with the experimental values. The bioinformatics POM analyses of the relative antiviral activities of these derivatives are reported for the first time.
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Affiliation(s)
- Andrey Bogoyavlenskiy
- Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Madina Alexyuk
- Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Pavel Alexyuk
- Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Vladimir Berezin
- Research and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Faisal A Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Taibi Ben Hadda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, MB 524, Oujda 60000, Morocco
| | - Alaa M Alqahtani
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Saleh A Ahmed
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Stefano Dall'Acqua
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35121 Padova, Italy
| | - Joazaizulfazli Jamalis
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, UTM, Johor Bahru 81310, Johor, Malaysia
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M. A. Kawsar S, Hosen MA, Ahmad S, El Bakri Y, Laaroussi H, Ben Hadda T, Almalki FA, Ozeki Y, Goumri-Said S. Potential SARS-CoV-2 RdRp inhibitors of cytidine derivatives: Molecular docking, molecular dynamic simulations, ADMET, and POM analyses for the identification of pharmacophore sites. PLoS One 2022; 17:e0273256. [PMID: 36441684 PMCID: PMC9704642 DOI: 10.1371/journal.pone.0273256] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/03/2022] [Indexed: 11/29/2022] Open
Abstract
The RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 is one of the optimum targets for antiviral drug design and development. The hydroxyl groups of cytidine structures were modified with different aliphatic and aromatic groups to obtain 5´-O-acyl and 2´,3´-di-O-acyl derivatives, and then, these derivatives were employed in molecular modeling, antiviral prediction, molecular docking, molecular dynamics, pharmacological and POM studies. Density functional theory (DFT) at the B3LYP/6-31G++ level analyzed biochemical behavior and molecular electrostatic potential (MESP) of the modified cytidine derivatives. The antiviral parameters of the mutated derivatives revealed promising drug properties compared with those of standard antiviral drugs. Molecular docking has determined binding affinities and interactions between the cytidine derivatives and SARS-CoV-2 RdRp. The modified derivatives strongly interacted with prime Pro620 and Lys621 residues. The binding conformation and interactions stability were investigated by 200 ns of molecular dynamics simulations and predicted the compounds to firmly dock inside the RdRp binding pocket. Interestingly, the binding residues of the derivatives were revealed in high equilibrium showing an enhanced binding affinity for the molecules. Intermolecular interactions are dominated by both Van der Waals and electrostatic energies. Finally, the pharmacokinetic characterization of the optimized inhibitors confirmed the safety of derivatives due to their improved kinetic properties. The selected cytidine derivatives can be suggested as potential inhibitors against SARS-CoV-2. The POM Theory supports the hypothesis above by confirming the existence of an antiviral (Oδ--O'δ-) pharmacophore site of Hits.
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Affiliation(s)
- Sarkar M. A. Kawsar
- Faculty of Science, Department of Chemistry, Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), University of Chittagong, Chittagong, Bangladesh
- * E-mail: (SMAK); (YEB); (SGS)
| | - Mohammed A. Hosen
- Faculty of Science, Department of Chemistry, Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), University of Chittagong, Chittagong, Bangladesh
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Youness El Bakri
- Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russian Federation
- * E-mail: (SMAK); (YEB); (SGS)
| | - Hamid Laaroussi
- Faculty of Sciences, Laboratory of Applied Chemistry & Environment, Mohammed Premier University, Oujda, Morocco
| | - Taibi Ben Hadda
- Faculty of Sciences, Laboratory of Applied Chemistry & Environment, Mohammed Premier University, Oujda, Morocco
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Umm AlQura University, Makkah, Saudi Arabia
| | - Faisal A. Almalki
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Umm AlQura University, Makkah, Saudi Arabia
| | - Yasuhiro Ozeki
- School of Sciences, Yokohama City University, Yokohama, Japan
| | - Souraya Goumri-Said
- Physics Department, College of Science, Alfaisal University, Riyadh, Saudi Arabia
- * E-mail: (SMAK); (YEB); (SGS)
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Abdellattif MH, Elkamhawy A, Hagar M, Hadda TB, Shehab WS, Mansy W, Belal A, Arief MMH, Hussien MA. Novel saccharin analogs as promising antibacterial and anticancer agents: synthesis, DFT, POM analysis, molecular docking, molecular dynamic simulations, and cell-based assay. Front Pharmacol 2022; 13:958379. [PMID: 36267293 PMCID: PMC9577234 DOI: 10.3389/fphar.2022.958379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/04/2022] [Indexed: 11/27/2022] Open
Abstract
Saccharine is a pharmacologically significant active scaffold for various biological activities, including antibacterial and anticancer activities. Herein, saccharinyl hydrazide (1) was synthesized and converted into 2-[(2Z)-2-(1,1-dioxo-1,2-dihydro-3H-1λ6,2- benzothiazole-3-ylidene) hydrazinyl] acetohydrazide (5), which was employed as a key precursor for synthesizing a novel series of small molecules bearing different moieties of monosaccharides, aldehydes, and anhydrides. Potent biological activities were found against Staphylococcus and Escherichia coli, and the results indicated that compounds 6c and 10a were the most active analogs with an inhibition zone diameter of 30–35 mm. In cell-based anticancer assay over Ovcar-3 and M-14 cell lines, compound 10a was the most potent analog with IC50 values of 7.64 ± 0.01 and 8.66 ± 0.01 µM, respectively. The Petra Orisis Molinspiration (POM) theoretical method was used to calculate the drug score of tested compounds and compare them with their experimental screening data. Theoretical DFT calculations were carried out in a gas phase in a set of B3LYP 6-311G (d,p). Molecular docking studies utilizing the MOE indicated the best binding mode with the highest energy interaction within the binding sites. The molecular docking for Ovcar-3 was carried out on the ovarian cancer protein (3W2S), while the molecular docking for M-14 melanoma was carried out on the melanoma cancer protein (2OPZ). The MD performed about 2ns simulations to validate selected compounds’ theoretical studies.
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Affiliation(s)
- Magda H. Abdellattif
- Department of Chemistry, College of Science, Taif University, Taif, Saudi Arabia
- *Correspondence: Magda H. Abdellattif, ; M. M. H. Arief,
| | - Ahmed Elkamhawy
- College of Pharmacy, Dongguk University-Seoul, Goyang, South Korea
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Mohamed Hagar
- Chemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Taibi Ben Hadda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
- Laboratory of Applied Chemistry and Environment, Faculty of Sciences, Mohammed Premier University, Oujda, Morocco
| | - Wesam S. Shehab
- Department of Chemistry, Faculty of Science, Zagazig University, Zagazig, Egypt
| | - Wael Mansy
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Amany Belal
- Department of Pharmaceutical Chemistry, College of Pharmacy Taif University, Taif, Saudi Arabia
| | - M. M. H. Arief
- Department of Chemistry, Faculty of Science, Benha University, Benha, Egypt
- *Correspondence: Magda H. Abdellattif, ; M. M. H. Arief,
| | - Mostafa A. Hussien
- Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Chemistry, Faculty of Science, Port Said University, Port Said, Egypt
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11
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Al-Otaibi JS, Sheena Mary Y, Shyma Mary Y, Soman S, Thirunavukkarasu M. Solvation Effects, Reactivity Studies and Molecular Dynamics of Two Phosphonic Acids – Theoretical Investigation. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2126504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Jamelah S. Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | | | | | - Sreejit Soman
- Stemskills Research and Education Lab Private Limited, Faridabad, India
| | - M. Thirunavukkarasu
- Department of Physics, Indo-American College, Cheyyar, India
- Department of Physics, Thiru A Govindasamy Govt. Arts College, Tindivanam, India
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12
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In silico drug design and molecular docking of novel amidophosphonates and sulfamidophosphonates as inhibitors of urokinase-type plasminogen activator. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Bechlem K, Berredjem M, Djouad SE, Sothea TO, Bouacida S, Marminon C, Hadda TB, Lebreton J, Bouzina A. Novel N-acylsulfamoyl-oxazolidin-2ones: Synthesis, antitumor activity, X-ray crystallographic study, molecular docking and POM analyses. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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Anowar Hosen M, Sultana Munia N, Al-Ghorbani M, Baashen M, Almalki FA, Ben Hadda T, Ali F, Mahmud S, Abu Saleh M, Laaroussi H, Kawsar SMA. Synthesis, antimicrobial, molecular docking and molecular dynamics studies of lauroyl thymidine analogs against SARS-CoV-2: POM study and identification of the pharmacophore sites. Bioorg Chem 2022; 125:105850. [PMID: 35533581 PMCID: PMC9065685 DOI: 10.1016/j.bioorg.2022.105850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/21/2022] [Accepted: 04/28/2022] [Indexed: 12/02/2022]
Abstract
Nucleoside precursors and nucleoside analogs occupy an important place in the treatment of viral respiratory pathologies, especially during the current COVID-19 pandemic. From this perspective, the present study has been designed to explore and evaluate the synthesis and spectral characterisation of 5́-O-(lauroyl) thymidine analogs 2–6 with different aliphatic and aromatic groups through comprehensive in vitro antimicrobial screening, cytotoxicity assessment, physicochemical aspects, molecular docking and molecular dynamics analysis, along with pharmacokinetic prediction. A unimolar one-step lauroylation of thymidine under controlled conditions furnished the 5́-O-(lauroyl) thymidine and indicated the selectivity at C-5́ position and the development of thymidine based potential antimicrobial analogs, which were further converted into four newer 3́-O-(acyl)-5́-O-(lauroyl) thymidine analogs in reasonably good yields. The chemical structures of the newly synthesised analogs were ascertained by analysing their physicochemical, elemental, and spectroscopic data. In vitro antimicrobial tests against five bacteria and two fungi, along with the prediction of activity spectra for substances (PASS), indicated promising antibacterial functionality for these thymidine analogs compared to antifungal activity. In support of this observation, molecular docking experiments have been performed against the main protease of SARS-CoV-2, and significant binding affinities and non-bonding interactions were observed against the main protease (6LU7, 6Y84 and 7BQY), considering hydroxychloroquine (HCQ) as standard. Moreover, the 100 ns molecular dynamics simulation process was performed to monitor the behaviour of the complex structure formed by the main protease under in silico physiological conditions to examine its stability over time, and this revealed a stable conformation and binding pattern in a stimulating environment of thymidine analogs. Cytotoxicity determination confirmed that compounds were found less toxic. Pharmacokinetic predictions were investigated to evaluate their absorption, distribution, metabolism and toxic properties, and the combination of pharmacokinetic and drug-likeness predictions has shown promising results in silico. The POM analysis shows the presence of an antiviral (O1δ-, O2δ-) pharmacophore site. Overall, the current study should be of great help in the development of thymidine-based, novel, multiple drug-resistant antimicrobial and COVID-19 drugs.
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Affiliation(s)
- Mohammed Anowar Hosen
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh
| | - Nasrin Sultana Munia
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh
| | - Mohammed Al-Ghorbani
- Department of Chemistry, Faculty of Science and Arts, Ulla, Taibah University, Medina, Saudi Arabia
| | - Mohammed Baashen
- Department of Chemistry, Science and Humanities College, Shaqra University, Saudi Arabia
| | - Faisal A Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, 21955 Makkah, Saudi Arabia
| | - Taibi Ben Hadda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, 21955 Makkah, Saudi Arabia; Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, MB 524, 60000 Oujda, Morocco
| | - Ferdausi Ali
- Department of Microbiology, Faculty of Biological Science, University of Chittagong, V, Bangladesh
| | - Shafi Mahmud
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md Abu Saleh
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Hamid Laaroussi
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, MB 524, 60000 Oujda, Morocco
| | - Sarkar M A Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh.
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15
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Sun JT, Li X, Yang TY, Lv M, Chen LY, Wei BG. In(OTf) 3-catalyzed N-α phosphonylation of N, O-acetals with triethyl phosphite. Org Biomol Chem 2022; 20:6571-6581. [PMID: 35904891 DOI: 10.1039/d2ob01196d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A practical approach to α-aminophosphonates has been developed through an In(OTf)3-catalyzed N-α phosphonylation of N,O-acetals with triethyl phosphite 7. Indoline and isoindoline N,O-acetals 6a-6j and 9a-9j and chain N,O-acetals 11a-11p were subjected to a Lewis acid catalyzed N-α phosphonylation process. As a result, the desired α-aminophosphonates 8a-8j, 10a-10j and 12a-12p were obtained in moderate to good yields.
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Affiliation(s)
- Jian-Ting Sun
- Department of Natural Medicine, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China. .,School of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, 333 Longteng Road, Shanghai, 201620 China.
| | - Xin Li
- Department of Natural Medicine, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China.
| | - Tian-Yu Yang
- Department of Natural Medicine, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China.
| | - Min Lv
- Department of Natural Medicine, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China.
| | - Ling-Yan Chen
- School of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, 333 Longteng Road, Shanghai, 201620 China.
| | - Bang-Guo Wei
- Department of Natural Medicine, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China.
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16
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Munia NS, Hosen MA, Azzam KMA, Al-Ghorbani M, Baashen M, Hossain MK, Ali F, Mahmud S, Shimu MSS, Almalki FA, Hadda TB, Laaroussi H, Naimi S, Kawsar SMA. Synthesis, antimicrobial, SAR, PASS, molecular docking, molecular dynamics and pharmacokinetics studies of 5'- O-uridine derivatives bearing acyl moieties: POM study and identification of the pharmacophore sites. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 41:1036-1083. [PMID: 35797068 DOI: 10.1080/15257770.2022.2096898] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/08/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Because of their superior antibacterial and pharmacokinetic capabilities, many nucleoside-based esters show potential against microorganisms, and may be used as pharmacological agents to address multidrug-resistant pathogenic problems. In this study, several aliphatic and aromatic groups were inserted to synthesize various 5'-O-decanoyluridine (2-5) and 5'-O-lauroyluridine derivatives (6-7) for antimicrobial, in silico computational, pharmacokinetic and POM (Petra/Osiris/Molinspiration). The chemical structures of the synthesized uridine derivatives were confirmed by physicochemical, elemental, and spectroscopic analyses. In vitro antimicrobial screening against five bacteria and two fungi, as well as the prediction of substance activity spectra (PASS), revealed that these uridine derivatives have promising antifungal properties when compared to the antibacterial activities. Density functional theory (DFT) was used to calculate the thermodynamic and physicochemical properties. Molecular docking was conducted against lanosterol 14a-demethylase CYP51A1 (3JUV) and Aspergillus flavus (1R4U) and revealed binding affinities and non-covalent interactions with the target. Then, a 150 ns molecular dynamic simulation was performed to confirm the behavior of the complex structure formed by microbial protein under in silico physiological conditions to examine its stability over time, which revealed a stable conformation and binding pattern in a stimulating environment of uridine derivatives. The acyl chain {CH3(CH2)9CO-} and {CH3(CH2)10CO-} in conjunction with sugar, was determined to have the most potent activity against bacterial and fungal pathogens in a structure-activity relationships (SAR) investigation. POM analyses were conducted with the presence of an antifungal (O δ- -- O' δ-) pharmacophore site. Overall, the present study might be useful for the development of uridine-based novel multidrug-resistant antimicrobial.
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Affiliation(s)
- Nasrin S Munia
- Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
| | - Mohammed A Hosen
- Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
| | - Khaldun M A Azzam
- Pharmacological and Diagnostic Research Center (PDRC), Department of Pharmaceutical Sciences, Faculty of Pharmacy, Al-Ahliyya Amman University, Amman, Jordan
| | - Mohammed Al-Ghorbani
- Department of Chemistry, Faculty of Science and Arts, Ulla, Taibah University, Medina, Saudi Arabia
| | - Mohammed Baashen
- Department of Chemistry, Science and Humanities College, Shaqra University, Shaqra, KSA
| | - Mohammed K Hossain
- Department of Pharmacy, Faculty of Biological Science, University of Chittagong, Chittagong, Bangladesh
| | - Ferdausi Ali
- Department of Microbiology, Faculty of Biological Science, University of Chittagong, Chittagong, Bangladesh
| | - Shafi Mahmud
- Department of Genome Science, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Mst S S Shimu
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Faisal A Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Taibi B Hadda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, Oujda, Morocco
| | - Hamid Laaroussi
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, Oujda, Morocco
| | - Souad Naimi
- Department of Biological Sciences, Sanofi-Aventis, Vitry, France
| | - Sarkar M A Kawsar
- Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
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17
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Synthesis, structural confirmation, antibacterial properties and bio-informatics computational analyses of new pyrrole based on 8-hydroxyquinoline. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132683] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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18
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Majid SA, Mir JM, Bhat MA, Shalla AH, Pandey A, Hadda TB, Abdellattif MH. A pair of carbazate derivatives as novel Schiff base ligands: DFT and POM theory supported spectroscopic and biological evaluation. J Biomol Struct Dyn 2022:1-17. [PMID: 35751130 DOI: 10.1080/07391102.2022.2090437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Schiff bases are mentioned as strongly important molecular scaffolds of industrial and medicinal purposes. Due to wide range applications of carbazate derivatives herein synthesis and characterization of a new Schiff base ligand, (E)-ethyl 2-(4-methoxybenzylidene)hydrazinecarboxylate and 4-(nitrobenzaldehyde)ethylcarbazate are reported. The compound was characterized on the basis of experimental and density functional theory calculations (using the B3LYP and 6-31 G(d,p)formalism combination). Among characterization techniques elemental analysis, FT-IR, UV-Vis and NMR spectroscopic evaluations were mainly employed to carry out the formulation of the compound. In addition to computational validation of characterization other significant molecular parameters were also evaluated including geometry optimization, frontier molecular orbital analysis (FMO) and Columbic interaction of different constituent atoms of the title compound. A good agreement has been found between DFT and experimental outcomes confined to prove the structure of the compound. Moreover, molecular docking and antimicrobial studies have proven the Schiff base as an effective bioactive compound.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sheikh Abdul Majid
- Department of Chemistry, Islamic University of Science and Technology Awantipora, Pulwama, Jammu and Kashmir, India
| | - Jan Mohammad Mir
- Department of Chemistry, Islamic University of Science and Technology Awantipora, Pulwama, Jammu and Kashmir, India.,Department of Chemistry and Pharmacy, RD University, Jabalpur, Madhya Pradesh, India
| | - Muzzaffar A Bhat
- Department of Chemistry, Islamic University of Science and Technology Awantipora, Pulwama, Jammu and Kashmir, India
| | - Aabid Hussain Shalla
- Department of Chemistry, Islamic University of Science and Technology Awantipora, Pulwama, Jammu and Kashmir, India
| | - Abhishek Pandey
- Department of Chemistry and Pharmacy, RD University, Jabalpur, Madhya Pradesh, India
| | - Taibi Ben Hadda
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, Oujda, Morocco
| | - Magda H Abdellattif
- Department of Chemistry, College of Science, Taif University, Al-Haweiah, Taif, Saudi Arabia
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19
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Prasetyo WE, Kusumaningsih T, Wibowo FR. Gaining deeper insights into 2,5-disubstituted furan derivatives as potent α-glucosidase inhibitors and discovery of putative targets associated with diabetes diseases using an integrative computational approach. Struct Chem 2022. [DOI: 10.1007/s11224-022-01994-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Bahadi R, Berredjem M, Redjemia R, Bouacida S, Amamra R, Meziani O, Zerrad C, Laichi Y, Bachari K, Ibrahim-Ouali M, Bouzina A. A green and novel method for the preparation of α-aminophosphonates using eggshell as catalyst. X-ray study. PHOSPHORUS SULFUR 2022. [DOI: 10.1080/10426507.2022.2085274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Rania Bahadi
- Laboratory of Applied Organic Chemistry LCOA, Synthesis of Biomolecules and Molecular Modelling Group, Badji-Mokhtar – Annaba University, Annaba, Algeria
| | - Malika Berredjem
- Laboratory of Applied Organic Chemistry LCOA, Synthesis of Biomolecules and Molecular Modelling Group, Badji-Mokhtar – Annaba University, Annaba, Algeria
| | - Rayenne Redjemia
- Laboratory of Applied Organic Chemistry LCOA, Synthesis of Biomolecules and Molecular Modelling Group, Badji-Mokhtar – Annaba University, Annaba, Algeria
| | - Sofiane Bouacida
- Unité de Recherche de Chimie de L’Environnement et Moléculaire Structurale, Université des Frères Mentouri, Constantine, Algeria
- Centre de Recherche Scientifique et Technique en Analyses Physico-chimiques (CRAPC), Bou-Ismail, Algeria
| | - Roumaissa Amamra
- Laboratory of Applied Organic Chemistry LCOA, Synthesis of Biomolecules and Molecular Modelling Group, Badji-Mokhtar – Annaba University, Annaba, Algeria
| | - Ouafa Meziani
- Laboratory of Applied Organic Chemistry LCOA, Synthesis of Biomolecules and Molecular Modelling Group, Badji-Mokhtar – Annaba University, Annaba, Algeria
| | - Chaima Zerrad
- Laboratory of Applied Organic Chemistry LCOA, Synthesis of Biomolecules and Molecular Modelling Group, Badji-Mokhtar – Annaba University, Annaba, Algeria
| | - Yacine Laichi
- Département des Sciences de La Matiére, Université Larbi Ben M'Hidi, Oum El Bouaghi, Algeria
| | - Khaldoun Bachari
- Département des Sciences de La Matiére, Université Larbi Ben M'Hidi, Oum El Bouaghi, Algeria
| | | | - Abdeslem Bouzina
- Laboratory of Applied Organic Chemistry LCOA, Synthesis of Biomolecules and Molecular Modelling Group, Badji-Mokhtar – Annaba University, Annaba, Algeria
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21
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Synthesis, characterization and bioactivity of novel 8-hydroxyquinoline derivatives: Experimental, molecular docking, DFT and POM analyses. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132688] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Chalkha M, Nakkabi A, Hadda TB, Berredjem M, Moussaoui AE, Bakhouch M, Saadi M, Ammari LE, Almalki FA, Laaroussi H, Jevtovic V, Yazidi ME. Crystallographic study, biological assessment and POM/Docking studies of pyrazoles-sulfonamide hybrids (PSH): Identification of a combined Antibacterial/Antiviral pharmacophore sites leading to in-silico screening the anti-Covid-19 activity. J Mol Struct 2022; 1267:133605. [PMID: 35782312 PMCID: PMC9237569 DOI: 10.1016/j.molstruc.2022.133605] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/03/2022] [Accepted: 06/27/2022] [Indexed: 01/14/2023]
Abstract
The discovery and development of new potent antimicrobial and antioxidant agents is an essential lever to protect living beings against pathogenic microorganisms and free radicals. In this regard, new functionalized pyrazoles have been synthesized using a simple and accessible approach. The synthesized aminobenzoylpyrazoles 3a-h and pyrazole-sulfonamides 4a-g were obtained in good yields and were evaluated in vitro for their antimicrobial and antioxidant activities. The structures of the synthesized compounds were determined using IR, NMR, and mass spectrometry. The structure of the compound 4b was further confirmed by single crystal X-ray diffraction. The results of the in vitro screening show that the synthesized pyrazoles 3 and 4 exhibit a promising antimicrobial and antioxidant activities. Among the tested compounds, pyrazoles 3a, 3f, 4e, 4f, and 4g have exhibited remarkable antimicrobial activity against some microorganisms. In addition, compounds 3a, 3c, 3e, 4a, 4d, 4f, and 4g have shown a significant antioxidant activity in comparison with the standard butylhydroxytoluene (BHT). Hence, compounds 3a, 4f, and 4g represent interesting dual acting antimicrobial and antioxidant agents. In fact, pyrazole derivatives bearing sulfonamide moiety (4a-g) have displayed an important antimicrobial activity compared to pyrazoles 3a-h, this finding could be attributed to the synergistic effect of the pyrazole and sulfonamide pharmacophores. Furthermore, Molecular docking results revealed a good interaction of the synthesized compounds with the target proteins and provided important information about their interaction modes with the target enzyme. The results of the POM bioinformatics investigations (Petra, Osiris, Molinspiration) show that the studied heterocycles present a very good non toxicity profile, an excellent bioavailability, and pharmacokinetics. Finally, an antiviral pharmacophore (O δ−, O δ−) was evaluated in the POM investigations and deserves all our attention to be tested against Covid-19 and its Omicron and Delta mutants.
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Affiliation(s)
- Mohammed Chalkha
- Engineering Laboratory of Organometallic and Molecular Materials and Environment (LIMOME), Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, P.O. Box 1796, Atlas, Fez, 30000, Morocco
| | - Asmae Nakkabi
- Engineering Laboratory of Organometallic and Molecular Materials and Environment (LIMOME), Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, P.O. Box 1796, Atlas, Fez, 30000, Morocco
- Laboratoire de Chimie des Matériaux et Biotechnologie des Produits Naturels, Faculté des Sciences, Université Moulay Ismail, BP 11201, Meknes 50000, Morocco
| | - Taibi Ben Hadda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, MB 524, Oujda 60000, Morocco
| | - Malika Berredjem
- Laboratoire de chimie organique appliquée (LCOA), Groupe de Synthèse de biomolécules et modélisation moléculaire, Université Badji-Mokhtar Annaba, BP 12, Annaba 23000, Algérie
| | - Abdelfattah El Moussaoui
- Laboratory of Biotechnology, Environment, Agri-Food, and Health (LBEAS), Faculty of Sciences, University Sidi Mohamed Ben Abdellah (USMBA), Fez 30050, Morocco
| | - Mohamed Bakhouch
- Laboratory of Bioorganic Chemistry, Department of Chemistry, Faculty of Sciences, Chouaïb Doukkali University, El Jadida 24000, Morocco
| | - Mohamed Saadi
- Laboratoire de Chimie Appliquée des Matériaux, Centres des Sciences des Matériaux, Faculty of Science, Mohammed V University, Avenue Ibn Battouta, BP. 1014, 100090 Rabat, Morocco
| | - Lahcen El Ammari
- Laboratoire de Chimie Appliquée des Matériaux, Centres des Sciences des Matériaux, Faculty of Science, Mohammed V University, Avenue Ibn Battouta, BP. 1014, 100090 Rabat, Morocco
| | - Faisal A Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Hamid Laaroussi
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, MB 524, Oujda 60000, Morocco
| | - Violeta Jevtovic
- Department of Chemistry, College of Science, University of Hail, Hail 81451, Saudi Arabia
| | - Mohamed El Yazidi
- Engineering Laboratory of Organometallic and Molecular Materials and Environment (LIMOME), Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, P.O. Box 1796, Atlas, Fez, 30000, Morocco
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23
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Nariya P, Kumar S, Seshadri S, Patel M, Thakore S. Novel Substituted Isoindolinones Derived from Lawsone: Synthesis, Characterization, Theoretical, Biological Activity and Docking Studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Prasetyo WE, Purnomo H, Sadrini M, Wibowo FR, Firdaus M, Kusumaningsih T. Identification of potential bioactive natural compounds from Indonesian medicinal plants against 3-chymotrypsin-like protease (3CL pro) of SARS-CoV-2: molecular docking, ADME/T, molecular dynamic simulations, and DFT analysis. J Biomol Struct Dyn 2022:1-18. [DOI: 10.1080/07391102.2022.2068071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Wahyu Eko Prasetyo
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Surakarta, Indonesia
| | - Heri Purnomo
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Surakarta, Indonesia
| | - Miracle Sadrini
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Surakarta, Indonesia
| | - Fajar Rakhman Wibowo
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Surakarta, Indonesia
| | - Maulidan Firdaus
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Surakarta, Indonesia
| | - Triana Kusumaningsih
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Sebelas Maret University, Surakarta, Indonesia
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25
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Bahadi R, Boughoula R, Berredjem M, Bachari K, Bouzina A, Bouacida S, Sbartai H, Benalliouche F, Redjemia R. A convenient synthesis, biological activity and X-ray crystallography of novel α-aminophosphonate derivatives. PHOSPHORUS SULFUR 2022. [DOI: 10.1080/10426507.2022.2064859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Rania Bahadi
- Laboratory of Applied Organic Chemistry, Synthesis of Biomolecules and Molecular Modelling Group, Department of Chemistry, Sciences Faculty, Badji-Mokhtar – Annaba University, Annaba, Algeria
| | - Rahma Boughoula
- Cellular Toxicology Laboratory, University of Badji Mokhtar, Annaba, Algeria
| | - Malika Berredjem
- Laboratory of Applied Organic Chemistry, Synthesis of Biomolecules and Molecular Modelling Group, Department of Chemistry, Sciences Faculty, Badji-Mokhtar – Annaba University, Annaba, Algeria
| | - Khaldoun Bachari
- Centre de Recherche Scientifique et Technique en Analyses Physico-chimiques (CRAPC), Bou-Ismail, Tipasa RP, Algeria
| | - Abdeslem Bouzina
- Laboratory of Applied Organic Chemistry, Synthesis of Biomolecules and Molecular Modelling Group, Department of Chemistry, Sciences Faculty, Badji-Mokhtar – Annaba University, Annaba, Algeria
| | - Sofiane Bouacida
- Unité de Recherche de Chimie de L’Environnement et Moléculaire Structurale, Université des Frères Mentouri, Constantine, Algérie
- Département des Sciences de La Matiére, Université Larbi Ben M’Hidi, Oum El Bouaghi, Algeria
| | - Hana Sbartai
- Cellular Toxicology Laboratory, University of Badji Mokhtar, Annaba, Algeria
| | - Fouzia Benalliouche
- Cellular Toxicology Laboratory, University of Badji Mokhtar, Annaba, Algeria
| | - Rayenne Redjemia
- Laboratory of Applied Organic Chemistry, Synthesis of Biomolecules and Molecular Modelling Group, Department of Chemistry, Sciences Faculty, Badji-Mokhtar – Annaba University, Annaba, Algeria
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26
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Liu J, Huang M, Hua Z, Ni J, Dong Y, Feng Z, Sun T, Chen C. Synergistic Combination: Promising Nanoplatform W‐POM NCs@ HKUST‐1 for Photothermal and Chemodynamic Reinforced Anti‐tumor Therapy. Appl Organomet Chem 2022. [DOI: 10.1002/aoc.6693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jiale Liu
- Aulin College, Northeast Forestry University China
| | | | - Zhongyu Hua
- Aulin College, Northeast Forestry University China
| | - Jiatong Ni
- Key Laboratory of Forest Plant Ecology, Ministry of Education College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University China
| | - Yi Dong
- Aulin College, Northeast Forestry University China
| | - Zeran Feng
- Aulin College, Northeast Forestry University China
| | - Tiedong Sun
- Aulin College, Northeast Forestry University China
- Key Laboratory of Forest Plant Ecology, Ministry of Education College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University China
| | - Chunxia Chen
- Key Laboratory of Forest Plant Ecology, Ministry of Education College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University China
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27
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Missioui M, Lgaz H, Guerrab W, Lee HS, Warad I, Mague JT, Ali IH, Essassi EM, Ramli Y. Synthesis of novel hybrid quinoxaline containing triazole and acetamide moieties by azide-alkyne click chemistry: Experimental and theoretical characterization. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132132] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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28
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Esharkawy ER, Almalki F, Hadda TB. In vitro potential antiviral SARS-CoV-19- activity of natural product thymohydroquinone and dithymoquinone from Nigella sativa. Bioorg Chem 2022; 120:105587. [PMID: 35026560 PMCID: PMC8719923 DOI: 10.1016/j.bioorg.2021.105587] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 12/19/2021] [Accepted: 12/26/2021] [Indexed: 12/12/2022]
Abstract
Inflammation, oxidation, and compromised immunity all increase the dangers of COVID-19, whereas many pharmaceutical protocols may lead to increased immunity such as ingesting from sources containing vitamin E and zinc. A global search for natural remedies to fight COVID-19 has emerged, to assist in the treatment of this infamous coronavirus. Nigella satvia is a world-renowned plant, an esteemed herbal remedy, which can be used as a liquid medicine to increase immunity while decreasing the dangers of acute respiratory distress syndrome. Thymoqinone (TQ), dithymoqinone (DTQ) and thymohydroquinone (THQ), are major compounds of the essential oil contained in N.sativa. A current study aims to discover the antiviral activity of two compounds, Thymohydroquinone and Dithymoquinone, which are synthesized through simple chemical procedures, deriving from thymoquinone, which happens to be a major compound of Nigella sativa. A half-maximal cytotoxic concentration, “CC50”, was calculated by MTT assay for each individual drug, The sample showed anti-SARS-CoV-2 activity at non-cytotoxic nanomolar concentrations in vitro with a low selectivity index (CC50/IC50 = 31.74/23.15 = 1.4), whereby Dimthymoquinone shows high cytotoxicity.
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29
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Antitumor activity, X-Ray crystallography, in silico study of some-sulfamido-phosphonates. Identification of pharmacophore sites. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131886] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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30
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Lafridi H, Almalki FA, Ben Hadda T, Berredjem M, Kawsar SMA, Alqahtani AM, Esharkawy ER, Lakhrissi B, Zgou H. In silico evaluation of molecular interactions between macrocyclic inhibitors with the HCV NS3 protease. Docking and identification of antiviral pharmacophore site. J Biomol Struct Dyn 2022; 41:2260-2273. [PMID: 35075979 DOI: 10.1080/07391102.2022.2029571] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An array of computational approaches DFT/QSAR/POM methods has been used for a better understanding of drug properties regarding 13 inhibitor derivatives containing either P2 cyclopentane P1 carboxylic acid moiety (1-9) or a P1 cyclopropyl acyl sulfonamide (10-13). To further recognize binding interactions and their activity trends, molecular docking studies were carried out with the use of HCV, which can be used to accurately predict the interactions of ligands with the receptor. The QSAR models are developed through the use of Multiple Linear Regression (MLR) together with Principal Component Analysis (PCA) methods. The statistical results indicate the multiple correlation coefficient R2 = 0.840, which shows favorable estimation stability, as well as showing a significant correlation between the HCV NS3 protease of the studied compounds and their electron-accepting ability. The POM analysis of the Physico-chemical properties of compounds 1-13, shows that they are bearing (O1, O2) and/or (O1, O2, O3) antiviral pockets, whereby all oxygen atoms are Osp2 and bearing negative charges. Similar to the reference ligand (F9K), the most active compound 10 was bound deeply into the binding cavity of NS3 protease making interactions with the residues Gly137, His57, Ala157, and His528. The anti-hepatitis pharmacophore site is similar to the anti-HIV pharmacophore site.
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Affiliation(s)
- Hind Lafridi
- Material Sciences, Processes, Environment and Modeling, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco.,Polydisciplinary Faculty, Ibn Zohr University, Ouarzazate, Morocco
| | - Faisal A Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm AlQura University, Makkah, Saudi Arabia
| | - Taibi Ben Hadda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm AlQura University, Makkah, Saudi Arabia.,Laboratory of Applied Chemistry and Environment, Faculty of Sciences, Mohammed Premier University, Oujda, Morocco
| | - Malika Berredjem
- Laboratory of Applied Organic Chemistry LCOA, Synthesis of Biomolecules and Molecular Modelling Group, Badji-Mokhtar - Annaba University, Annaba, Algeria
| | - Sarkar M A Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
| | - Ali M Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Kingdom of Saudi Arabia
| | - Eman R Esharkawy
- Department of Plant Ecology and Range Management, Ecology and Dry Lands Agriculture Division, Desert Research Center, Mathef El-Mataria, Egypt.,Department of Chemistry, Science Faculty for Girls, Northern Border University ARAR, North Region, Saudi Arabia
| | - Brahim Lakhrissi
- Laboratory of Organic Chemistry, Catalysis, and Environment, Department of Chemistry, Faculty of Sciences, Ibn Tofaïl University, Kenitra, Morocco
| | - Hsaine Zgou
- Polydisciplinary Faculty, Ibn Zohr University, Ouarzazate, Morocco
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31
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Elsisi DM, Ragab A, Elhenawy AA, Farag AA, Ali AM, Ammar YA. Experimental and theoretical investigation for 6-Morpholinosulfonylquinoxalin-2(1H)-one and its haydrazone derivate: Synthesis, characterization, tautomerization and antimicrobial evaluation. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131314] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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32
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Moussaoui O, Byadi S, Eddine Hachim M, Sghyar R, Bahsis L, Moslova K, Aboulmouhajir A, Rodi YK, Podlipnik Č, Hadrami EMEL, Chakroune S. Selective synthesis of novel quinolones-amino esters as potential antibacterial and antifungal agents: Experimental, mechanistic study, docking and molecular dynamic simulations. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130652] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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33
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Guerfi M, Berredjem M, Bahadi R, Djouad SE, Bouzina A, Aissaoui M. An efficient synthesis, characterization, DFT study and molecular docking of novel sulfonylcycloureas. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130327] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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34
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Ben Hadda T, Berredjem M, Almalki FA, Rastija V, Jamalis J, Emran TB, Abu-Izneid T, Esharkawy E, Rodriguez LC, Alqahtani AM. How to face COVID-19: proposed treatments based on remdesivir and hydroxychloroquine in the presence of zinc sulfate. Docking/DFT/POM structural analysis. J Biomol Struct Dyn 2021; 40:9429-9442. [PMID: 34033727 PMCID: PMC8171014 DOI: 10.1080/07391102.2021.1930161] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Remdesivir and hydroxychloroquine derivatives form two important classes of heterocyclic compounds. They are known for their anti-malarial biological activity. This research aims to analyze the physicochemical properties of remdesivir and hydroxychloroquine compounds by the computational approach. DFT, docking, and POM analyses also identify antiviral pharmacophore sites of both compounds. The antiviral activity of hydroxychloroquine compound's in the presence of zinc sulfate and azithromycin is evaluated through its capacity to coordinate transition metals (M = Cu, Ni, Zn, Co, Ru, Pt). The obtained bioinformatic results showed the potent antiviral/antibacterial activity of the prepared mixture (Hydroxychloroquine/Azithromycin/Zinc sulfate) for all the opportunistic Gram-positive, Gram-negative in the presence of coronavirus compared with the complexes Polypyridine-Ruthenium-di-aquo. The postulated zinc(II) complex of hydroxychloroquine derivatives are indeed an effective antibacterial and antiviral agent against coronavirus and should be extended to other pathogens. The combination of a pharmacophore site with a redox [Metal(OH2)2] moiety is of crucial role to fight against viruses and bacteria strains. [Formula: see text]Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Taibi Ben Hadda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia,Laboratory of Applied Chemistry & Environment, Faculty of Science, University Mohammed the first, Oujda, Morocco,CONTACT Taibi Ben Hadda Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Almukkarramah 21955, Saudi Arabia; Malika Berredjem Laboratory of Applied Organic Chemistry LCOA, Synthesis of Biomolecules and Molecular Modelling Group, Badji-Mokhtar - Annaba University, Box 12, 23000, Annaba, Algeria
| | - Malika Berredjem
- Laboratory of Applied Organic Chemistry LCOA, Synthesis of Biomolecules and Molecular Modelling Group, Badji-Mokhtar - Annaba University, Annaba, Algeria,CONTACT Taibi Ben Hadda Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Almukkarramah 21955, Saudi Arabia; Malika Berredjem Laboratory of Applied Organic Chemistry LCOA, Synthesis of Biomolecules and Molecular Modelling Group, Badji-Mokhtar - Annaba University, Box 12, 23000, Annaba, Algeria
| | - Faisal A. Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Vesna Rastija
- Department of Agroecology and Environmental Protection, Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Joazaizulfazli Jamalis
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh,Drug Discovery, GUSTO A Research Group, Chittagong, Bangladesh
| | - Tareq Abu-Izneid
- Pharmaceutical Sciences, College of Pharmacy, Al Ain University, Al Ain, UAE
| | - Eman Esharkawy
- Department of Plant Ecology and Range Management, Ecology and Dry Lands Agriculture Division, Desert Research Center, Mathef El-Mataria, Egypt,Department of Chemistry, Science Faculty for Girls, Northern Border University ARAR, North Region, Saudi Arabia
| | - Luis Cruz Rodriguez
- ELIDAN Dynamic LLC, Tampa, FL, USA,ELIDAN Genome SAS, Montereau Fault Yonne, France,Environmental Biotechnology Department, ExCELab Co, Ltd, St Ann, Jamaica
| | - Ali M. Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
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35
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Cetin A. In silico studies on stilbenolignan analogues as SARS-CoV-2 Mpro inhibitors. Chem Phys Lett 2021; 771:138563. [PMID: 33776065 PMCID: PMC7983322 DOI: 10.1016/j.cplett.2021.138563] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/16/2022]
Abstract
COVID-19, a new strain of coronavirus family, was identified at the end of 2019 in China. The COVID-19 virus spread rapidly all over the world. Scientists strive to find virus-specific antivirals for the treatment of COVID-19. The present study reports a molecular docking study of the stilbenolignans and SARS-CoV-2 main protease (SARS-CoV-2 Mpro) inhibitors. The detailed interactions between the stilbenolignan analogues and SARS-CoV-2 Mpro inhibitors were determined as hydrophobic bonds, hydrogen bonds and electronic bonds, inhibition activity, ligand efficiency, bonding type and distance and etc. The binding energies of the stilbenolignan analogues were obtained from the molecular docking of SARS-CoV-2 Mpro. Lehmbachol D, Maackolin, Gnetucleistol, Gnetifolin F, Gnetofuran A and Aiphanol were found to be -7.7, -8.2, -7.3, -8.5, -8.0 and -7.3 kcal/mol, respectively. Osirus, Molinspiration and SwissADME chemoinformatic tools were used to examine ADMET properties, pharmacokinetic parameters and toxicological characteristics of the stilbenolignan analogues. All analogues obey the Lipinski's rule of five. Furthermore, stilbenolignan analogues were studied to predict their binding affinities against SARS-CoV-2 Mpro using molecular modeling and simulation techniques, and the binding free energy calculations of all complexes were calculated using the molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) method. With the data presented here it has been observed that these analogues may be a good candidate for SARS-CoV-2 Mpro in vivo studies, so more research can be done on stilbenolignan analogues.
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36
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Abdellattif MH, Abdel-Rahman AAH, Arief MMH, Mouneir SM, Ali A, Hussien MA, Okasha RM, Afifi TH, Hagar M. Novel 2-Hydroselenonicotinonitriles and Selenopheno[2, 3-b]pyridines: Efficient Synthesis, Molecular Docking-DFT Modeling, and Antimicrobial Assessment. Front Chem 2021; 9:672503. [PMID: 34041224 PMCID: PMC8141565 DOI: 10.3389/fchem.2021.672503] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 03/31/2021] [Indexed: 11/16/2022] Open
Abstract
Selenium containing heterocyclic compounds gained great interest as bioactive molecules as of late. This report explores the design, synthesis, characterization, and antimicrobial screening of new pyridine derivatives endowed with selenium moieties. A one-pot multicomponent system with a solvent-free, microwave irradiation environment was employed to afford this series. The spectroscopic techniques were exploited to verify the structures of the synthesized derivatives. Additionally, the agar diffusion method was employed to determine the antimicrobial activity of all the desired compounds. Of all the synthesized molecules, 9b, 12b, 14f, and 16d exhibited well to remarkable antibacterial and antifungal activities. Moreover, derivative 14f demonstrated the most potent antibacterial and antifungal performance. The results were also supported by molecular docking studies, utilizing the MOE (molecular operating environment) which revealed the best binding mode with the highest energy interaction within the binding pocket. Lastly, theoretical DFT calculations were carried out in a gas phase at B3LYP 6-311G (d,p) basis set to predict the molecular geometries and chemical reactivity descriptors. DFT results have been used to illustrate that molecular docking findings and biological activity assessments.
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Affiliation(s)
- Magda H Abdellattif
- Department of Chemistry, College of Science, Deanship of Scientific Research, Taif University, Taif, Saudi Arabia
| | | | | | - Samar M Mouneir
- Department of Pharmacology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Amena Ali
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Mostafa A Hussien
- Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Chemistry, Faculty of Science, Port Said University, Port Said, Egypt
| | - Rawda M Okasha
- Department of Chemistry, Faculty of Science, Taibah University, Medina, Saudi Arabia
| | - Tarek H Afifi
- Department of Chemistry, Faculty of Science, Taibah University, Medina, Saudi Arabia
| | - Mohamed Hagar
- Chemistry Department, College of Sciences, Taibah University, Yanbu, Saudi Arabia.,Chemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
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37
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Hachim ME, Oubella A, Byadi S, Fawzi M, Laamari Y, Bahsis L, Aboulmouhajir A, Morjani H, Podlipnik Č, Auhmani A, Ait Itto MY. Newly synthesized (R)-carvone-derived 1,2,3-triazoles: structural, mechanistic, cytotoxic and molecular docking studies. J Biomol Struct Dyn 2021; 40:7205-7217. [DOI: 10.1080/07391102.2021.1894984] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Mouhi Eddine Hachim
- Équipe de modélisation moléculaire et de spectroscopie, Faculté des sciences, Université de Chouaïb Doukkali, El Jadida, Morocco
| | - Ali Oubella
- Département de Chimie, Faculté desSciences, Laboratoire de Synthèse Organique et Physico-Chimie Moléculaire, Marrakech, Morocco
| | - Said Byadi
- Équipe de spectroscopie d'extraction et de valorisation, Synthèse organique, Laboratoire d'extraction et de valorisation, Faculté des sciences d'Ain Chock, Université Hassan II, Casablanca, Morocco
| | - Mourad Fawzi
- Département de Chimie, Faculté desSciences, Laboratoire de Synthèse Organique et Physico-Chimie Moléculaire, Marrakech, Morocco
| | - Yassine Laamari
- Département de Chimie, Faculté desSciences, Laboratoire de Synthèse Organique et Physico-Chimie Moléculaire, Marrakech, Morocco
| | - Lahoucine Bahsis
- Laboratoire de Chimie de Coordination et d'Analytique, Département de Chimie, Faculté des Sciences d’El Jadida, Université Chouaïb Doukkali, El Jadida, Morocco
| | - Aziz Aboulmouhajir
- Équipe de modélisation moléculaire et de spectroscopie, Faculté des sciences, Université de Chouaïb Doukkali, El Jadida, Morocco
- Équipe de spectroscopie d'extraction et de valorisation, Synthèse organique, Laboratoire d'extraction et de valorisation, Faculté des sciences d'Ain Chock, Université Hassan II, Casablanca, Morocco
| | - Hamid Morjani
- BioSpectroscopie Translationnelle, BioSpecT - EA7506, UFR de Pharmacie, Université de Reims Champagne-Ardenne, Reims Cedex, France
| | - Črtomir Podlipnik
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Aziz Auhmani
- Département de Chimie, Faculté desSciences, Laboratoire de Synthèse Organique et Physico-Chimie Moléculaire, Marrakech, Morocco
| | - My Youssef Ait Itto
- Département de Chimie, Faculté desSciences, Laboratoire de Synthèse Organique et Physico-Chimie Moléculaire, Marrakech, Morocco
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38
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Abd-El-Aziz AS, Alsaggaf A, Assirey E, Naqvi A, Okasha RM, Afifi TH, Hagar M. A New Family of Benzo[ h]Chromene Based Azo Dye: Synthesis, In-Silico and DFT Studies with In Vitro Antimicrobial and Antiproliferative Assessment. Int J Mol Sci 2021; 22:2807. [PMID: 33802075 PMCID: PMC7998172 DOI: 10.3390/ijms22062807] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/03/2021] [Accepted: 03/03/2021] [Indexed: 12/27/2022] Open
Abstract
The high biological activity of the chromene compounds coupled with the intriguing optical features of azo chromophores prompted our desire to construct novel derivatives of chromene incorporating azo moieties 4a-l, which have been prepared via a three-component reaction of 1-naphthalenol-4-[(4-ethoxyphenyl) azo], 1, with the benzaldehyde derivatives and malononitrile. The structural identities of the azo-chromene 4a-l were confirmed on the basis of their spectral data and elemental analysis, and a UV-visible study was performed in a Dimethylformamide (DMF) solution for these molecules. Additionally, the antimicrobial activity was investigated against four human pathogens (Gram-positive and Gram-negative bacteria) and four fungi, employing an agar well diffusion method, with their minimum inhibitory concentrations being reported. Molecules 4a, 4g, and 4h were discovered to be more efficacious against Syncephalastrum racemosum (RCMB 05922) in comparison to the reference drugs, while compounds 4b and 4h demonstrated the highest inhibitory activity against Escherichia coli (E. coli) in evaluation against the reference drugs. Moreover, their cytotoxicity was assessed against three different human cell lines, including human colon carcinoma (HCT-116), human hepatocellular carcinoma (HepG-2), and human breast adenocarcinoma (MCF-7) with a selection of molecules illustrating potency against the HCT-116 and MCF-7 cell lines. Furthermore, the molecular modeling results depicted the binding interactions of the synthesized compounds 3b and 3h in the active site of the E. coli DNA gyrase B enzyme with a clear SAR (structure-activity relationship) analysis. Lastly, the density functional theory's (DFTs) theoretical calculations were performed to quantify the energy levels of the Frontier Molecular Orbitals (FMOs) and their energy gaps, dipole moments, and molecular electrostatic potentials. These data were utilized in the chemical descriptor estimations to confirm the biological activity.
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Affiliation(s)
- Alaa S. Abd-El-Aziz
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada; (A.A.); (E.A.)
| | - Azhaar Alsaggaf
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada; (A.A.); (E.A.)
- Department of Chemistry, Taibah University, Madinah 30002, Saudi Arabia; (A.N.); (R.M.O.)
| | - Eman Assirey
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada; (A.A.); (E.A.)
- Department of Chemistry, Taibah University, Madinah 30002, Saudi Arabia; (A.N.); (R.M.O.)
| | - Arshi Naqvi
- Department of Chemistry, Taibah University, Madinah 30002, Saudi Arabia; (A.N.); (R.M.O.)
| | - Rawda M. Okasha
- Department of Chemistry, Taibah University, Madinah 30002, Saudi Arabia; (A.N.); (R.M.O.)
| | - Tarek H. Afifi
- Department of Chemistry, Taibah University, Madinah 30002, Saudi Arabia; (A.N.); (R.M.O.)
| | - Mohamed Hagar
- Department of Chemistry, College of Sciences, Taibah University, Yanbu 30799, Saudi Arabia;
- Department of Chemistry, Faculty of Science, Alexandria University, Alexandria 21321, Egypt
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39
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Cuesta SA, Mora JR, Márquez EA. In Silico Screening of the DrugBank Database to Search for Possible Drugs against SARS-CoV-2. Molecules 2021; 26:1100. [PMID: 33669720 PMCID: PMC7923184 DOI: 10.3390/molecules26041100] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/11/2021] [Accepted: 02/16/2021] [Indexed: 12/29/2022] Open
Abstract
Coronavirus desease 2019 (COVID-19) is responsible for more than 1.80 M deaths worldwide. A Quantitative Structure-Activity Relationships (QSAR) model is developed based on experimental pIC50 values reported for a structurally diverse dataset. A robust model with only five descriptors is found, with values of R2 = 0.897, Q2LOO = 0.854, and Q2ext = 0.876 and complying with all the parameters established in the validation Tropsha's test. The analysis of the applicability domain (AD) reveals coverage of about 90% for the external test set. Docking and molecular dynamic analysis are performed on the three most relevant biological targets for SARS-CoV-2: main protease, papain-like protease, and RNA-dependent RNA polymerase. A screening of the DrugBank database is executed, predicting the pIC50 value of 6664 drugs, which are IN the AD of the model (coverage = 79%). Fifty-seven possible potent anti-COVID-19 candidates with pIC50 values > 6.6 are identified, and based on a pharmacophore modelling analysis, four compounds of this set can be suggested as potent candidates to be potential inhibitors of SARS-CoV-2. Finally, the biological activity of the compounds was related to the frontier molecular orbitals shapes.
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Affiliation(s)
- Sebastián A. Cuesta
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Colegio Politécnico, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 170901, Ecuador;
| | - José R. Mora
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Colegio Politécnico, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 170901, Ecuador;
| | - Edgar A. Márquez
- Grupo de Investigaciones en Química y Biología, Departamento de Química y Biología, Facultad de Ciencias Exactas, Universidad del Norte, Carrera 51B, Km 5, vía Puerto Colombia, Barranquilla 081007, Colombia
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40
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Synthesis, Cytotoxic Activity, Crystal Structure, DFT Studies and Molecular Docking of 3-Amino-1-(2,5-dichlorophenyl)-8-methoxy-1H-benzo[f]chromene-2-carbonitrile. CRYSTALS 2021. [DOI: 10.3390/cryst11020184] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The target compound 3-amino-1-(2,5-d ichlorophenyl)-8-methoxy-1H-benzo[f]-chromene-2-carbonitrile (4) was synthesized via a reaction of 6-methoxynaphthalen-2-ol (1), 2,5-dichlorobenzaldehyde (2), and malononitrile (3) in ethanolic piperidine solution under microwave irradiation. The newly synthesized β-enaminonitrile was characterized by FT-IR, 1H NMR, 13C NMR, mass spectroscopy, elemental analysis and X-ray diffraction data. Its cytotoxic activity was evaluated against three different human cancer cell lines MDA-MB-231, A549, and MIA PaCa-2 in comparison to the positive controls etoposide and camptothecin employing the XTT cell viability assay. The analysis of the Hirshfeld surface was utilized to visualize the reliability of the crystal package. The obtained results confirmed that the tested molecule revealed promising cytotoxic activities against the three cancer cell lines. Furthermore, theoretical calculations (DFT) were carried out with the Becke3-Lee-Yang-parr (B3LYP) level using 6-311++G(d,p) basis. The optimization geometry for molecular structures was in agreement with the X-ray structure data. The HOMO-LUMO energy gap of the studied system was discussed. The intermolecular-interactions were studied through analysis of the topological-electron-density(r) using the QTAIM and NCI methods. The novel compound exhibited favorable ADMET properties and its molecular modeling analysis showed strong interaction with DNA methyltransferase 1.
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41
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Al Sheikh Ali A, Khan D, Naqvi A, Al-blewi FF, Rezki N, Aouad MR, Hagar M. Design, Synthesis, Molecular Modeling, Anticancer Studies, and Density Functional Theory Calculations of 4-(1,2,4-Triazol-3-ylsulfanylmethyl)-1,2,3-triazole Derivatives. ACS OMEGA 2021; 6:301-316. [PMID: 33458482 PMCID: PMC7807778 DOI: 10.1021/acsomega.0c04595] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/09/2020] [Indexed: 05/07/2023]
Abstract
New conjugates of substituted 1,2,3-triazoles linked to 1,2,4-triazoles were synthesized starting from the appropriate S-propargylated 1,2,4-triazoles 7 and 8. Ligation of 1,2,4-triazoles to the 1,2,3-triazole core was performed through Cu(I)-catalyzed cycloaddition of 1,2,4-triazole-based alkyne side chain 7 and/or 8 with several un/functionalized alkyl- and/or aryl-substituted azides 9-15 to afford the desired 1,4-disubstituted 1,2,3-triazoles 16-27, using both classical and microwave methods. After their spectroscopic characterization (infrared, 1H, 13C nuclear magnetic resonance, and elemental analyses), an anticancer screening was carried out against some cancer cell lines including human colon carcinoma (Caco-2 and HCT116), human cervical carcinoma (HeLa), and human breast adenocarcinoma (MCF-7). The outcomes of this exploration revealed that compounds 17, 22, and 25 had a significant anticancer activity against MCF-7 and Caco-2 cancer cell lines with IC50 values of 0.31 and 4.98 μM, respectively, in relation to the standard reference drug, doxorubicin. Enzyme-docking examination was executed onto cyclin-dependent kinase 2; a promising aim for cancer medication. Synthesized compounds acquiring highest potency showcased superior interactions with the active site residue of the target protein and exhibited minimum binding energy. Finally, the density functional theory (DFT) calculations were carried out to confirm the outcomes of the molecular docking and the experimental findings. The chemical reactivity descriptors such as softness (δ), global hardness (η), electronegativity (χ), and electrophilicity were calculated from the levels of the predicted frontier molecular orbitals and their energy gap. The DFT results and the molecular docking calculation results explained the activity of the most expectedly active compounds 17, 22, and 25.
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Affiliation(s)
- Adeeb Al Sheikh Ali
- Department
of Chemistry, Faculty of Science, Taibah
University, Al-Madinah
Al-Munawarah 30002, Saudi
Arabia
| | - Daoud Khan
- Department
of Chemistry, Faculty of Science, Taibah
University, Al-Madinah
Al-Munawarah 30002, Saudi
Arabia
| | - Arshi Naqvi
- Department
of Chemistry, Faculty of Science, Taibah
University, Al-Madinah
Al-Munawarah 30002, Saudi
Arabia
| | - Fawzia Faleh Al-blewi
- Department
of Chemistry, Faculty of Science, Taibah
University, Al-Madinah
Al-Munawarah 30002, Saudi
Arabia
| | - Nadjet Rezki
- Department
of Chemistry, Faculty of Science, Taibah
University, Al-Madinah
Al-Munawarah 30002, Saudi
Arabia
| | - Mohamed Reda Aouad
- Department
of Chemistry, Faculty of Science, Taibah
University, Al-Madinah
Al-Munawarah 30002, Saudi
Arabia
| | - Mohamed Hagar
- Chemistry
Department, College of Sciences, Yanbu, Taibah University, Yanbu 30799, Saudi Arabia
- Chemistry
Department, Faculty of Science, Alexandria
University, Alexandria 21321, Egypt
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42
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Kusumaningsih T, Prasetyo WE, Wibowo FR, Firdaus M. Toward an efficient and eco-friendly route for the synthesis of dimeric 2,4-diacetyl phloroglucinol and its potential as a SARS-CoV-2 main protease antagonist: insight from in silico studies. NEW J CHEM 2021. [DOI: 10.1039/d0nj06114j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Dimeric 2,4-diacetyl phloroglucinol derivatives were synthesized under green chemistry protocols and found to be the potential inhibitor of 3CLpro of SARS-CoV-2.
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Affiliation(s)
- Triana Kusumaningsih
- Department of Chemistry
- Faculty of Mathematics and Natural Sciences
- Sebelas Maret University
- Surakarta
- Indonesia
| | - Wahyu E. Prasetyo
- Department of Chemistry
- Faculty of Mathematics and Natural Sciences
- Sebelas Maret University
- Surakarta
- Indonesia
| | - Fajar R. Wibowo
- Department of Chemistry
- Faculty of Mathematics and Natural Sciences
- Sebelas Maret University
- Surakarta
- Indonesia
| | - Maulidan Firdaus
- Department of Chemistry
- Faculty of Mathematics and Natural Sciences
- Sebelas Maret University
- Surakarta
- Indonesia
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43
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Bouchareb F, Berredjem M, Bouzina A, Guerfi M. Ultrasound-promoted, rapid and green synthesis of phosphonamide derivatives under catalyst and solvent-free conditions. PHOSPHORUS SULFUR 2020. [DOI: 10.1080/10426507.2020.1854254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Fouzia Bouchareb
- Laboratory of Applied Organic Chemistry, Synthesis of Biomolecules and Molecular Modelling Group, Faculty of Sciences, Department of Chemistry, Badji-Mokhtar – Annaba University, Annaba, Algeria
- Department of Chemistry, Faculty of Sciences and Technology, Chadli Bendjedid – EL Tarf University, El Tarf, Algeria
| | - Malika Berredjem
- Laboratory of Applied Organic Chemistry, Synthesis of Biomolecules and Molecular Modelling Group, Faculty of Sciences, Department of Chemistry, Badji-Mokhtar – Annaba University, Annaba, Algeria
| | - Abdeslem Bouzina
- Laboratory of Applied Organic Chemistry, Synthesis of Biomolecules and Molecular Modelling Group, Faculty of Sciences, Department of Chemistry, Badji-Mokhtar – Annaba University, Annaba, Algeria
| | - Meriem Guerfi
- Laboratory of Applied Organic Chemistry, Synthesis of Biomolecules and Molecular Modelling Group, Faculty of Sciences, Department of Chemistry, Badji-Mokhtar – Annaba University, Annaba, Algeria
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44
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Abad N, Lgaz H, Atioglu Z, Akkurt M, Mague JT, Ali IH, Chung IM, Salghi R, Essassi EM, Ramli Y. Synthesis, crystal structure, hirshfeld surface analysis, DFT computations and molecular dynamics study of 2-(benzyloxy)-3-phenylquinoxaline. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128727] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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45
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Synthesis, biological activity and POM/DFT/docking analyses of annulated pyrano[2,3-d]pyrimidine derivatives: Identification of antibacterial and antitumor pharmacophore sites. Bioorg Chem 2020; 106:104480. [PMID: 33279245 DOI: 10.1016/j.bioorg.2020.104480] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/27/2020] [Accepted: 11/15/2020] [Indexed: 12/17/2022]
Abstract
New annulated pyrano[2,3-d]pyrimidine derivatives were synthesized with hydroxyl, methoxy, bromine, nitrile and nitro substituents on its skeleton. The correlated electronic effect of substituents on the magnitude of antibacterial activity was noted. The electron donating substituents (namely; 4-OH, 4-OCH3, 4-Br) and electron withdrawing substituents (4-NO2) on phenyl ring in the pyrano[2,3-d]pyrimidine skeleton exerted different influence on its antimicrobial activity against some Gram-positive and Gram-negative bacteria such as Pseudomonas aureus, E. coli, Staphylococcus aureus, Klebsiella pneumonia and Bacillus cereus. All the pyrano[2,3-d]pyrimidines were characterized by spectroscopic analyses. Antibacterial screening revealed that the presence of heteroaryl, cyano and amino groups on pyrano[2,3-d]pyrimidine skeleton increases its penetrating power on the bacterial cell wall so that the product becomes more biologically active. So the the nature of electron withdrawing or electro-donnor Impact of substituents should be taken in consideration in drug design. Hydrolysis of -CRN to amide restored vital Intramolecular interaction like ortho-nitrophenyl and ONOδ-…NHδ+/amide link, offering a crucial template for antibacterial NH, HO-pharmacophore sites, which ultimately elevated innate antimicrobial profiles. POM combinatorial analysis of tangible electronic contributions due to armed annulated pyrano[2,3-d]pyrimidines concluded their broad antimicrobial activity and viable/prominent drug score index through perspective parameters particularly: inter atomic distance/linkers, steric, electronic, polar parameters, and with a different polarising effect of electron donating/withdrawing environments of substituents. Furthermore, an anti-Kinase pharmacophore site (OCNHCO) was evaluated in continuation of the POM investigations. All synthesized products verified fewer side effects than standard streptomycin, but facile implication in selective cancer media (viz. breast or leucemia still needs to be screened).
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46
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Grib I, Berredjem M, Rachedi KO, Djouad SE, Bouacida S, Bahadi R, Ouk TS, Kadri M, Ben Hadda T, Belhani B. Novel N-sulfonylphthalimides: Efficient synthesis, X-ray characterization, spectral investigations, POM analyses, DFT computations and antibacterial activity. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128423] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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47
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Modelling the Anti-Methicillin-Resistant Staphylococcus Aureus (MRSA) Activity of Cannabinoids: A QSAR and Docking Study. CRYSTALS 2020. [DOI: 10.3390/cryst10080692] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Twenty-four cannabinoids active against MRSA SA1199B and XU212 were optimized at WB97XD/6-31G(d,p), and several molecular descriptors were obtained. Using a multiple linear regression method, several mathematical models with statistical significance were obtained. The robustness of the models was validated, employing the leave-one-out cross-validation and Y-scrambling methods. The entire data set was docked against penicillin-binding protein, iso-tyrosyl tRNA synthetase, and DNA gyrase. The most active cannabinoids had high affinity to penicillin-binding protein (PBP), whereas the least active compounds had low affinities for all of the targets. Among the cannabinoid compounds, Cannabinoid 2 was highlighted due to its suitable combination of both antimicrobial activity and higher scoring values against the selected target; therefore, its docking performance was compared to that of oxacillin, a commercial PBP inhibitor. The 2D figures reveal that both compounds hit the protein in the active site with a similar type of molecular interaction, where the hydroxyl groups in the aromatic ring of cannabinoids play a pivotal role in the biological activity. These results provide some evidence that the anti-Staphylococcus aureus activity of these cannabinoids may be related to the inhibition of the PBP protein; besides, the robustness of the models along with the docking and Quantitative Structure–Activity Relationship (QSAR) results allow the proposal of three new compounds; the predicted activity combined with the scoring values against PBP should encourage future synthesis and experimental testing.
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48
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Bechlem K, Aissaoui M, Belhani B, Rachedi KO, Bouacida S, Bahadi R, Djouad SE, Ben Mansour R, Bouaziz M, Almalki F, Ben Hadda T, Berredjem M. Synthesis, X-ray crystallographic study and molecular docking of new α-sulfamidophosphonates: POM analyses of their cytotoxic activity. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.127990] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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49
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Elsharkawy ER, Almalki F, Ben Hadda T, Rastija V, Lafridi H, Zgou H. DFT calculations and POM analyses of cytotoxicity of some flavonoids from aerial parts of Cupressus sempervirens: Docking and identification of pharmacophore sites. Bioorg Chem 2020; 100:103850. [PMID: 32460177 DOI: 10.1016/j.bioorg.2020.103850] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/08/2020] [Accepted: 04/10/2020] [Indexed: 11/30/2022]
Abstract
Two known polyphenols named apigenin 7-O-β-d-glucopyranoside (S1) and querctine-3-O-glucoside (S2), along with another two new compounds apigenin 4'-geranyl-8-glucopyranosyl-7-O-α-glucopyranoside (S3) and apigenin 4'-pernyl-8-glucopyranosyl -7-O-α-glucopyranoside (S4), were isolated from the leaves of Cupressus sempervirens. Structure elucidation of the isolated polyphenols was established on the basis of detailed spectroscopic analysis like 1D and 2D NMR analyses including 1H NMR, 13C NMR, COSY, DEPT, HMQC, UV, and Electron Spray Ionization Mass Spectroscopy (ESI-MS). Density Functional Theory (DFT) of computational, Petra/Osiris/Molinspiration (POM), and docking analyses methods were applied in the structural validation of new isolated compounds. The isolated compounds S1-S4 showed significant cytotoxicity against human hepatocellular liver carcinoma HepG2 cells, MCF-7, HC116 and A549.
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Affiliation(s)
- Eman R Elsharkawy
- Chemistry Department, Faculty of Science, Northern Borders University, Arar, Saudi Arabia; Ecophysiology Unit, Plant Ecology and Ranges Department, Desert Research Center, Cairo, Egypt.
| | - Faisal Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm AlQura University, Makkah 21955, Saudi Arabia.
| | - Taibi Ben Hadda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm AlQura University, Makkah 21955, Saudi Arabia; Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, MB 524, 60000 Oujda, Morocco.
| | - Vesna Rastija
- Department of Agroecology and Environmental Protection, Faculty of Agrobiotehnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, Vladimira Preloga 1, Osijek, Croatia.
| | - Hind Lafridi
- Material Sciences, Processes, Environment & Modeling, Polydisciplinary Faculty, Ibn Zohr University, Ouarzazate, Morocco; Ibn Zohr University, Faculty of Sciences, B.P. 8106, 80090 Agadir, Morocco.
| | - Hsaine Zgou
- Ibn Zohr University, Faculty of Sciences, B.P. 8106, 80090 Agadir, Morocco.
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50
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Synthesis of a novel phenytoin derivative: Crystal structure, Hirshfeld surface analysis and DFT calculations. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127630] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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