1
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Nematollahi MH, Mehrabani M, Hozhabri Y, Mirtajaddini M, Iravani S. Antiviral and antimicrobial applications of chalcones and their derivatives: From nature to greener synthesis. Heliyon 2023; 9:e20428. [PMID: 37810815 PMCID: PMC10556610 DOI: 10.1016/j.heliyon.2023.e20428] [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: 05/08/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/10/2023] Open
Abstract
Chalcones and their derivatives have been widely studied due to their versatile pharmacological and biological activities, such as anti-inflammatory, antibacterial, antiviral, and antitumor effects. These compounds have shown suitable antiviral effects through the selective targeting of a variety of viral enzymes, including lactate dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), fumarate reductase, protein tyrosine phosphatase, topoisomerase-II, protein kinases, integrase/protease, and lactate/isocitrate dehydrogenase, among others. Chalcones and their derivatives have displayed excellent potential for combating pathogenic bacteria and fungi (especially, multidrug-resistant bacteria). However, relevant mechanisms should be further explored, focusing on inhibitory effects against DNA gyrase B, UDP-N-acetylglucosamine enolpyruvyl transferase (MurA), and efflux pumps (e.g., NorA), among others. In addition, the antifungal and antiparasitic activities of these compounds (e.g., antitrypanosomal and antileishmanial properties) have prompted additional explorations. Nonetheless, systematic analysis of the relevant mechanisms, biosafety issues, and pharmacological properties, as well as clinical translation studies, are vital for practical applications. Herein, recent advancements pertaining to the antibacterial, antiviral, antiparasitic, and antifungal activities of chalcones and their derivatives are deliberated, focusing on the relevant mechanisms of action, crucial challenges, and future prospects. Furthermore, due to the great importance of greener and more sustainable synthesis of these valuable compounds, especially on an industrial scale, the progress made in this field has been briefly discussed. Hopefully, this review can serve as a catalyst for researchers to delve deeper into the exploration and designing of novel chalcone compounds with medicinal properties, especially against pathogenic viruses and multidrug-resistant bacteria as major causes of concern for human health.
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Affiliation(s)
- Mohammad Hadi Nematollahi
- Herbal and Traditional Medicines Research Center, School of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Mehrnaz Mehrabani
- Physiology Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Yaser Hozhabri
- Applied Cellular and Molecular Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Maryamossadat Mirtajaddini
- Physiology Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Siavash Iravani
- Independent Researcher, W Nazar ST, Boostan Ave, Isfahan, Iran
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2
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Wang S, Wang Y, Ge C, Sun R, Wang H, Yan H. Insight for the synthesis and crystal structure of diazatetraasterane derivatives: Experimental and theoretical studies. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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3
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Valipour M. Recruitment of chalcone's potential in drug discovery of anti-SARS-CoV-2 agents. Phytother Res 2022; 36:4477-4490. [PMID: 36208000 PMCID: PMC9874432 DOI: 10.1002/ptr.7651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/09/2022] [Accepted: 09/22/2022] [Indexed: 01/27/2023]
Abstract
Chalcone is an interesting scaffold found in the structure of many naturally occurring molecules. Medicinal chemists are commonly interested in designing new chalcone-based structures because of having the α, β-unsaturated ketone functional group, which allows these compounds to participate in Michael's reaction and create strong covalent bonds at the active sites of the targets. Some studies have identified several natural chalcone-based compounds with the ability to inhibit the severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus proteases. A few years after the advent of the coronavirus disease 2019 pandemic and the publication of many findings in this regard, there is some evidence that suggests chalcone scaffolding has great potential for use in the design and development of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) inhibitors. Artificial placement of this scaffold in the structure of optimized anti-SARS-CoV-2 compounds can potentially provide irreversible inhibition of the viral cysteine proteases 3-chymotrypsin-like protease and papain-like protease by creating Michael interaction. Despite having remarkable capabilities, the use of chalcone scaffold in drug design and discovery of SARS-CoV-2 inhibitors seems to have been largely neglected. This review addresses issues that could lead to further consideration of chalcone scaffolding in the structure of SARS-CoV-2 protease inhibitors in the future.
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Affiliation(s)
- Mehdi Valipour
- Razi Drug Research Center, Iran University of Medical SciencesTehranIran
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4
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Véras JH, Do Vale CR, Luiz Cardoso Bailão EF, Dos Anjos MM, Cardoso CG, de Oliveira MG, de Paula JR, de Oliveira GR, Silva CRE, Chen-Chen L. Protective effects and DNA repair induction of a coumarin-chalcone hybrid against genotoxicity induced by mutagens. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2022; 85:937-951. [PMID: 36068785 DOI: 10.1080/15287394.2022.2120585] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Coumarins and chalcones are compounds widely found in plants or obtained by synthetic methods which possess several biological properties including antioxidant, anti-inflammatory, and antitumor effects. A series of coumarin-chalcone hybrids were synthesized to improve their biological actions and reduce potential adverse effects. Considering the applications of these molecules, a coumarin-chalcone hybrid [7-methoxy-3-(E)-3-(3,4,5-trimethoxyphenyl) acryloyl-2 H-chromen-2-one] (4-MET) was synthesized and the genotoxic, cytotoxic, and protective effects assessed against damage induced by different mutagens. First, in silico tools were used to predict biological activity of 4-MET which indicated a chemopreventive potential. Subsequently, the genotoxic/antigenotoxic activities of 4-MET were determined both in vitro (Ames test) and in vivo (micronucleus (MN) test and comet assay). In addition, molecular docking simulations were performed between 4-MET and glutathione reductase, an important cellular detoxifying enzyme. Our results indicated that 4-MET was not mutagenic in the Ames test; however, when co-treated with sodium azide or 4-nitroquinoline 1-oxide (4-NQO), 4-MET significantly reduced the harmful actions of these mutagens. Except for a cytotoxic effect after 120 hr treatment, 4-MET alone did not produce cytotoxicity or genotoxicity in the MN test and comet assay. Nonetheless, all treatments of 4-MET with cyclophosphamide (CPA) showed a chemoprotective effect against DNA damage induced by CPA. Further, molecular docking analysis indicated a strong interaction between 4-MET and the catalytic site of glutathione reductase. These effects may be related to (1) damage prevention, (2) interaction with detoxifying enzymes, and (3) DNA-repair induction. Therefore, data demonstrated that 4-MET presents a favorable profile to be used in chemopreventive therapies.
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Affiliation(s)
- Jefferson Hollanda Véras
- Laboratory of Radiobiology and Mutagenesis, Department of Genetics, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
| | - Camila Regina Do Vale
- Laboratory of Radiobiology and Mutagenesis, Department of Genetics, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
| | | | | | - Clever Gomes Cardoso
- Laboratory of Radiobiology and Mutagenesis, Department of Genetics, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
| | | | | | | | - Carolina Ribeiro E Silva
- Laboratory of Radiobiology and Mutagenesis, Department of Genetics, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
| | - Lee Chen-Chen
- Laboratory of Radiobiology and Mutagenesis, Department of Genetics, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
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5
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Said MA, Riyadh SM, Al-Kaff NS, Nayl AA, Khalil KD, Bräse S, Gomha SM. Synthesis and greener pastures biological study of bis-thiadiazoles as potential Covid-19 drug candidates. ARAB J CHEM 2022; 15:104101. [PMID: 35845755 PMCID: PMC9272579 DOI: 10.1016/j.arabjc.2022.104101] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 07/02/2022] [Indexed: 12/12/2022] Open
Abstract
A novel series of bis- (Abdelhamid et al., 2017, Banerjee et al., 2018, Bharanidharan et al., 2022)thiadiazoles was synthesized from the reaction of precursor dimethyl 2,2'-(1,2-diphenylethane-1,2-diylidene)-bis(hydrazine-1-carbodithioate) and hydrazonyl chlorides in ethanol under ultrasonic irradiation. Spectral tools (IR. NMR, MS, elemental analyses, molecular dynamic simulation, DFT and LUMO and HOMO) were used to elucidate the structure of the isolated products. Molecular docking for the precursor, 3 and ligands 6a-i to two COVID-19 important proteins Mpro and RdRp was compared with two approved drugs, Remdesivir and Ivermectin. The binding affinity varied between the ligands and the drugs. The highest recorded binding affinity of 6c with Mpro was (-9.2 kcal/mol), followed by 6b and 6a, (-8.9 and -8.5 kcal/mol), respectively. The lowest recorded binding affinity was (-7.0 kcal/mol) for 6 g. In comparison, the approved drugs showed binding affinity (-7.4 and -7.7 kcal/mol), for Remdesivir and Ivermectin, respectively, which are within the range of the binding affinity of our ligands. The binding affinity of the approved drug Ivermectin against RdRp recoded the highest (-8.6 kcal/mol), followed by 6a, 6 h, and 6i are the same have (-8.2 kcal/mol). The lowest reading was found for compound 3 ligand (-6.3 kcal/mol). On the other side, the amino acids also differed between the compounds studied in this project for both the viral proteins. The ligand 6a forms three H-bonds with Thr 319(A), Sr 255(A) and Arg 457(A), whereas Ivermectin forms three H-bonds with His 41(A), Gly143(A) and Gln 18(A) for viral Mpro. The RdRp amino acids residues could be divided into four groups based on the amino acids that interact with hydrogen or hydrophobic interactions. The first group contained 6d, 6b, 6 g, and Remdesivir with 1-4 hydrogen bonds and hydrophobic interactions 1 to 10. Group 2 is 6a and 6f exhibited 1 and 3 hydrogen bonds and 15 and 14 hydrophobic interactions. Group 3 has 6e and Ivermectin shows 4 and 3 hydrogen bonds, respectively and 11 hydrophobic interactions for both compounds. The last group contains ligands 3, 6c, 6 h, and 6i gave 1-3 hydrogen bonds and 6c and 3 recorded the highest number of hydrophobic interactions, 14 for both 6c and 6 h. Pro Tox-II estimated compounds' activities as Hepatoxic, Carcinogenic and Mutagenic, revealing that 6f-h were inactive in all five similar to that found with Remdesivir and Ivermectin. The drug-likeness prediction was carried out by studying physicochemical properties, lipophilicity, size, polarity, insolubility, unsaturation, and flexibility. Generally, some properties of the ligands were comparable to that of the standards used in this study, Remdesivir and Ivermectin.
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Affiliation(s)
- Musa A Said
- Department of Chemistry, Faculty of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia
| | - Sayed M Riyadh
- Department of Chemistry, Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Nadia S Al-Kaff
- Department of Biology, Faculty of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia
| | - A A Nayl
- Department of Chemistry, College of Science, Jouf University, P.O. Box 2014, Sakaka, Aljouf, Saudi Arabia
| | - Khaled D Khalil
- Department of Chemistry, Faculty of Science, Cairo University, Giza 12613, Egypt.,Department of Chemistry, Faculty of Science, Taibah University, Al-Madinah Almunawrah, Yanbu 46423, Saudi Arabia
| | - Stefan Bräse
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76133 Karlsruhe, Germany.,Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Director Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Sobhi M Gomha
- Department of Chemistry, Faculty of Science, Cairo University, Giza 12613, Egypt.,Department of Chemistry, Faculty of Science, Islamic University of Madinah, Madinah 42351, Saudi Arabia
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6
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Elkanzi NAA, Hrichi H, Alolayan RA, Derafa W, Zahou FM, Bakr RB. Synthesis of Chalcones Derivatives and Their Biological Activities: A Review. ACS OMEGA 2022; 7:27769-27786. [PMID: 35990442 PMCID: PMC9386807 DOI: 10.1021/acsomega.2c01779] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/21/2022] [Indexed: 05/27/2023]
Abstract
Chalcone derivatives are considered valuable species because they possess a ketoethylenic moiety, CO-CH=CH-. Due to the presence of a reactive α,β-unsaturated carbonyl group, chalcones and their derivatives possess a wide spectrum of antiproliferative, antifungal, antibacterial, antiviral, antileishmanial, and antimalarial pharmacological properties. Recent developments in heterocyclic chemistry have led to the synthesis of chalcone derivatives, which had been biologically investigated toward certain disease targets. The major aspect of this review is to present the most recent synthesis of chalcones bearing N, O, and/or S heterocycles, revealing their biological potential during the past decade (2010-2021). Based on a review of the literature, many chalcone-heterocycle hybrids appear to exhibit promise as future drug candidates owing to their similar or superior activities compared to those of the standards. Thus, this review may prove to be beneficial for the development and design of new potent therapeutic drugs based on previously developed strategies.
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Affiliation(s)
- Nadia A. A. Elkanzi
- Chemistry
Department, College of Science, Jouf University, Sakaka 2014, Saudi Arabia
| | - Hajer Hrichi
- Chemistry
Department, College of Science, Jouf University, Sakaka 2014, Saudi Arabia
| | - Ruba A. Alolayan
- Chemistry
Department, College of Science, Jouf University, Sakaka 2014, Saudi Arabia
| | - Wassila Derafa
- Chemistry
Department, College of Science, Jouf University, Sakaka 2014, Saudi Arabia
| | - Fatin M. Zahou
- Biology
Department, College of Science, Jouf University, Sakaka 2014, Saudi Arabia
| | - Rania B. Bakr
- Department
of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt
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7
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Azo-based Multifunctional Molecules and Their Copper(II) Complexes as Potential Inhibitors Against Alzheimer’s Disease: XRD/Hirshfeld Analysis/ DFT/Molecular Docking/Cytotoxicity. INORG CHEM COMMUN 2022. [DOI: 10.1016/j.inoche.2022.109535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Panahi Y, Dadkhah M, Talei S, Gharari Z, Asghariazar V, Abdolmaleki A, Matin S, Molaei S. Can anti-parasitic drugs help control COVID-19? Future Virol 2022. [PMID: 35359702 PMCID: PMC8940209 DOI: 10.2217/fvl-2021-0160] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 02/28/2022] [Indexed: 01/18/2023]
Abstract
Novel COVID-19 is a public health emergency that poses a serious threat to people worldwide. Given the virus spreading so quickly, novel antiviral medications are desperately needed. Repurposing existing drugs is the first strategy. Anti-parasitic drugs were among the first to be considered as a potential treatment option for this disease. Even though many papers have discussed the efficacy of various anti-parasitic drugs in treating COVID-19 separately, so far, no single study comprehensively discussed these drugs. This study reviews some anti-parasitic recommended drugs to treat COVID-19, in terms of function and in vitro as well as clinical results. Finally, we briefly review the advanced techniques, such as artificial intelligence, that have been used to find effective drugs for the treatment of COVID-19.
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Affiliation(s)
- Yasin Panahi
- Department of Pharmacology & Toxicology, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Masoomeh Dadkhah
- Pharmaceutical Sciences Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Sahand Talei
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Gharari
- Department of Biotechnology, Faculty of Biological Sciences, Al-Zahra University, Tehran, Iran
| | - Vahid Asghariazar
- Deputy of Research & Technology, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Arash Abdolmaleki
- Department of Engineering Sciences, Faculty of Advanced Technologies, University of Mohaghegh Ardabili, Namin, Iran.,Bio Science & Biotechnology Research center (BBRC), Sabalan University of Advanced Technologies (SUAT), Namin, Iran
| | - Somayeh Matin
- Department of Internal Medicine, Imam Khomeini Hospital, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Soheila Molaei
- Pharmaceutical Sciences Research Center, Ardabil University of Medical Sciences, Ardabil, Iran.,Zoonoses Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
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9
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Mahesha, Udaya Kumar AH, Vindya KG, Pampa KJ, Rangappa KS, Lokanath NK. Structure-property relationship in thioxotriaza-spiro derivative: Crystal structure and molecular docking analysis against SARS-CoV-2 main protease. J Mol Struct 2022; 1250:131746. [PMID: 34697506 PMCID: PMC8520729 DOI: 10.1016/j.molstruc.2021.131746] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 12/11/2022]
Abstract
Detailed structural and non-covalent interactions in thioxotriaza-spiroderivative (DZ2) are investigated by single crystal structure anslysis and computational approaches. Its results were compared with the previously reported spiroderivative (DZ1). The crystal structure analysis revealed various C–H…O, N–H…O, C–H…N and N–H…S hydrogen bonds involved in constructing several dimeric motifs to stabilize the crystal packing. The differences and similarities in the relative contribution of non-covalent interactions in DZ1 and DZ2 compounds are compared using the Hirshfeld surface analysis and 2D fingerprint plots. The binding energies of specific molecular pairs and homodimers have been obtained using molecule–molecule interaction energy calculation. The hierarchy and topology of pair-wise intermolecular interactions are visualized through energy frameworks. The nature and strength of intra and intermolecular interactions were characterized using non-covalent interaction index analysis and the quantum theory of atoms in molecule approach. Further, molecular docking of compounds (DZ1 and DZ2) with SARS-CoV-2 main protease for COVID-19 is performed. And the superposition of these ligands and inhibitor N3, which is docked into the binding pocket of 7BQY, is presented. The binding affinity of −6.7 kcal/mol is observed, attributed to hydrogen bonding and hydrophobic interactions between the ligand and the amino acid residues of the receptor.
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Affiliation(s)
- Mahesha
- Department of Studies in Physics, University of Mysore, Manasagangotri, Mysuru, Karnataka 570 006, India
| | - A H Udaya Kumar
- Department of Studies in Physics, University of Mysore, Manasagangotri, Mysuru, Karnataka 570 006, India
| | - K G Vindya
- Department of Studies in Chemistry, University of Mysore, Manasagangotri, Mysuru, Karnataka 570 006, India
| | - K J Pampa
- Department of Biotechnology, University of Mysore, Manasagangotri, Mysuru, Karnataka 570 006, India
| | - K S Rangappa
- Department of Studies in Chemistry, University of Mysore, Manasagangotri, Mysuru, Karnataka 570 006, India
| | - N K Lokanath
- Department of Studies in Physics, University of Mysore, Manasagangotri, Mysuru, Karnataka 570 006, India
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10
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Missioui M, Said MA, Demirtaş G, Mague JT, Al-Sulami A, Al-Kaff NS, Ramli Y. A possible potential COVID-19 drug candidate: Diethyl 2-(2-(2-(3-methyl-2-oxoquinoxalin-1(2H)-yl)acetyl)hydrazono)malonate: Docking of disordered independent molecules of a novel crystal structure, HSA/DFT/XRD and cytotoxicity. ARAB J CHEM 2022; 15:103595. [PMID: 34909067 PMCID: PMC8627592 DOI: 10.1016/j.arabjc.2021.103595] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/24/2021] [Indexed: 01/25/2023] Open
Abstract
This study reports the synthesis, characterization and importance of a novel diethyl 2-(2-(2-(3-methyl-2-oxoquinoxalin-1(2H)-yl)acetyl)hydrazono)malonate (MQOAHM). Two independent molecular structures of the disordered MQOAHM have been established by XRD‑single‑crystal analysis in a ratio of 0.596(3)/0.404(3), MQOAHM (a) and MQOAHM (b), respectively. MQOAHM was characterized by means of various spectroscopic tools ESI-MS, IR, 1H &13C NMR analyses. Density Functional Theory (DFT) method, B3LYP, 6-311++G(d,p) basis set was used to optimize MQOAHM molecule. The obtained theoretical structure and experimental structure were superimposed on each other, and the correlation between them was calculated. The Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO) were created, and the energy gap between these orbitals was calculated. For analyzing intermolecular interactions, Molecular Electrostatic Potential (MEP) and Hirshfeld Surface Analysis were studied. For a fair comparative study, the two forms of the title compound were docked together with 18 approved drugs and N3 under precisely the same conditions. The disordered molecule structure's binding scores against 7BQY were -7.0 and -6.9 kcal/mol-1 for MQOAHM (a) and MQOAHM (b), respectively. Both the forms show almost identical superimposed structures and scores indicating that the disorder of the molecule, in this study, has no obvious effect. The high binding score of the molecule was attributed to the multi-hydrogen bond and hydrophobic interactions between the ligand and the receptor's active amino acid residues. Worth pointing out here that the aim of using the free energy in Silico molecular docking approach is to rank the title molecule compared to the wide range of approved drugs and a well-established ligand N3. The binding scores of all the molecules used in this study are ranged from -9.9 to -4.5 kcal/mol-1. These results and the supporting statistical analyses suggest that this malonate-based ligand merits further research in the context of possible therapeutic agents for COVID-19. Cheap computational techniques, PASS, Way2drug and ADMET, online software tools, were used in this study to uncover the title compound's potential biological activities and cytotoxicity.
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Affiliation(s)
- Mohcine Missioui
- Laboratory of Medicinal Chemistry, Drug Sciences Research Center, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Morocco
| | - Musa A. Said
- College of Science, Taibah University, PO Box 30002, Al-Madinah Al Munawarah, 1417, Saudi Arabia
| | - Güneş Demirtaş
- Ondokuz Mayıs University, Faculty of Arts and Sciences, Department of Physics, 55139 Samsun, Turkey
| | - Joel T. Mague
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA
| | - Ahlam Al-Sulami
- Department of Chemistry, College of Science, University of Jeddah, Jeddah 21589, Saudi Arabia
| | - Nadia S. Al-Kaff
- College of Science, Taibah University, PO Box 30002, Al-Madinah Al Munawarah, 1417, Saudi Arabia
| | - Youssef Ramli
- Laboratory of Medicinal Chemistry, Drug Sciences Research Center, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Morocco,Corresponding author
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11
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Abu-Melha S, Edrees MM, Said MA, Riyadh SM, Al-Kaff NS, Gomha SM. Potential COVID-19 Drug Candidates Based on Diazinyl-Thiazol-Imine Moieties: Synthesis and Greener Pastures Biological Study. Molecules 2022; 27:molecules27020488. [PMID: 35056802 PMCID: PMC8777737 DOI: 10.3390/molecules27020488] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/25/2021] [Accepted: 12/28/2021] [Indexed: 12/23/2022] Open
Abstract
A novel series of 1-aryl-N-[4-phenyl-5-(arylazo)thiazol-2-yl)methanimines has been synthesized via the condensation of 2-amino-4-phenyl-5-arylazothiazole with various aromatic aldehydes. The synthesized imines were characterized by spectroscopic techniques, namely 1H and 13C-NMR, FTIR, MS, and Elemental Analysis. A molecular comparative docking study for 3a-f was calculated, with reference to two approved drugs, Molnupiravir and Remdesivir, using 7BQY (Mpro; PDB code 7BQY; resolution: 1.7 A°) under identical conditions. The binding scores against 7BQY were in the range of -7.7 to -8.7 kcal/mol for 3a-f. The high scores of the compounds indicated an enhanced binding affinity of the molecules to the receptor. This is due to the hydrophobic interactions and multi-hydrogen bonds between 3a-f ligands and the receptor's active amino acid residues. The main aim of using in silco molecular docking was to rank 3a-f with respect to the approved drugs, Molnupiravir and Remdesivir, using free energy methods as greener pastures. A further interesting comparison presented the laydown of the ligands before and after molecular docking. These results and other supporting statistical analyses suggested that ligands 3a-f deserve further investigation in the context of potential therapeutic agents for COVID-19. Free-cost, PASS, SwissADME, and Way2drug were used in this research paper to determine the possible biological activities and cytotoxicity of 3a-f.
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Affiliation(s)
- Sraa Abu-Melha
- Department of Chemistry, Faculty of Science, King Khalid University, Abha 61413, Saudi Arabia; (S.A.-M.); (M.M.E.)
| | - Mastoura Mohamed Edrees
- Department of Chemistry, Faculty of Science, King Khalid University, Abha 61413, Saudi Arabia; (S.A.-M.); (M.M.E.)
- Department of Organic Chemistry, National Organization for Drug Control and Research (NODCAR), Giza 12311, Egypt
| | - Musa A. Said
- Department of Chemistry, Faculty of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia;
- Correspondence: (M.A.S.); (S.M.G.)
| | - Sayed M. Riyadh
- Department of Chemistry, Faculty of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia;
- Department of Chemistry, Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Nadia S. Al-Kaff
- Department of Biology, Faculty of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia;
| | - Sobhi M. Gomha
- Department of Chemistry, Faculty of Science, Cairo University, Giza 12613, Egypt
- Department of Chemistry, Faculty of Science, Islamic University of Madinah, Al-Madinah Al-Munawarah 42351, Saudi Arabia
- Correspondence: (M.A.S.); (S.M.G.)
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12
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Missioui M, Said MA, Demirtaş G, Mague JT, Ramli Y. Docking of disordered independent molecules of novel crystal structure of (N-(4-methoxyphenyl)-2-(3-methyl-2-oxo-3,4-dihydroquinoxalin-1(2H)-yl)acetamide as anti-COVID-19 and anti-Alzheimer's disease. Crystal structure, HSA/DFT/XRD. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131420] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Manas Bandyopadhyay, Sengupta U, Periyasamy M, Mukhopadhyay S, Hasija A, Chopra D, Özdemir N, Said MA, Bera MK. Cu(II)(PhOMe-Salophen) Complex: Greener Pasture Biological Study, XRD/HAS Interactions, and MEP. RUSS J INORG CHEM+ 2022; 67. [PMCID: PMC10028762 DOI: 10.1134/s0036023623700274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
PhOMe-salophen (1b) (salophen is N,N-bis(salycilidene)-1,2-phenylenediamine with two tert-butyl on each ring) and Cu(II) complex with PhOMe-salophen (1c) have been synthesized and characterized using various tools, including X-ray diffraction for the Cu(II)-complex (1c, C43H52CuN2O3)). The copper complex has been obtained by Cu2+ templated approach using 1b. PhOMe-salophen (1b) has been obtained in reasonably high yield using a mixture of the Schiff-base, 1a, Pd(OAc)2, PPh3, Na2CO3, 4-methoxyphenylboronic acid in benzene. We focus in this research work on the electronic and structural properties of the Cu–Schiff base complex. The tetra-coordinate τ4 index was calculated, indicating almost a perfect square planner in agreement with X-ray diffraction results. MEP reveals the maximum positive regions in 1/-associated with the azomethine and methoxyphenyl C–H bonds with an average value of 0.03 a.u. Hirshfeld surface analysis (HSA) was also studied to highlight the significant inter-atomic contacts and their percentage contribution through 2D Fingerprint plot. In a fair comparative molecular docking study, 1b and 1c were docked together with N-[{(5-methylisoxazol-3-yl)-carbonyl}alanyl}-l-valyl]-N1-((1R,2Z)-4-(benzyloxy)-4-oxo-1-[{(3R)-2-oxopyrrolidin-3-yl}methyl]but-2-enyl)-l-leucinamide, N3 against main protease Mpro, (PDB code 7BQY) using the same parameters and conditions. Interesting here to use the free energy, in silico, molecular docking approach, which aims to rank our molecules with respect to the well-known inhibitor, N3. The binding scores of 1b, 1c, N3 are –7.8, –9.0, and –8.4 kcal/mol, respectively. These preliminary results propose that ligands deserve additional study in the context of possible remedial agents for COVID-19.
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Affiliation(s)
- Manas Bandyopadhyay
- Department of Chemistry, Indian Institute of Engineering Science and Technology (IIEST), Shibpur P.O. Botanic Garden, 7111103 Howrah, India
| | - Utsav Sengupta
- Department of Chemistry, Indian Institute of Engineering Science and Technology (IIEST), Shibpur P.O. Botanic Garden, 7111103 Howrah, India
| | - Muthaimanoj Periyasamy
- Department of Mining Engineering, Indian Institute of Engineering Science and Technology (IIEST), Shibpur, P.O. Botanic Garden, 7111103 Howrah, India
| | - Sudipta Mukhopadhyay
- Department of Mining Engineering, Indian Institute of Engineering Science and Technology (IIEST), Shibpur, P.O. Botanic Garden, 7111103 Howrah, India
| | - Avantika Hasija
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Bhopal Bypass Rd, Bhauri, 462066 Bhopal, Madhya Pradesh India
| | - Deepak Chopra
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Bhopal Bypass Rd, Bhauri, 462066 Bhopal, Madhya Pradesh India
| | - Namık Özdemir
- Department of Mathematics and Science Education, Faculty of Education, Ondokuz Mayıs University, 55139 Samsun, Turkey
| | - Musa A. Said
- Department of Chemistry, Faculty of Science, Taibah University, 30002 Al-Madinah Al-Munawarah, Saudi Arabia
- Institut fuer Anorganische Chemie, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Mrinal K. Bera
- Department of Chemistry, Indian Institute of Engineering Science and Technology (IIEST), Shibpur P.O. Botanic Garden, 7111103 Howrah, India
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Said MA, Khan DJO, Al-blewi FF, Al-Kaff NS, Ali AA, Rezki N, Aouad MR, Hagar M. New 1,2,3-Triazole Scaffold Schiff Bases as Potential Anti-COVID-19: Design, Synthesis, DFT-Molecular Docking, and Cytotoxicity Aspects. Vaccines (Basel) 2021; 9:vaccines9091012. [PMID: 34579249 PMCID: PMC8472185 DOI: 10.3390/vaccines9091012] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/24/2021] [Accepted: 09/01/2021] [Indexed: 11/16/2022] Open
Abstract
Schiff bases encompassing a 1,2,3-triazole motif were synthesized using an efficient multi-step synthesis. The formations of targeted Schiff base ligands were confirmed by different spectroscopic techniques (FT-IR, 1H NMR, 13C NMR, and CHN analysis). The spectral data analysis revealed that the newly designed hydrazones exist as a mixture of trans-E and cis-E diastereomers. Densityfunctional theory calculations (DFT) for the Schiff bases showed that the trans-trans form has the lowest energy structure with maximum stability compared to the other possible geometrical isomers that could be present due to the orientation of the amidic NH-C=O group. The energy differences between the trans-trans on one side and syn-syn and syn-trans isomers on the other side were 9.26 and 5.56 kcal/mol, respectively. A quantitative structure-activity relationship investigation was also performed in terms of density functional theory. The binding affinities of the newly synthesized bases are, maybe, attributed to the presence of hydrogen bonds together with many hydrophobic interactions between the ligands and the active amino acid residue of the receptor. The superposition of the inhibitor N3 and an example ligand into the binding pocket of 7BQY is also presented. Further interesting comparative docking analyses were performed. Quantitative structure-activity relationship calculations are presented, illustrating possible inhibitory activity. Further computer-aided cytotoxicity analysis by Drug2Way and PASS online software was carried out for Schiff base ligands against various cancer cell lines. Overall, the results of this study suggest that these Schiff base derivatives may be considered for further investigation as possible therapeutic agents for COVID-19.
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Affiliation(s)
- Musa A. Said
- Department of Chemistry, College of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia; (D.J.O.K.); (F.F.A.-b.); (A.A.A.); (N.R.)
- Correspondence: (M.A.S.); (M.R.A.)
| | - Daoud J. O. Khan
- Department of Chemistry, College of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia; (D.J.O.K.); (F.F.A.-b.); (A.A.A.); (N.R.)
| | - Fawzia F. Al-blewi
- Department of Chemistry, College of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia; (D.J.O.K.); (F.F.A.-b.); (A.A.A.); (N.R.)
| | - Nadia S. Al-Kaff
- Department of Biology, College of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia;
| | - Adeeb A. Ali
- Department of Chemistry, College of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia; (D.J.O.K.); (F.F.A.-b.); (A.A.A.); (N.R.)
| | - Nadjet Rezki
- Department of Chemistry, College of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia; (D.J.O.K.); (F.F.A.-b.); (A.A.A.); (N.R.)
| | - Mohamed Reda Aouad
- Department of Chemistry, College of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia; (D.J.O.K.); (F.F.A.-b.); (A.A.A.); (N.R.)
- Correspondence: (M.A.S.); (M.R.A.)
| | - Mohamed Hagar
- Chemistry Department, College of Sciences, Taibah University, Yanbu 30799, Saudi Arabia;
- Chemistry Department, Faculty of Science, Alexandria University, Alexandria 21321, Egypt
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Naresh P, Pramodh B, Naveen S, Ganguly S, Panda J, Sunitha K, Maniukiewicz W, Lokanath N. Cis and trans isomers of 1-(5-bromothiophen-2-yl)-3-(10-chloroanthracen-9-yl)prop-2-en-1-one: Synthesis and characterization. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Virtual screenings of the bioactive constituents of tea, prickly chaff, catechu, lemon, black pepper, and synthetic compounds with the main protease (Mpro) and human angiotensin-converting enzyme 2 (ACE 2) of SARS-CoV-2. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2021; 7:121. [PMID: 34150913 PMCID: PMC8204119 DOI: 10.1186/s43094-021-00275-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/07/2021] [Indexed: 12/24/2022] Open
Abstract
Background COVID-19 has mutation capability, and there are no specific drug therapies that are available to fight or inhibit the proteins of this virus. The present study aims to investigate the binding affinity of the bioactive and synthetic compounds with the main protease (Mpro) enzymes and angiotensin-converting enzyme 2 (ACE 2) by computational approach. PASS prediction, pharmacokinetics, and toxicological properties prediction studies were performed through the Google PASS prediction and Swiss ADME/T website. Besides, molecular docking studies were accomplished by BIOVIA Discovery Studio 2020, UCSF Chimera, and PyRx autodock vina. Results The docking scores were inferred and the selected compounds showed results varying from −3.2 to −9.8 (kcal/mol). Theaflavin scored the highest docking score to the 5REB, 6VW1, and 1R42 enzymes and showed the binding affinity as −6.3 kcal/mol, −9.8 kcal/mol, and −8.6 kcal/mol, respectively. Again, kaempferol showed the best binding affinity to the 7BQY (−7.1 kcal/mol) and 6Y2FB (−6.6 kcal/mol) enzymes. All the chemical constituents showed better probability in action in pass prediction analysis. Besides, no ligands (except theaflavin) have any conflict with Lipinski’s rules of five, which authorized the drug probability of these ligands. Conclusion Therefore, the selected compounds could be considered a potential herbal treatment source against SARS-CoV-2.
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Alaşalvar C, Öztürk N, Gökce H, Güder A, Menteşe E, Bektaş H. Synthesis, structural, spectral, antioxidant, bioactivity and molecular docking investigations of a novel triazole derivative. J Biomol Struct Dyn 2021; 40:6642-6655. [PMID: 33594957 DOI: 10.1080/07391102.2021.1887764] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The structural, spectroscopic and electronic properties of 4-(4-nitrophenyl)-5-(pyridin-3-yl)-2,4-dihydro-3H-1,2,4-triazole-3-thione have been analyzed by using single crystal X-ray diffraction (SCXRD), 1H and 13C NMR chemical shifts and FT-IR spectroscopic methods both theoretically and experimentally. The tautomeric (thiol and thione) energetic analysis results, structural optimization parameters (bond lengths and angles), vibrational wavenumbers, proton and carbon NMR chemical shifts, UV-Vis. parameters, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) analyses and Molecular Electrostatic Potential (MEP) surface have been calculated by using DFT/B3LYP quantum chemical method with 6-311++G(2d,2p) basis set to compare with the experimental results. The computed geometry parameters, vibrational wavenumbers, and NMR chemical shifts have been in good agreement with the experimental results. It should be noted that the radical scavenging activities of the title compound have been evaluated by using different test methods i.e. 2,2-Diphenyl-1-picrylhydrazyl (DPPH), N,N-dimethyl-p-phenylenediamine (DMPD) and 2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonate) (ABTS). According to obtained results, the title compound displayed DPPH (SC50 19.42 ± 0.11 μg/mL), DMPD (SC50 21.13 ± 0.08 μg/mL) and ABTS (SC50 38.17 ± 0.25 μg/mL) scavenging activities. Also, these results have been compared with Butylated hydroxyanisole (BHA), Rutin (RUT) and Trolox (TRO) used as standard compounds. The physicochemical, pharmacokinetic, and toxicity features of the compound have been determined by using drug-likeness and in silico ADMET investigations. The interaction results with SARS-CoV-2 main protease (Mpro) of the title ligand compound have been analyzed via the help of molecular docking study.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Can Alaşalvar
- Technical Science Vocational High School, Giresun University, Giresun, Turkey
| | - Nuri Öztürk
- Dereli Vocational School, Giresun University, Giresun, Turkey
| | - Halil Gökce
- Vocational High School of Health Services, Giresun University, Giresun, Turkey
| | - Aytaç Güder
- Vocational High School of Health Services, Giresun University, Giresun, Turkey
| | - Emre Menteşe
- Faculty of Art and Science, Recep Tayyip Erdogan University, Rize, Turkey
| | - Hakan Bektaş
- Faculty of Art and Science, Giresun University, Giresun, Turkey
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