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Mansour MA, AboulMagd AM, Abbas SH, Abdel-Aziz M, Abdel-Rahman HM. Quinazoline-chalcone hybrids as HDAC/EGFR dual inhibitors: Design, synthesis, mechanistic, and in-silico studies of potential anticancer activity against multiple myeloma. Arch Pharm (Weinheim) 2024; 357:e2300626. [PMID: 38297894 DOI: 10.1002/ardp.202300626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/02/2024] [Accepted: 01/05/2024] [Indexed: 02/02/2024]
Abstract
Two new series of quinazoline-chalcone hybrids were designed, synthesized as histone deacetylase (HDAC)/epidermal growth factor receptor (EGFR) dual inhibitors, and screened in vitro against the NCI 60 human cancer cell line panel. The most potent derivative, compound 5e bearing a 3,4,5-trimethoxyphenyl chalcone moiety, showed the most effective growth inhibition value against the panel of NCI 60 human cancer cell lines. Thus, it was selected for further investigation for NCI 5 log doses. Interestingly, this trimethoxy-substituted analog inhibited the proliferation of Roswell Park Memorial Institute (RPMI)-8226 cells by 96%, at 10 µM with IC50 = 9.09 ± 0.34 µM and selectivity index = 7.19 against normal blood cells. To confirm the selectivity of this compound, it was evaluated against a panel of tyrosine kinase enzymes. Mechanistically, it successfully and selectively inhibited HDAC6, HDAC8, and EGFR with IC50 = 0.41 ± 0.015, 0.61 ± 0.027, and 0.09 ± 0.004 µM, respectively. Furthermore, the selected derivative induced apoptosis via the mitochondrial apoptotic pathway by raising the Bax/Bcl-2 ratio and activating caspases 3, 7, and 9. Also, the flow cytometry analysis of RPMI-8226 cells showed that the trimethoxy-substituted analog produced cell cycle arrest in the G1 and S phases at 55.82%. Finally, an in silico study was performed to explore the binding interaction of the most active compound within the zinc-containing binding site of HDAC6 and HDAC8.
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Affiliation(s)
- Mostafa A Mansour
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Nahda University in Beni-Suef (NUB), Beni-Suef, Egypt
| | - Asmaa M AboulMagd
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Nahda University in Beni-Suef (NUB), Beni-Suef, Egypt
| | - Samar H Abbas
- Medicinal Chemistry Department, Faculty of Pharmacy, Minia University, Minia, Egypt
| | - Mohamed Abdel-Aziz
- Medicinal Chemistry Department, Faculty of Pharmacy, Minia University, Minia, Egypt
| | - Hamdy M Abdel-Rahman
- Medicinal Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut, Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Badr University in Assiut (BUA), Assiut, Egypt
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2
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AbdelSamad AL, El-Saadi MT, Gouda AM, AboulMagd AM. Pyrrolizine/indolizine-bearing (un)substituted isoindole moiety: design, synthesis, antiproliferative and MDR reversal activities, and in silico studies. RSC Adv 2023; 13:30753-30770. [PMID: 37869384 PMCID: PMC10587743 DOI: 10.1039/d3ra05310e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 10/08/2023] [Indexed: 10/24/2023] Open
Abstract
Two new series of pyrrolizine/indolizine derivative-bearing (un)substituted isoindole moiety were designed and synthesized. The anticancer potential of the new compounds was evaluated against hepatocellular carcinoma (HepG-2), colorectal carcinoma, colon cancer (HCT-116), and breast cancer (MCF-7) cell lines. Compounds 6d and 6o were the most potent derivatives with IC50 values ranging from 6.02 to 13.87 μM against HePG-2, HCT-116, and MCF-7 cell lines. Moreover, methyl analog of the fluoro-substituted indolizine derivative 6m revealed significant antiproliferative activity against HePG-2, HCT-116, and MCF-7 cancer cell lines with IC50 values of 11.97, 28.37, and 19.87 μM, respectively. The most active anticancer analogs, 6d, 6m, and 6o, were inspected for their putative mechanism of action by estimating their epidermal growth factor receptor (EGFR) and cyclin-dependent kinase (CDK 2) inhibitory activities. Thus, compound 6o displayed the most inhibitory activity against EGFR and CDK 2 with IC50 values of 62 and 118 nM, respectively. Additionally, the quantitative real-time PCR analysis for the P-glycoprotein effect of compounds 6d, 6m, and 6o was performed, in which compound 6o illustrated significant down-regulation of P-gp against the HepG-2 cell line by 0.2732 fold. Mechanistic studies for the most active compounds involving the reversal doxorubicin (DOX) effect of compounds 6d, 6m, and 6o were performed, which illustrated cytotoxic activity with IC50 22.27, 3.88, and 8.79 μM, respectively. Moreover, the apoptotic activity of the most active derivative 6o on HCT-116 cancer cells showed accumulation in the G1 and S phases of the cell cycle.
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Affiliation(s)
- Amr L AbdelSamad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Nahda University in Beni-Suef (NUB) Beni-Suef 62513 Egypt
| | - Mohammed T El-Saadi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Beni-Suef University Beni-Suef 62514 Egypt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Sinai University-Kantra Branch Ismailia Egypt
| | - Ahmed M Gouda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Beni-Suef University Beni-Suef 62514 Egypt
| | - Asmaa M AboulMagd
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Nahda University in Beni-Suef (NUB) Beni-Suef 62513 Egypt
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3
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Ahmed HS, Abouzeid H, Mansour MA, Owis AI, Amin E, Darwish HW, Alanazi AS, Naguib IA, Afifi N. Antioxidant and Anti-Aging Phytoconstituents from Faucaria tuberculosa: In Vitro and In Silico Studies. Molecules 2023; 28:6895. [PMID: 37836738 PMCID: PMC10574154 DOI: 10.3390/molecules28196895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
Research targeting natural cosmeceuticals is now increasing due to the safety and/or limited side effects of natural products that are highly valued in cosmetology. Within a research program exploring botanical sources for valuable skincare antioxidant components, the current study investigated the phytochemical content and the biological potential of Faucaria tuberculosa. Phytochemical investigation of F. tuberculosa extract resulted in purification and characterization of six phytoconstituents, including a new one. The structure of the new constituent was elucidated as (-) catechin-(2→1',4→2')-phloroglucinol (4). The structural identity of all isolated compounds were confirmed on the basis of extensive physical and spectral (1D, 2D-NMR and HRESIMS) investigations. The ethanolic extract exhibits a rich content of total phenolics (TPC) and total flavonoids (TFC), estimated as 32 ± 0.034 mg GAE/g and 43 ± 0.004 mg RE/g, respectively. In addition, the antioxidant (ABTS and FRAP), antihyaluronidase and antityrosinase activities of all purified phytoconstituents were evaluated. The results noted (-) catechin-(2→1',4→2') phloroglucinol (4) and phloroglucinol (1) for their remarkable antioxidant activity, while isorhamnetin 3-O-rutinoside (3) and 3,5-dihydroxyphenyl β-D-glucopyranoside (2) achieved the most potent inhibitory activity against tyrosinase (IC50 22.09 ± 0.7 µM and 29.96 ± 0.44 µM, respectively) and hyaluronidase enzymes (IC50 49.30 ± 1.57 µM and 62.58 ± 0.92, respectively) that remarkably exceeds the activity of the standard drugs kojic acid (IC50 = 65.21 ± 0.47 µM) and luteolin, (IC50 = 116.16 ± 1.69 µM), respectively. A molecular docking study of the two active compounds (3 and 2) highlighted their high potential to bind to the active sites of the two enzymes involved in the study.
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Affiliation(s)
- Hayam S. Ahmed
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt (A.I.O.)
| | - Hala Abouzeid
- Department of Pharmacognosy, Faculty of Pharmacy, Port Said University, Port Said 42515, Egypt
| | - Mostafa A. Mansour
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Nahda University, Beni-Suef 62521, Egypt
| | - Asmaa I. Owis
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt (A.I.O.)
- Department of Pharmacognosy, Faculty of Pharmacy, Heliopolis University for Sustainable Development, Cairo 11785, Egypt
| | - Elham Amin
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt (A.I.O.)
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Qassim University, Buraydah 51452, Saudi Arabia
| | - Hany W. Darwish
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ashwag S. Alanazi
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Ibrahim A. Naguib
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Naglaa Afifi
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt (A.I.O.)
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4
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Manikanttha M, Deepti K, Tej MB, Tej MB, Gopi Reddy A, Kapavarapu R, Barange DK, V Basaveswara Rao M, Pal M. Ultrasound assisted Cu-catalyzed Ullmann-Goldberg type coupling-cyclization in a single pot: Synthesis and in silico evaluation of 11 H-pyrido[2,1- b]quinazolin-11-ones against SARS-CoV-2 RdRp. J Mol Struct 2023; 1280:135044. [PMID: 36743447 PMCID: PMC9884102 DOI: 10.1016/j.molstruc.2023.135044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/13/2023] [Accepted: 01/26/2023] [Indexed: 01/30/2023]
Abstract
The in silico evaluation of 11H-pyrido[2,1-b]quinazolin-11-one derivatives against SARS-CoV-2 RdRp was undertaken based on the reports on antiviral activities of this class of compounds in addition to the promising interactions of the antiviral drug penciclovir as well as quinazoline derivatives with SARS-CoV-2 RdRp in silico. The target compounds were prepared via an Ullmann-Goldberg type coupling followed by the subsequent cyclization (involving amidation) in a single pot. The methodology involved a CuI-catalyzed reaction of 2-iodobenzoate ester with 2-aminopyridine or quinolin-2-amine or thiazol-2-amine under ultrasound to give the expected products in acceptable (51-93%) yields. The molecular interactions of the synthesized 11H-pyrido[2,1-b]quinazolin-11-one derivatives with the SARS-CoV-2 RdRp (PDB: 7AAP) were evaluated in silico. The study suggested that though none of these compounds showed interactions better than penciclovir but the compound 3a and 3n appeared to be comparable along with 3b seemed to be nearly comparable to favipiravir and remdesivir. The compound 3n with the best binding energy (-79.85 Kcal/mol) participated in the H-bond interactions through its OMe group with THR556 as well as ARG624 and via the N-5 atom with the residue SER682. The in silico studies further suggested that majority of the compounds interacted with the main cavity of active site pocket whereas 3h and 3o that showed relatively lower binding energies (-66.06 and -66.28 Kcal/mol) interacted with the shallow cavity underneath the active site of SARS CoV-2 RdRp. The study also revealed that a OMe group was favourable for interaction with respect to its position in the order C-8 > C-1 > C-2. Further, the presence of a fused quinoline ring was tolerated whereas a fused thiazole ring decreased the interaction significantly. The in silico predictions of pharmacokinetic properties of 3a, 3b and 3n indicated that besides the BBB (Blood Brain Barrier) penetration potential these molecules may show a good overall ADME. Overall, the regioisomers 3a, 3b and 3n have emerged as molecules of possible interest in the context of targeting COVID-19.
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Affiliation(s)
- Matta Manikanttha
- Department of Chemistry, Koneru Lakshmaiah Education Foundation, Greenfields, Vaddeswaram, Guntur, Andhra Pradesh 522 502, India
| | - Kolli Deepti
- Department of Chemistry, Koneru Lakshmaiah Education Foundation, Greenfields, Vaddeswaram, Guntur, Andhra Pradesh 522 502, India
| | - Mandava Bhuvan Tej
- Department of Healthcare informatics, Sacred Heart University, 5151 Park Avenue, Fair fields, Connecticut CT06825, USA
| | - Mandava Bhagya Tej
- Department of MBBS, NRI Academi of Medical Sciences, Chinakakani, Guntur, Andhra Pradesh 522503, India
| | - A. Gopi Reddy
- Department of Pharmaceutical Chemistry, SANA College of Pharmacy, Kodad, Telangana, India
| | - Ravikumar Kapavarapu
- Department of Pharmaceutical Chemistry and Phytochemistry, Nirmala College of Pharmacy, Mangalagiri, Andhra Pradesh, India
| | | | - M. V Basaveswara Rao
- Department of Chemistry, Krishna University, Krishna District, Andhra Pradesh, India,Corresponding authors
| | - Manojit Pal
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Hyderabad 500046, India,Corresponding authors
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5
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Shaaban S, Abdou A, Alhamzani AG, Abou-Krisha MM, Al-Qudah MA, Alaasar M, Youssef I, Yousef TA. Synthesis and in Silico Investigation of Organoselenium-Clubbed Schiff Bases as Potential Mpro Inhibitors for the SARS-CoV-2 Replication. Life (Basel) 2023; 13:life13040912. [PMID: 37109441 PMCID: PMC10141725 DOI: 10.3390/life13040912] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 04/03/2023] Open
Abstract
Since the first report of the organoselenium compound, ebselen, as a potent inhibitor of the SARS-CoV-2 Mpro main protease by Z. Jin et al. (Nature, 2020), different OSe analogs have been developed and evaluated for their anti-COVID-19 activities. Herein, organoselenium-clubbed Schiff bases were synthesized in good yields (up to 87%) and characterized using different spectroscopic techniques. Their geometries were studied by DFT using the B3LYP/6–311 (d, p) approach. Ten FDA-approved drugs targeting COVID-19 were used as model pharmacophores to interpret the binding requirements of COVID-19 inhibitors. The antiviral efficiency of the novel organoselenium compounds was assessed by molecular docking against the 6LU7 protein to investigate their possible interactions. Our results showed that the COVID-19 primary protease bound to organoselenium ligands with high binding energy scores ranging from −8.19 to −7.33 Kcal/mol for 4c and 4a to −6.10 to −6.20 Kcal/mol for 6b and 6a. Furthermore, the docking data showed that 4c and 4a are good Mpro inhibitors. Moreover, the drug-likeness studies, including Lipinski’s rule and ADMET properties, were also assessed. Interestingly, the organoselenium candidates manifested solid pharmacokinetic qualities in the ADMET studies. Overall, the results demonstrated that the organoselenium-based Schiff bases might serve as possible drugs for the COVID-19 epidemic.
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Ang D, Kendall R, Atamian HS. Virtual and In Vitro Screening of Natural Products Identifies Indole and Benzene Derivatives as Inhibitors of SARS-CoV-2 Main Protease (M pro). Biology (Basel) 2023; 12:biology12040519. [PMID: 37106720 PMCID: PMC10135783 DOI: 10.3390/biology12040519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/25/2023] [Accepted: 03/26/2023] [Indexed: 04/29/2023]
Abstract
The rapid spread of the coronavirus disease 2019 (COVID-19) resulted in serious health, social, and economic consequences. While the development of effective vaccines substantially reduced the severity of symptoms and the associated deaths, we still urgently need effective drugs to further reduce the number of casualties associated with SARS-CoV-2 infections. Machine learning methods both improved and sped up all the different stages of the drug discovery processes by performing complex analyses with enormous datasets. Natural products (NPs) have been used for treating diseases and infections for thousands of years and represent a valuable resource for drug discovery when combined with the current computation advancements. Here, a dataset of 406,747 unique NPs was screened against the SARS-CoV-2 main protease (Mpro) crystal structure (6lu7) using a combination of ligand- and structural-based virtual screening. Based on 1) the predicted binding affinities of the NPs to the Mpro, 2) the types and number of interactions with the Mpro amino acids that are critical for its function, and 3) the desirable pharmacokinetic properties of the NPs, we identified the top 20 candidates that could potentially inhibit the Mpro protease function. A total of 7 of the 20 top candidates were subjected to in vitro protease inhibition assay and 4 of them (4/7; 57%), including two beta carbolines, one N-alkyl indole, and one Benzoic acid ester, had significant inhibitory activity against Mpro protease. These four NPs could be developed further for the treatment of COVID-19 symptoms.
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Affiliation(s)
- Dony Ang
- Computational and Data Sciences Program, Chapman University, Orange, CA 92866, USA
- Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
| | - Riley Kendall
- Computational and Data Sciences Program, Chapman University, Orange, CA 92866, USA
- Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
| | - Hagop S Atamian
- Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
- Biological Sciences Program, Chapman University, Orange, CA 92866, USA
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Bhat D, Spoorthy L, Sharanya R, Siddesh M, Mahesha, Kumar AU, Lokanath N. Influence of hydroxyl group in stabilizing the Schiff base crystal structure: Crystal structure, computational and molecular docking studies. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Fayyazi N, Mostashari-Rad T, Ghasemi JB, Ardakani MM, Kobarfard F. Molecular dynamics simulation, 3D-pharmacophore and scaffold hopping analysis in the design of multi-target drugs to inhibit potential targets of COVID-19. J Biomol Struct Dyn 2022; 40:11787-11808. [PMID: 34405765 DOI: 10.1080/07391102.2021.1965914] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
SARS-CoV-2 has posed serious threat to the health and has inflicted huge costs in the world. Discovering potent compounds is a critical step to inhibit coronavirus. 3CLpro and RdRp are the most conserved targets associated with COVID-19. In this study, three-dimensional pharmacophore modeling, scaffold hopping, molecular docking, structure-based virtual screening, QSAR-based ADMET predictions and molecular dynamics analysis were used to identify inhibitors for these targets. Binding free energies estimated by molecular docking for each ligand in different binding sites of RdRp were used to predict the active site. Previously reported active 3CLpro and RdRp inhibitors were used to build a pharmacophore model to develop different scaffolds. Structure-based simulations and pharmacophore modeling based on Hip Hop algorithm converged in a state that suggest hydrogen bond acceptor and donor features have a critical role in the two binding sites. Further validations indicated that the best pharmacophore model has fairly good correlation values compared with approved inhibitors. Structure-based simulation results approved that GLu166 and Gln189 in 3CLpro and Lys551 and Glu811 in RdRp, are critical residues for dual activities. Ten compounds were extracted from pharmacophore-based virtual screening in six databases. The results, gained by repurposing approach, suggest the effectiveness of these ten compounds with different scaffolds as possible inhibitors of the two targets. Some quinoline-based hybrid derivatives also were designed. QSAR descriptors plot predicted that the scaffolds have had accepted pharmacokinetic profiles. Multiple molecular dynamics simulations in 100 ns and MM/PBSA studies of some reference inhibitors and the novel compounds in complex with both targets demonstrated stable complexes and confirmed the interaction modes. Based on different computational methods, COVID-19 multi-target inhibitors are proposed. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Neda Fayyazi
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan, Iran.,Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tahereh Mostashari-Rad
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan, Iran.,Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jahan B Ghasemi
- College of Sciences, Faculty of Chemistry, University of Tehran, Tehran, Iran
| | - Mehran Mirabzadeh Ardakani
- Department of Traditional Pharmacy, Faculty of Pharmacy, Tehran University of Medical Science, Tehran, Iran
| | - Farzad Kobarfard
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Medicinal Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Bayoumi NA, El-Shehry MF. Pyrazole derivatives as potent EGFR inhibitors: synthesis, biological evaluation and in silico and biodistribution study. Future Med Chem 2022; 14:1755-69. [PMID: 36524436 DOI: 10.4155/fmc-2022-0242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Aim: Synthesis of pyrazole derivatives as EGFR inhibitors. Materials & methods: Cytotoxicity and EGFR inhibitory effect were evaluated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide and EGFR kits, respectively. The biodistribution of radioiodinated compound nanoparticles in tumor-bearing mice was studied. Results: The IC50 values of compound 4a against HepG2 cells and EGFR were 0.15 ± 0.03 and 0.31 ± 0.008 μM, respectively, while those of erlotinib were 0.73 ± 0.04 and 0.11 ± 0.008 μM, respectively. The binding scores of compound 4a and erlotinib to EGFR were -9.52 and -10.23 Kcal/mol, respectively. The maximum tumor uptake of radioiodinated compound after intravenous nanoparticle injection was 6.7 ± 0.3% radioactivity/g. Conclusion: Compound 4a is a promising antitumor agent with a potential EGFR inhibitory effect.
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Borg H, Belal F, Draz ME. Facile fabrication of a portable PANI-NFs/c-MWCNT nano-composite electrochemical sensor for gefitinib: application to human plasma. Anal Methods 2022; 14:4721-4729. [PMID: 36354173 DOI: 10.1039/d2ay01426b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
A novel potentiometric solid contact (SC) sensor was developed to determine the anticancer drug gefitinib by employing a polyaniline nanofibers/carboxylated multi-walled carbon nanotube (PANI-NFs/c-MWCNT) nano-composite as an ion to electron transducer. The FDA approved gefitinib as the first line treatment of non-small cell lung cancer (NSCLC) that represents 90% of lung carcinomas. The PANI-NFs/C-MWCNT nano-composite was synthesized and characterized using Fourier transform infrared spectroscopy (FTIR) and transmission electron microscopy (TEM). Twenty-three polyvinyl chloride (PVC) based sensors were fabricated through a systematic approach using different plasticizers and cationic exchangers to investigate their effects on the performance of the developed sensors. The incorporation of calix[8]arene (CX-8) notably enhanced the sensitivity of the developed sensor, confirmed by the docking study. The optimized sensor attained a fast and stable Nernstian slope of 29.14 mV per decade over the concentration range from 1.0 × 10-2 to 1.5 × 10-6 M with a LOD of 1.0 × 10-6 M. The proposed method represents the first potentiometric sensor for GEF assay according to the authors' knowledge. It was validated as per the IUPAC guidelines and efficiently applied to determine GEF in its tablets and human plasma. This encourages quality control, bioavailability, and clinical centers to utilize the portable GEF sensor in its routine analysis.
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Affiliation(s)
- Hadir Borg
- Institute of Physical Chemistry and Electrochemistry, Leibniz Universität Hannover, Callinstraße 3A, 30167, Hannover, Germany.
- Laboratory of Nano and Quantum Engineering, Leibniz Universität Hannover, Schneiderberg 39, 30167, Hannover, Germany
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, University of Mansoura, Mansoura, 35516, Egypt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa, Egypt
| | - Fathalla Belal
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, University of Mansoura, Mansoura, 35516, Egypt
| | - Mohammed E Draz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa, Egypt
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11
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Elsamra RMI, Masoud MS, Ramadan AM. Designing metal chelates of halogenated sulfonamide Schiff bases as potent nonplatinum anticancer drugs using spectroscopic, molecular docking and biological studies. Sci Rep 2022; 12:20192. [PMID: 36424449 PMCID: PMC9691640 DOI: 10.1038/s41598-022-24512-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/16/2022] [Indexed: 11/27/2022] Open
Abstract
In this contribution, five Ni(II) complexes have been synthesized from sulfonamide-based Schiff bases (SB1-SB5) that comprise bromo or iodo substituents in the salicylidene moiety. The chemical structures of these compounds were extensively elucidated by different analytical and physicochemical studies. All ligands act as bidentate chelators with ON binding mode yielding octahedral, square planar, or tetrahedral geometries. The phenolic OH at δ 12.80 ppm in the free Schiff base SB2 vanishes in the 1H NMRspectrum of diamagnetic complex [Ni(SB2-H)2] favoring the OH deprotonation prior to the chelation with Ni(II) ion. The appearance of twin molecular ion peaks ([M - 1]+ and [M + 1]+) is due to the presence of bromine isotopes (79Br and 81Br) in the mass spectra of most cases. Also, the thermal decomposition stages of all complexes confirmed their high thermal stability and ended with the formation of NiO residue of mass 6.42% to 14.18%. Besides, antimicrobial activity and cytotoxicity of the ligands and some selected complexes were evaluated. Among the ligands, SB4 showed superior antimicrobial efficacy with MIC values of 0.46, 7.54, and 0.95 µM against B. subtilis, E. coli, and A. fumigatus strains, respectively. The consortium of different substituents as two bromine atoms either at positions 3 and/or 5 on the phenyl ring and a thiazole ring is one of the reasons behind the recorded optimal activity. Moreover, there is a good correlation between the cytotoxicity screening (IC50) and molecular docking simulation outcomes that predicted a strong binding of SB2 (16.0 μM), SB4 (18.8 μM), and SB5 (6.32 μM) to the breast cancer protein (3s7s). Additionally, [Ni(SB4-H)2] (4.33 µM) has nearly fourfold potency in comparison with cisplatin (19.0 μM) against breast carcinoma cells (MCF-7) and is highly recommended as a promising, potent, as well as low-cost non-platinum antiproliferative agent after further drug authorization processes.
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Affiliation(s)
- Rehab M. I. Elsamra
- grid.7155.60000 0001 2260 6941Chemistry Department, Faculty of Science, Alexandria University, P.O. Box 426, Alexandria, 21321 Egypt
| | - Mamdouh S. Masoud
- grid.7155.60000 0001 2260 6941Chemistry Department, Faculty of Science, Alexandria University, P.O. Box 426, Alexandria, 21321 Egypt
| | - Ahmed M. Ramadan
- grid.7155.60000 0001 2260 6941Chemistry Department, Faculty of Science, Alexandria University, P.O. Box 426, Alexandria, 21321 Egypt
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Abdel-Azziz IA, Amin NH, El-Saadi MT, Abdel-Rahman HM. Design, synthesis and mechanistic studies of benzophenones hydrazone derivatives as cathepsin inhibitors. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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13
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Zekeya N, Mamiro B, Ndossi H, Mallya RC, Kilonzo M, Kisingo A, Mtambo M, Kideghesho J, Chilongola J. Screening and evaluation of cytotoxicity and antiviral effects of secondary metabolites from water extracts of Bersama abyssinica against SARS-CoV-2 Delta. BMC Complement Med Ther 2022; 22:280. [PMID: 36289484 PMCID: PMC9598020 DOI: 10.1186/s12906-022-03754-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 10/07/2022] [Indexed: 11/10/2022] Open
Abstract
Background Bersama abyssinica is a common herb in Africa, with diverse medical uses in different areas. The plant is well-known in Tanzania for treating respiratory disorders such as TB, tonsillitis, bronchitis, and asthma, and it has lately been utilized to treat COVID-19 symptoms. Water extract of leaf and stem bark has been registered as an herbal medication known as 'Coviba Dawa' in Tanzania for the relief of bacterial respiratory infections. The extracts, however, have not been scientifically tested for their anti-viral activities. The aim of this work was to test for the cytotoxicity and antiviral effects of bioactive ingredients from B. abyssinica extracts against the Delta variant of the SARS-CoV-2 coronavirus. Methods B. abyssinica leaves and stem bark were dried under shade in room temperature and then pulverized to obtain small pieces before soaking into different solvents. One hundred grams of each, leaves and stem bark, were extracted in petroleum ether, dichloromethane, ethyl acetate and methanol. Water extract was obtained by decoction of stem bark and leaves into water. Phenols, flavonoids, tannins, and antioxidants were confirmed as components of the extracts. Analysis of polar extracts of bark stem bark and leaves was done. Antiviral screening and cytotoxicity experiments were conducted in a Biosafety Level 3 (BSL-3) Laboratory facility according to International Standard Operating Procedures (SOPs). Results By the use of LC–MS/MS analysis, this study confirmed the existence of four phenolic compounds in B. abyssinica water extract; 2,4-di-tert-butylphenol, 4-formyl-2-methoxyphenyl propionate, 7,8-Dihydroxy-4-methylcoumarin, and 2,3, 6-trimethoxyflavone with antioxidant activity. This study showed that, while the water extracts of B. abyssinica had significant antiviral activity against SARS Cov2 virus, it showed no cytotoxicity effect on Vero E6 cells. In particular, the water extract (Coviba dawa) showed 75% while ethylacetate fraction of B. abyssinica leaves showed a 50% in vitro viral inhibition, indicating that these substances may be useful for the development of future anti-viral agents. Conclusion We therefore recommend isolation of compounds for further profiling and development with a broader concentration range. We further recommend studies that determine the antiviral activity of extracts of B.abyssinica on other viral pathogens of clinical concern. Supplementary Information The online version contains supplementary material available at 10.1186/s12906-022-03754-3.
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Affiliation(s)
- Never Zekeya
- grid.442468.80000 0001 0566 9529Department of Wildlife Management, College of African Wildlife Management, CAWM, P.O. Box 3031, Mweka, Moshi, Kilimanjaro Tanzania
| | - Bertha Mamiro
- grid.463666.70000 0001 0358 5436Tanzania Industrial Research and Development Organization (TIRDO), P.O. Box 23235, Msasani, Dar es Salaam, Tanzania
| | - Humphrey Ndossi
- grid.463666.70000 0001 0358 5436Tanzania Industrial Research and Development Organization (TIRDO), P.O. Box 23235, Msasani, Dar es Salaam, Tanzania
| | - Rehema Chande Mallya
- grid.25867.3e0000 0001 1481 7466School of Pharmacy and Pharmacognosy, Muhimbili University of Health and Allied Sciences, P.O. Box 65014, Dar es salaam, Tanzania
| | - Mhuji Kilonzo
- grid.442459.a0000 0001 1998 2954University of Dodoma, Dodoma, Tanzania
| | - Alex Kisingo
- grid.442468.80000 0001 0566 9529Department of Wildlife Management, College of African Wildlife Management, CAWM, P.O. Box 3031, Mweka, Moshi, Kilimanjaro Tanzania
| | - Mkumbukwa Mtambo
- grid.463666.70000 0001 0358 5436Tanzania Industrial Research and Development Organization (TIRDO), P.O. Box 23235, Msasani, Dar es Salaam, Tanzania
| | - Jafari Kideghesho
- grid.442468.80000 0001 0566 9529Department of Wildlife Management, College of African Wildlife Management, CAWM, P.O. Box 3031, Mweka, Moshi, Kilimanjaro Tanzania
| | - Jaffu Chilongola
- grid.412898.e0000 0004 0648 0439Kilimanjaro Christian Medical University College, P.O. Box 2240, Moshi, Kilimanjaro Tanzania
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Parvarinezhad S, Salehi M, Kubicki M, Eshaghi Malekshah R. Experimental and theoretical studies of new Co (III) complexes of hydrazide derivatives proposed as multi‐target inhibitors of SARS‐COV‐2. Appl Organomet Chem 2022; 36:e6836. [PMID: 35945928 PMCID: PMC9353290 DOI: 10.1002/aoc.6836] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 07/04/2022] [Accepted: 07/15/2022] [Indexed: 11/06/2022]
Affiliation(s)
| | - Mehdi Salehi
- Department of Chemistry, Faculty of Science Semnan University Semnan Iran
| | - Maciej Kubicki
- Department of Chemistry Adam Mickiewicz University Poznan Poland
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Abdizadeh R, Hadizadeh F, Abdizadeh T. Evaluation of apigenin-based biflavonoid derivatives as potential therapeutic agents against viral protease (3CLpro) of SARS-CoV-2 via molecular docking, molecular dynamics and quantum mechanics studies. J Biomol Struct Dyn 2022:1-31. [PMID: 35848354 DOI: 10.1080/07391102.2022.2098821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the causative agent of the pandemic COVID-19 disease that affects human respiratory function. Despite the scientific progression made in the development of the vaccine, there is an urgent need for the discovery of antiviral drugs for better performance at different stages of SARS-CoV-2 reproduction. The main protease (Mpro or 3CLpro) plays a pivotal role in the life cycle of the virus, making it an attractive target for the development of antiviral agents effective against the new strains of coronaviruses (CoVs). In this study, a series of apigenin-based natural biflavonoid derivatives as potential inhibitors of coronaviruses 3CLpro was investigated by in silico approaches. For this purpose, the molecular docking was performed to analyze the interaction of the natural biflavonoids with SARS-Cov-2 main protease and for further investigation, docking to the 3CLpro of SARS-CoV and MERS-CoV. Based on docking scores and comparison with the reference inhibitors (ritonavir and lopinavir), more than half of the biflavonoids had strong interactions with the residues of the binding pocket of the coronaviruses 3CLpro and exhibited better binding affinities toward the main protease than ritonavir and lopinavir. The top biflavonoids were further explored through molecular dynamics simulation, binding free energy calculation and residual energy contributions estimated by the MM-PBSA. Also, drug likeness property investigation by Swiss ADME tools and density functional theory (DFT) calculations were performed. The results confirmed that the 3CLpro-amentoflavone, 3CLpro-bilobetin, 3CLpro-ginkgetin, and 3CLpro-sotetsuflavone complexes possess a large amount of dynamic properties such as high stability, significant binding energy and fewer conformation fluctuations. Also, the pharmacokinetics and drug-likeness studies and HOMO-LUMO and DFT descriptor values indicated a promising result of the selected natural biflavonoids. Overall findings indicate that the apigenin-based biflavonoids may inhibit COVID-19 by significant interactions in the binding pocket and those results can pave the way in drug discovery although the effectiveness of these bioactive compounds should be further validated by in-vitro and in-vivo investigations. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rahman Abdizadeh
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Farzin Hadizadeh
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Tooba Abdizadeh
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
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16
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Ramasamy S, Rajan AT. Unraveling the Pharmaceutical Benefits of Freshly Prepared Amino Acid-Based Schiff Bases Via DFT, In Silico Molecular Docking and ADMET. J Fluoresc 2022. [PMID: 35749028 DOI: 10.1007/s10895-022-02987-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 05/31/2022] [Indexed: 10/17/2022]
Abstract
A series of amino acid-based Schiff bases have been synthesized using a facile condensation between benzil (a diketone) and amino acid in the presence of a base. The formation of Schiff base compounds has been ensured by elemental analysis, FT-IR, 1H-NMR, 13C-NMR and UV-Vis. spectra. Density Functional Theory (DFT) calculations have been explored in order to get intuition into the molecular structure and chemical reactivity of the compounds. The DFT, optimized structure of the compounds, has been used to attain the molecular docking studies with DNA structure to find the favorable mode of interaction. In silico ADME/Tox profile of the compounds has been predicted using pkCSM web tools, exhibiting suitable values of absorption, distribution, and metabolism. These obtained parameters are connected to bioavailability. In addition, toxicity, skin sensitization and cardiotoxicity (hERG) analysis have been performed for evaluating the drug-like character of the prepared Schiff bases. The findings obtained from this study may find applications in the field focusing on the production of efficient and harmless pharmacological drugs.
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17
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El-Sayed NNE, Almaneai NM, Ben Bacha A, El-Ashrey MK, Al-Zaben MI, Almarhoon ZM. Biological Evaluation, Molecular Docking Analyses, and ADME Profiling of Certain New Quinazolinones as Anti-colorectal Agents. ACS Omega 2022; 7:18443-18458. [PMID: 35694504 PMCID: PMC9178606 DOI: 10.1021/acsomega.2c00812] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Colorectal carcinogenesis is a complex process, which is linked to dysregulation of human secretory phospholipases A2 (hsPLA2-G-IIA, hsPLA2-G-V, and hsPLA2-G-X), proteases (cathepsin-B, collagenase, thrombin, elastase, and trypsin), carbohydrate hydrolyzing enzymes (α-amylase and α-glucosidase), and free radical generating enzyme (xanthine oxidoreductase (XOR)). Therefore, some new quinazolinones were synthesized and evaluated as inhibitors against this array of enzymes as well as cytotoxic agents on LoVo and HCT-116 cells of colorectal cancer. Compounds 3g, 10, 8, 3c, and 1c exhibited promising cytotoxic effects with IC50 values ranging from 206.07 to 459.79 μM. Nine compounds showed promising enzymatic inhibitory effects, 3b, 3d, 3f, 5, 1a, and 12 (α-amylase), 8 (thrombin, elastase and trypsin), 10 (hsPLA2-G-IIA and hsPLA2-G-V), and 3f (α-glucosidase and XOR). Therefore, the most active inhibitors, were subjected to validated molecular docking studies to identify their affinities and binding modes. The expected physicochemical and pharmacokinetic features of the active candidates, 1a, 1c, 3b, 3c, 3d, 3f, 3g, 5, 8, 10, and 12 were predicted using bioavailability radar charts and boiled-egg graphical representations along with the Lipinski rule of five filter. Collectively, these studies showed the significance of derivatives 1c, 3b, 3c, 3d, 8, 10, and 12 as lead scaffolds for further optimization to develop enzymes inhibitors and anti-colorectal agents.
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Affiliation(s)
- Nahed N. E. El-Sayed
- National
Organization for Drug Control and Research, Egyptian Drug Authority, 51 Wezaret El-Zerra Street, Giza 35521, Egypt
| | - Norah M. Almaneai
- Department
of Chemistry, College of Science, King Saud
University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abir Ben Bacha
- Biochemistry
Department, College of Science, King Saud
University, P. O. Box 22452, Riyadh 11495, Saudi Arabia
- Laboratory
of Plant Biotechnology Applied to Crop Improvement, Faculty of Science
of Sfax, University of Sfax, Sfax 3038, Tunisia
| | - Mohamed K. El-Ashrey
- Pharmaceutical
Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr Elini Street, Cairo 11562, Egypt
- Medicinal
Chemistry Department, Faculty of Pharmacy, King Salman International University, Ras-Sedr, South Sinai, Egypt
| | - Maha I. Al-Zaben
- Department
of Chemistry, College of Science, King Saud
University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Zainab M. Almarhoon
- Department
of Chemistry, College of Science, King Saud
University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
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Mohamed HS, Amin NH, El-saadi MT, Abdel-rahman HM. Design, synthesis, biological assessment, and in-Silico studies of 1,2,4-triazolo[1,5-a]pyrimidine derivatives as tubulin polymerization inhibitors. Bioorg Chem 2022; 121:105687. [DOI: 10.1016/j.bioorg.2022.105687] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/10/2022] [Accepted: 02/13/2022] [Indexed: 12/20/2022]
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El-hawary SS, Mohammed R, Taher MA, Abouzid SF, Mansour MA, Almahmoud SA, Huwaimel B, Amin E. Characterization of Promising Cytotoxic Metabolites from Tabebuia guayacan Hemsl.: Computational Prediction and In Vitro Testing. Plants 2022; 11:888. [PMID: 35406868 PMCID: PMC9002841 DOI: 10.3390/plants11070888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/15/2022] [Accepted: 03/21/2022] [Indexed: 11/16/2022]
Abstract
Genus Tabebuia is famous for its traditional uses and valuable phytoconstituents. Our previous investigation of Tabebuia species noted the promising anticancer activity of T. guayacan Hemsl. leaves extract, however, the mechanism underlying the observed anticancer activity is still unexplored. The current research was designed to explore the phytochemical content as well as to address the phytoconstituent(s) responsible for the recorded anticancer activity. Accordingly, sixteen compounds were isolated, and their structures were elucidated using different spectroscopic techniques. The drug-likeness of the isolated compounds, as well as their binding affinity with four anticancer drug target receptors: CDK-2/6, topoisomerase-1, and VEGFR-2, were evaluated. Additionally, the most promising compounds were in vitro evaluated for inhibitory activities against CDK-2/6 and VEGFR-2 enzymes using kinase assays method. Corosolic acid (3) and luteolin-7-O-β-glucoside (16) were the most active inhibitors against CDK-2 (−13.44 kcal/mol) and topoisomerase 1 (−13.83 kcal/mol), respectively. Meanwhile, quercetin 3-O-β-xyloside (10) scored the highest binding free energies against both CDK-6 (−16.23 kcal/mol) as well as against VEGFR-2 protein targets (−10.39 kcal/mol). Molecular dynamic simulation indicated that quercetin 3-O-β-xyloside (10) exhibited the least fluctuations and deviations from the starting binding pose with RMSD (2.6 Å). Interestingly, in vitro testing results confirmed the potent activity of 10 (IC50 = 0.154 µg/mL) compared to IC50 = 0.159 µg/mL of the reference drug ribociclib. These findings suggest the three noted compounds (3, 10, and 16) for further in vivo anticancer studies.
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Iacopetta D, Ceramella J, Catalano A, Saturnino C, Pellegrino M, Mariconda A, Longo P, Sinicropi MS, Aquaro S. COVID-19 at a Glance: An Up-to-Date Overview on Variants, Drug Design and Therapies. Viruses 2022; 14:v14030573. [PMID: 35336980 PMCID: PMC8950852 DOI: 10.3390/v14030573] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 02/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a member of the Coronavirus family which caused the worldwide pandemic of human respiratory illness coronavirus disease 2019 (COVID-19). Presumably emerging at the end of 2019, it poses a severe threat to public health and safety, with a high incidence of transmission, predominately through aerosols and/or direct contact with infected surfaces. In 2020, the search for vaccines began, leading to the obtaining of, to date, about twenty COVID-19 vaccines approved for use in at least one country. However, COVID-19 continues to spread and new genetic mutations and variants have been discovered, requiring pharmacological treatments. The most common therapies for COVID-19 are represented by antiviral and antimalarial agents, antibiotics, immunomodulators, angiotensin II receptor blockers, bradykinin B2 receptor antagonists and corticosteroids. In addition, nutraceuticals, vitamins D and C, omega-3 fatty acids and probiotics are under study. Finally, drug repositioning, which concerns the investigation of existing drugs for new therapeutic target indications, has been widely proposed in the literature for COVID-19 therapies. Considering the importance of this ongoing global public health emergency, this review aims to offer a synthetic up-to-date overview regarding diagnoses, variants and vaccines for COVID-19, with particular attention paid to the adopted treatments.
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Affiliation(s)
- Domenico Iacopetta
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy; (D.I.); (J.C.); (M.P.); (M.S.S.); (S.A.)
| | - Jessica Ceramella
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy; (D.I.); (J.C.); (M.P.); (M.S.S.); (S.A.)
| | - Alessia Catalano
- Department of Pharmacy-Drug Sciences, University of Bari “Aldo Moro”, 70126 Bari, Italy
- Correspondence: ; Tel.: +39-0805442746
| | - Carmela Saturnino
- Department of Science, University of Basilicata, 85100 Potenza, Italy; (C.S.); (A.M.)
| | - Michele Pellegrino
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy; (D.I.); (J.C.); (M.P.); (M.S.S.); (S.A.)
| | - Annaluisa Mariconda
- Department of Science, University of Basilicata, 85100 Potenza, Italy; (C.S.); (A.M.)
| | - Pasquale Longo
- Department of Chemistry and Biology, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy;
| | - Maria Stefania Sinicropi
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy; (D.I.); (J.C.); (M.P.); (M.S.S.); (S.A.)
| | - Stefano Aquaro
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy; (D.I.); (J.C.); (M.P.); (M.S.S.); (S.A.)
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Haribabu J, Garisetti V, Malekshah RE, Srividya S, Gayathri D, Bhuvanesh N, Mangalaraja RV, Echeverria C, Karvembu R. Design and synthesis of heterocyclic azole based bioactive compounds: Molecular structures, quantum simulation, and mechanistic studies through docking as multi-target inhibitors of SARS-CoV-2 and cytotoxicity. J Mol Struct 2022; 1250:131782. [PMID: 34697505 PMCID: PMC8528790 DOI: 10.1016/j.molstruc.2021.131782] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/16/2021] [Accepted: 10/19/2021] [Indexed: 01/04/2023]
Abstract
Two heterocyclic azole compounds, 3-(2,3-dihydrobenzo[d]thiazol-2-yl)-4H-chromen-4-one (SVS1) and 5-(1H-indol-3-yl)-4-methyl-2,4-dihydro-3H-1,2,4-triazole-3-thione (SVS2) were obtained unexpectedly from 2-aminothiophenol and 4-oxo-4H-chromene-3-carbaldehyde (for SVS1), and (E)-2-((1H-indol-3-yl)methylene)-N-methylhydrazine-1-carbothioamide in the presence of anhydrous FeCl3 (for SVS2), respectively. The compounds were well characterized by analytical and spectroscopic tools. The molecular structures of both the compounds were determined by single crystal X-ray diffraction (XRD) study. The results obtained from density functional theory (DFT) study revealed the molecular geometry and electron distribution of the compounds, which were correlated well with the three-dimensional structures obtained from the single crystal XRD. DMol3 was used to calculate quantum chemical parameters [chemical potential (µ), global hardness (η), global softness (σ), absolute electronegativity (χ) and electrophilicity index (ω)] of SVS1 and SVS2. Molecular docking study was performed to elucidate the binding ability of SVS1 and SVS2 with SARS-CoV-2 main protease and human angiotensin-converting enzyme-2 (ACE-2) molecular targets. Interestingly, the binding efficiency of the compounds with the molecular targets was comparable with that of remdesivir (SARS-CoV-2), chloroquine and hydroxychloroquine. SVS1 showed better docking energy than SVS2. The molecular docking study was complemented by molecular dynamics simulation study of SARS-CoV-2 main protease-SVS1 complex, which further exemplified the binding ability of SVS1 with the target. In addition, SVS1, SVS2 and cisplatin were assessed for their cytotoxicity against a panel of three human cancer cells such as HepG-2 (hepatic carcinoma), T24 (bladder) and EA.hy926 (endothelial), as well as Vero (kidney epithelial cells extracted from an African green monkey) normal cells using MTT assay. The results showed that SVS2 has significant cytotoxicity against HepG-2 and EA.hy926 cells with the IC50 values of 33.8 μM (IC50 = 49.9 μM-cisplatin and 8.6 μM-doxorubicin) and 29.2 (IC50 = 26.6 μM-cisplatin and 3.8 μM-doxorubicin), respectively.
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Affiliation(s)
- Jebiti Haribabu
- Department of Chemistry, National Institute of Technology, Tiruchirappalli 620015, India,Facultad de Medicina, Universidad de Atacama, Los Carreras 1579, 1532502 Copiapo, Chile
| | - Vasavi Garisetti
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600025, India
| | - Rahime Eshaghi Malekshah
- Medical Biomaterial Research Centre (MBRC), Tehran University of Medical Sciences, Tehran, Iran,Department of Chemistry, Iran University of Science and Technology, Tehran 16846‒13114, Iran
| | - Swaminathan Srividya
- Department of Chemistry, National Institute of Technology, Tiruchirappalli 620015, India
| | - Dasararaju Gayathri
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600025, India
| | - Nattamai Bhuvanesh
- Department of Chemistry, Texas A & M University, College Station, TX 77842, USA
| | - Ramalinga Viswanathan Mangalaraja
- Advanced Ceramics and Nanotechnology Laboratory, Department of Materials Engineering, Faculty of Engineering, University of Concepcion, Concepcion, Chile
| | - Cesar Echeverria
- Facultad de Medicina, Universidad de Atacama, Los Carreras 1579, 1532502 Copiapo, Chile,Corresponding authors
| | - Ramasamy Karvembu
- Department of Chemistry, National Institute of Technology, Tiruchirappalli 620015, India,Corresponding authors
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Karthic A, Kesarwani V, Singh RK, Yadav PK, Chaturvedi N, Chauhan P, Yadav BS, Kushwaha SK. Computational Analysis Reveals Monomethylated Triazolopyrimidine as a Novel Inhibitor of SARS-CoV-2 RNA-Dependent RNA Polymerase (RdRp). Molecules 2022; 27:801. [PMID: 35164069 DOI: 10.3390/molecules27030801] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/03/2022] [Accepted: 01/07/2022] [Indexed: 01/18/2023] Open
Abstract
The human population is still facing appalling conditions due to several outbreaks of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) virus. The absence of specific drugs, appropriate vaccines for mutants, and knowledge of potential therapeutic agents makes this situation more difficult. Several 1, 2, 4-triazolo [1, 5-a] pyrimidine (TP)-derivative compounds were comprehensively studied for antiviral activities against RNA polymerase of HIV, HCV, and influenza viruses, and showed immense pharmacological interest. Therefore, TP-derivative compounds can be repurposed against the RNA-dependent RNA polymerase (RdRp) protein of SARS-CoV-2. In this study, a meta-analysis was performed to ensure the genomic variability and stability of the SARS-CoV-2 RdRp protein. The molecular docking of natural and synthetic TP compounds to RdRp and molecular dynamic (MD) simulations were performed to analyse the dynamic behaviour of TP compounds at the active site of the RdRp protein. TP compounds were also docked against other non-structural proteins (NSP1, NSP2, NSP3, NSP5, NSP8, NSP13, and NSP15) of SARS-CoV-2. Furthermore, the inhibition potential of TP compounds was compared with Remdesivir and Favipiravir drugs as a positive control. Additionally, TP compounds were analysed for inhibitory activity against SARS-CoV RdRp protein. This study demonstrates that TP analogues (monomethylated triazolopyrimidine and essramycin) represent potential lead molecules for designing an effective inhibitor to control viral replication. Furthermore, in vitro and in vivo studies will strengthen the use of these inhibitors as suitable drug candidates against SARS-CoV-2.
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Abstract
Abstract
The rapid growth and revolution in the area of emerging therapeutics has been able to save the life of millions of patients globally. Besides these developments, the microbes are consistently struggling for their own survival and hence becoming quite more sturdy and incurable to existing drugs. Covid-19 virus and Black Fungus are recent examples of failure of medical preparations and strength of these viruses beyond the imagination of medical practitioners. Henceforth the study has made an extensive survey of exiting literature on heterocyclic schiff bases and their transition metal complexes to look for their potential applicability as antimicrobial agents. The inherent physiognomies of the essential properties of these transition metal complexes including thermodynamic, kinetic and chelating are comparatively modifiable as per requirements. The study has found that the biological applications of these transition metal complexes are well suited to be used as antibacterial and antifungal agents.
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Saeedi S, Rahmati A, Chavoshpour-Natanzi Z. Synthesis of pyrazolo[5′,1′:2,3]imidazo[1,5- c]quinazolin-6(5 H)-ones and molecular docking study of their affinity against the COVID-19 main protease. RSC Adv 2022; 12:19579-19589. [PMID: 35919373 PMCID: PMC9264878 DOI: 10.1039/d2ra03179e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/23/2022] [Indexed: 01/13/2023] Open
Abstract
A novel series of fused pyrazolo[5′,1′:2,3]imidazo[1,5-c]quinazolin-6(5H)-ones were synthesized and their affinity against the COVID-19 main protease was investigated using molecular docking study and compared to that of some used clinical drugs.
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Affiliation(s)
- Shaghayegh Saeedi
- Department of Chemistry, University of Isfahan, P. O. Box 81746-73441, Isfahan, Iran
| | - Abbas Rahmati
- Department of Chemistry, University of Isfahan, P. O. Box 81746-73441, Isfahan, Iran
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Mohan B, Choudhary M. Synthesis, crystal structure, computational study and anti-virus effect of mixed ligand copper (II) complex with ONS donor Schiff base and 1, 10-phenanthroline. J Mol Struct 2021; 1246:131246. [PMID: 34658419 DOI: 10.1016/j.molstruc.2021.131246] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/31/2021] [Accepted: 08/03/2021] [Indexed: 12/16/2022]
Abstract
This work deals with the synthesis, crystal structure, computational study and antiviral potential of mixed ligand copper(II) complex [Cu(L)(phen)](1), (where, H2L = (Z)-N'-((E)-2-hydroxy-3,5-diiodobenzylidene)-N,N-dimethylcarbamohydrazonothioic acid, phen = 1,10-phenanthroline). The Schiff base ligand (H2L) is coordinated with Cu(II) ion in O, N, S-tridentate mode. The copper complex (1) crystallized in the monoclinic system of the space group P21/c with eight molecules in the unit cell and reveals a square pyramidal geometry. Furthermore, we also perform quantum chemical calculations to get insights into the structure-property relationship and functional properties of ligand (H2L) and its copper (II) complex [Cu(L)(phen)](1). Complex [Cu(L)(phen)](1) was also virtually designed in-silico evaluation by Swiss-ADME. Additionally, inspiring by recent developments to find a potential inhibitor for the COVID-19 virus, we have also performed molecular docking study of ligand and its copper complex (1) to see if our compounds shows an affinity for the main protease (Mpro) of COVID-19 spike protein (PDB ID: 7C8U). Interestingly, the results are found quite encouraging where the binding affinity and inhibition constant were found to be -7.14 kcal/mol and 5.82 μM for ligand (H2L) and -6.18 kcal/mol and 0.76 μM for complex [Cu(L)(phen)](1) with Mpro protein. This binding affinity is reasonably well as compared to recently known antiviral drugs. For instance, the binding affinity of ligand and complex was found to be better than docking results of chloroquine (-6.293 kcal/mol), hydroxychloroquine (-5.573 kcal/mol) and remdesivir (-6.352 kcal/mol) with Mpro protein. The present study may offer the technological solutions and potential inhibition to the COVID-19 virus in the ongoing and future challenges of the global community. In the framework of synthesis and characterization of mixed ligand copper (II) complex; the major conclusions can be drawn as follow.
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Lochab A, Thareja R, Gadre SD, Saxena R. Potential Protein and Enzyme Targets for In‐silico Development and Repurposing of Drug Against Coronaviruses. ChemistrySelect 2021. [DOI: 10.1002/slct.202103350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Amit Lochab
- Department of Chemistry Kirori Mal College University of Delhi Delhi India
| | - Rakhi Thareja
- Department of Chemistry St. Stephens College University of Delhi Delhi India
| | - Sangeeta D. Gadre
- Department of Physics Kirori Mal College University of Delhi Delhi India
| | - Reena Saxena
- Department of Chemistry Kirori Mal College University of Delhi Delhi India
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27
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Draz ME, Naguib IA, Saad AS. Computational ionophore selection during optimization of a portable calixarene based sensor for direct assay of levamisole residues in livestock products. J Electroanal Chem (Lausanne) 2021. [DOI: 10.1016/j.jelechem.2021.115546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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28
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Badawy MAS, Abdelall EKA, El-Nahass ES, Abdellatif KRA, Abdel-Rahman HM. Design, synthesis, biological assessment and in silico ADME prediction of new 2-(4-(methylsulfonyl) phenyl) benzimidazoles as selective cyclooxygenase-2 inhibitors. RSC Adv 2021; 11:27659-27673. [PMID: 35480694 PMCID: PMC9037807 DOI: 10.1039/d1ra04756f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 07/30/2021] [Indexed: 11/22/2022] Open
Abstract
A novel series of benzimidazole derivatives wherein 4-(methylsulfonyl) phenyl pharmacophore attached via its C-2 position was designed and synthesized. These compounds were evaluated in vitro as cyclooxygenase-1(COX-1)/cyclooxygenese-2(COX-2) inhibitors. Furthermore, the synthesized compounds were also in vivo evaluated for their anti-inflammatory activity and ulcerogenic liability. Examination of histopathological lesions was also performed to evaluate the cariogenic effect of most active compounds. In silico prediction of physicochemical properties, ADME, and drug-likeness profiles were also studied. Several compounds as 11b, 11k, 12b, and 12d showed selective inhibition to (COX-2) isozyme. Compound 11b showed the most potent (COX-2) inhibitory activity with (IC50 = 0.10 μM) and selectivity index (SI = 134); the tested compounds also have shown good anti-inflammatory activity. Regarding the ulcerogenic liability, compound 11b was also safest one (Ulcer Index) (UI = 0.83). The results of the molecular docking studies is closely related to the results of the in vitro COX-2 inhibitory activities. A novel series of benzimidazole derivatives wherein 4-(methylsulfonyl) phenyl pharmacophore attached via its C-2 position was designed and synthesized.![]()
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Affiliation(s)
- Mohamed A S Badawy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Nahda University (NUB) Beni-Suef 62513 Egypt +2001066394559
| | - Eman K A Abdelall
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Beni-Suef University Beni-Suef 62514 Egypt
| | - El-Shaymaa El-Nahass
- Department of Pathology, Faculty of Veterinary Medicine, Beni-Suef University Beni-Suef 62511 Egypt
| | - Khaled R A Abdellatif
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Beni-Suef University Beni-Suef 62514 Egypt.,Pharmaceutical Sciences Department, IbnSina National College for Medical Studies Jeddah Kingdom of Saudi Arabia
| | - Hamdy M Abdel-Rahman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Nahda University (NUB) Beni-Suef 62513 Egypt +2001066394559.,Department of Medicinal Chemistry, Faculty of Pharmacy, Assiut University Assiut 71526 Egypt
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29
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Ma JT, Wang LS, Chai Z, Chen XF, Tang BC, Chen XL, He C, Wu YD, Wu AX. Access to 2-arylquinazolines via catabolism/reconstruction of amino acids with the insertion of dimethyl sulfoxide. Chem Commun (Camb) 2021; 57:5414-5417. [PMID: 33949486 DOI: 10.1039/d1cc00623a] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quinazoline skeletons are synthesized by amino acid catabolism/reconstruction combined with the insertion/cyclization of dimethyl sulfoxide for the first time. The amino acid acts as a carbon and nitrogen source through HI-mediated catabolism and is then reconstructed using aromatic amines and dimethyl sulfoxide (DMSO) as a one-carbon synthon. This protocol is of great significance for the further study of the conversion of amino acids.
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Affiliation(s)
- Jin-Tian Ma
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - Li-Sheng Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - Zhi Chai
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - Xin-Feng Chen
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - Bo-Cheng Tang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - Xiang-Long Chen
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - Cai He
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - Yan-Dong Wu
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - An-Xin Wu
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
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Patel S, Srivastav AK, Gupta SK, Kumar U, Mahapatra SK, Gajjar PN, Banerjee I. Carbon nanotubes for rapid capturing of SARS-COV-2 virus: revealing a mechanistic aspect of binding based on computational studies. RSC Adv 2021; 11:5785-5800. [PMID: 35423109 PMCID: PMC8694767 DOI: 10.1039/d0ra08888a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/25/2021] [Indexed: 12/15/2022] Open
Abstract
We investigate the binding interactions of synthesized multi-walled carbon nanotubes (MWCNTs) with SARS-CoV-2 virus. Two essential components of the SARS-CoV-2 structure i.e.6LU7 (main protease of SARS-CoV-2) and 6LZG (spike receptor-binding domain complexed with its receptor ACE2) were used for computational studies. MWCNTs of different morphologies (zigzag, armchair and chiral) were synthesized through a thermal chemical vapour deposition process as a function of pyrolysis temperature. A direct correlation between radius to volume ratio of the synthesized MWCNTs and the binding energies for all three (zigzag, armchair and chiral) conformations were observed in our computational studies. Our result suggests that MWCNTs interact with the active sites of the main protease along with the host angiotensin-converting enzyme2 (ACE2) receptors. Furthermore, it is also observed that MWCNTs have significant binding affinities towards SARS-CoV-2. However, the highest free binding energy of -87.09 kcal mol-1 with 6LZG were shown by the armchair MWCNTs with SARS-CoV-2 through the simulated molecular dynamic trajectories, which could alter the SARS-CoV-2 structure with higher accuracy. The radial distribution function also confirms the density variation as a function of distance from a reference particle of MWCNTs for the study of interparticle interactions of the MWCNT and SARS-CoV-2. Due to these interesting attributes, such MWCNTs could find potential application in personal protective equipment (PPE) and diagnostic kits.
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Affiliation(s)
- Shivkumar Patel
- School of Nano Sciences, Central University of Gujarat Gandhinagar 382030 India
| | | | - Sanjeev K Gupta
- Computational Materials and Nanoscience Group, Department of Physics, St. Xavier's College Ahmedabad 380009 India
| | - Umesh Kumar
- School of Nano Sciences, Central University of Gujarat Gandhinagar 382030 India
| | - S K Mahapatra
- Department of Physics, Central University of Punjab Bathinda 151001 India
| | - P N Gajjar
- Department of Physics, University School of Sciences, Gujarat University Ahmedabad 380009 India
| | - I Banerjee
- School of Nano Sciences, Central University of Gujarat Gandhinagar 382030 India
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31
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Tam NM, Nam PC, Quang DT, Tung NT, Vu VV, Ngo ST. Binding of inhibitors to the monomeric and dimeric SARS-CoV-2 Mpro. RSC Adv 2021; 11:2926-2934. [PMID: 35424256 PMCID: PMC8694027 DOI: 10.1039/d0ra09858b] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/04/2021] [Indexed: 11/29/2022] Open
Abstract
SARS-CoV-2 rapidly infects millions of people worldwide since December 2019. There is still no effective treatment for the virus, resulting in the death of more than one million patients. Inhibiting the activity of SARS-CoV-2 main protease (Mpro), 3C-like protease (3CLP), is able to block the viral replication and proliferation. In this context, our study has revealed that in silico screening for inhibitors of SARS-CoV-2 Mpro can be reliably done using the monomeric structure of the Mpro instead of the dimeric one. Docking and fast pulling of ligand (FPL) simulations for both monomeric and dimeric forms correlate well with the corresponding experimental binding affinity data of 24 compounds. The obtained results were also confirmed via binding pose and noncovalent contact analyses. Our study results show that it is possible to speed up computer-aided drug design for SARS-CoV-2 Mpro by focusing on the monomeric form instead of the larger dimeric one.
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Affiliation(s)
- Nguyen Minh Tam
- Computational Chemistry Research Group, Ton Duc Thang University Ho Chi Minh City Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University Ho Chi Minh City Vietnam
| | - Pham Cam Nam
- Department of Chemistry, The University of Danang, University of Science and Technology Danang Vietnam
| | | | - Nguyen Thanh Tung
- Institute of Materials Science, Vietnam Academy of Science and Technology Hanoi Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology Hanoi Vietnam
| | - Van V Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University Ho Chi Minh City Vietnam
| | - Son Tung Ngo
- Faculty of Applied Sciences, Ton Duc Thang University Ho Chi Minh City Vietnam
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University Ho Chi Minh City Vietnam
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