51
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Ma C, Tan H, Choza J, Wang Y, Wang J. Validation and invalidation of SARS-CoV-2 main protease inhibitors using the Flip-GFP and Protease-Glo luciferase assays. Acta Pharm Sin B 2022; 12:1636-1651. [PMID: 34745850 PMCID: PMC8558150 DOI: 10.1016/j.apsb.2021.10.026] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/24/2021] [Accepted: 10/14/2021] [Indexed: 12/14/2022] Open
Abstract
SARS-CoV-2 main protease (Mpro) is one of the most extensively exploited drug targets for COVID-19. Structurally disparate compounds have been reported as Mpro inhibitors, raising the question of their target specificity. To elucidate the target specificity and the cellular target engagement of the claimed Mpro inhibitors, we systematically characterize their mechanism of action using the cell-free FRET assay, the thermal shift-binding assay, the cell lysate Protease-Glo luciferase assay, and the cell-based FlipGFP assay. Collectively, our results have shown that majority of the Mpro inhibitors identified from drug repurposing including ebselen, carmofur, disulfiram, and shikonin are promiscuous cysteine inhibitors that are not specific to Mpro, while chloroquine, oxytetracycline, montelukast, candesartan, and dipyridamole do not inhibit Mpro in any of the assays tested. Overall, our study highlights the need of stringent hit validation at the early stage of drug discovery.
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52
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Fellowes T, White JM. Simulating chalcogen bonding using molecular mechanics: a pseudoatom approach to model ebselen. J Mol Model 2022; 28:66. [PMID: 35201444 PMCID: PMC8867462 DOI: 10.1007/s00894-021-05023-5] [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: 08/23/2021] [Accepted: 12/29/2021] [Indexed: 11/30/2022]
Abstract
The organoselenium compound ebselen has recently been investigated as a treatment for COVID-19; however, efforts to model ebselen in silico have been hampered by the lack of an efficient and accurate method to assess its binding to biological macromolecules. We present here a Generalized Amber Force Field modification which incorporates classical parameters for the selenium atom in ebselen, as well as a positively charged pseudoatom to simulate the σ-hole, a quantum mechanical phenomenon that dominates the chemistry of ebselen. Our approach is justified using an energy decomposition analysis of a number of density functional theory–optimized structures, which shows that the σ-hole interaction is primarily electrostatic in origin. Finally, our model is verified by conducting molecular dynamics simulations on a number of simple complexes, as well as the clinically relevant enzyme SOD1 (superoxide dismutase), which is known to bind to ebselen. Ebselen is an organoselenium drug that has shown promise for the treatment of a number of conditions. Computational modelling of drug-target complexes is commonly performed to determine the likely mechanism of action, however this is difficult in the case of ebselen, as an important mode of interaction is not simulated using current techniques. We present here an extension to common methods, which accurately captures this interaction. ![]()
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Affiliation(s)
- Thomas Fellowes
- Bio21 Institute and School of Chemistry, University of Melbourne, Parkville, Australia.
| | - Jonathan M White
- Bio21 Institute and School of Chemistry, University of Melbourne, Parkville, Australia
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53
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Jiang H, Yang P, Zhang J. Potential Inhibitors Targeting Papain-Like Protease of SARS-CoV-2: Two Birds With One Stone. Front Chem 2022; 10:822785. [PMID: 35281561 PMCID: PMC8905519 DOI: 10.3389/fchem.2022.822785] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/28/2022] [Indexed: 12/23/2022] Open
Abstract
Severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2), the pathogen of the Coronavirus disease-19 (COVID-19), is still devastating the world causing significant chaos to the international community and posing a significant threat to global health. Since the first outbreak in late 2019, several lines of intervention have been developed to prevent the spread of this virus. Nowadays, some vaccines have been approved and extensively administered. However, the fact that SARS-CoV-2 rapidly mutates makes the efficacy and safety of this approach constantly under debate. Therefore, antivirals are still needed to combat the infection of SARS-CoV-2. Papain-like protease (PLpro) of SARS-CoV-2 supports viral reproduction and suppresses the innate immune response of the host, which makes PLpro an attractive pharmaceutical target. Inhibition of PLpro could not only prevent viral replication but also restore the antiviral immunity of the host, resulting in the speedy recovery of the patient. In this review, we describe structural and functional features on PLpro of SARS-CoV-2 and the latest development in searching for PLpro inhibitors. Currently available inhibitors targeting PLpro as well as their structural basis are also summarized.
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Affiliation(s)
- Haihai Jiang
- School of Basic Medical Sciences, Nanchang University, Nanchang, China
- *Correspondence: Haihai Jiang, ; Jin Zhang,
| | - Peiyao Yang
- Queen Mary School, Nanchang University, Nanchang, China
| | - Jin Zhang
- School of Basic Medical Sciences, Nanchang University, Nanchang, China
- *Correspondence: Haihai Jiang, ; Jin Zhang,
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54
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Liang JJ, Pitsillou E, Ververis K, Guallar V, Hung A, Karagiannis TC. Investigation of small molecule inhibitors of the SARS-CoV-2 papain-like protease by all-atom microsecond modelling, PELE Monte Carlo simulations, and in vitro activity inhibition. Chem Phys Lett 2022; 788:139294. [PMID: 34961797 PMCID: PMC8693950 DOI: 10.1016/j.cplett.2021.139294] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/03/2021] [Accepted: 12/15/2021] [Indexed: 12/16/2022]
Abstract
The SARS-CoV-2 papain-like (PLpro) protease is essential for viral replication. We investigated potential antiviral effects of hypericin relative to the well-known noncovalent PLpro inhibitor GRL-0617. Molecular dynamics and PELE Monte Carlo simulations highlight favourable binding of hypericin and GRL-0617 to the naphthalene binding pocket of PLpro. Although not potent as GRL-0617 (45.8 vs 1.6 µM for protease activity, respectively), in vitro fluorogenic enzymatic assays with hypericin show concentration-dependent inhibition of both PLpro protease and deubiquitinating activities. Given its use in supplementations and the FDA conditional approval of a synthetic version, further evaluation of hypericin as a potential SARS-CoV-2 antiviral is warranted.
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Affiliation(s)
- Julia J. Liang
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia,School of Science, STEM College, RMIT University, VIC 3001, Australia
| | - Eleni Pitsillou
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia,School of Science, STEM College, RMIT University, VIC 3001, Australia
| | - Katherine Ververis
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - Victor Guallar
- Barcelona Supercomputing Center, Jordi Girona 29, E-08034 Barcelona, Spain,ICREA, Passeig Lluís Companys 23, E-08010 Barcelona, Spain
| | - Andrew Hung
- School of Science, STEM College, RMIT University, VIC 3001, Australia
| | - Tom C. Karagiannis
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia,Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3052, Australia,Corresponding author at: Head Epigenomic Medicine Program, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
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55
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Musalov MV, Potapov VA, Maylyan AA, Khabibulina AG, Zinchenko SV, Amosova SV. Selenium Dihalides Click Chemistry: Highly Efficient Stereoselective Addition to Alkynes and Evaluation of Glutathione Peroxidase-Like Activity of Bis( E-2-halovinyl) Selenides. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27031050. [PMID: 35164315 PMCID: PMC8838769 DOI: 10.3390/molecules27031050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/29/2022] [Accepted: 01/31/2022] [Indexed: 11/23/2022]
Abstract
Highly efficient stereoselective syntheses of novel bis(E-2-chlorovinyl) selenides and bis(E-2-bromovinyl) selenides in quantitative yields by reactions of selenium dichloride and dibromide with alkynes were developed. The reactions proceeded at room temperature as anti-addition giving products exclusively with (E)-stereochemistry. The glutathione peroxidase-like activity of the obtained products was estimated and compounds with high activity were found. The influence of substituents in the products on their glutathione peroxidase-like activity was discussed.
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56
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Lv Z, Cano KE, Jia L, Drag M, Huang TT, Olsen SK. Targeting SARS-CoV-2 Proteases for COVID-19 Antiviral Development. Front Chem 2022; 9:819165. [PMID: 35186898 PMCID: PMC8850931 DOI: 10.3389/fchem.2021.819165] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 12/20/2021] [Indexed: 12/18/2022] Open
Abstract
The emergence of severe acute respiratory syndrome (SARS-CoV-2) in 2019 marked the third occurrence of a highly pathogenic coronavirus in the human population since 2003. As the death toll surpasses 5 million globally and economic losses continue, designing drugs that could curtail infection and disease progression is critical. In the US, three highly effective Food and Drug Administration (FDA)-authorized vaccines are currently available, and Remdesivir is approved for the treatment of hospitalized patients. However, moderate vaccination rates and the sustained evolution of new viral variants necessitate the ongoing search for new antivirals. Several viral proteins have been prioritized as SARS-CoV-2 antiviral drug targets, among them the papain-like protease (PLpro) and the main protease (Mpro). Inhibition of these proteases would target viral replication, viral maturation, and suppression of host innate immune responses. Knowledge of inhibitors and assays for viruses were quickly adopted for SARS-CoV-2 protease research. Potential candidates have been identified to show inhibitory effects against PLpro and Mpro, both in biochemical assays and viral replication in cells. These results encourage further optimizations to improve prophylactic and therapeutic efficacy. In this review, we examine the latest developments of potential small-molecule inhibitors and peptide inhibitors for PLpro and Mpro, and how structural biology greatly facilitates this process.
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Affiliation(s)
- Zongyang Lv
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Kristin E. Cano
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Lijia Jia
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Tony T. Huang
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, United States
| | - Shaun K. Olsen
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
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57
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Ma C, Wang J. Validation and Invalidation of SARS-CoV-2 Papain-like Protease Inhibitors. ACS Pharmacol Transl Sci 2022; 5:102-109. [PMID: 35178512 PMCID: PMC8806001 DOI: 10.1021/acsptsci.1c00240] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Indexed: 12/19/2022]
Abstract
![]()
SARS-CoV-2
encodes two viral cysteine proteases, the main protease
(Mpro) and the papain-like protease (PLpro),
both of which are validated antiviral drug targets. PLpro is involved in the cleavage of viral polyproteins as well as immune
modulation by removing ubiquitin and interferon-stimulated gene product
15 (ISG15) from host proteins. Therefore, targeting PLpro might be a two-pronged approach. Several compounds including YM155,
cryptotanshinone, tanshinone I, dihydrotanshinone I, tanshinone IIA,
SJB2-043, 6-thioguanine, and 6-mercaptopurine were recently identified
as SARS-CoV-2 PLpro inhibitors through high-throughput
screenings. In this study, we aim to validate/invalidate the reported
PLpro inhibitors using a combination of PLpro target-specific assays including enzymatic FRET assay, thermal shift
binding assay (TSA), and cell-based FlipGFP assay. Collectively, our
results showed that all compounds tested either did not show binding
or led to denaturation of PLpro in the TSA binding assay,
which might explain their weak enzymatic inhibition in the FRET assay.
In addition, none of the compounds showed cellular PLpro inhibition as revealed by the FlipGFP assay. Therefore, more efforts
are needed to search for potent and specific SARS-CoV-2 PLpro inhibitors.
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Affiliation(s)
- Chunlong Ma
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
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58
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Structure-based inhibitor design and repurposing clinical drugs to target SARS-CoV-2 proteases. Biochem Soc Trans 2022; 50:151-165. [PMID: 35015073 DOI: 10.1042/bst20211180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 01/01/2023]
Abstract
SARS-CoV-2, the coronavirus responsible for the current COVID-19 pandemic, encodes two proteases, 3CLpro and PLpro, two of the main antiviral research targets. Here we provide an overview of the structures and functions of 3CLpro and PLpro and examine strategies of structure-based drug designing and drug repurposing against these proteases. Rational structure-based drug design enables the generation of potent and target-specific antivirals. Drug repurposing offers an attractive prospect with an accelerated turnaround. Thus far, several protease inhibitors have been identified, and some candidates are undergoing trials that may well prove to be effective antivirals against SARS-CoV-2.
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59
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Yin J, Li C, Ye C, Ruan Z, Liang Y, Li Y, Wu J, Luo Z. Advances in the development of therapeutic strategies against COVID-19 and perspectives in the drug design for emerging SARS-CoV-2 variants. Comput Struct Biotechnol J 2022; 20:824-837. [PMID: 35126885 PMCID: PMC8802458 DOI: 10.1016/j.csbj.2022.01.026] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/18/2022] [Accepted: 01/27/2022] [Indexed: 12/15/2022] Open
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60
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Kamińska K, Wojaczyńska E. Synthesis of new chiral N-heterocyclic diselenides and their application in the alkoxyselenylation reaction. NEW J CHEM 2022. [DOI: 10.1039/d2nj01434c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Novel chiral diselenides based on a cyclic or bicyclic backbone were applied in the highly diastereoselective methoxyselenylation of styrene.
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Affiliation(s)
- Karolina Kamińska
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50 370 Wrocław, Poland
| | - Elżbieta Wojaczyńska
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50 370 Wrocław, Poland
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61
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Atazanavir Is a Competitive Inhibitor of SARS-CoV-2 M pro, Impairing Variants Replication In Vitro and In Vivo. Pharmaceuticals (Basel) 2021; 15:ph15010021. [PMID: 35056078 PMCID: PMC8777605 DOI: 10.3390/ph15010021] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 11/17/2022] Open
Abstract
Atazanavir (ATV) has already been considered as a potential repurposing drug to 2019 coronavirus disease (COVID-19); however, there are controversial reports on its mechanism of action and effectiveness as anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Through the pre-clinical chain of experiments: enzymatic, molecular docking, cell-based and in vivo assays, it is demonstrated here that both SARS-CoV-2 B.1 lineage and variant of concern gamma are susceptible to this antiretroviral. Enzymatic assays and molecular docking calculations showed that SARS-CoV-2 main protease (Mpro) was inhibited by ATV, with Morrison’s inhibitory constant (Ki) 1.5-fold higher than GC376 (a positive control) dependent of the catalytic water (H2Ocat) content. ATV was a competitive inhibitor, increasing the Mpro’s Michaelis–Menten (Km) more than sixfold. Cell-based assays indicated that different lineages of SARS-CoV-2 is susceptible to ATV. Using oral administration of ATV in mice to reach plasmatic exposure similar to humans, transgenic mice expression in human angiotensin converting enzyme 2 (K18-hACE2) were partially protected against lethal challenge with SARS-CoV-2 gamma. Moreover, less cell death and inflammation were observed in the lung from infected and treated mice. Our studies may contribute to a better comprehension of the Mpro/ATV interaction, which could pave the way to the development of specific inhibitors of this viral protease.
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Abstract
The development of effective antiviral therapy for COVID-19 is critical for those awaiting vaccination, as well as for those who do not respond robustly to vaccination. This review summarizes 1 year of progress in the race to develop antiviral therapies for COVID-19, including research spanning preclinical and clinical drug development efforts, with an emphasis on antiviral compounds that are in clinical development or that are high priorities for clinical development. The review is divided into sections on compounds that inhibit SARS-CoV-2 enzymes, including its polymerase and proteases; compounds that inhibit virus entry, including monoclonal antibodies; interferons; and repurposed drugs that inhibit host processes required for SARS-CoV-2 replication. The review concludes with a summary of the lessons to be learned from SARS-CoV-2 drug development efforts and the challenges to continued progress.
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Affiliation(s)
- Kaiming Tao
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
| | - Philip L. Tzou
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
| | - Janin Nouhin
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
| | - Hector Bonilla
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
| | - Prasanna Jagannathan
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
| | - Robert W. Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
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63
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Krishna Cheerala VS, Ghanta P, Neelakantan SC. Design, synthesis and in silico screening of benzoxazole-thiazolidinone hybrids as potential inhibitors of SARS-CoV-2 proteases. RSC Adv 2021; 11:39328-39342. [PMID: 35492479 PMCID: PMC9044413 DOI: 10.1039/d1ra07504g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 11/04/2021] [Indexed: 11/21/2022] Open
Abstract
Hybrid molecules in the recent years have gained significant importance in drug research as promising therapeutic agents. We report a novel combination of two such bioactive scaffolds (benzoxazole and 4-thiazolidinone B-T hybrids) as inhibitors of SARS-CoV-2. The study uses an in silico approach to identify the potential of B-T hybrids as possible inhibitors of the SARS-CoV-2 proteases. Molecular docking was employed to identify the interactions of B-T hybrids with the two proteases - 3CLp (the 3-chymotrypsin-like protease) and PLp (the papain-like protease). Docking results of the screened 81 hybrids indicated that BT10 and BT14 interacted with the catalytic dyad residue of 3CLp (Cys145) with the best binding energy. MD simulations revealed that BT10 formed stable interactions via 4 hydrogen bonds with the catalytic site residues of 3CLp. In the case of PLp, BT27 and MBT9 interacted with the catalytic triad residue of PLp (His272) with high binding energy. MD simulations demonstrated that the reference drug Tipranavir relocated to the thumb region of the protease whereas BT27 remained in the active site of PLp stabilized by 2 hydrogen bonds, while MBT9 relocated to the BL2 loop of the palm region. The MM-PBSA and interaction entropy (IE) analysis indicated that BT14 exhibited the best ΔG (of -6.83 kcal mol-1) with 3CLp, while BT27 exhibited the best ΔG (of -7.76 kcal mol-1) with PLp. A four-step synthetic procedure was employed to synthesize the B-T hybrids starting from ammonium thiocyanate. The short-listed compounds in the case of 3CLp were synthesized and characterized using IR, NMR, and HRMS spectroscopic techniques.
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Affiliation(s)
- Vijay Sai Krishna Cheerala
- Department of Chemistry, Sri Sathya Sai Institute of Higher Learning Brindavan Campus Bangalore 560067 India
| | - Prasanth Ghanta
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning Prasanthi Nilayam Campus, Puttaparthi 515134 India
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64
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Maniak H, Talma M, Giurg M. Inhibitory Potential of New Phenolic Hydrazide-Hydrazones with a Decoy Substrate Fragment towards Laccase from a Phytopathogenic Fungus: SAR and Molecular Docking Studies. Int J Mol Sci 2021; 22:ijms222212307. [PMID: 34830189 PMCID: PMC8617976 DOI: 10.3390/ijms222212307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 01/22/2023] Open
Abstract
Laccase from pathogenic fungi participates in both the delignification and neutralization of phytoantibiotics. Furthermore, it interferes with the hormone signaling in plants and catalyzes melanization. Infections of these pathogens contribute to loss in forestry, agriculture, and horticulture. As there is still a need to expand knowledge on efficient defense strategies against phytopathogenic fungi, the present study aimed to reveal more information on the molecular mechanisms of laccase inhibition with natural and natural-like carboxylic acid semi-synthetic derivatives. A set of hydrazide-hydrazones derived from carboxylic acids, generally including electron-rich arene units that serve as a decoy substrate, was synthesized and tested with laccase from Trametes versicolor. The classic synthesis of the title inhibitors proceeded with good to almost quantitative yield. Ninety percent of the tested molecules were active in the range of KI = 8–233 µM and showed different types of action. Such magnitude of inhibition constants qualified the hydrazide-hydrazones as strong laccase inhibitors. Molecular docking studies supporting the experimental data explained the selected derivatives’ interactions with the enzyme. The results are promising in developing new potential antifungal agents mitigating the damage scale in the plant cultivation, gardening, and horticulture sectors.
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Affiliation(s)
- Halina Maniak
- Department of Micro, Nano and Bioprocess Engineering, Faculty of Chemistry, Wroclaw University of Science and Technology, Norwida 4/6, 50-373 Wrocław, Poland
- Correspondence: (H.M.); (M.G.); Tel.: +48-713203314 (H.M.); +48-713203616 (M.G.)
| | - Michał Talma
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland;
| | - Mirosław Giurg
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
- Correspondence: (H.M.); (M.G.); Tel.: +48-713203314 (H.M.); +48-713203616 (M.G.)
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65
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Huff S, Kummetha IR, Tiwari SK, Huante MB, Clark AE, Wang S, Bray W, Smith D, Carlin AF, Endsley M, Rana TM. Discovery and Mechanism of SARS-CoV-2 Main Protease Inhibitors. J Med Chem 2021; 65:2866-2879. [PMID: 34570513 PMCID: PMC8491550 DOI: 10.1021/acs.jmedchem.1c00566] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The emergence of a new coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), presents an urgent public health crisis. Without available targeted therapies, treatment options remain limited for COVID-19 patients. Using medicinal chemistry and rational drug design strategies, we identify a 2-phenyl-1,2-benzoselenazol-3-one class of compounds targeting the SARS-CoV-2 main protease (Mpro). FRET-based screening against recombinant SARS-CoV-2 Mpro identified six compounds that inhibit proteolysis with nanomolar IC50 values. Preincubation dilution experiments and molecular docking determined that the inhibition of SARS-CoV-2 Mpro can occur by either covalent or noncovalent mechanisms, and lead E04 was determined to inhibit Mpro competitively. Lead E24 inhibited viral replication with a nanomolar EC50 value (844 nM) in SARS-CoV-2-infected Vero E6 cells and was further confirmed to impair SARS-CoV-2 replication in human lung epithelial cells and human-induced pluripotent stem cell-derived 3D lung organoids. Altogether, these studies provide a structural framework and mechanism of Mpro inhibition that should facilitate the design of future COVID-19 treatments.
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Affiliation(s)
- Sarah Huff
- Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - Indrasena Reddy Kummetha
- Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - Shashi Kant Tiwari
- Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - Matthew B Huante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Alex E Clark
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - Shaobo Wang
- Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - William Bray
- Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - Davey Smith
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - Aaron F Carlin
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
| | - Mark Endsley
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Tariq M Rana
- Division of Genetics, Department of Pediatrics, Center for Drug Discovery Innovation, Program in Immunology, Institute for Genomic Medicine, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States.,Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, 9500 Gilman Drive MC 0762, La Jolla, California 92093, United States
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Plavec Z, Pöhner I, Poso A, Butcher SJ. Virus structure and structure-based antivirals. Curr Opin Virol 2021; 51:16-24. [PMID: 34564030 PMCID: PMC8460353 DOI: 10.1016/j.coviro.2021.09.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/13/2021] [Accepted: 09/12/2021] [Indexed: 01/18/2023]
Abstract
Structure-based antiviral developments in the past two years have been dominated by the structure determination and inhibition of SARS-CoV-2 proteins and new lead molecules for picornaviruses. The SARS-CoV-2 spike protein has been targeted successfully with antibodies, nanobodies, and receptor protein mimics effectively blocking receptor binding or fusion. The two most promising non-structural proteins sharing strong structural and functional conservation across virus families are the main protease and the RNA-dependent RNA polymerase, for which design and reuse of broad range inhibitors already approved for use has been an attractive avenue. For picornaviruses, the increasing recognition of the transient expansion of the capsid as a critical transition towards RNA release has been targeted through a newly identified, apparently widely conserved, druggable, interprotomer pocket preventing viral entry. We summarize some of the key papers in these areas and ponder the practical uses and contributions of molecular modeling alongside empirical structure determination.
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Affiliation(s)
- Zlatka Plavec
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland; Helsinki Institute of Life Sciences-Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
| | - Ina Pöhner
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Antti Poso
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland; University Hospital Tübingen, Department of Internal Medicine VII, Tübingen, Germany
| | - Sarah J Butcher
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland; Helsinki Institute of Life Sciences-Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
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Abstract
Abstract
Ebselen is a well-known synthetic compound mimicking glutathione peroxidase (GPx), which catalyses some vital reactions that protect against oxidative damage. Based on a large number of in vivo and in vitro studies, various mechanisms have been proposed to explain its actions on multiple targets. It targets thiol-related compounds, including cysteine, glutathione, and thiol proteins (e.g., thioredoxin and thioredoxin reductase). Owing to this, ebselen is a unique multifunctional agent with important effects on inflammation, apoptosis, oxidative stress, cell differentiation, immune regulation and neurodegenerative disease, with anti-microbial, detoxifying and anti-tumour activity. This review summarises the current understanding of the multiple biological processes and molecules targeted by ebselen, and its pharmacological applications.
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Parise A, Romeo I, Russo N, Marino T. The Se-S Bond Formation in the Covalent Inhibition Mechanism of SARS-CoV-2 Main Protease by Ebselen-like Inhibitors: A Computational Study. Int J Mol Sci 2021; 22:9792. [PMID: 34575955 PMCID: PMC8467846 DOI: 10.3390/ijms22189792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 12/20/2022] Open
Abstract
The inhibition mechanism of the main protease (Mpro) of SARS-CoV-2 by ebselen (EBS) and its analog with a hydroxyl group at position 2 of the benzisoselenazol-3(2H)-one ring (EBS-OH) was studied by using a density functional level of theory. Preliminary molecular dynamics simulations on the apo form of Mpro were performed taking into account both the hydrogen donor and acceptor natures of the Nδ and Nε of His41, a member of the catalytic dyad. The potential energy surfaces for the formation of the Se-S covalent bond mediated by EBS and EBS-OH on Mpro are discussed in detail. The EBS-OH shows a distinctive behavior with respect to EBS in the formation of the noncovalent complex. Due to the presence of canonical H-bonds and noncanonical ones involving less electronegative atoms, such as sulfur and selenium, the influence on the energy barriers and reaction energy of the Minnesota hybrid meta-GGA functionals M06, M06-2X and M08HX, and the more recent range-separated hybrid functional wB97X were also considered. The knowledge of the inhibition mechanism of Mpro by the small protease inhibitors EBS or EBS-OH can enlarge the possibilities for designing more potent and selective inhibitor-based drugs to be used in combination with other antiviral therapies.
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Affiliation(s)
- Angela Parise
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy; (A.P.); (I.R.); (N.R.)
- Institut de Chimie Physique UMR8000, Université Paris-Saclay, CNRS, 91405 Orsay, France
| | - Isabella Romeo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy; (A.P.); (I.R.); (N.R.)
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy; (A.P.); (I.R.); (N.R.)
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy; (A.P.); (I.R.); (N.R.)
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Serrano-Aparicio N, Moliner V, Świderek K. On the Origin of the Different Reversible Characters of Salinosporamide A and Homosalinosporamide A in the Covalent Inhibition of the Human 20S Proteasome. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Natalia Serrano-Aparicio
- Biocomp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Vicent Moliner
- Biocomp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Katarzyna Świderek
- Biocomp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
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Wang Z, Yang L, Zhao XE. Co-crystallization and structure determination: An effective direction for anti-SARS-CoV-2 drug discovery. Comput Struct Biotechnol J 2021; 19:4684-4701. [PMID: 34426762 PMCID: PMC8373586 DOI: 10.1016/j.csbj.2021.08.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 07/29/2021] [Accepted: 08/17/2021] [Indexed: 01/18/2023] Open
Abstract
Safer and more-effective drugs are urgently needed to counter infections with the highly pathogenic SARS-CoV-2, cause of the COVID-19 pandemic. Identification of efficient inhibitors to treat and prevent SARS-CoV-2 infection is a predominant focus. Encouragingly, using X-ray crystal structures of therapeutically relevant drug targets (PLpro, Mpro, RdRp, and S glycoprotein) offers a valuable direction for anti-SARS-CoV-2 drug discovery and lead optimization through direct visualization of interactions. Computational analyses based primarily on MMPBSA calculations have also been proposed for assessing the binding stability of biomolecular structures involving the ligand and receptor. In this study, we focused on state-of-the-art X-ray co-crystal structures of the abovementioned targets complexed with newly identified small-molecule inhibitors (natural products, FDA-approved drugs, candidate drugs, and their analogues) with the assistance of computational analyses to support the precision design and screening of anti-SARS-CoV-2 drugs.
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Key Words
- 3CLpro, 3C-Like protease
- ACE2, angiotensin-converting enzyme 2
- COVID-19, coronavirus disease 2019
- Candidate drugs
- Co-crystal structures
- DyKAT, dynamic kinetic asymmetric transformation
- EBOV, Ebola virus
- EC50, half maximal effective concentration
- EMD, Electron Microscopy Data
- FDA, U.S. Food and Drug Administration
- FDA-approved drugs
- HCoV-229E, human coronavirus 229E
- HPLC, high-performance liquid chromatography
- IC50, half maximal inhibitory concentration
- MD, molecular dynamics
- MERS-CoV, Middle East respiratory syndrome coronavirus
- MMPBSA, molecular mechanics Poisson-Boltzmann surface area
- MTase, methyltransferase
- Mpro, main protease
- Natural products
- Nsp, nonstructural protein
- PDB, Protein Data Bank
- PLpro, papain-like protease
- RTP, ribonucleoside triphosphate
- RdRp, RNA-dependent RNA polymerase
- SAM, S-adenosylmethionine
- SARS-CoV, severe acute respiratory syndrome coronavirus
- SARS-CoV-2
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- SI, selectivity index
- Ugi-4CR, Ugi four-component reaction
- cryo-EM, cryo-electron microscopy
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Affiliation(s)
- Zhonglei Wang
- Key Laboratory of Green Natural Products and Pharmaceutical Intermediates in Colleges and Universities of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, PR China
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, PR China
| | - Liyan Yang
- School of Physics and Physical Engineering, Qufu Normal University, Qufu 273165, PR China
| | - Xian-En Zhao
- Key Laboratory of Green Natural Products and Pharmaceutical Intermediates in Colleges and Universities of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, PR China
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Durdagi S, Dağ Ç, Dogan B, Yigin M, Avsar T, Buyukdag C, Erol I, Ertem FB, Calis S, Yildirim G, Orhan MD, Guven O, Aksoydan B, Destan E, Sahin K, Besler SO, Oktay L, Shafiei A, Tolu I, Ayan E, Yuksel B, Peksen AB, Gocenler O, Yucel AD, Can O, Ozabrahamyan S, Olkan A, Erdemoglu E, Aksit F, Tanisali G, Yefanov OM, Barty A, Tolstikova A, Ketawala GK, Botha S, Dao EH, Hayes B, Liang M, Seaberg MH, Hunter MS, Batyuk A, Mariani V, Su Z, Poitevin F, Yoon CH, Kupitz C, Sierra RG, Snell EH, DeMirci H. Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing. Structure 2021; 29:1382-1396.e6. [PMID: 34403647 PMCID: PMC8367086 DOI: 10.1016/j.str.2021.07.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/19/2021] [Accepted: 07/20/2021] [Indexed: 02/06/2023]
Abstract
The COVID-19 pandemic has resulted in 198 million reported infections and more than 4 million deaths as of July 2021 (covid19.who.int). Research to identify effective therapies for COVID-19 includes: (1) designing a vaccine as future protection; (2) de novo drug discovery; and (3) identifying existing drugs to repurpose them as effective and immediate treatments. To assist in drug repurposing and design, we determine two apo structures of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease at ambient temperature by serial femtosecond X-ray crystallography. We employ detailed molecular simulations of selected known main protease inhibitors with the structures and compare binding modes and energies. The combined structural and molecular modeling studies not only reveal the dynamics of small molecules targeting the main protease but also provide invaluable opportunities for drug repurposing and structure-based drug design strategies against SARS-CoV-2.
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Affiliation(s)
- Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey.
| | - Çağdaş Dağ
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - Berna Dogan
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey
| | - Merve Yigin
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - Timucin Avsar
- Department of Medical Biology, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey
| | - Cengizhan Buyukdag
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - Ismail Erol
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey; Department of Chemistry, Gebze Technical University, Kocaeli 41400, Turkey
| | - Fatma Betul Ertem
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - Seyma Calis
- Department of Medical Biology, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey; Department of Molecular Biology - Genetics and Biotechnology, Istanbul Technical University, Istanbul 34469, Turkey
| | - Gunseli Yildirim
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - Muge D Orhan
- Department of Medical Biology, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey
| | - Omur Guven
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - Busecan Aksoydan
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey; Neuroscience Program, Graduate School of Health Sciences, Bahcesehir University, Istanbul 34734, Turkey
| | - Ebru Destan
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - Kader Sahin
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey
| | - Sabri O Besler
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - Lalehan Oktay
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey
| | - Alaleh Shafiei
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - Ilayda Tolu
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey
| | - Esra Ayan
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - Busra Yuksel
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - Ayse B Peksen
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - Oktay Gocenler
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - Ali D Yucel
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - Ozgur Can
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - Serena Ozabrahamyan
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - Alpsu Olkan
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey; School of Medicine, Bahcesehir University, Istanbul 34734, Turkey
| | - Ece Erdemoglu
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey; Faculty of Medicine, Mersin University, Mersin 33070, Turkey
| | - Fulya Aksit
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - Gokhan Tanisali
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | | | - Anton Barty
- Deutsches Elektronen-Synchrotron, Notkestrasse 85, Hamburg 22607, Germany
| | | | - Gihan K Ketawala
- Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA; Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Sabine Botha
- Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA; Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | - E Han Dao
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, CA 94025, USA
| | - Brandon Hayes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Matthew H Seaberg
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Alex Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Valerio Mariani
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Zhen Su
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; Department of Applied Physics, Stanford University, Stanford, CA, USA
| | - Frederic Poitevin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Christopher Kupitz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Edward H Snell
- Hauptman-Woodward Medical Research Institute, University at Buffalo, 700 Ellicott St, Buffalo, NY, USA; Materials Design and Innovation, SUNY at Buffalo, 700 Ellicott St., Buffalo, NY, USA
| | - Hasan DeMirci
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey; Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, CA 94025, USA; Koc University Isbank Center for Infectious Diseases (KUISCID), 34450, Istanbul, Turkey.
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72
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Al-Kuraishy HM, Al-Gareeb AI, Alkazmi L, Alexiou A, Batiha GES. Levamisole Therapy in COVID-19. Viral Immunol 2021; 34:722-725. [PMID: 34388031 DOI: 10.1089/vim.2021.0042] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) a global infectious disease caused by severe acute respiratory coronavirus 2 (SARS-CoV-2) affects various organs, primarily the respiratory system, and presented with pulmonary manifestations such as acute lung injury (ALI) and acute respiratory distress syndrome. Levamisole (LVM) is an anthelminthic drug; it has immune-modulating effects through induction of type 1 immune response. Based on these findings several recent studies highlighted that LVM might be effective in preventing and treating SARS-CoV-2 infections. The aim of this report is to illustrate the potential role of LVM in SARS-CoV-2 infection and in the management of COVID-19. Different studies proposed that LVM may inhibit proliferation of SARS-CoV-2 through inhibition of papain-like protease. LVM may prevent ALI and acute kidney injury through activation of glucocorticoid receptors. In general, LVM has strong immune stimulant effects by modulating cellular and humoral immune responses. This effect is beneficial in the early phase of COVID-19 and harmful in the late phase. In the early phase, immune stimulation facilitates SARS-CoV-2 clearance and tissue repair, however, in the late phase, immune stimulation in COVID-19 may increase propagation risk of cytokine storm. In conclusion, LVM therapy in COVID-19 has bidirectional effects, beneficial in the early phase and harmful effects in the late phase of COVID-19. Clinical trial and prospective studies are warranted in this regard to confirm the efficacy and timing administration of LVM in the management of COVID-19.
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Affiliation(s)
- Hayder M Al-Kuraishy
- Department of Clinical Pharmacology and Therapeutic, College of Medicine, ALmustansiriyiah University, Baghdad, Iraq
| | - Ali I Al-Gareeb
- Department of Clinical Pharmacology and Therapeutic, College of Medicine, ALmustansiriyiah University, Baghdad, Iraq
| | - Luay Alkazmi
- Biology Department, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Athanasios Alexiou
- Department of Social Studies and Arts, Novel Global Community Educational Foundation, Hebersham, Australia.,AFNP Med Austria, Wien, Austria
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, AlBeheira, Egypt
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73
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Tupikina EY, Karpov VV, Tolstoy PM. On the influence of water molecules on the outer electronic shells of R-SeH, R-Se(-) and R-SeOH fragments in the selenocysteine amino acid residue. Phys Chem Chem Phys 2021; 23:13965-13970. [PMID: 34143160 DOI: 10.1039/d1cp01345a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this computational work (MP2/aug-cc-pVTZ) we investigated the features of the outer electronic shells of R-SeH, R-Se(-) and R-SeOH fragments (R = CH3), which can be considered as simplified models for the forms of the active centres of glutathione peroxidases GPx along their catalytic pathway (reduction of peroxides). It is shown that the preferential direction of a nucleophilic attack on the R-Se(-) fragment by a peroxide molecule is determined by the presence of the electron-depleted region of the selenium atom in front of the C-Se bond and nucleophilic attack can be facilitated by the solvation of R-Se(-) by water molecules. Such solvation does not block the direction of potential nucleophilic attack and also leads to the increase of the maximal value of the molecular electrostatic potential on the selenium atom. It was shown that the 77Se NMR chemical shift is sensitive both to the oxidation state and the hydration state of the selenium-containing fragment.
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Affiliation(s)
- Elena Yu Tupikina
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Emb. 7/9, Saint Petersburg, 199034, Russia.
| | - Valerii V Karpov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Emb. 7/9, Saint Petersburg, 199034, Russia.
| | - Peter M Tolstoy
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Emb. 7/9, Saint Petersburg, 199034, Russia.
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74
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Ebselen and Analogues: Pharmacological Properties and Synthetic Strategies for Their Preparation. Molecules 2021; 26:molecules26144230. [PMID: 34299505 PMCID: PMC8306772 DOI: 10.3390/molecules26144230] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 02/06/2023] Open
Abstract
Ebselen is the leader of selenorganic compounds, and starting from its identification as mimetic of the key antioxidant enzyme glutathione peroxidase, several papers have appeared in literature claiming its biological activities. It was the subject of several clinical trials and it is currently in clinical evaluation for the treatment of COVID-19 patients. Given our interest in the synthesis and pharmacological evaluation of selenorganic derivatives with this review, we aimed to collect all the papers focused on the biological evaluation of ebselen and its close analogues, covering the timeline between 2016 and most of 2021. Our analysis evidences that, even if it lacks specificity when tested in vitro, being able to bind to every reactive cysteine, it proved to be always well tolerated in vivo, exerting no sign of toxicity whatever the administered doses. Besides, looking at the literature, we realized that no review article dealing with the synthetic approaches for the construction of the benzo[d][1,2]-selenazol-3(2H)-one scaffold is available; thus, a section of the present review article is completely devoted to this specific topic.
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75
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Mechanistic Insight into SARS-CoV-2 Mpro Inhibition by Organoselenides: The Ebselen Case Study. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11146291] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The main protease (Mpro) of SARS-CoV-2 is a current target for the inhibition of viral replication. Through a combined Docking and Density Functional Theory (DFT) approach, we investigated in-silico the molecular mechanism by which ebselen (IUPAC: 2-phenyl-1,2-benzoselenazol-3-one), the most famous and pharmacologically active organoselenide, inhibits Mpro. For the first time, we report on a mechanistic investigation in an enzyme for the formation of the covalent -S-Se- bond between ebselen and a key enzymatic cysteine. The results highlight the strengths and weaknesses of ebselen and provide hints for a rational drug design of bioorganic selenium-based inhibitors.
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76
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Sun LY, Chen C, Su J, Li JQ, Jiang Z, Gao H, Chigan JZ, Ding HH, Zhai L, Yang KW. Ebsulfur and Ebselen as highly potent scaffolds for the development of potential SARS-CoV-2 antivirals. Bioorg Chem 2021; 112:104889. [PMID: 33915460 PMCID: PMC8026246 DOI: 10.1016/j.bioorg.2021.104889] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 01/25/2023]
Abstract
The emerging COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has raised a global catastrophe. To date, there is no specific antiviral drug available to combat this virus, except the vaccine. In this study, the main protease (Mpro) required for SARS-CoV-2 viral replication was expressed and purified. Thirty-six compounds were tested as inhibitors of SARS-CoV-2 Mpro by fluorescence resonance energy transfer (FRET) technique. The half-maximal inhibitory concentration (IC50) values of Ebselen and Ebsulfur analogs were obtained to be in the range of 0.074-0.91 μM. Notably, the molecules containing furane substituent displayed higher inhibition against Mpro, followed by Ebselen 1i (IC50 = 0.074 μM) and Ebsulfur 2k (IC50 = 0.11 μM). The action mechanism of 1i and 2k were characterized by enzyme kinetics, pre-incubation and jump dilution assays, as well as fluorescent labeling experiments, which suggested that both compounds covalently and irreversibly bind to Mpro, while molecular docking suggested that 2k formed an SS bond with the Cys145 at the enzymatic active site. This study provides two very potent scaffolds Ebsulfur and Ebselen for the development of covalent inhibitors of Mpro to combat COVID-19.
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Affiliation(s)
- Le-Yun Sun
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Cheng Chen
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Jianpeng Su
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Jia-Qi Li
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Zhihui Jiang
- Department of Pharmacy, General Hospital of Southern Theatre Command of PLA, Guangzhou 510010, PR China
| | - Han Gao
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Jia-Zhu Chigan
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Huan-Huan Ding
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Le Zhai
- Shaanxi Key Laboratory of Phytochemistry, College of Chemistry and Chemical Engineering, Baoji University of Arts and Sciences, Baoji 72101, Shaanxi Province, PR China
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China.
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Inhibitors of Coronavirus 3CL Proteases Protect Cells from Protease-Mediated Cytotoxicity. J Virol 2021; 95:e0237420. [PMID: 33910954 DOI: 10.1128/jvi.02374-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We describe a mammalian cell-based assay to identify coronavirus 3CL protease (3CLpro) inhibitors. This assay is based on rescuing protease-mediated cytotoxicity and does not require live virus. By enabling the facile testing of compounds across a range of 15 distantly related coronavirus 3CLpro enzymes, we identified compounds with broad 3CLpro-inhibitory activity. We also adapted the assay for use in compound screening and in doing so uncovered additional severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) 3CLpro inhibitors. We observed strong concordance between data emerging from this assay and those obtained from live-virus testing. The reported approach democratizes the testing of 3CLpro inhibitors by developing a simplified method for identifying coronavirus 3CLpro inhibitors that can be used by the majority of laboratories, rather than the few with extensive biosafety infrastructure. We identified two lead compounds, GC376 and compound 4, with broad activity against all 3CL proteases tested, including 3CLpro enzymes from understudied zoonotic coronaviruses. IMPORTANCE Multiple coronavirus pandemics have occurred over the last 2 decades. This has highlighted a need to be proactive in the development of therapeutics that can be readily deployed in the case of future coronavirus pandemics. We developed and validated a simplified cell-based assay for the identification of chemical inhibitors of 3CL proteases encoded by a wide range of coronaviruses. This assay is reporter free, does not require specialized biocontainment, and is optimized for performance in high-throughput screening. By testing reported 3CL protease inhibitors against a large collection of 3CL proteases with variable sequence similarity, we identified compounds with broad activity against 3CL proteases and uncovered structural insights into features that contribute to their broad activity. Furthermore, we demonstrated that this assay is suitable for identifying chemical inhibitors of proteases from families other than 3CL proteases.
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Gediz Erturk A, Sahin A, Bati Ay E, Pelit E, Bagdatli E, Kulu I, Gul M, Mesci S, Eryilmaz S, Oba Ilter S, Yildirim T. A Multidisciplinary Approach to Coronavirus Disease (COVID-19). Molecules 2021; 26:3526. [PMID: 34207756 PMCID: PMC8228528 DOI: 10.3390/molecules26123526] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/04/2021] [Accepted: 06/04/2021] [Indexed: 02/07/2023] Open
Abstract
Since December 2019, humanity has faced an important global threat. Many studies have been published on the origin, structure, and mechanism of action of the SARS-CoV-2 virus and the treatment of its disease. The priority of scientists all over the world has been to direct their time to research this subject. In this review, we highlight chemical studies and therapeutic approaches to overcome COVID-19 with seven different sections. These sections are the structure and mechanism of action of SARS-CoV-2, immunotherapy and vaccine, computer-aided drug design, repurposing therapeutics for COVID-19, synthesis of new molecular structures against COVID-19, food safety/security and functional food components, and potential natural products against COVID-19. In this work, we aimed to screen all the newly synthesized compounds, repurposing chemicals covering antiviral, anti-inflammatory, antibacterial, antiparasitic, anticancer, antipsychotic, and antihistamine compounds against COVID-19. We also highlight computer-aided approaches to develop an anti-COVID-19 molecule. We explain that some phytochemicals and dietary supplements have been identified as antiviral bioproducts, which have almost been successfully tested against COVID-19. In addition, we present immunotherapy types, targets, immunotherapy and inflammation/mutations of the virus, immune response, and vaccine issues.
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Affiliation(s)
- Aliye Gediz Erturk
- Department of Chemistry, Faculty of Arts and Sciences, Ordu University, Altınordu, Ordu 52200, Turkey;
| | - Arzu Sahin
- Department of Basic Medical Sciences—Physiology, Faculty of Medicine, Uşak University, 1-EylulUşak 64000, Turkey;
| | - Ebru Bati Ay
- Department of Plant and Animal Production, Suluova Vocational School, Amasya University, Suluova, Amasya 05100, Turkey;
| | - Emel Pelit
- Department of Chemistry, Faculty of Arts and Sciences, Kırklareli University, Kırklareli 39000, Turkey;
| | - Emine Bagdatli
- Department of Chemistry, Faculty of Arts and Sciences, Ordu University, Altınordu, Ordu 52200, Turkey;
| | - Irem Kulu
- Department of Chemistry, Faculty of Basic Sciences, Gebze Technical University, Kocaeli 41400, Turkey;
| | - Melek Gul
- Department of Chemistry, Faculty of Arts and Sciences, Amasya University, Ipekkoy, Amasya 05100, Turkey
| | - Seda Mesci
- Scientific Technical Application and Research Center, Hitit University, Çorum 19030, Turkey;
| | - Serpil Eryilmaz
- Department of Physics, Faculty of Arts and Sciences, Amasya University, Ipekkoy, Amasya 05100, Turkey;
| | - Sirin Oba Ilter
- Food Processing Department, Suluova Vocational School, Amasya University, Suluova, Amasya 05100, Turkey;
| | - Tuba Yildirim
- Department of Biology, Faculty of Arts and Sciences, Amasya University, Ipekkoy, Amasya 05100, Turkey;
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79
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Abdellattif MH, Abdel-Rahman AAH, Arief MMH, Mouneir SM, Ali A, Hussien MA, Okasha RM, Afifi TH, Hagar M. Novel 2-Hydroselenonicotinonitriles and Selenopheno[2, 3-b]pyridines: Efficient Synthesis, Molecular Docking-DFT Modeling, and Antimicrobial Assessment. Front Chem 2021; 9:672503. [PMID: 34041224 PMCID: PMC8141565 DOI: 10.3389/fchem.2021.672503] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 03/31/2021] [Indexed: 11/16/2022] Open
Abstract
Selenium containing heterocyclic compounds gained great interest as bioactive molecules as of late. This report explores the design, synthesis, characterization, and antimicrobial screening of new pyridine derivatives endowed with selenium moieties. A one-pot multicomponent system with a solvent-free, microwave irradiation environment was employed to afford this series. The spectroscopic techniques were exploited to verify the structures of the synthesized derivatives. Additionally, the agar diffusion method was employed to determine the antimicrobial activity of all the desired compounds. Of all the synthesized molecules, 9b, 12b, 14f, and 16d exhibited well to remarkable antibacterial and antifungal activities. Moreover, derivative 14f demonstrated the most potent antibacterial and antifungal performance. The results were also supported by molecular docking studies, utilizing the MOE (molecular operating environment) which revealed the best binding mode with the highest energy interaction within the binding pocket. Lastly, theoretical DFT calculations were carried out in a gas phase at B3LYP 6-311G (d,p) basis set to predict the molecular geometries and chemical reactivity descriptors. DFT results have been used to illustrate that molecular docking findings and biological activity assessments.
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Affiliation(s)
- Magda H Abdellattif
- Department of Chemistry, College of Science, Deanship of Scientific Research, Taif University, Taif, Saudi Arabia
| | | | | | - Samar M Mouneir
- Department of Pharmacology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Amena Ali
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Mostafa A Hussien
- Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Chemistry, Faculty of Science, Port Said University, Port Said, Egypt
| | - Rawda M Okasha
- Department of Chemistry, Faculty of Science, Taibah University, Medina, Saudi Arabia
| | - Tarek H Afifi
- Department of Chemistry, Faculty of Science, Taibah University, Medina, Saudi Arabia
| | - Mohamed Hagar
- Chemistry Department, College of Sciences, Taibah University, Yanbu, Saudi Arabia.,Chemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
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