1
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Ruiz-Moreno AJ, Cedillo-González R, Cordova-Bahena L, An Z, Medina-Franco JL, Velasco-Velázquez MA. Consensus Pharmacophore Strategy For Identifying Novel SARS-Cov-2 M pro Inhibitors from Large Chemical Libraries. J Chem Inf Model 2024; 64:1984-1995. [PMID: 38472094 PMCID: PMC10966741 DOI: 10.1021/acs.jcim.3c01439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 02/24/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main Protease (Mpro) is an enzyme that cleaves viral polyproteins translated from the viral genome and is critical for viral replication. Mpro is a target for anti-SARS-CoV-2 drug development, and multiple Mpro crystals complexed with competitive inhibitors have been reported. In this study, we aimed to develop an Mpro consensus pharmacophore as a tool to expand the search for inhibitors. We generated a consensus model by aligning and summarizing pharmacophoric points from 152 bioactive conformers of SARS-CoV-2 Mpro inhibitors. Validation against a library of conformers from a subset of ligands showed that our model retrieved poses that reproduced the crystal-binding mode in 77% of the cases. Using models derived from a consensus pharmacophore, we screened >340 million compounds. Pharmacophore-matching and chemoinformatics analyses identified new potential Mpro inhibitors. The candidate compounds were chemically dissimilar to the reference set, and among them, demonstrating the relevance of our model. We evaluated the effect of 16 candidates on Mpro enzymatic activity finding that seven have inhibitory activity. Three compounds (1, 4, and 5) had IC50 values in the midmicromolar range. The Mpro consensus pharmacophore reported herein can be used to identify compounds with improved activity and novel chemical scaffolds against Mpro. The method developed for its generation is provided as an open-access code (https://github.com/AngelRuizMoreno/ConcensusPharmacophore) and can be applied to other pharmacological targets.
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Affiliation(s)
- Angel J. Ruiz-Moreno
- School
of Medicine, Universidad Nacional Autónoma
de México, Mexico
City 04510, Mexico
| | - Raziel Cedillo-González
- School
of Medicine, Universidad Nacional Autónoma
de México, Mexico
City 04510, Mexico
- Graduate
Program in Biochemical Sciences, Universidad
Nacional Autónoma de México, Mexico City 04510, Mexico
- DIFACQUIM
Research Group, School of Chemistry, Universidad
Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Luis Cordova-Bahena
- School
of Medicine, Universidad Nacional Autónoma
de México, Mexico
City 04510, Mexico
- Consejo
Nacional de Humanidades, Ciencias y Tecnología, Mexico City 03940, Mexico
| | - Zhiqiang An
- Texas
Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - José L. Medina-Franco
- DIFACQUIM
Research Group, School of Chemistry, Universidad
Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Marco A. Velasco-Velázquez
- School
of Medicine, Universidad Nacional Autónoma
de México, Mexico
City 04510, Mexico
- Texas
Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas 77030, United States
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2
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Fernandes GFS, Lopes JR, Dos Santos JL, Scarim CB. Phthalimide as a versatile pharmacophore scaffold: Unlocking its diverse biological activities. Drug Dev Res 2023; 84:1346-1375. [PMID: 37492986 DOI: 10.1002/ddr.22094] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/03/2023] [Accepted: 07/07/2023] [Indexed: 07/27/2023]
Abstract
Phthalimide, a pharmacophore exhibiting diverse biological activities, holds a prominent position in medicinal chemistry. In recent decades, numerous derivatives of phthalimide have been synthesized and extensively studied for their therapeutic potential across a wide range of health conditions. This comprehensive review highlights the latest developments in medicinal chemistry, specifically focusing on phthalimide-based compounds that have emerged within the last decade. These compounds showcase promising biological activities, including anti-inflammatory, anti-Alzheimer, antiepileptic, antischizophrenia, antiplatelet, anticancer, antibacterial, antifungal, antimycobacterial, antiparasitic, anthelmintic, antiviral, and antidiabetic properties. The physicochemical profiles of the phthalimide derivatives were carefully analyzed using the online platform pkCSM, revealing the remarkable versatility of this scaffold. Therefore, this review emphasizes the potential of phthalimide as a valuable scaffold for the development of novel therapeutic agents, providing avenues for the exploration and design of new compounds.
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Affiliation(s)
| | - Juliana R Lopes
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
| | - Jean L Dos Santos
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
| | - Cauê B Scarim
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
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3
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Hussein MA, Borik RM, Nafie MS, Abo-Salem HM, Boshra SA, Mohamed ZN. Structure Activity Relationship and Molecular Docking of Some Quinazolines Bearing Sulfamerazine Moiety as New 3CLpro, cPLA2, sPLA2 Inhibitors. Molecules 2023; 28:6052. [PMID: 37630304 PMCID: PMC10460087 DOI: 10.3390/molecules28166052] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 07/28/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
The current work was conducted to synthesize several novel anti-inflammatory quinazolines having sulfamerazine moieties as new 3CLpro, cPLA2, and sPLA2 inhibitors. The thioureido derivative 3 was formed when compound 2 was treated with sulfamerazine. Also, compound 3 was reacted with NH2-NH2 in ethanol to produce the N-aminoquinazoline derivative. Additionally, derivative 4 was reacted with 4-hydroxy-3-methoxybenzaldehyde, ethyl chloroacetate, and/or diethyl oxalate to produce quinazoline derivatives 5, 6, and 12, respectively. The results of the pharmacological study indicated that the synthesized 4-6 and 12 derivatives showed good 3CLpro, cPLA2, and sPLA2 inhibitory activity. The IC50 values of the target compounds 4-6, and 12 against the SARS-CoV-2 main protease were 2.012, 3.68, 1.18, and 5.47 µM, respectively, whereas those of baicalein and ivermectin were 1.72 and 42.39 µM, respectively. The IC50 values of the target compounds 4-6, and 12 against sPLA2 were 2.84, 2.73, 1.016, and 4.45 µM, respectively, whereas those of baicalein and ivermectin were 0.89 and 109.6 µM, respectively. The IC50 values of the target compounds 4-6, and 12 against cPLA2 were 1.44, 2.08, 0.5, and 2.39 µM, respectively, whereas those of baicalein and ivermectin were 3.88 and 138.0 µM, respectively. Also, incubation of lung cells with LPS plus derivatives 4-6, and 12 caused a significant decrease in levels of sPLA2, cPLA2, IL-8, TNF-α, and NO. The inhibitory activity of the synthesized compounds was more pronounced compared to baicalein and ivermectin. In contrast to ivermectin and baicalein, bioinformatics investigations were carried out to establish the possible binding interactions between the newly synthesized compounds 2-6 and 12 and the active site of 3CLpro. Docking simulations were utilized to identify the binding affinity and binding mode of compounds 2-6 and 12 with the active sites of 3CLpro, sPLA2, and cPLA2 enzymes. Our findings demonstrated that all compounds had outstanding binding affinities, especially with the key amino acids of the target enzymes. These findings imply that compound 6 is a potential lead for the development of more effective SARS-CoV-2 Mpro inhibitors and anti-COVID-19 quinazoline derivative-based drugs. Compound 6 was shown to have more antiviral activity than baicalein and against 3CLpro. Furthermore, the IC50 value of ivermectin against the SARS-CoV-2 main protease was revealed to be 42.39 µM, indicating that it has low effectiveness.
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Affiliation(s)
- Mohammed Abdalla Hussein
- Biotechnology Department, Faculty of Applied Heath Science Technology, October 6 University, Giza 28125, Egypt;
| | - Rita M. Borik
- Chemistry Department, Faculty of Science (Female Section), Jazan University, Jazan 82621, Saudi Arabia;
| | - Mohamed S. Nafie
- Chemistry Department (Biochemistry Program), Faculty of Science, Suez Canal University, Ismailia 41522, Egypt;
| | - Heba M. Abo-Salem
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Giza 28125, Egypt;
| | - Sylvia A. Boshra
- Department of Biochemistry, Faculty of Pharmacy, October 6 University, Giza 28125, Egypt
| | - Zahraa N. Mohamed
- Medical Laboratory Department, Faculty of Applied Medical Sciences, October 6 University, Giza 28125, Egypt;
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4
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Gupta Y, Savytskyi OV, Coban M, Venugopal A, Pleqi V, Weber CA, Chitale R, Durvasula R, Hopkins C, Kempaiah P, Caulfield TR. Protein structure-based in-silico approaches to drug discovery: Guide to COVID-19 therapeutics. Mol Aspects Med 2023; 91:101151. [PMID: 36371228 PMCID: PMC9613808 DOI: 10.1016/j.mam.2022.101151] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
Abstract
With more than 5 million fatalities and close to 300 million reported cases, COVID-19 is the first documented pandemic due to a coronavirus that continues to be a major health challenge. Despite being rapid, uncontrollable, and highly infectious in its spread, it also created incentives for technology development and redefined public health needs and research agendas to fast-track innovations to be translated. Breakthroughs in computational biology peaked during the pandemic with renewed attention to making all cutting-edge technology deliver agents to combat the disease. The demand to develop effective treatments yielded surprising collaborations from previously segregated fields of science and technology. The long-standing pharmaceutical industry's aversion to repurposing existing drugs due to a lack of exponential financial gain was overrun by the health crisis and pressures created by front-line researchers and providers. Effective vaccine development even at an unprecedented pace took more than a year to develop and commence trials. Now the emergence of variants and waning protections during the booster shots is resulting in breakthrough infections that continue to strain health care systems. As of now, every protein of SARS-CoV-2 has been structurally characterized and related host pathways have been extensively mapped out. The research community has addressed the druggability of a multitude of possible targets. This has been made possible due to existing technology for virtual computer-assisted drug development as well as new tools and technologies such as artificial intelligence to deliver new leads. Here in this article, we are discussing advances in the drug discovery field related to target-based drug discovery and exploring the implications of known target-specific agents on COVID-19 therapeutic management. The current scenario calls for more personalized medicine efforts and stratifying patient populations early on for their need for different combinations of prognosis-specific therapeutics. We intend to highlight target hotspots and their potential agents, with the ultimate goal of using rational design of new therapeutics to not only end this pandemic but also uncover a generalizable platform for use in future pandemics.
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Affiliation(s)
- Yash Gupta
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | - Oleksandr V Savytskyi
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; In Vivo Biosystems, Eugene, OR, USA
| | - Matt Coban
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | | | - Vasili Pleqi
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | - Caleb A Weber
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Rohit Chitale
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA; The Council on Strategic Risks, 1025 Connecticut Ave NW, Washington, DC, USA
| | - Ravi Durvasula
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | | | - Prakasha Kempaiah
- Department of Medicine, Infectious Diseases, Mayo Clinic, Jacksonville, FL, USA
| | - Thomas R Caulfield
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Department of QHS Computational Biology, Mayo Clinic, Jacksonville, FL, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA; Department of Neurosurgery, Mayo Clinic, Jacksonville, FL, USA.
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5
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Asiedu SO, Gupta Y, Nicolaescu V, Gula H, Caulfield TR, Durvasula R, Kempaiah P, Kwofie SK, Wilson MD. Mycolactone: A Broad Spectrum Multitarget Antiviral Active in the Picomolar Range for COVID-19 Prevention and Cure. Int J Mol Sci 2023; 24:ijms24087151. [PMID: 37108313 PMCID: PMC10139166 DOI: 10.3390/ijms24087151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/25/2023] [Accepted: 03/29/2023] [Indexed: 04/29/2023] Open
Abstract
We have previously shown computationally that Mycolactone (MLN), a toxin produced by Mycobacterium ulcerans, strongly binds to Munc18b and other proteins, presumably blocking degranulation and exocytosis of blood platelets and mast cells. We investigated the effect of MLN on endocytosis using similar approaches, and it bound strongly to the N-terminal of the clathrin protein and a novel SARS-CoV-2 fusion protein. Experimentally, we found 100% inhibition up to 60 nM and 84% average inhibition at 30 nM in SARS-CoV-2 live viral assays. MLN was also 10× more potent than remdesivir and molnupiravir. MLN's toxicity against human alveolar cell line A549, immortalized human fetal renal cell line HEK293, and human hepatoma cell line Huh7.1 were 17.12%, 40.30%, and 36.25%, respectively. The cytotoxicity IC50 breakpoint ratio versus anti-SARS-CoV-2 activity was more than 65-fold. The IC50 values against the alpha, delta, and Omicron variants were all below 0.020 µM, and 134.6 nM of MLN had 100% inhibition in an entry and spread assays. MLN is eclectic in its actions through its binding to Sec61, AT2R, and the novel fusion protein, making it a good drug candidate for treating and preventing COVID-19 and other similarly transmitted enveloped viruses and pathogens.
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Affiliation(s)
- Seth Osei Asiedu
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra P.O. Box GA 337, Ghana
| | - Yash Gupta
- Department of Medicine, Division of Infectious Diseases, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - Vlad Nicolaescu
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL 60637, USA
| | - Haley Gula
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL 60637, USA
| | - Thomas R Caulfield
- Department of Neuroscience, Division of QHS Computational Biology, Mayo Clinic, Jacksonville, FL 32224, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ravi Durvasula
- Department of Medicine, Division of Infectious Diseases, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - Prakasha Kempaiah
- Department of Medicine, Division of Infectious Diseases, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - Samuel K Kwofie
- Department of Biomedical Engineering, School of Engineering, University of Ghana, Legon, Accra P.O. Box 77, Ghana
| | - Michael D Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra P.O. Box GA 337, Ghana
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6
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In Silico Binding of 2-Aminocyclobutanones to SARS-CoV-2 Nsp13 Helicase and Demonstration of Antiviral Activity. Int J Mol Sci 2023; 24:ijms24065120. [PMID: 36982188 PMCID: PMC10049026 DOI: 10.3390/ijms24065120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/22/2023] [Accepted: 03/02/2023] [Indexed: 03/10/2023] Open
Abstract
The landscape of viral strains and lineages of SARS-CoV-2 keeps changing and is currently dominated by Delta and Omicron variants. Members of the latest Omicron variants, including BA.1, are showing a high level of immune evasion, and Omicron has become a prominent variant circulating globally. In our search for versatile medicinal chemistry scaffolds, we prepared a library of substituted ɑ-aminocyclobutanones from an ɑ-aminocyclobutanone synthon (11). We performed an in silico screen of this actual chemical library as well as other virtual 2-aminocyclobutanone analogs against seven SARS-CoV-2 nonstructural proteins to identify potential drug leads against SARS-CoV-2, and more broadly against coronavirus antiviral targets. Several of these analogs were initially identified as in silico hits against SARS-CoV-2 nonstructural protein 13 (Nsp13) helicase through molecular docking and dynamics simulations. Antiviral activity of the original hits as well as ɑ-aminocyclobutanone analogs that were predicted to bind more tightly to SARS-CoV-2 Nsp13 helicase are reported. We now report cyclobutanone derivatives that exhibit anti-SARS-CoV-2 activity. Furthermore, the Nsp13 helicase enzyme has been the target of relatively few target-based drug discovery efforts, in part due to a very late release of a high-resolution structure accompanied by a limited understanding of its protein biochemistry. In general, antiviral agents initially efficacious against wild-type SARS-CoV-2 strains have lower activities against variants due to heavy viral loads and greater turnover rates, but the inhibitors we are reporting have higher activities against the later variants than the wild-type (10–20X). We speculate this could be due to Nsp13 helicase being a critical bottleneck in faster replication rates of the new variants, so targeting this enzyme affects these variants to an even greater extent. This work calls attention to cyclobutanones as a useful medicinal chemistry scaffold, and the need for additional focus on the discovery of Nsp13 helicase inhibitors to combat the aggressive and immune-evading variants of concern (VOCs).
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7
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Anjani, Kumar S, Rathi B, Poonam. Recent updates on the biological efficacy of approved drugs and potent synthetic compounds against SARS-CoV-2. RSC Adv 2023; 13:3677-3687. [PMID: 36756584 PMCID: PMC9890797 DOI: 10.1039/d2ra06834f] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 01/16/2023] [Indexed: 01/27/2023] Open
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), also known as COVID-19, has triggered a global pandemic that has prompted severe public health concerns. Researchers worldwide are continuously trying to find options that could be effective against COVID-19. The main focus of research during the initial phase of the pandemic was to use the already approved drugs as supportive care, and efforts were made to find new therapeutic options. Nirmatrelvir (PF-07321332), a Pfizer chemical, recently received approval for usage in conjunction with ritonavir. This mini-review summarises the biological effectiveness of vital synthetic compounds and FDA-approved medications against SARS-CoV-2. Understanding how functional groups are included in the creation of synthetic compounds could help enhance the biological activity profile of those compounds to increase their efficacy against SARS-CoV-2. This opened the way for researchers to explore opportunities to develop better therapeutics by investigating synthetic analogs.
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Affiliation(s)
- Anjani
- Department of Chemistry, Chaudhary Charan Singh Haryana Agricultural University Hisar Haryana-125004 India
| | - Sumit Kumar
- Department of Chemistry, Miranda House, University of Delhi Delhi-110007 India
| | - Brijesh Rathi
- Laboratory for Translational Chemistry and Drug Discovery, Hansraj College, University of Delhi Delhi-110007 India
- Delhi School of Public Health, Institute of Eminence, University of Delhi Delhi-110007 India
| | - Poonam
- Department of Chemistry, Miranda House, University of Delhi Delhi-110007 India
- Delhi School of Public Health, Institute of Eminence, University of Delhi Delhi-110007 India
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8
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Yang Z, Cai X, Ye Q, Zhao Y, Li X, Zhang S, Zhang L. High-Throughput Screening for the Potential Inhibitors of SARS-CoV-2 with Essential Dynamic Behavior. Curr Drug Targets 2023; 24:532-545. [PMID: 36876836 DOI: 10.2174/1389450124666230306141725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 11/09/2022] [Accepted: 01/11/2023] [Indexed: 03/07/2023]
Abstract
Global health security has been challenged by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic. Due to the lengthy process of generating vaccinations, it is vital to reposition currently available drugs in order to relieve anti-epidemic tensions and accelerate the development of therapies for Coronavirus Disease 2019 (COVID-19), the public threat caused by SARS-CoV-2. High throughput screening techniques have established their roles in the evaluation of already available medications and the search for novel potential agents with desirable chemical space and more cost-effectiveness. Here, we present the architectural aspects of highthroughput screening for SARS-CoV-2 inhibitors, especially three generations of virtual screening methodologies with structural dynamics: ligand-based screening, receptor-based screening, and machine learning (ML)-based scoring functions (SFs). By outlining the benefits and drawbacks, we hope that researchers will be motivated to adopt these methods in the development of novel anti- SARS-CoV-2 agents.
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Affiliation(s)
- Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Xinhui Cai
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Qiushi Ye
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Yizhen Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Xuhua Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
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9
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Bouzina A, Berredjem M, Bouacida S, Bachari K, Marminon C, Borgne ML, Bouaziz Z, Bouone YO. Synthesis, in silico study (DFT, ADMET) and crystal structure of novel sulfamoyloxy-oxazolidinones: Interaction with SARS-CoV-2. J Mol Struct 2022; 1257:132579. [PMID: 35153333 PMCID: PMC8817226 DOI: 10.1016/j.molstruc.2022.132579] [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: 12/11/2021] [Revised: 01/28/2022] [Accepted: 02/03/2022] [Indexed: 12/16/2022]
Abstract
A new series of sulfamoyloxyoxazolidinone (SOO) derivatives have been synthesized and characterized by single-crystal X-ray diffraction, NMR, IR, MS and EA. Chemical reactivity and geometrical characteristics of the target compounds were investigated using DFT method. The possible binding mode between SOO and Main protease (Mpro) of SARS-CoV-2 and their reactivity were studied using molecular docking simulation. Single crystal X-ray diffraction showed that SOO crystallizes in a monoclinic system with P 2 1 space group. The binding energy of the SARS-CoV-2/Mpro-SOO complex and the calculated inhibition constant using docking simulation showed that the active SOO molecule has the ability to inhibit SARS-CoV2. We studied the prediction of absorption, distribution, properties of metabolism, excretion and toxicity (ADMET) of the synthesized molecules.
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Affiliation(s)
- Abdeslem Bouzina
- Department of Chemistry, Laboratory of Applied Organic Chemistry, Synthesis of Biomolecules and Molecular Modelling Group, Sciences Faculty, Badji-Mokhtar-Annaba University, Box 12, Annaba 23000, Algeria
| | - Malika Berredjem
- Department of Chemistry, Laboratory of Applied Organic Chemistry, Synthesis of Biomolecules and Molecular Modelling Group, Sciences Faculty, Badji-Mokhtar-Annaba University, Box 12, Annaba 23000, Algeria
| | - Sofiane Bouacida
- Unité de Recherche de Chimie de L'Environnement et Moléculaire Structurale, Université des Fréres Mentouri, Constantine 25000, Algeria
- Département des Sciences de La Matiére, Université Larbi Ben M'Hidi, Oum El Bouaghi 04000, Algeria
| | - Khaldoun Bachari
- Centre de Recherche Scientifique et Technique en Analyses Physico-Chimiques (CRAPC), BP384, Bou-Ismail, Tipasa RP 42004, Algeria
| | - Christelle Marminon
- Small Molecules for Biological Targets Team, Centre de Recherche en Cancérologie de Lyon, Centre Léon Bérard, CNRS 5286, INSERM 1052, Université Claude Bernard Lyon 1, Univ Lyon, Lyon 69373, France
| | - Marc Le Borgne
- Small Molecules for Biological Targets Team, Centre de Recherche en Cancérologie de Lyon, Centre Léon Bérard, CNRS 5286, INSERM 1052, Université Claude Bernard Lyon 1, Univ Lyon, Lyon 69373, France
| | - Zouhair Bouaziz
- Faculté de Pharmacie-ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry, SFR Santé Lyon-Est CNRS UMS3453-INSERM US7, Université de Lyon, Université Lyon 1, CEDEX 8, Lyon 69373, France
| | - Yousra Ouafa Bouone
- Department of Chemistry, Laboratory of Applied Organic Chemistry, Synthesis of Biomolecules and Molecular Modelling Group, Sciences Faculty, Badji-Mokhtar-Annaba University, Box 12, Annaba 23000, Algeria
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10
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da Silva-Júnior EF, Zhan P. Current trends in designing antiviral agents against emerging and re-emerging RNA viruses. Bioorg Med Chem 2022; 62:116741. [PMID: 35397970 PMCID: PMC8975753 DOI: 10.1016/j.bmc.2022.116741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
| | - Peng Zhan
- School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
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11
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Kumar S, Sharma N, Dantas WM, do Nascimento JCF, Maus H, de Oliveira RN, Pandit U, Singh AP, Schirmeister T, Hazari PP, Pena L, Poonam, Rathi B. A potent candidate against Zika virus infection: Synthesis, bioactivity, radiolabeling and biodistribution studies. NEW J CHEM 2022. [DOI: 10.1039/d2nj02482a] [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
Compound VI exhibits potent activity against Zika virus infection combined with favorable cellular uptake and biodistribution without apparent cytotoxicity in a mouse model.
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Affiliation(s)
- Sumit Kumar
- Department of Chemistry, Miranda House, University of Delhi, Delhi, 110007, India
| | - Neha Sharma
- Har Gobind Khorana Centre For Chemical Biology, Department of Chemistry, Hansraj College, University of Delhi, Delhi, 110007, India
| | - Willyenne Marilia Dantas
- Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, 50670-420, Pernambuco, Brazil
- Department of Chemistry, Federal Rural University of Pernambuco, Dois Irmãos, 52171-900, Recife, Brazil
| | | | - Hannah Maus
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, 55128, Mainz, Germany
| | | | - Unnat Pandit
- Special Centre for Systems Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Agam P. Singh
- Infectious Diseases Laboratory, National Institute of Immunology, New Delhi, 110067, India
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, 55128, Mainz, Germany
| | - Puja Panwar Hazari
- Division of Cyclotron and Radiopharmaceutical Sciences Institute of Nuclear Medicine and Allied Sciences, New Delhi, 110054, India
| | - Lindomar Pena
- Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, 50670-420, Pernambuco, Brazil
| | - Poonam
- Department of Chemistry, Miranda House, University of Delhi, Delhi, 110007, India
- Delhi School of Public Health, Institution of Eminence, University of Delhi, Delhi, 110007, India
| | - Brijesh Rathi
- Har Gobind Khorana Centre For Chemical Biology, Department of Chemistry, Hansraj College, University of Delhi, Delhi, 110007, India
- Delhi School of Public Health, Institution of Eminence, University of Delhi, Delhi, 110007, India
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12
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Upadhyay C, Sharma N, Kumar S, Sharma PP, Fontinha D, Chhikara BS, Mukherjee B, Kumar D, Prudencio M, Singh AP, Poonam. Synthesis of the new analogs of morpholine and their antiplasmodial evaluation against the human malaria parasite Plasmodium falciparum. NEW J CHEM 2022. [DOI: 10.1039/d1nj04198c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A series of morpholine analogs functionalized with hydroxyethylamine (HEA) pharmacophore was synthesized and assayed for the initial screening against Plasmodium falciparum 3D7 in culture, which suggested that analog 6k is a hit molecule with an inhibitory concentration of 5.059 ± 0.2036 μM.
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Affiliation(s)
- Charu Upadhyay
- Department of Chemistry, Miranda House, University of Delhi, Delhi, India
| | - Neha Sharma
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College University Enclave, University of Delhi, Delhi 110007, India
| | - Sumit Kumar
- Department of Chemistry, Miranda House, University of Delhi, Delhi, India
| | - Prem Prakash Sharma
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College University Enclave, University of Delhi, Delhi 110007, India
| | - Diana Fontinha
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | | | - Budhaditya Mukherjee
- School of Medical Science and Technology, IIT Kharagpur, Kharagpur-721302, India
| | - Dhruv Kumar
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University Uttar Pradesh, Noida, India
| | - Miguel Prudencio
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Agam P. Singh
- Infectious Diseases Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Poonam
- Department of Chemistry, Miranda House, University of Delhi, Delhi, India
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