1
|
Wu HT, Wu BX, Fang ZX, Wu Z, Hou YY, Deng Y, Cui YK, Liu J. Lomitapide repurposing for treatment of malignancies: A promising direction. Heliyon 2024; 10:e32998. [PMID: 38988566 PMCID: PMC11234027 DOI: 10.1016/j.heliyon.2024.e32998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 06/12/2024] [Accepted: 06/12/2024] [Indexed: 07/12/2024] Open
Abstract
The development of novel drugs from basic science to clinical practice requires several years, much effort, and cost. Drug repurposing can promote the utilization of clinical drugs in cancer therapy. Recent studies have shown the potential effects of lomitapide on treating malignancies, which is currently used for the treatment of familial hypercholesterolemia. We systematically review possible functions and mechanisms of lomitapide as an anti-tumor compound, regarding the aspects of apoptosis, autophagy, and metabolism of tumor cells, to support repurposing lomitapide for the clinical treatment of tumors.
Collapse
Affiliation(s)
- Hua-Tao Wu
- Department of General Surgery, the First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, China
- The Breast Center, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China
| | - Bing-Xuan Wu
- Department of General Surgery, the First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, China
- The Breast Center, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China
| | - Ze-Xuan Fang
- The Breast Center, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China
- Department of Physiology/Changjiang Scholar's Laboratory, Shantou University Medical College, Shantou, 515041, China
| | - Zheng Wu
- The Breast Center, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China
- Department of Physiology/Changjiang Scholar's Laboratory, Shantou University Medical College, Shantou, 515041, China
| | - Yan-Yu Hou
- The Breast Center, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China
- Department of Physiology/Changjiang Scholar's Laboratory, Shantou University Medical College, Shantou, 515041, China
| | - Yu Deng
- Department of General Surgery, the First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, China
- The Breast Center, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China
| | - Yu-Kun Cui
- The Breast Center, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China
| | - Jing Liu
- The Breast Center, Cancer Hospital of Shantou University Medical College, Shantou, 515041, China
- Department of Physiology/Changjiang Scholar's Laboratory, Shantou University Medical College, Shantou, 515041, China
| |
Collapse
|
2
|
Rieder GS, Nogara PA, Omage FB, Duarte T, Dalla Corte CL, da Rocha JBT. Computational analysis of the interactions between Ebselen and derivatives with the active site of the main protease from SARS-CoV-2. Comput Biol Chem 2023; 107:107956. [PMID: 37748316 DOI: 10.1016/j.compbiolchem.2023.107956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/27/2023]
Abstract
The main protease (Mpro) of the novel coronavirus SARS-CoV-2 is a key target for developing antiviral drugs. Ebselen (EbSe) is a selenium-containing compound that has been shown to inhibit Mpro in vitro by forming a covalent bond with the cysteine (Cys) residue in the active site of the enzyme. However, EbSe can also bind to other proteins, like albumin, and low molecular weight compounds that have free thiol groups, such as Cys and glutathione (GSH), which may affect its availability and activity. In this study, we analyzed the Mpro interaction with EbSe, its analogues, and its metabolites with Cys, GSH, and albumin by molecular docking. We also simulated the electronic structure of the generated molecules by density functional theory (DFT) and explored the stability of EbSe and one of its best derivatives, EbSe-2,5-MeClPh, in the catalytic pocket of Mpro through covalent docking and molecular dynamics. Our results show that EbSe and its analogues bound to GSH/albumin have larger distance between the selenium atom of the ligands and the sulfur atom of Cys145 of Mpro than the other compounds. This suggests that EbSe and its GSH/albumin-analogues may have less affinity for the active site of Mpro. EbSe-2,5-MeClPh was found one of the best molecules, and in molecular dynamics simulations, it showed to undergo more conformational changes in the active site of Mpro, in relation to EbSe, which remained stable in the catalytic pocket. Moreover, this study also reveals that all compounds have the potential to interact closely with the active site of Mpro, providing us with a concept of which derivatives may be promising for in vitro analysis in the future. We propose that these compounds are potential covalent inhibitors of Mpro and that organoselenium compounds are molecules that should be studied for their antiviral properties.
Collapse
Affiliation(s)
- Guilherme Schmitt Rieder
- Postgraduate Program in Biological Sciences: Toxicological Biochemistry, Federal University of Santa Maria, 97105-900 Santa Maria, RS, Brazil
| | - Pablo Andrei Nogara
- Federal Institute of Education, Science and Technology Sul-rio-grandense (IFSul), Bagé 96418-400, RS, Brazil
| | - Folorunsho Bright Omage
- Biological Chemistry Laboratory, Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil; Computational Biology Research Group, Embrapa Agricultural Informatics, Campinas, São Paulo, Brazil
| | - Tâmie Duarte
- Postgraduate Program in Biological Sciences: Toxicological Biochemistry, Federal University of Santa Maria, 97105-900 Santa Maria, RS, Brazil
| | - Cristiane Lenz Dalla Corte
- Postgraduate Program in Biological Sciences: Toxicological Biochemistry, Federal University of Santa Maria, 97105-900 Santa Maria, RS, Brazil
| | - João Batista Teixeira da Rocha
- Postgraduate Program in Biological Sciences: Toxicological Biochemistry, Federal University of Santa Maria, 97105-900 Santa Maria, RS, Brazil; Department of Biochemistry, Institute of Basic Health Science, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil, 90035-003.
| |
Collapse
|
3
|
Stagnoli S, Macari G, Corsi P, Capone B, Vidaurrazaga A, Ereño-Orbea J, Ardá A, Polticelli F, Jiménez-Barbero J, Abrescia NGA, Coluzza I. Targeting the Spike: Repurposing Mithramycin and Dihydroergotamine to Block SARS-CoV-2 Infection. ACS OMEGA 2023; 8:43490-43499. [PMID: 38027314 PMCID: PMC10666140 DOI: 10.1021/acsomega.3c02921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/15/2023] [Indexed: 12/01/2023]
Abstract
The urgency to find complementary therapies to current SARS-CoV-2 vaccines, whose effectiveness is preserved over time and not compromised by the emergence of new and emerging variants, has become a critical health challenge. We investigate the possibility of jamming the opening of the Receptor Binding Domain (RBD) of the spike protein of SARS-CoV-2 with small compounds. Through in silico screening, we identified two potential candidates that would lock the Receptor Binding Domain (RBD) in a closed configuration, preventing the virus from infecting the host cells. We show that two drugs already approved by the FDA, mithramycin and dihydroergotamine, can block infection using concentrations in the μM range in cell-based assays. Further STD-NMR experiments support dihydroergotamine's direct interaction with the spike protein. Overall, our results indicate that repurposing of these compounds might lead to potential clinical drug candidates for the treatment of SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Soledad Stagnoli
- Structure
and Cell Biology of Viruses Lab, Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research
and Technology Alliance (BRTA), 48160 Derio, Spain
| | - Gabriele Macari
- Department
of Sciences, University of Rome Tre, 00154 Rome, Italy
| | - Pietro Corsi
- Department
of Sciences, University of Rome Tre, 00154 Rome, Italy
| | - Barbara Capone
- Department
of Sciences, University of Rome Tre, 00154 Rome, Italy
| | - Ander Vidaurrazaga
- Structure
and Cell Biology of Viruses Lab, Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research
and Technology Alliance (BRTA), 48160 Derio, Spain
| | - June Ereño-Orbea
- Chemical
Glycobiology Laboratory, CIC bioGUNE, BRTA, 48160 Derio, Spain
- IKERBASQUE,
Basque Foundation for Science, 48009 Bilbao, Spain
| | - Ana Ardá
- Chemical
Glycobiology Laboratory, CIC bioGUNE, BRTA, 48160 Derio, Spain
| | - Fabio Polticelli
- Department
of Sciences, University of Rome Tre, 00154 Rome, Italy
- National
Institute of Nuclear Physics, Roma Tre Section, 00154 Rome, Italy
| | - Jesús Jiménez-Barbero
- Chemical
Glycobiology Laboratory, CIC bioGUNE, BRTA, 48160 Derio, Spain
- IKERBASQUE,
Basque Foundation for Science, 48009 Bilbao, Spain
- Centro
de
Investigación Biomédica En Red de Enfermedades Respiratorias.
(CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department
of Organic & Inorganic Chemistry, Faculty
of Science and Technology University of the Basque Country, EHU-UPV, 48940 Leioa, Spain
| | - Nicola GA Abrescia
- Structure
and Cell Biology of Viruses Lab, Center
for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research
and Technology Alliance (BRTA), 48160 Derio, Spain
- IKERBASQUE,
Basque Foundation for Science, 48009 Bilbao, Spain
- Centro
de Investigación Biomédica en Red de Enfermedades Hepáticas
y Digestivas (CIBERehd), Instituto de Salud
Carlos III, 28029 Madrid, Spain
| | - Ivan Coluzza
- IKERBASQUE,
Basque Foundation for Science, 48009 Bilbao, Spain
- Computational
Soft Matter and Biophysics Lab, Basque Center
for Materials, Applications and Nanostructures (BCMaterials), Buil. Martina Casiano, Pl. 3 Parque
Científico UPV/EHU Barrio Sarriena, 48940 Leioa, Spain
| |
Collapse
|
4
|
De Vita S, Chini MG, Bifulco G, Lauro G. Target identification by structure-based computational approaches: Recent advances and perspectives. Bioorg Med Chem Lett 2023; 83:129171. [PMID: 36739998 DOI: 10.1016/j.bmcl.2023.129171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 12/15/2022] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
Abstract
The use of computational techniques in the early stages of drug discovery has recently experienced a boost, especially in the target identification step. Finding the biological partner(s) for new or existing synthetic and/or natural compounds by "wet" approaches may be challenging; therefore, preliminary in silico screening is even more recommended. After a brief overview of some of the most known target identification techniques, recent advances in structure-based computational approaches for target identification are reported in this digest, focusing on Inverse Virtual Screening and its recent applications. Moreover, future perspectives concerning the use of such methodologies, coupled or not with other approaches, are analyzed.
Collapse
Affiliation(s)
- Simona De Vita
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy
| | - Maria Giovanna Chini
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche (IS), Italy
| | - Giuseppe Bifulco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy.
| | - Gianluigi Lauro
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy.
| |
Collapse
|
5
|
Firouzi R, Ashouri M. Identification of Potential Anti‐COVID‐19 Drug Leads from Medicinal Plants through Virtual High‐Throughput Screening. ChemistrySelect 2023. [DOI: 10.1002/slct.202203865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- Rohoullah Firouzi
- Department of Physical Chemistry Chemistry and Chemical Engineering Research Center of Iran Tehran Iran
| | - Mitra Ashouri
- Department of Physical Chemistry School of Chemistry College of Science University of Tehran Tehran Iran
| |
Collapse
|
6
|
Paul DS, Karthe P. Improved docking of peptides and small molecules in iMOLSDOCK. J Mol Model 2023; 29:12. [DOI: 10.1007/s00894-022-05413-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022]
|
7
|
Pharmacophore model-aided virtual screening combined with comparative molecular docking and molecular dynamics for identification of marine natural products as SARS-CoV-2 papain-like protease inhibitors. ARAB J CHEM 2022; 15:104334. [PMID: 36246784 PMCID: PMC9554199 DOI: 10.1016/j.arabjc.2022.104334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 10/03/2022] [Indexed: 11/24/2022] Open
Abstract
Targeting SARS-CoV-2 papain-like protease using inhibitors is a suitable approach for inhibition of virus replication and dysregulation of host anti-viral immunity. Engaging all five binding sites far from the catalytic site of PLpro is essential for developing a potent inhibitor. We developed and validated a structure-based pharmacophore model with 9 features of a potent PLpro inhibitor. The pharmacophore model-aided virtual screening of the comprehensive marine natural product database predicted 66 initial hits. This hit library was downsized by filtration through a molecular weight filter of ≤ 500 g/mol. The 50 resultant hits were screened by comparative molecular docking using AutoDock and AutoDock Vina. Comparative molecular docking enables benchmarking docking and relieves the disparities in the search and scoring functions of docking engines. Both docking engines retrieved 3 same compounds at different positions in the top 1 % rank, hence consensus scoring was applied, through which CMNPD28766, aspergillipeptide F emerged as the best PLpro inhibitor. Aspergillipeptide F topped the 50-hit library with a pharmacophore-fit score of 75.916. Favorable binding interactions were predicted between aspergillipeptide F and PLpro similar to the native ligand XR8-24. Aspergillipeptide F was able to engage all the 5 binding sites including the newly discovered BL2 groove, site V. Molecular dynamics for quantification of Cα-atom movements of PLpro after ligand binding indicated that it exhibits highly correlated domain movements contributing to the low free energy of binding and a stable conformation. Thus, aspergillipeptide F is a promising candidate for pharmaceutical and clinical development as a potent SARS-CoV-2 PLpro inhibitor.
Collapse
Key Words
- CMNPD, comprehensive marine natural product database
- Consensus scoring
- DCCM, dynamic cross-correlation matrix
- H, hydrophobic
- HBA, hydrogen bond acceptor
- HBD, hydrogen bond donor
- MD, molecular dynamics
- MMGBSA, molecular mechanics generalized Born and surface area continuum solvation
- MW, molecular weight
- Marine natural products
- Molecular docking
- Molecular dynamics
- PCA, principal component analysis
- PI, positive ionization
- PLpro, SARS-CoV-2 papain-like protease
- Pharmacophore model
- SARS-CoV-2 PLpro
- TG, Total gain
- ns, nanoseconds
- ps, picoseconds
Collapse
|
8
|
Geng Z, Yang Y, Yang S, Zhou J, Lyu H. Purification of rutin by supercritical fluid simulated moving bed chromatography. CAN J CHEM ENG 2022. [DOI: 10.1002/cjce.24237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Zhongfeng Geng
- Key Laboratory for Green Chemical Technology of Ministry of Education, R&D Center for Petrochemical Technology Tianjin University Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering Tianjin China
| | - Yuzhu Yang
- Key Laboratory for Green Chemical Technology of Ministry of Education, R&D Center for Petrochemical Technology Tianjin University Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering Tianjin China
| | - Shuyuan Yang
- Key Laboratory for Green Chemical Technology of Ministry of Education, R&D Center for Petrochemical Technology Tianjin University Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering Tianjin China
| | - Jinyi Zhou
- Key Laboratory for Green Chemical Technology of Ministry of Education, R&D Center for Petrochemical Technology Tianjin University Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering Tianjin China
| | - Huisheng Lyu
- Key Laboratory for Green Chemical Technology of Ministry of Education, R&D Center for Petrochemical Technology Tianjin University Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering Tianjin China
| |
Collapse
|
9
|
Borges EL, Goulart HA, Perin G, Schneider PH, Rieder GS, Nogara PA, da Rocha JBT. One-Pot Synthesis and in Silico Molecular Docking Studies of Arylselanyl Hydrazides as Potential Antituberculosis Agents. Chem Biodivers 2022; 19:e202100793. [PMID: 35293125 DOI: 10.1002/cbdv.202100793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 03/14/2022] [Indexed: 11/06/2022]
Abstract
The present study reports a simple two-step method for the synthesis of arylselanyl hydrazide derivatives using hypophosphorous acid and polyethylene glycol (H3 PO2 /PEG-400) as an alternative reducing system and hydrazine hydrate (NH2 NH2 ⋅xH2 O/50-60 %). This single-vessel procedure was employed with methyl acrylate 2a and methyl bromoacetate 2b using diaryl diselenides to generate the nucleophile species to produce, respectively, 3-(arylselanyl)propane-hydrazides 4a-e and 2-(arylselanyl)acetohydrazides 5a-e with good yields by accelerating the reduction of -Se-Se- bond, when compared to available methods. The synthesized molecules are structurally similar to the isoniazid (INH). Therefore, we perform in silico molecular docking studies, using the lactoperoxidase enzyme, in order to verify whether the INH Se derivatives could interact in a similar way to INH at the active site of the mammalian enzyme. The in silico results indicated a similar type of interaction of the arylselanyl hydrazide derivatives with that of INH. In view of the similar in silico interaction of the selenium derivatives of INH, the arylselanyl hydrazide derivatives reported here should be tested against Mycobacterium tuberculosis in vitro.
Collapse
Affiliation(s)
- Elton L Borges
- Grupo de Pesquisa em Síntese Orgânica da Região Amazônica (LASORA, DAEPA), Fundação Universidade Federal de Rondônia (UNIR), Rua da Paz 4376, 76916-000, Presidente Médici, RO, Brazil
| | - Helen A Goulart
- Laboratório de Síntese Orgânica Limpa (LASOL, CCQFA), Universidade Federal de Pelotas (UFPel), PO Box 354, 96010-900, Pelotas, RS, Brazil
| | - Gelson Perin
- Laboratório de Síntese Orgânica Limpa (LASOL, CCQFA), Universidade Federal de Pelotas (UFPel), PO Box 354, 96010-900, Pelotas, RS, Brazil
| | - Paulo H Schneider
- Instituto de Química, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970, Porto Alegre, RS, Brazil
| | - Guilherme S Rieder
- Programa de Pós-graduação em Ciências Biológicas: Bioquímica Toxicológica, Universidade Federal de Santa Maria (UFSM), 97105-90, Santa Maria, RS, Brazil
| | - Pablo A Nogara
- Programa de Pós-graduação em Ciências Biológicas: Bioquímica Toxicológica, Universidade Federal de Santa Maria (UFSM), 97105-90, Santa Maria, RS, Brazil
| | - João B T da Rocha
- Programa de Pós-graduação em Ciências Biológicas: Bioquímica Toxicológica, Universidade Federal de Santa Maria (UFSM), 97105-90, Santa Maria, RS, Brazil
| |
Collapse
|
10
|
Kittakoop P, Darshana D, Sangsuwan R, Mahidol C. Alkaloids and Alkaloid-Like Compounds are Potential Scaffolds of Antiviral Agents against SARS-CoV-2 (COVID-19) Virus. HETEROCYCLES 2022. [DOI: 10.3987/rev-22-sr(r)3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
11
|
Azam F, Eid EEM, Almutairi A. Targeting SARS-CoV-2 main protease by teicoplanin: A mechanistic insight by docking, MM/GBSA and molecular dynamics simulation. J Mol Struct 2021; 1246:131124. [PMID: 34305175 PMCID: PMC8286173 DOI: 10.1016/j.molstruc.2021.131124] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 07/05/2021] [Accepted: 07/14/2021] [Indexed: 12/16/2022]
Abstract
First emerged in late December 2019, the outbreak of novel severe acute respiratory syndrome corona virus-2 (SARS-CoV-2) pandemic has instigated public-health emergency around the globe. Till date there is no specific therapeutic agent for this disease and hence, the world is craving to identify potential antiviral agents against SARS-CoV-2. The main protease (MPro) is considered as an attractive drug target for rational drug design against SARS-CoV-2 as it is known to play a crucial role in the viral replication and transcription. Teicoplanin is a glycopeptide class of antibiotic which is regularly used for treating Gram-positive bacterial infections, has shown potential therapeutic efficacy against SARS-CoV-2 in vitro. Therefore, in this study, a mechanistic insight of intermolecular interactions between teicoplanin and SARS-CoV-2 MPro has been scrutinized by molecular docking. Both monomeric and dimeric forms of MPro was used in docking involving blind as well as defined binding site based on the known inhibitor. Binding energies of teicoplanin-MPro complexes were estimated by Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) computations from docking and simulated trajectories. The dynamic and thermodynamics constraints of docked drug in complex with target proteins under specific physiological conditions was ascertained by all-atom molecular dynamics simulation of 100 ns trajectory. Root mean square deviation and fluctuation of carbon α chain justified the stability of the bound complex in biological environments. The outcomes of current study are supposed to be fruitful in rational design of antiviral drugs against SARS-CoV-2.
Collapse
|
12
|
Chini MG, Lauro G, Bifulco G. Addressing the Target Identification and Accelerating the Repositioning of Anti‐Inflammatory/Anti‐Cancer Organic Compounds by Computational Approaches. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Maria Giovanna Chini
- Department of Biosciences and Territory University of Molise C.da Fonte Lappone 86090 Pesche (IS) Italy
| | - Gianluigi Lauro
- Department of Pharmacy University of Salerno Via Giovanni Paolo II 132 84084 Fisciano (SA) Italy
| | - Giuseppe Bifulco
- Department of Pharmacy University of Salerno Via Giovanni Paolo II 132 84084 Fisciano (SA) Italy
| |
Collapse
|
13
|
Aatif M, Muteeb G, Alsultan A, Alshoaibi A, Khelif BY. Dieckol and Its Derivatives as Potential Inhibitors of SARS-CoV-2 Spike Protein (UK Strain: VUI 202012/01): A Computational Study. Mar Drugs 2021; 19:242. [PMID: 33922914 PMCID: PMC8145291 DOI: 10.3390/md19050242] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 02/06/2023] Open
Abstract
The high risk of morbidity and mortality associated with SARS-CoV-2 has accelerated the development of many potential vaccines. However, these vaccines are designed against SARS-CoV-2 isolated in Wuhan, China, and thereby may not be effective against other SARS-CoV-2 variants such as the United Kingdom variant (VUI-202012/01). The UK SARS-CoV-2 variant possesses D614G mutation in the Spike protein, which impart it a high rate of infection. Therefore, newer strategies are warranted to design novel vaccines and drug candidates specifically designed against the mutated forms of SARS-CoV-2. One such strategy is to target ACE2 (angiotensin-converting enzyme2)-Spike protein RBD (receptor binding domain) interaction. Here, we generated a homology model of Spike protein RBD of SARS-CoV-2 UK strain and screened a marine seaweed database employing different computational approaches. On the basis of high-throughput virtual screening, standard precision, and extra precision molecular docking, we identified BE011 (Dieckol) as the most potent compounds against RBD. However, Dieckol did not display drug-like properties, and thus different derivatives of it were generated in silico and evaluated for binding potential and drug-like properties. One Dieckol derivative (DK07) displayed good binding affinity for RBD along with acceptable physicochemical, pharmacokinetic, drug-likeness, and ADMET properties. Analysis of the RBD-DK07 interaction suggested the formation of hydrogen bonds, electrostatic interactions, and hydrophobic interactions with key residues mediating the ACE2-RBD interaction. Molecular dynamics simulation confirmed the stability of the RBD-DK07 complex. Free energy calculations suggested the primary role of electrostatic and Van der Waals' interaction in stabilizing the RBD-DK07 complex. Thus, DK07 may be developed as a potential inhibitor of the RBD-ACE2 interaction. However, these results warrant further validation by in vitro and in vivo studies.
Collapse
Affiliation(s)
- Mohammad Aatif
- Department of Public Health, College of Applied Medical Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia;
| | - Ghazala Muteeb
- Department of Nursing, College of Applied Medical Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia;
| | - Abdulrahman Alsultan
- Department of Biomedical Sciences, College of Applied Medical Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia;
| | - Adil Alshoaibi
- Department of Physics, College of Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia;
| | - Bachir Yahia Khelif
- Department of Public Health, College of Applied Medical Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia;
| |
Collapse
|
14
|
Kumar S, Singh B, Kumari P, Kumar PV, Agnihotri G, Khan S, Kant Beuria T, Syed GH, Dixit A. Identification of multipotent drugs for COVID-19 therapeutics with the evaluation of their SARS-CoV2 inhibitory activity. Comput Struct Biotechnol J 2021; 19:1998-2017. [PMID: 33841751 PMCID: PMC8025584 DOI: 10.1016/j.csbj.2021.04.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/04/2021] [Accepted: 04/04/2021] [Indexed: 12/12/2022] Open
Abstract
The SARS-CoV2 is a highly contagious pathogen that causes COVID-19 disease. It has affected millions of people globally with an average lethality of ~3%. There is an urgent need of drugs for the treatment of COVID-19. In the current studies, we have used bioinformatics techniques to screen the FDA approved drugs against nine SARS-CoV2 proteins to identify drugs for repurposing. Additionally, we analyzed if the identified molecules can also affect the human proteins whose expression in lung changed during SARS-CoV2 infection. Targeting such genes may also be a beneficial strategy to curb disease manifestation. We have identified 74 molecules that can bind to various SARS-CoV2 and human host proteins. We experimentally validated our in-silico predictions using vero E6 cells infected with SARS-CoV2 virus. Interestingly, many of our predicted molecules viz. capreomycin, celecoxib, mefloquine, montelukast, and nebivolol showed good activity (IC50) against SARS-CoV2. We hope that these studies may help in the development of new therapeutic options for the treatment of COVID-19.
Collapse
Affiliation(s)
- Sugandh Kumar
- Institute of Life Science, Nalco Square, Bhubaneswar, Odisha 751023, India
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT) University, Bhubaneswar, Odisha 751024, India
| | - Bharati Singh
- Institute of Life Science, Nalco Square, Bhubaneswar, Odisha 751023, India
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT) University, Bhubaneswar, Odisha 751024, India
| | - Pratima Kumari
- Institute of Life Science, Nalco Square, Bhubaneswar, Odisha 751023, India
- Regional Centre for Biotechnology (RCB), 3rd Milestone, Faridabad-Gurgaon, Haryana 121001, India
| | - Preethy V. Kumar
- Institute of Life Science, Nalco Square, Bhubaneswar, Odisha 751023, India
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT) University, Bhubaneswar, Odisha 751024, India
| | - Geetanjali Agnihotri
- School of Chemical Technology, Kalinga Institute of Industrial Technology (KIIT) University, Bhubaneswar, Odisha 751024, India
| | - Shaheerah Khan
- Institute of Life Science, Nalco Square, Bhubaneswar, Odisha 751023, India
- Regional Centre for Biotechnology (RCB), 3rd Milestone, Faridabad-Gurgaon, Haryana 121001, India
| | - Tushar Kant Beuria
- Institute of Life Science, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Gulam Hussain Syed
- Institute of Life Science, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Anshuman Dixit
- Institute of Life Science, Nalco Square, Bhubaneswar, Odisha 751023, India
| |
Collapse
|
15
|
Targeting multiple conformations of SARS-CoV2 Papain-Like Protease for drug repositioning: An in-silico study. Comput Biol Med 2021; 131:104295. [PMID: 33662683 PMCID: PMC7902231 DOI: 10.1016/j.compbiomed.2021.104295] [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: 12/24/2020] [Revised: 02/15/2021] [Accepted: 02/19/2021] [Indexed: 12/16/2022]
Abstract
Papain-Like Protease (PLpro) is a key protein for SARS-CoV-2 viral replication which is the cause of the emerging COVID-19 pandemic. Targeting PLpro can suppress viral replication and provide treatment options for COVID-19. Due to the dynamic nature of its binding site loop, PLpro multiple conformations were generated through a long-range 1 micro-second molecular dynamics (MD) simulation. Clustering the MD trajectory enabled us to extract representative structures for the conformational space generated. Adding to the MD representative structures, X-ray structures were involved in an ensemble docking approach to screen the FDA approved drugs for a drug repositioning endeavor. Guided by our recent benchmarking study of SARS-CoV-2 PLpro, FRED docking software was selected for such a virtual screening task. The results highlighted potential consensus binders to many of the MD clusters as well as the newly introduced X-ray structure of PLpro complexed with a small molecule. For instance, three drugs Benserazide, Dobutamine and Masoprocol showed a superior consensus enrichment against the PLpro conformations. Further MD simulations for these drugs complexed with PLpro suggested the superior stability and binding of dobutamine and masoprocol inside the binding site compared to Benserazide. Generally, this approach can facilitate identifying drugs for repositioning via targeting multiple conformations of a crucial target for the rapidly emerging COVID-19 pandemic.
Collapse
|
16
|
El Hassab MA, Ibrahim TM, Shoun AA, Al-Rashood ST, Alkahtani HM, Alharbi A, Eskandrani RO, Eldehna WM. In silico identification of potential SARS COV-2 2′-O-methyltransferase inhibitor: fragment-based screening approach and MM-PBSA calculations. RSC Adv 2021; 11:16026-16033. [PMID: 35481212 PMCID: PMC9029993 DOI: 10.1039/d1ra01809d] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 04/12/2021] [Indexed: 12/22/2022] Open
Abstract
In the present era, there are many efforts trying to face the emerging and successive waves of the COVID-19 pandemic. This has led to considering new and unusual targets for SARS CoV-2. 2′-O-Methyltransferase (nsp16) is a key and attractive target in the SARS CoV-2 life cycle since it is responsible for the viral RNA protection via a cap formation process. In this study, we propose a new potential inhibitor for SARS COV-2 2′-O-methyltransferase (nsp16). A fragment library was screened against the co-crystal structure of the SARS COV-2 2′-O-methyltransferase complexed with Sinefungin (nsp16 – PDB ID: 6WKQ), and consequently the best proposed fragments were linked via a de novo approach to build molecule AP-20. Molecule AP-20 displayed a superior docking score to Sinefungin and reproduced the key interactions in the binding site of 2′-O-methyltransferase. Three molecular dynamic simulations of the 2′-O-methyltransferase apo structure and its complexed forms with AP-20 and Sinefungin were performed for 150 nano-seconds to provide insights on the dynamic nature of such setups and to assess the stability of the proposed AP-20/enzyme complex. AP-20/enzyme complex demonstrated better stability for the ligand–enzyme complex compared to Sinefungin in a respective setup. Furthermore, MM-PBSA binding free energy calculations showed a better profile for AP-20/enzyme complex compared to Sinefungin/enzyme complex emphasizing the potential inhibitory effect of AP-20 on SARS COV-2 2′-O-methyltransferase. We endorse our designed molecule AP-20 to be further explored via experimental evaluations to confront the spread of the emerging COVID-19. Also, in silico ADME profiling has ascribed to AP-20 an excellent safety and metabolic stability profile. The identification of AP-20 as a potential SARS COV-2 2′-O-methyltransferase inhibitor: fragment-based screening approach and MM-PBSA calculations.![]()
Collapse
Affiliation(s)
- Mahmoud A. El Hassab
- Department of Pharmaceutical Chemistry
- School of Pharmacy
- Badr University in Cairo (BUC)
- Cairo
- Egypt
| | - Tamer M. Ibrahim
- Department of Pharmaceutical Chemistry
- Faculty of Pharmacy
- Kafrelsheikh University
- Kafrelsheikh
- Egypt
| | - Aly A. Shoun
- Department of Microbiology & Immunology
- Faculty of Pharmacy
- Sinai University
- North Sinai
- Egypt
| | - Sara T. Al-Rashood
- Department of Pharmaceutical Chemistry
- College of Pharmacy
- King Saud University
- Riyadh
- Saudi Arabia
| | - Hamad M. Alkahtani
- Department of Pharmaceutical Chemistry
- College of Pharmacy
- King Saud University
- Riyadh
- Saudi Arabia
| | - Amal Alharbi
- Department of Pharmaceutical Chemistry
- College of Pharmacy
- King Saud University
- Riyadh
- Saudi Arabia
| | - Razan O. Eskandrani
- Department of Pharmaceutical Chemistry
- College of Pharmacy
- King Saud University
- Riyadh
- Saudi Arabia
| | - Wagdy M. Eldehna
- Department of Pharmaceutical Chemistry
- Faculty of Pharmacy
- Kafrelsheikh University
- Kafrelsheikh
- Egypt
| |
Collapse
|