1
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El-Hddad SSA, Sobhy MH, El-Morsy A, Shoman NA, El-Adl K. Quinazolines and thiazolidine-2,4-dions as SARS-CoV-2 inhibitors: repurposing, in silico molecular docking and dynamics simulation. RSC Adv 2024; 14:13237-13250. [PMID: 38655479 PMCID: PMC11037030 DOI: 10.1039/d4ra02029d] [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: 03/16/2024] [Accepted: 04/18/2024] [Indexed: 04/26/2024] Open
Abstract
This paper presents an extensive analysis of COVID-19 with a specific focus on VEGFR-2 inhibitors as potential treatments. The investigation includes an overview of computational methodologies employed in drug repurposing and highlights in silico research aimed at developing treatments for SARS-CoV-2. The study explores the possible effects of twenty-eight established VEGFR-2 inhibitors, which include amide and urea linkers, against SARS-CoV-2. Among these, nine inhibitors exhibit highly promising in silico outcomes (designated as 3-6, 11, 24, 26, 27, and sorafenib) and are subjected to extensive molecular dynamics (MD) simulations to evaluate the binding modes and affinities of these inhibitors to the SARS-CoV-2 Mpro across a 100 ns timeframe. Additionally, MD simulations are conducted to ascertain the binding free energy of the most compelling ligand-pocket complexes identified through docking studies. The findings provide valuable understanding regarding the dynamic and thermodynamic properties of the interactions between ligands and pockets, reinforcing the outcomes of the docking studies and presenting promising prospects for the creation of therapeutic treatments targeting COVID-19.
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Affiliation(s)
- Sanadelaslam S A El-Hddad
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Omar Almukhtar University Al Bayda 991 Libya
| | - Mohamed H Sobhy
- Chemistry Department, Faculty of Pharmacy, Heliopolis University for Sustainable Development Cairo Egypt
| | - Ahmed El-Morsy
- Pharmaceutical Chemistry Department, College of Pharmacy, The Islamic University Najaf Iraq
| | - Nabil A Shoman
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Ahram Canadian University Giza Egypt
| | - Khaled El-Adl
- Chemistry Department, Faculty of Pharmacy, Heliopolis University for Sustainable Development Cairo Egypt
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University Cairo11884 Egypt
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2
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Donati G, Viviano M, D'Amore VM, Cipriano A, Diakogiannaki I, Amato J, Tomassi S, Brancaccio D, Russomanno P, Di Leva FS, Arosio D, Seneci P, Taliani S, Magiera-Mularz K, Musielak B, Skalniak L, Holak TA, Castellano S, La Pietra V, Marinelli L. A combined approach of structure-based virtual screening and NMR to interrupt the PD-1/PD-L1 axis: Biphenyl-benzimidazole containing compounds as novel PD-L1 inhibitors. Arch Pharm (Weinheim) 2024; 357:e2300583. [PMID: 38110703 DOI: 10.1002/ardp.202300583] [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: 10/10/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/20/2023]
Abstract
Immunotherapy has emerged as a game-changing approach for cancer treatment. Although monoclonal antibodies (mAbs) targeting the programmed cell death protein 1/programmed cell death protein 1 ligand 1 (PD-1/PD-L1) axis have entered the market revolutionizing the treatment landscape of many cancer types, small molecules, although presenting several advantages including the possibility of oral administration and/or reduced costs, struggled to enter in clinical trials, suffering of water insolubility and/or inadequate potency compared with mAbs. Thus, the search for novel scaffolds for both the design of effective small molecules and possible synergistic strategies is an ongoing field of interest. In an attempt to find novel chemotypes, a virtual screening approach was employed, resulting in the identification of new chemical entities with a certain binding capability, the most versatile of which was the benzimidazole-containing compound 10. Through rational design, a small library of its derivatives was synthesized and evaluated. The homogeneous time-resolved fluorescence (HTRF) assay revealed that compound 17 shows the most potent inhibitory activity (IC50 ) in the submicromolar range and notably, differently from the major part of PD-L1 inhibitors, exhibits satisfactory water solubility properties. These findings highlight the potential of benzimidazole-based compounds as novel promising candidates for PD-L1 inhibition.
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Affiliation(s)
- Greta Donati
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Monica Viviano
- Department of Pharmacy, University of Salerno, Fisciano, Italy
| | | | | | | | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Stefano Tomassi
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Diego Brancaccio
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | | | | | - Daniela Arosio
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), Consiglio Nazionale delle Ricerche (CNR), Milan, Italy
| | | | | | | | - Bogdan Musielak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Cracow, Poland
| | - Lukasz Skalniak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Cracow, Poland
| | - Tad A Holak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Cracow, Poland
| | | | - Valeria La Pietra
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Luciana Marinelli
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
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3
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Temizer AB, Uludoğan G, Özçelik R, Koulani T, Ozkirimli E, Ulgen KO, Karali N, Özgür A. Exploring data-driven chemical SMILES tokenization approaches to identify key protein-ligand binding moieties. Mol Inform 2024; 43:e202300249. [PMID: 38196065 DOI: 10.1002/minf.202300249] [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: 09/19/2023] [Revised: 11/13/2023] [Accepted: 01/06/2024] [Indexed: 01/11/2024]
Abstract
Machine learning models have found numerous successful applications in computational drug discovery. A large body of these models represents molecules as sequences since molecular sequences are easily available, simple, and informative. The sequence-based models often segment molecular sequences into pieces called chemical words, analogous to the words that make up sentences in human languages, and then apply advanced natural language processing techniques for tasks such as de novo drug design, property prediction, and binding affinity prediction. However, the chemical characteristics and significance of these building blocks, chemical words, remain unexplored. To address this gap, we employ data-driven SMILES tokenization techniques such as Byte Pair Encoding, WordPiece, and Unigram to identify chemical words and compare the resulting vocabularies. To understand the chemical significance of these words, we build a language-inspired pipeline that treats high affinity ligands of protein targets as documents and selects key chemical words making up those ligands based on tf-idf weighting. The experiments on multiple protein-ligand affinity datasets show that despite differences in words, lengths, and validity among the vocabularies generated by different subword tokenization algorithms, the identified key chemical words exhibit similarity. Further, we conduct case studies on a number of target to analyze the impact of key chemical words on binding. We find that these key chemical words are specific to protein targets and correspond to known pharmacophores and functional groups. Our approach elucidates chemical properties of the words identified by machine learning models and can be used in drug discovery studies to determine significant chemical moieties.
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Affiliation(s)
- Asu Busra Temizer
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, İstanbul University, İstanbul, Turkey
- Department of Pharmaceutical Chemistry, Institute of Health Sciences, İstanbul University, İstanbul, Turkey
| | - Gökçe Uludoğan
- Department of Computer Engineering, Boğaziçi University, İstanbul, Turkey
| | - Rıza Özçelik
- Department of Computer Engineering, Boğaziçi University, İstanbul, Turkey
| | - Taha Koulani
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, İstanbul University, İstanbul, Turkey
- Department of Pharmaceutical Chemistry, Institute of Health Sciences, İstanbul University, İstanbul, Turkey
| | - Elif Ozkirimli
- Science and Research Informatics, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Kutlu O Ulgen
- Department of Chemical Engineering, Boğaziçi University, İstanbul, Turkey
| | - Nilgun Karali
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, İstanbul University, İstanbul, Turkey
| | - Arzucan Özgür
- Department of Computer Engineering, Boğaziçi University, İstanbul, Turkey
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4
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El-Hddad S, Sobhy M, Ayoub A, El-Adl K. In silico molecular docking, dynamics simulation and repurposing of some VEGFR-2 inhibitors based on the SARS-CoV-2-main-protease inhibitor N3. J Biomol Struct Dyn 2023; 41:9267-9281. [PMID: 36399002 DOI: 10.1080/07391102.2022.2148000] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/09/2022] [Indexed: 11/21/2022]
Abstract
The global and rapid spread of the novel human coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has brought immediate urgency to the discovery of favorable targets for COVID-19 treatment. Here, we consider drug reuse as an attractive methodology for drug discovery by reusing existing drugs to treat diseases other than their initial indications. Here, we review current information concerning the global health issue of COVID-19 including VEGFR-2 inhibitors. Besides, we describe computational approaches to be used in drug repurposing and highlight examples of in silico studies of drug development efforts against SARS-CoV-2. The present study suggests the potential anti-SARS-CoV-2 activities of 35 reported VEGFR-2 inhibitors containing the amide and urea linkers. Nineteen members revealed the best in silico results and hence, were subjected to further molecular dynamics (MD) simulation for their inhibitory activities against SARS-CoV-2 Mpro across 100 ns. Furthermore, MD simulations followed by calculations of the free energy of binding were also carried out for the most promising ligand-pocket complexes from docking studies to clarify some information on their dynamic and thermodynamic properties and approve the docking results. These results we obtained probably provided an excellent lead candidate for the development of therapeutic drugs against COVID-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sanadelaslam El-Hddad
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Omar Almukhtar University, Al Bayda, Libya
| | - Mohamed Sobhy
- Chemistry Department, Faculty of Pharmacy, Heliopolis University for Sustainable Development, Cairo, Egypt
| | - Ahmed Ayoub
- HTuO Biosciences Inc., Vancouver, BC, Canada
| | - Khaled El-Adl
- Chemistry Department, Faculty of Pharmacy, Heliopolis University for Sustainable Development, Cairo, Egypt
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
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5
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Marinescu M. Benzimidazole-Triazole Hybrids as Antimicrobial and Antiviral Agents: A Systematic Review. Antibiotics (Basel) 2023; 12:1220. [PMID: 37508316 PMCID: PMC10376251 DOI: 10.3390/antibiotics12071220] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
Bacterial infections have attracted the attention of researchers in recent decades, especially due to the special problems they have faced, such as their increasing diversity and resistance to antibiotic treatment. The emergence and development of the SARS-CoV-2 infection stimulated even more research to find new structures with antimicrobial and antiviral properties. Among the heterocyclic compounds with remarkable therapeutic properties, benzimidazoles, and triazoles stand out, possessing antimicrobial, antiviral, antitumor, anti-Alzheimer, anti-inflammatory, analgesic, antidiabetic, or anti-ulcer activities. In addition, the literature of the last decade reports benzimidazole-triazole hybrids with improved biological properties compared to the properties of simple mono-heterocyclic compounds. This review aims to provide an update on the synthesis methods of these hybrids, along with their antimicrobial and antiviral activities, as well as the structure-activity relationship reported in the literature. It was found that the presence of certain groups grafted onto the benzimidazole and/or triazole nuclei (-F, -Cl, -Br, -CF3, -NO2, -CN, -CHO, -OH, OCH3, COOCH3), as well as the presence of some heterocycles (pyridine, pyrimidine, thiazole, indole, isoxazole, thiadiazole, coumarin) increases the antimicrobial activity of benzimidazole-triazole hybrids. Also, the presence of the oxygen or sulfur atom in the bridge connecting the benzimidazole and triazole rings generally increases the antimicrobial activity of the hybrids. The literature mentions only benzimidazole-1,2,3-triazole hybrids with antiviral properties. Both for antimicrobial and antiviral hybrids, the presence of an additional triazole ring increases their biological activity, which is in agreement with the three-dimensional binding mode of compounds. This review summarizes the advances of benzimidazole triazole derivatives as potential antimicrobial and antiviral agents covering articles published from 2000 to 2023.
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Affiliation(s)
- Maria Marinescu
- Department of Organic Chemistry, Biochemistry and Catalysis, Faculty of Chemistry, University of Bucharest, 030018 Bucharest, Romania
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6
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Vazquez-Rodriguez S, Ramírez-Contreras D, Noriega L, García-García A, Sánchez-Gaytán BL, Melendez FJ, Castro ME, de Azevedo WF, González-Vergara E. Interaction of copper potential metallodrugs with TMPRSS2: A comparative study of docking tools and its implications on COVID-19. Front Chem 2023; 11:1128859. [PMID: 36778030 PMCID: PMC9909424 DOI: 10.3389/fchem.2023.1128859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 01/17/2023] [Indexed: 01/28/2023] Open
Abstract
SARS-CoV-2 is the virus responsible for the COVID-19 pandemic. For the virus to enter the host cell, its spike (S) protein binds to the ACE2 receptor, and the transmembrane protease serine 2 (TMPRSS2) cleaves the binding for the fusion. As part of the research on COVID-19 treatments, several Casiopeina-analogs presented here were looked at as TMPRSS2 inhibitors. Using the DFT and conceptual-DFT methods, it was found that the global reactivity indices of the optimized molecular structures of the inhibitors could be used to predict their pharmacological activity. In addition, molecular docking programs (AutoDock4, Molegro Virtual Docker, and GOLD) were used to find the best potential inhibitors by looking at how they interact with key amino acid residues (His296, Asp 345, and Ser441) in the catalytic triad. The results show that in many cases, at least one of the amino acids in the triad is involved in the interaction. In the best cases, Asp435 interacts with the terminal nitrogen atoms of the side chains in a similar way to inhibitors such as nafamostat, camostat, and gabexate. Since the copper compounds localize just above the catalytic triad, they could stop substrates from getting into it. The binding energies are in the range of other synthetic drugs already on the market. Because serine protease could be an excellent target to stop the virus from getting inside the cell, the analyzed complexes are an excellent place to start looking for new drugs to treat COVID-19.
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Affiliation(s)
- Sergio Vazquez-Rodriguez
- Centro de Química del Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Diego Ramírez-Contreras
- Centro de Química del Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Lisset Noriega
- Laboratorio de Química Teórica, Depto. de Fisicoquímica, Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico,Departamento de Física Aplicada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Mexico
| | - Amalia García-García
- Centro de Química del Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico,Departamento de Química Inorgánica, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Brenda L. Sánchez-Gaytán
- Centro de Química del Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Francisco J. Melendez
- Laboratorio de Química Teórica, Depto. de Fisicoquímica, Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - María Eugenia Castro
- Centro de Química del Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico,*Correspondence: María Eugenia Castro, ; Enrique González-Vergara,
| | - Walter Filgueira de Azevedo
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Enrique González-Vergara
- Centro de Química del Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico,*Correspondence: María Eugenia Castro, ; Enrique González-Vergara,
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7
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Kolade SO, Izunobi JU, Gordon AT, Hosten EC, Olasupo IA, Ogunlaja AS, Asekun OT, Familoni OB. N-Cycloamino substituent effects on the packing architecture of ortho-sulfanilamide molecular crystals and their in silico carbonic anhydrase II and IX inhibitory activities. Acta Crystallogr C 2022; 78:730-742. [PMID: 36468556 PMCID: PMC9720883 DOI: 10.1107/s2053229622010130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
In the search for new `sulfa drugs' with therapeutic properties, o-nitrosulfonamides and N-cycloamino-o-sulfanilamides were synthesized and characterized using techniques including 1H NMR, 13C NMR and FT-IR spectroscopy, and single-crystal X-ray diffraction (SC-XRD). The calculated density functional theory (DFT)-optimized geometry of the molecules showed similar conformations to those obtained by SC-XRD. Molecular docking of N-piperidinyl-o-sulfanilamide and N-indolinyl-o-sulfanilamide supports the notion that o-sulfanilamides are able to bind to human carbonic anhydrase II and IX inhibitors (hCA II and IX; PDB entries 4iwz and 5fl4). Hirshfeld surface analyses and DFT studies of three o-nitrosulfonamides {1-[(2-nitrophenyl)sulfonyl]pyrrolidine, C10H12N2O4S, 1, 1-[(2-nitrophenyl)sulfonyl]piperidine, C11H14N2O4S, 2, and 1-[(2-nitrophenyl)sulfonyl]-2,3-dihydro-1H-indole, C14H12N2O4S, 3} and three N-cycloamino-o-sulfanilamides [2-(pyrrolidine-1-sulfonyl)aniline, C10H14N2O2S, 4, 2-(piperidine-1-sulfonyl)aniline, C11H16N2O2S, 5, and 2-(2,3-dihydro-1H-indole-1-sulfonyl)aniline, C14H14N2O2S, 6] suggested that forces such as hydrogen bonding and π-π interactions hold molecules together and further showed that charge transfer could promote bioactivity and the ability to form biological interactions at the piperidinyl and phenyl moieties.
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Affiliation(s)
- Sherif O. Kolade
- Department of Chemistry, University of Lagos, Akoka-Yaba, Lagos, Nigeria,Department of Chemistry, Nelson Mandela University, Port Elizabeth, 6031, South Africa
| | | | - Allen T. Gordon
- Department of Chemistry, Nelson Mandela University, Port Elizabeth, 6031, South Africa
| | - Eric C. Hosten
- Department of Chemistry, Nelson Mandela University, Port Elizabeth, 6031, South Africa
| | - Idris A. Olasupo
- Department of Chemistry, University of Lagos, Akoka-Yaba, Lagos, Nigeria
| | - Adeniyi S. Ogunlaja
- Department of Chemistry, Nelson Mandela University, Port Elizabeth, 6031, South Africa,Correspondence e-mail: ,
| | - Olayinka T. Asekun
- Department of Chemistry, University of Lagos, Akoka-Yaba, Lagos, Nigeria
| | - Oluwole B. Familoni
- Department of Chemistry, University of Lagos, Akoka-Yaba, Lagos, Nigeria,Correspondence e-mail: ,
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8
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Cipriano A, Milite C, Feoli A, Viviano M, Pepe G, Campiglia P, Sarno G, Picaud S, Imaide S, Makukhin N, Filippakopoulos P, Ciulli A, Castellano S, Sbardella G. Discovery of Benzo[d]imidazole-6-sulfonamides as Bromodomain and Extra-Terminal Domain (BET) Inhibitors with Selectivity for the First Bromodomain. ChemMedChem 2022; 17:e202200343. [PMID: 36040095 PMCID: PMC9826262 DOI: 10.1002/cmdc.202200343] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/29/2022] [Indexed: 01/11/2023]
Abstract
The bromodomain and extra-terminal (BET) family of proteins includes BRD2, BRD3, BRD4, and the testis-specific protein, BRDT, each containing two N-terminal tandem bromodomain (BRD) modules. Potent and selective inhibitors targeting the two bromodomains are required to elucidate their biological role(s), with potential clinical applications. In this study, we designed and synthesized a series of benzimidazole-6-sulfonamides starting from the azobenzene compounds MS436 (7 a) and MS611 (7 b) that exhibited preference for the first (BD1) over the second (BD2) BRD of BET family members. The most-promising compound (9 a) showed good binding potency and improved metabolic stability and selectivity towards BD1 with respect to the parent compounds.
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Affiliation(s)
- Alessandra Cipriano
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Ciro Milite
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Alessandra Feoli
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Monica Viviano
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Giacomo Pepe
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Pietro Campiglia
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Giuliana Sarno
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Sarah Picaud
- Nuffield Department of MedicineOxford UniversityOX3 7DQOxfordUK
| | - Satomi Imaide
- Division of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EH, ScotlandUK,Discovery Technology Research LaboratoriesOno Pharmaceutical Co., Ltd.618-8585OsakaJapan
| | - Nikolai Makukhin
- Division of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EH, ScotlandUK,Oncology R&DTumour Targeted DeliveryAstraZenecaQMB Innovation Centre42 New RoadLondonE1 2AXUK
| | | | - Alessio Ciulli
- Division of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EH, ScotlandUK
| | - Sabrina Castellano
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
| | - Gianluca Sbardella
- Department of PharmacyUniversity of Salernovia Giovanni Paolo II 13284084Fisciano (SA)Italy
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9
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Arif N, Shafiq Z, Mahmood K, Rafiq M, Naz S, Shahzad SA, Farooq U, Bahkali AH, Elgorban AM, Yaqub M, El-Gokha A. Synthesis, Biological Evaluation, and In Silico Studies of Novel Coumarin-Based 4 H,5 H-pyrano[3,2- c]chromenes as Potent β-Glucuronidase and Carbonic Anhydrase Inhibitors. ACS OMEGA 2022; 7:28605-28617. [PMID: 35990487 PMCID: PMC9386806 DOI: 10.1021/acsomega.2c03528] [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: 06/06/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
The search for novel heterocyclic compounds with a natural product skeleton as potent enzyme inhibitors against clinical hits is our prime concern in this study. Here, a simple and facile two-step strategy has been designed to synthesize a series of novel coumarin-based dihydropyranochromenes (12a-12m) in a basic moiety. The synthesized compounds were thus characterized through spectroscopic techniques and screened for inhibition potency against the cytosolic hCA II isoform and β-glucuronidase. Few of these compounds were potent inhibitors of hCA II and β-glucuronidase with varying IC50 values ranging from 4.55 ± 0.22 to 21.77 ± 3.32 μM and 440.1 ± 1.17 to 971.3 ± 0.05 μM, respectively. Among the stream of synthesized compounds, 12e and 12i were the most potent inhibitors of β-glucuronidase, while 12h, 12i, and 12j showed greater potency against hCA II. In silico docking studies illustrated the significance of substituted groups on the pyranochromene skeleton and binding pattern of these highly potent compounds inside enzyme pockets.
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Affiliation(s)
- Nadia Arif
- Institute
of Chemical Sciences, Organic Chemistry Division, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Zahid Shafiq
- Institute
of Chemical Sciences, Organic Chemistry Division, Bahauddin Zakariya University, Multan 60800, Pakistan
- Department
of Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Khalid Mahmood
- Institute
of Chemical Sciences, Organic Chemistry Division, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Muhammad Rafiq
- Institute
of Chemical Sciences, Organic Chemistry Division, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Sadia Naz
- Department
of Chemistry, COMSATS University Islamabad,
Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Sohail Anjum Shahzad
- Department
of Chemistry, COMSATS University Islamabad,
Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Umar Farooq
- Department
of Chemistry, COMSATS University Islamabad,
Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Ali H. Bahkali
- Department
of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdallah M. Elgorban
- Department
of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Muhammad Yaqub
- Institute
of Chemical Sciences, Organic Chemistry Division, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Ahmed El-Gokha
- Department
of Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
- Chemistry
Department, Faculty of Science, Menoufia
University, Shebin El-Kom 32512, Egypt
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10
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Alves Borges Leal AL, Fonseca Bezerra C, Ferreira E Silva AK, Everson da Silva L, Bezerra LL, Almeida-Neto FW, Marinho EM, Celedonio Fernandes CF, Nunes da Rocha M, Marinho MM, Coutinho HDM, Barreto HM, Rafaela Freitas Dotto A, Amaral WD, Santos HSD, Lima-Neto PD, Marinho ES. Seasonal variation of the composition of essential oils from Piper cernuum Vell and Piper rivinoides Kunth, ADMET study, DFT calculations, molecular docking and dynamics studies of major components as potent inhibitors of the heterodimer methyltransferase complex NSP16-NSP10 SARS COV-2 protein. J Biomol Struct Dyn 2022:1-19. [PMID: 35943030 DOI: 10.1080/07391102.2022.2107072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Coronavirus disease (COVID-19) has the virus that causes the SARS-CoV-2 severe acute respiratory syndrome, which has reached a pandemic proportion, with thousands of deaths worldwide already registered. It has no standardized effective clinical treatment, arousing the urgent need for the discovery of bioactive compounds for the treatment of symptoms of COVID-19. In this context, the present study aimed to evaluate the influence of seasonality on the yield and chemical composition of the essential oils of Piper cernuum and Piper rivinoides as well as to evaluate the anti-SARS-CoV-2 potential of the major components of each oil by molecular docking and quantum chemical calculation (Density Functional Theory method), being possible indicate that the winter and autumn periods, the seasons of the year where it is possible to obtain the highest percentage of Piper cernuum and Piper rivinoides oils, respectively. Regarding the anti-SARS-Cov-2 potential, the present work showed that the dihydroagarofuran present in Piper cernuum, presented a strong interaction with amino acid residues from Mpro, presenting a potential similar to Remdesivir, a drug for clinical use. Regarding methyltransferase, dihydroagarofuran (Piper cernuum) and myristicin (Piper rivinoids) showed better affinity, with important interactions at the active site of the inhibitor Sinefugin, suggesting a potential inhibitory effect of the heterodimer methyltransferase complex NSP16-NSP10 SARS Cov-2. Molecular docking and molecular dynamics studies represent an initial step, being indicative for future in vitro studies of dihydroagarofuran and myristicin, as possible pharmacological tools for COVID-19.
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Affiliation(s)
- Antonio Linkoln Alves Borges Leal
- Department of Biological Chemistry, Regional University of Cariri, Crato, Ceará, Brazil.,Departament of Parasitology and Microbial, Federal University of Piauí, Teresina, Piauí, Brazil
| | - Camila Fonseca Bezerra
- Department of Antibiotics, Drug Planning and Synthesis Laboratory - LPSF, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | | | - Luiz Everson da Silva
- Postgraduate Program in Sustainable Territorial Development, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Lucas Lima Bezerra
- Department of Analytical Chemistry and Physical Chemistry - UFC, PICI Campus, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Francisco Wagner Almeida-Neto
- Department of Analytical Chemistry and Physical Chemistry - UFC, PICI Campus, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Emanuelle Machado Marinho
- Department of Analytical Chemistry and Physical Chemistry - UFC, PICI Campus, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Carla Freire Celedonio Fernandes
- Multi-User Laboratory for Research and Development, Antibody and Nanocorp Platform, Foundation Oswaldo Cruz-Fiocruz, Eusébio, Ceará, Brazil
| | - Matheus Nunes da Rocha
- Department of Chemistry, Group of Theoretical Chemistry and Electrochemistry, FAFIDAM Campus, State University of Ceará, Limoeiro do Norte, Ceará, Brazil
| | - Marcia Machado Marinho
- Department of Biological Chemistry, Regional University of Cariri, Crato, Ceará, Brazil.,Chemistry Course, Laboratory of Natural Products and Synthesis and of Organic Compounds - LBPNSB, Betânia Campus, State University of Vale do Acaraú, Sobral, Ceará, Brazil
| | - Henrique D M Coutinho
- Department of Biological Chemistry, Regional University of Cariri, Crato, Ceará, Brazil
| | | | - Ana Rafaela Freitas Dotto
- Postgraduate Program in Sustainable Territorial Development, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Wanderlei do Amaral
- Department of Chemical Engineering, Curitiba, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Hélcio Silva Dos Santos
- Department of Biological Chemistry, Regional University of Cariri, Crato, Ceará, Brazil.,Chemistry Course, Laboratory of Natural Products and Synthesis and of Organic Compounds - LBPNSB, Betânia Campus, State University of Vale do Acaraú, Sobral, Ceará, Brazil
| | - Pedro de Lima-Neto
- Department of Analytical Chemistry and Physical Chemistry - UFC, PICI Campus, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Emmanuel Silva Marinho
- Department of Chemistry, Group of Theoretical Chemistry and Electrochemistry, FAFIDAM Campus, State University of Ceará, Limoeiro do Norte, Ceará, Brazil
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11
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2-Phenyl substituted Benzimidazole derivatives: Design, synthesis, and evaluation of their antiproliferative and antimicrobial activities. Med Chem Res 2022. [DOI: 10.1007/s00044-022-02900-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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12
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Synthesis of Benzimidazole-Sulfonyl Derivatives and Their Biological Activities. Biochem Res Int 2022; 2022:7255299. [PMID: 35425644 PMCID: PMC9005321 DOI: 10.1155/2022/7255299] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/21/2022] [Indexed: 12/26/2022] Open
Abstract
Currently, the synthesis of new compounds with potential bioactivities has become a central issue in the drug discovery arena. Among these new compounds, benzimidazole-sulfonyl scaffolds have vital applications in the fields of pharmaceuticals industries. Benzimidazole and sulfonyl compounds have remarkable biological activities, such as antibacterial, antifungal, anti-inflammatory, antiproliferative, carbonic anhydrase inhibitory, and α-amylase inhibitory activities. Furthermore, recent literature mentions the synthesis and bioactivities of some benzimidazole-sulfonyl hybrids. In this review, we focus on reviewing the synthesis of these hybrid scaffolds and their various types of biological activities of the compounds.
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13
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Saadiq M, Uddin G, Latif A, Ali M, Akbar N, Ammara, Ali S, Ahmad M, Zahoor M, Khan A, Al-Harrasi A. Synthesis, Bioactivity Assessment, and Molecular Docking of Non-sulfonamide Benzimidazole-Derived N-Acylhydrazone Scaffolds as Carbonic Anhydrase-II Inhibitors. ACS OMEGA 2022; 7:705-715. [PMID: 35036737 PMCID: PMC8756595 DOI: 10.1021/acsomega.1c05362] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/06/2021] [Indexed: 04/06/2024]
Abstract
This research reports the synthesis of new benzimidazole-derived N-acylhydrazones (NAH), their characterization using various spectroscopic methods, and in vitro evaluation as potent carbonic anhydrase-II inhibitors. Among the target compounds (9-29), few showed higher inhibition than the standard acetazolamide (IC50: 18.6 ± 0.43 μM), for example, compound 9 (IC50: 13.3 ± 1.25 μM), 10 (IC50: 17.2 ± 1.24 μM), 12 (IC50: 14.6 ± 0.62 μM), and 15 (IC50: 14.5 ± 1.05 μM). Molecular docking was performed on the most active compounds, which revealed their binding interactions with the active site of the enzyme, thus supporting the experimental findings.
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Affiliation(s)
- Muhammad Saadiq
- Institute
of Chemical Sciences, University of Peshawar, Peshawar, Khyber Pakhtunkhwa 25120, Pakistan
| | - Ghias Uddin
- Institute
of Chemical Sciences, University of Peshawar, Peshawar, Khyber Pakhtunkhwa 25120, Pakistan
| | - Abdul Latif
- Department
of Chemistry, University of Malakand, Dir (Lower), Chakdara, Khyber
Pakhtunkhwa 18800, Pakistan
| | - Mumtaz Ali
- Department
of Chemistry, University of Malakand, Dir (Lower), Chakdara, Khyber
Pakhtunkhwa 18800, Pakistan
| | - Nazia Akbar
- Department
of Biotechnology & Genetic Engineering, Hazara University, Mansehra, Khyber Pakhtunkhwa, 21120, Pakistan
| | - Ammara
- Department
of Chemistry, University of Malakand, Dir (Lower), Chakdara, Khyber
Pakhtunkhwa 18800, Pakistan
| | - Sardar Ali
- Department
of Chemistry, University of Malakand, Dir (Lower), Chakdara, Khyber
Pakhtunkhwa 18800, Pakistan
| | - Manzoor Ahmad
- Department
of Chemistry, University of Malakand, Dir (Lower), Chakdara, Khyber
Pakhtunkhwa 18800, Pakistan
| | - Mohammad Zahoor
- Department
of Biochemistry, University of Malakand, Dir (Lower), Chakdara, Khyber
Pakhtunkhwa 18800, Pakistan
| | - Ajmal Khan
- UoN
Chair of Oman’s Medicinal Plants and Marine Natural Products, University of Nizwa, Nizwa 616, Sultanate
of Oman
| | - Ahmed Al-Harrasi
- UoN
Chair of Oman’s Medicinal Plants and Marine Natural Products, University of Nizwa, Nizwa 616, Sultanate
of Oman
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14
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Hamed MIA, Darwish KM, Soltane R, Chrouda A, Mostafa A, Abo Shama NM, Elhady SS, Abulkhair HS, Khodir AE, Elmaaty AA, Al-Karmalawy AA. β-Blockers bearing hydroxyethylamine and hydroxyethylene as potential SARS-CoV-2 Mpro inhibitors: rational based design, in silico, in vitro, and SAR studies for lead optimization. RSC Adv 2021; 11:35536-35558. [PMID: 35493159 PMCID: PMC9043270 DOI: 10.1039/d1ra04820a] [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] [Received: 06/21/2021] [Accepted: 10/26/2021] [Indexed: 02/05/2023] Open
Abstract
The global COVID-19 pandemic became more threatening especially after the introduction of the second and third waves with the current large expectations for a fourth one as well. This urged scientists to rapidly develop a new effective therapy to combat SARS-CoV-2. Based on the structures of β-adrenergic blockers having the same hydroxyethylamine and hydroxyethylene moieties present in the HIV-1 protease inhibitors which were found previously to inhibit the replication of SARS-CoV, we suggested that they may decrease the SARS-CoV-2 entry into the host cell through their ability to decrease the activity of RAAS and ACE2 as well. Herein, molecular docking of twenty FDA-approved β-blockers was performed targeting SARS-CoV-2 Mpro. Results showed promising inhibitory activities especially for Carvedilol (CAR) and Nebivolol (NEB) members. Moreover, these two drugs together with Bisoprolol (BIS) as an example from the lower active ones were subjected to molecular dynamics simulations at 100 ns. Great stability across the whole 100 ns timeframe was observed for the top docked ligands, CAR and NEB, over BIS. Conformational analysis of the examined drugs and hydrogen bond investigation with the pocket's crucial residues confirm the great affinity and confinement of CAR and NEB within the Mpro binding site. Moreover, the binding-free energy analysis and residue-wise contribution analysis highlight the nature of ligand–protein interaction and provide guidance for lead development and optimization. Furthermore, the examined three drugs were tested for their in vitro inhibitory activities towards SARS-CoV-2. It is worth mentioning that NEB achieved the most potential anti-SARS-CoV-2 activity with an IC50 value of 0.030 μg ml−1. Besides, CAR was found to have a promising inhibitory activity with an IC50 of 0.350 μg ml−1. Also, the IC50 value of BIS was found to be as low as 15.917 μg ml−1. Finally, the SARS-CoV-2 Mpro assay was performed to evaluate and confirm the inhibitory effects of the tested compounds (BIS, CAR, and NEB) towards the SARS-CoV-2 Mpro enzyme. The obtained results showed very promising SARS-CoV-2 Mpro inhibitory activities of BIS, CAR, and NEB (IC50 = 118.50, 204.60, and 60.20 μg ml−1, respectively) compared to lopinavir (IC50 = 73.68 μg ml−1) as a reference standard. Hydroxyethylamine and hydroxyethylene moieties of β-blockers exert potential SARS-CoV-2 inhibitory effects: rational-based design and in silico, in vitro, and SAR Studies.![]()
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Affiliation(s)
- Mohammed I A Hamed
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, Fayoum University Fayoum 63514 Egypt
| | - Khaled M Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University Ismailia 41522 Egypt
| | - Raya Soltane
- Department of Basic Sciences, Adham University College, Umm Al-Qura University Saudi Arabia .,Faculty of Sciences, Tunis El Manar University Tunisia
| | - Amani Chrouda
- Department of Chemistry, College of Science Al-Zulfi, Majmaah University Al-Majmaah 11952 Saudi Arabia .,Laboratory of Interfaces and Advanced Materials, Faculty of Sciences, Monastir University Monastir 5000 Tunisia.,Institute of Analytical Sciences, UMR CNRS-UCBL-ENS 5280 5 Rue la Doua 69100 Villeurbanne CEDEX France
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre Dokki Cairo 12622 Egypt
| | - Noura M Abo Shama
- Center of Scientific Excellence for Influenza Viruses, National Research Centre Dokki Cairo 12622 Egypt
| | - Sameh S Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University Jeddah 21589 Saudi Arabia
| | - Hamada S Abulkhair
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy (Boys), Al-Azhar University Nasr City 11884 Cairo Egypt .,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Horus University-Egypt New Damietta 34518 Egypt
| | - Ahmed E Khodir
- Department of Pharmacology, Faculty of Pharmacy, Horus University-Egypt New Damietta 34518 Egypt
| | - Ayman Abo Elmaaty
- Department of Medicinal Chemistry, Faculty of Pharmacy, Port Said University Port Said 42526 Egypt
| | - Ahmed A Al-Karmalawy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Horus University-Egypt New Damietta 34518 Egypt
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15
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Baglini E, Ravichandran R, Berrino E, Salerno S, Barresi E, Marini AM, Viviano M, Castellano S, Da Settimo F, Supuran CT, Cosconati S, Taliani S. Tetrahydroquinazole-based secondary sulphonamides as carbonic anhydrase inhibitors: synthesis, biological evaluation against isoforms I, II, IV, and IX, and computational studies. J Enzyme Inhib Med Chem 2021; 36:1874-1883. [PMID: 34340614 PMCID: PMC8344263 DOI: 10.1080/14756366.2021.1956913] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
A library of variously decorated N-phenyl secondary sulphonamides featuring the bicyclic tetrahydroquinazole scaffold was synthesised and biologically evaluated for their inhibitory activity against human carbonic anhydrase (hCA) I, II, IV, and IX. Of note, several compounds were identified showing submicromolar potency and excellent selectivity for the tumour-related hCA IX isoform. Structure-activity relationship data attained for various substitutions were rationalised by molecular modelling studies in terms of both inhibitory activity and selectivity.
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Affiliation(s)
- Emma Baglini
- Department of Pharmacy, University of Pisa, Pisa, Italy
| | | | - Emanuela Berrino
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | | | | | | | - Monica Viviano
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno, Fisciano, Italy
| | - Sabrina Castellano
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno, Fisciano, Italy
| | | | - Claudiu T Supuran
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Sandro Cosconati
- DiSTABiF, University of Campania Luigi Vanvitelli, Caserta, Italy
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16
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Coutinho TDNP, Barroso FDD, da Silva CR, da Silva AR, Cabral VPDF, Sá LGDAV, Cândido TM, da Silva LJ, Ferreira TL, da Silva WMB, Silva J, Marinho ES, Cavalcanti BC, Moraes MO, Nobre Júnior H, Andrade Neto JBD. EFFECTS OF KETAMINE IN METHICILLIN RESISTANT S. aureus AND IN SILICO INTERACTION WITH SORTASE A. Can J Microbiol 2021; 67:885-893. [PMID: 34314621 DOI: 10.1139/cjm-2021-0093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is one of the main human pathogens and is responsible for many diseases ranging from skin infections to more invasive infections. These infections are dangerous and expensive to treat because these strains are resistant to a large number of conventional antibiotics. Having said that, Antibacterial effect of ketamine against MRSA strains, its mechanism of action and in silico interaction with sortase A was evaluated. The antibacterial effect of ketamine was assessed by the broth microdilution method. Subsequently, the mechanism of action was assessed using flow cytometry and molecular docking assays with sortase A. Our results showed that Ketamine has a significant antibacterial activity against MRSA strains in the range of 2.49 to 3.73 mM. Their mechanism of action involves alterations in the membrane integrity and DNA damage, reducing cell viability that provoke death by apoptosis. In addition, Ketamine compound had affinity for S. aureus sortase A. These results indicate that this compound can be an alternative to develop new strategies to combat of infections caused by MRSA.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Jacilene Silva
- State University of Ceara, 67843, Fortaleza, CE, Brazil;
| | | | | | | | - Hélio Nobre Júnior
- Federal University of Ceará, Department of Clinical and Toxicological Analysis, Rua Capitão Francisco Pedro, 1210 - Rodolfo Teófilo, Fortaleza, Brazil, 60430-370;
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17
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Salerno S, Amendola G, Angeli A, Baglini E, Barresi E, Marini AM, Ravichandran R, Viviano M, Castellano S, Novellino E, Da Settimo F, Supuran CT, Cosconati S, Taliani S. Inhibition studies on carbonic anhydrase isoforms I, II, IV and IX with N-arylsubstituted secondary sulfonamides featuring a bicyclic tetrahydroindazole scaffold. Eur J Med Chem 2021; 220:113490. [PMID: 33975138 DOI: 10.1016/j.ejmech.2021.113490] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/24/2021] [Accepted: 04/17/2021] [Indexed: 12/15/2022]
Abstract
Carbonic Anhydrases (CAs) are pharmaceutically relevant targets for the treatment of several disease conditions. The ubiquitous localization of these enzymes and the high homology shared by the different isoforms represent substantial impediments for the discovery of potential drugs devoid of off-target side effects. As a consequence, substantial efforts are still needed to allow for the full realization of the pharmacological potential of CA modulators. In this contribution, starting from our previous studies, we describe the synthesis of a set of new bicyclic tetrahydroindazoles featuring a secondary sulfonamide. Biological evaluation of the inhibitory activity against the hCA I, II, IV, and IX isoforms allowed drawing a structure-activity relationship profile that was rationalized through theoretical studies. This allowed dissecting the new molecules into the single portions influencing the zinc chelation properties and the selectivity profile thereby offering a new platform for the discovery of new isotype selective CA inhibitors.
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Affiliation(s)
| | - Giorgio Amendola
- DiSTABiF, University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Andrea Angeli
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, Sesto Fiorentino (Florence), Italy
| | - Emma Baglini
- Department of Pharmacy, University of Pisa, Pisa, Italy
| | | | | | | | - Monica Viviano
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno, Fisciano (SA), Italy
| | - Sabrina Castellano
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno, Fisciano (SA), Italy
| | - Ettore Novellino
- Department of Pharmacy, University Federico II of Naples, Naples, Italy
| | | | - Claudiu T Supuran
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, Sesto Fiorentino (Florence), Italy
| | - Sandro Cosconati
- DiSTABiF, University of Campania Luigi Vanvitelli, Caserta, Italy.
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18
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Rocha MND, Alves DR, Marinho MM, Morais SMD, Marinho ES. Virtual Screening of Citrus Flavonoid Tangeretin: A Promising Pharmacological Tool for the Treatment and Prevention of Zika fever and COVID-19. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416521500137] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
It is of great importance for the pharmaceutical industry to find therapeutic substances extracted from natural sources, which are abundant, obtained with low costs and presenting the antiviral potential for the treatment of Zika virus (ZIKV) and COVID-19. Tangeretin (TAN) is a citrus polymethoxyflavone from Citrus reticulata peel oil with known antiviral activities, whose physico-chemical properties are not reported. The present study aimed to investigate by a theoretical screening of electronic, structural properties and pharmacodynamic and pharmacokinetic parameters that characterize TAN as a therapeutic drug in the treatment and prevention of zika fever and COVID-19. The molecule reached its minimum energy-forming state of [Formula: see text]795.85747[Formula: see text]kJ/mol and the HOMO and LUMO boundary orbitals reactivity descriptors suggest that the compound is stable and does not tend to be reactive in intermolecular interactions. The ligand connects to the NS1 ZIKV receptor with strong H-bond interactions, also connects with the NS5 ZIKV receptor in a competitive effect with the SAM inhibitor and acts in a supplementary effect with the N3 inhibitor and the BRT drug in the Mpro SARS-CoV-2 receptor. The properties of ADMET shows that the compound suffers few amounts of drug alterations because it inhibits the metabolic enzymes CYP2C9 and CYP3A4 and penetrates the central nervous system, without accumulation of drug residues in the blood or in the lumen in the gastrointestinal tract, without risk of toxicity to the patient. With the results obtained, it is possible to identify TAN as a promising pharmacological tool for the treatment and prevention of Zika fever and COVID-19.
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Affiliation(s)
- Matheus Nunes da Rocha
- Group of Theoretical Chemistry and Electrochemical, FAFIDAM, Ceará State University, Limoeiro do Norte, Ceará, Brazil
| | - Daniela Ribeiro Alves
- Animal Health Research Center, Ceará State University, Campus Itaperi, Fortaleza, Ceará, Brazil
| | - Marcia Machado Marinho
- Iguatu Faculty of Education, Science and Letters/FECLI, State University of Ceará Iguatu, Ceará, Brazil
| | - Selene Maia de Morais
- Animal Health Research Center, Ceará State University, Campus Itaperi, Fortaleza, Ceará, Brazil
| | - Emmanuel Silva Marinho
- Group of Theoretical Chemistry and Electrochemical, FAFIDAM, Ceará State University, Limoeiro do Norte, Ceará, Brazil
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19
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Abstract
Coumarins constitute a relatively new class of inhibitors of the zinc enzyme carbonic anhydrase (CA, EC 4.2.1.1), possessing a unique inhibition mechanism, acting as "prodrug inhibitors." They undergo the hydrolysis of the lactone ring mediated by the esterase activity of CA. The formed 2-hydroxy-cinnamic acids thereafter bind within a very particular part of the enzyme active site, at its entrance, where a high variability of amino acid residues among the different mammalian CA isoforms is present, and where other inhibitors classes were not seen bound earlier. This explains why coumarins are among the most isoform-selective CA inhibitors known to date among the many chemotypes endowed with such biological activity. As coumarins are widespread secondary metabolites in some bacteria, plants, fungi, and ascidians, many such compounds from various natural sources have been investigated for their CA inhibitory properties and for possible biomedical applications, mainly as anticancer agents targeting hypoxic tumours.
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Affiliation(s)
- Claudiu T Supuran
- Section of Pharmaceutical and Nutraceutical Sciences, Neurofarba Department, Università degli Studi di Firenze, Florence, Italy
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20
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Ersan RH, Alagoz MA, Dogen A, Duran N, Burmaoglu S, Algul O. Bisbenzoxazole Derivatives: Design, Synthesis, in Vitro Antimicrobial, Antiproliferative Activity, and Molecular Docking Studies. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2020.1852589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Ronak Haj Ersan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Mersin University, Mersin, Turkey
| | - Mehmet Abdullah Alagoz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Inonu University, Malatya, Turkey
| | - Aylin Dogen
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Mersin University, Mersin, Turkey
| | - Nizami Duran
- Department of Medical Microbiology, Medical Faculty, Mustafa Kemal University, Antakya-Hatay, Turkey
| | - Serdar Burmaoglu
- Department of Chemistry, Faculty of Science, Ataturk University, Erzurum, Turkey
| | - Oztekin Algul
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Mersin University, Mersin, Turkey
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21
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Marinho EM, Batista de Andrade Neto J, Silva J, Rocha da Silva C, Cavalcanti BC, Marinho ES, Nobre Júnior HV. Virtual screening based on molecular docking of possible inhibitors of Covid-19 main protease. Microb Pathog 2020; 148:104365. [PMID: 32619669 PMCID: PMC7834391 DOI: 10.1016/j.micpath.2020.104365] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/22/2020] [Accepted: 06/25/2020] [Indexed: 02/07/2023]
Abstract
Coronavirus (COVID-19) is an enveloped RNA virus that is diversely found in humans and that has now been declared a global pandemic by the World Health Organization. Thus, there is an urgent need to develop effective therapies and vaccines against this disease. In this context, this study aimed to evaluate in silico the molecular interactions of drugs with therapeutic indications for treatment of COVID-19 (Azithromycin, Baricitinib and Hydroxychloroquine) and drugs with similar structures (Chloroquine, Quinacrine and Ruxolitinib) in docking models from the SARS-CoV-2 main protease (M-pro) protein. The results showed that all inhibitors bound to the same enzyme site, more specifically in domain III of the SARS-CoV-2 main protease. Therefore, this study allows proposing the use of baricitinib and quinacrine, in combination with azithromycin; however, these computer simulations are just an initial step for conceiving new projects for the development of antiviral molecules.
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Affiliation(s)
- Emanuelle Machado Marinho
- Department of Analytical Chemistry and Physical Chemistry, Group of Theoretical Chemistry (GQT), Science Center, Federal University of Ceará, Fortaleza, CE, 60.455-760, Brazil
| | - João Batista de Andrade Neto
- School of Pharmacy, Laboratory of Bioprospection in Antimicrobial Molecules (LABIMAN), Federal University of Ceara, Fortaleza, CE, Brazil; Christus University Center (UNICHRISTUS), Fortaleza, CE, Brazil; Drug Research and Development Center, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Jacilene Silva
- Department of Chemistry, Group of Theoretical Chemistry and Electrochemistry (GQTE), State University of Ceará, Limoeiro do Norte, Ceará, Brazil
| | - Cecília Rocha da Silva
- School of Pharmacy, Laboratory of Bioprospection in Antimicrobial Molecules (LABIMAN), Federal University of Ceara, Fortaleza, CE, Brazil; Drug Research and Development Center, Federal University of Ceará, Fortaleza, CE, Brazil
| | | | - Emmanuel Silva Marinho
- Department of Chemistry, Group of Theoretical Chemistry and Electrochemistry (GQTE), State University of Ceará, Limoeiro do Norte, Ceará, Brazil
| | - Hélio Vitoriano Nobre Júnior
- School of Pharmacy, Laboratory of Bioprospection in Antimicrobial Molecules (LABIMAN), Federal University of Ceara, Fortaleza, CE, Brazil; Drug Research and Development Center, Federal University of Ceará, Fortaleza, CE, Brazil.
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Aparna Y, Nirmala G, Subhashini NJP, Sharada LN, Sreekanth S. Synthesis and Antimicrobial Activity of Novel
Bis-1,2,3-triazol-1H-4-yl-substituted Aryl
Benzimidazole-2-thiol Derivatives. RUSS J GEN CHEM+ 2020. [DOI: 10.1134/s1070363220080186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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