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Xiong F, Zhang Y, Jiao J, Zhu Y, Mo T, Li Y. Towards new bioactive fluorine-containing 1,3,4-oxadiazole-amide derivatives: synthesis, antibacterial activity, molecular docking and molecular dynamics simulation study. Mol Divers 2025; 29:1079-1089. [PMID: 38900333 DOI: 10.1007/s11030-024-10893-x] [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: 03/22/2024] [Accepted: 05/09/2024] [Indexed: 06/21/2024]
Abstract
Through the approach of molecular hybridization, this study rationally designed and synthesized new trifluoromethyl-1,3,4-oxadiazole amide derivatives, denoted as 1a-1n. The findings reveal that these novel molecules exhibit potent inhibitory effects against various bacterial strains. Thereinto, compounds 1c, 1d, 1i, 1j and 1n, demonstrate relatively superior antimicrobial performance against B. cereus FM314, with a minimum inhibitory concentration (MIC) of 0.03907 μg/mL. Molecular docking analysis suggests the potential importance of the Ser57 and Thr125 amino acid residues (PDB ID: 4EI9) in contributing to the inhibitory activity against B. cereus. The consistency of these results was further corroborated through subsequent molecular dynamics simulations and MMPBSA validations. The insights gained from this study serve to facilitate the rational design and efficient development of novel eco-friendly antimicrobial inhibitors based on the trifluoromethyl-1,3,4-oxadiazole amide scaffold.
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Affiliation(s)
- Fei Xiong
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, 200093, People's Republic of China.
| | - Yanjun Zhang
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, 200093, People's Republic of China
| | - Jinlong Jiao
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, People's Republic of China
| | - Yiren Zhu
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, 200093, People's Republic of China
| | - Tianlu Mo
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, People's Republic of China.
| | - Yeji Li
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, 200093, People's Republic of China
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2
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Jiang H, Xia H, Wang Z, Xiong F. Discovery of Severe Acute Respiratory Syndrome Coronavirus 2 Main Protease Inhibitors through Rational Design of Novel Fluorinated 1,3,4-oxadiazole Amide Derivatives: An In-Silico Study. Chem Biodivers 2025:e202403179. [PMID: 39853882 DOI: 10.1002/cbdv.202403179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2024] [Revised: 12/23/2024] [Accepted: 01/24/2025] [Indexed: 01/26/2025]
Abstract
As severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) variants continue to emerge, there is an urgent need to develop more effective antiviral drugs capable of combating the COVID-19 pandemic. The main protease (Mpro) of SARS-CoV-2 is an evolutionarily conserved drug discovery target. The present study mainly focused on chemoinformatics computational methods to investigate the efficacy of our newly designed trifluoromethyl-1,3,4-oxadiazole amide derivatives as SARS-CoV-2 Mpro inhibitors. Drug-likeness absorption, distribution, metabolism, excretion, and toxicity analysis, molecular docking simulation, density functional theory (DFT), and molecular dynamics simulation methods were included. A comprehensive drug-likeness analysis was performed on the 14 newly designed compounds (1a-1n), and this series of small molecule inhibitors showed potential anti-SARS-CoV-2 activity. In order to reveal the mechanism of drug interaction, these novel compounds were classified by structure, and molecular docking simulations were performed. The results showed good interactions and identified the key amino acid residue GLY-143. Further DFT analysis using B3LYP-D3BJ functional and 6-311 + + G (d, p) basis set was performed to optimize the optimal configuration of the Mpro inhibitors, and the infrared spectrum of the vibration frequency was analyzed to clearly understand the structure and stability of the drug. The electrostatic potential map was analyzed to predict the reactivity of functional groups and protein-substrate interactions. The frontier molecular orbital analysis and density of states map showed the reactivity level and stability of the drug itself, among which 1i had the smallest energy gap difference (ΔEgap = 3.64 ev), showing good reactivity. The analysis of global reactivity descriptors such as electrophilic index (ω) and chemical potential (μ) also showed that our newly designed Mpro inhibitors had stronger interactions. Molecular dynamics simulation further revealed the stable binding of the Mpro inhibitors in a solvent environment. The binding free energy results calculated by Molecular Mechanics / Poisson Boltzmann Surface Area (MM/PBSA) all exceeded the Food and Drug Administration-approved standard reference drug (Nirmatrelvir), and the free energy landscape and principal component analysis also further described the energy sites formed during the binding process between the drug molecule and the ligand-protein and the changes in conformation. These new series of small molecule inhibitors studied in this work will provide the necessary theoretical basis for the synthesis and activity evaluation of novel SARS-CoV-2 Mpro inhibitors.
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Affiliation(s)
- Huiying Jiang
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Heping Xia
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Zhonghua Wang
- Shanghai Engineering Research Center of Green Fluoropharmaceutical Technology, School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, P. R. China
| | - Fei Xiong
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
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3
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Ahadi H, Shokrzadeh M, Hosseini-Khah Z, Ghassemi Barghi N, Ghasemian M, Emami S. Conversion of antibacterial quinolone drug levofloxacin to potent cytotoxic agents. J Biochem Mol Toxicol 2023:e23334. [PMID: 36843476 DOI: 10.1002/jbt.23334] [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: 06/20/2022] [Revised: 01/03/2023] [Accepted: 02/10/2023] [Indexed: 02/28/2023]
Abstract
Levofloxacin, the optical S-(-) isomer of ofloxacin, is a broad-spectrum antibacterial agent widely used to control various infections caused by Gram-positive and Gram-negative bacteria. While the COOH group is necessary for antibacterial activity, its modification can offer anticancer activity to the fluoroquinolone framework. Therefore, several levofloxacin carboxamides 11a-j and 12 containing 5-substituted-1,3,4-thiadiazole residue were synthesized and screened in vitro for their anticancer activity. The in vitro MTT viability assay revealed that the most compounds had significant activity against cancer cells MCF-7, A549, and SKOV3. In particular, the 3-chloro- and 4-fluoro- benzyl derivatives (11b and 11h), with IC50 values of 1.69-4.76 μM were as potent as or better than doxorubicin. It should be noted that the mother quinolone levofloxacin showed no activity on the tested cancer cell lines. The SAR analysis demonstrated that the 3-chloro or 4-fluoro substituent on the S-benzyl moiety had positive effect on the activity. Further in vitro evaluations of the most promising compounds 11b and 11h by flow cytometric analysis and comet test revealed the ability of compounds in the induction of apoptosis and blockage of the cell proliferation at the G1-phase by nuclear fragmentation and DNA degradation in cancer cells. The obtained results demonstrated that the alteration of 6-COOH functional group in the levofloxacin structure and conjugation with a proper heterocyclic pharmacophore is a good strategy to obtain new anticancer agents.
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Affiliation(s)
- Hamideh Ahadi
- Department of Medicinal Chemistry, Student Research Committee, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mohammad Shokrzadeh
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Zahra Hosseini-Khah
- Diabetes Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Nasrin Ghassemi Barghi
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Majid Ghasemian
- Department of Clinical Biochemistry, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Saeed Emami
- Department of Medicinal Chemistry and Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
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4
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Wei S, Zhao T, Wang J, Zhai X. Approach in Improving Potency and Selectivity of Kinase Inhibitors: Allosteric Kinase Inhibitors. Mini Rev Med Chem 2021; 21:991-1003. [PMID: 33355051 DOI: 10.2174/1389557521666201222144355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 09/21/2020] [Accepted: 10/16/2020] [Indexed: 11/22/2022]
Abstract
Allostery is an efficient and particular regulatory mechanism to regulate protein functions. Different from conserved orthosteric sites, allosteric sites have a distinctive functional mechanism to form the complex regulatory network. In drug discovery, kinase inhibitors targeting the allosteric pockets have received extensive attention for the advantages of high selectivity and low toxicity. The approval of trametinib as the first allosteric inhibitor validated that allosteric inhibitors could be used as effective therapeutic drugs for the treatment of diseases. To date, a wide range of allosteric inhibitors have been identified. In this perspective, we outline different binding modes and potential advantages of allosteric inhibitors. In the meantime, the research processes of typical and novel allosteric inhibitors are described briefly in terms of structure-activity relationships, ligand-protein interactions, and in vitro and in vivo activity. Additionally, challenges, as well as opportunities, are also presented.
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Affiliation(s)
- Shangfei Wei
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Tianming Zhao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Jie Wang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xin Zhai
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
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5
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Ahadi H, Shokrzadeh M, Hosseini-Khah Z, Ghassemi Barghi N, Ghasemian M, Emadi E, Zargari M, Razzaghi-Asl N, Emami S. Synthesis and biological assessment of ciprofloxacin-derived 1,3,4-thiadiazoles as anticancer agents. Bioorg Chem 2020; 105:104383. [PMID: 33130342 DOI: 10.1016/j.bioorg.2020.104383] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/10/2020] [Accepted: 10/13/2020] [Indexed: 01/01/2023]
Abstract
The quinolone-3-carboxylic acid scaffold is essential structure for antibacterial activity of fluoroquinolones such as ciprofloxacin. Modification of 3-carboxylic functionality in this structure can be used for switching its activity from antibacterial to anticancer. Accordingly, a series of C-3 modified ciprofloxacin derivatives containing N-(5-(benzylthio)-1,3,4-thiadiazol-2-yl)-carboxamide moiety was synthesized as novel anticancer agents. Most of compounds showed significant activity against MCF-7, A549 and SKOV-3 cancer cells in the MTT assay. In particular, compounds 13a-e and 13g were found to be as potent as standard drug doxorubicin against MCF-7 cell line (IC50s = 3.26-3.90 µM). Furthermore, the 4-fluorobenzyl derivatives 13h and 14b with IC50 values of 3.58 and 2.79 µM exhibited the highest activity against SKOV-3 and A549 cells, being as potent as doxorubicin. Two promising compounds 13e and 13g were further tested for their apoptosis inducing activity and cell cycle arrest. Both compounds could significantly induce apoptosis in MCF-7 cells, while compound 13e was more potent apoptosis inducer resulting in an 18-fold increase in the proportion of apoptotic cells at the IC50 concentration in MCF-7 cells. The cell cycle analysis revealed that compounds 13e and 13g could increase cell portions in the sub-G1 phase, inducing oligonucleosomal DNA fragmentation and apoptosis confirmed by comet assay.
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Affiliation(s)
- Hamideh Ahadi
- Department of Medicinal Chemistry, Student Research Committee, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mohammad Shokrzadeh
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Zahra Hosseini-Khah
- Diabetes Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Nasrin Ghassemi Barghi
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Majid Ghasemian
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences (SBMU), Tehran, Iran
| | - Elnaz Emadi
- Molecular and Cell Biology Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mehryar Zargari
- Molecular and Cell Biology Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Nima Razzaghi-Asl
- Department of Medicinal Chemistry, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Saeed Emami
- Department of Medicinal Chemistry and Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran.
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6
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Carofiglio F, Trisciuzzi D, Gambacorta N, Leonetti F, Stefanachi A, Nicolotti O. Bcr-Abl Allosteric Inhibitors: Where We Are and Where We Are Going to. Molecules 2020; 25:E4210. [PMID: 32937901 PMCID: PMC7570842 DOI: 10.3390/molecules25184210] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 12/12/2022] Open
Abstract
The fusion oncoprotein Bcr-Abl is an aberrant tyrosine kinase responsible for chronic myeloid leukemia and acute lymphoblastic leukemia. The auto-inhibition regulatory module observed in the progenitor kinase c-Abl is lost in the aberrant Bcr-Abl, because of the lack of the N-myristoylated cap able to bind the myristoyl binding pocket also conserved in the Bcr-Abl kinase domain. A way to overcome the occurrence of resistance phenomena frequently observed for Bcr-Abl orthosteric drugs is the rational design of allosteric ligands approaching the so-called myristoyl binding pocket. The discovery of these allosteric inhibitors although very difficult and extremely challenging, represents a valuable option to minimize drug resistance, mostly due to the occurrence of mutations more frequently affecting orthosteric pockets, and to enhance target selectivity with lower off-target effects. In this perspective, we will elucidate at a molecular level the structural bases behind the Bcr-Abl allosteric control and will show how artificial intelligence can be effective to drive the automated de novo design towards off-patent regions of the chemical space.
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Affiliation(s)
- Francesca Carofiglio
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
| | - Daniela Trisciuzzi
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
- Molecular Horizon srl, Via Montelino 32, 06084 Bettona, Italy
| | - Nicola Gambacorta
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
| | - Francesco Leonetti
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
| | - Angela Stefanachi
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
| | - Orazio Nicolotti
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
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7
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Ostapiuk YV, Frolov DA, Vasylyschyn RY, Matiychuk VS. Synthesis and antitumor activities of new N-(5-benzylthiazol-2-yl)-2-(heteryl-5-ylsulfanyl)-acetamides. ACTA ACUST UNITED AC 2018. [DOI: 10.7124/bc.000971] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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8
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Docking optimization, variance and promiscuity for large-scale drug-like chemical space using high performance computing architectures. Drug Discov Today 2016; 21:1672-1680. [DOI: 10.1016/j.drudis.2016.06.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 05/12/2016] [Accepted: 06/21/2016] [Indexed: 12/27/2022]
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9
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Radi M, Schneider R, Fallacara AL, Botta L, Crespan E, Tintori C, Maga G, Kissova M, Calgani A, Richters A, Musumeci F, Rauh D, Schenone S. A cascade screening approach for the identification of Bcr-Abl myristate pocket binders active against wild type and T315I mutant. Bioorg Med Chem Lett 2016; 26:3436-40. [DOI: 10.1016/j.bmcl.2016.06.051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/16/2016] [Accepted: 06/18/2016] [Indexed: 01/17/2023]
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10
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Balti M, Efrit ML, Leadbeater NE. Preparation of vinyl ethers using a Wittig approach, and their subsequent hydrogenation employing continuous-flow processing. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.03.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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11
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Fallacara AL, Tintori C, Radi M, Schenone S, Botta M. Insight into the allosteric inhibition of Abl kinase. J Chem Inf Model 2014; 54:1325-38. [PMID: 24787133 DOI: 10.1021/ci500060k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Abl kinase inhibitors targeting the ATP binding pocket are currently used as a front-line therapy for the treatment of chronic myelogenous leukemia (CML), but their use has significant limitation because of the development of drug resistance (especially due to the T315I mutation). Two compounds (GNF-2 and BO1) have been found able to inhibit the Abl activity through a peculiar mechanism of action. Particularly, GNF-2 acts as allosteric inhibitor against Bcr-Abl wild type (wt), but it has no activity against the gatekeeper mutant T315I. Its activity against the last mutant reappears when used together with an ATP-competitive inhibitor such as Imatinib or Nilotinib. A crystal structure of GNF-2 bound to the Abl myristoyl pocket (MP) has been released. On the contrary, BO1 shows an ATP-competitive/mixed mechanism of action against the wt, while it acts as an allosteric inhibitor against T315I. In order to better understand the mechanism of Abl allosteric inhibition, MD simulations and MM/GBSA analysis were performed on Abl wt and T315I in complex with GNF-2 and BO1, and the results were compared to those found for the natural myristoyl ligand. Similarly to that observed for the myristoyl group, the binding of an allosteric inhibitor to the MP promotes the formation of a compact and inhibited conformation of the wt protein, characterized by the stabilization of the intramolecular interactions that occur between SH2-SH3 and kinase domains. Conversely, an overall higher flexibility was observed with the Abl T315I mutant, especially in the case of GNF-2. Our analysis highlighted differences in the dynamic behavior of GNF-2 and BO1 which could explain the different biological profiles of the two allosteric inhibitors against the T315I mutant.
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Affiliation(s)
- Anna Lucia Fallacara
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena , Via Aldo Moro 2, 53100 Siena, Siena, Italy
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12
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Peruzzotti C, Borrelli S, Ventura M, Pantano R, Fumagalli G, Christodoulou MS, Monticelli D, Luzzani M, Fallacara AL, Tintori C, Botta M, Passarella D. Probing the binding site of abl tyrosine kinase using in situ click chemistry. ACS Med Chem Lett 2013; 4:274-7. [PMID: 24900659 DOI: 10.1021/ml300394w] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 01/15/2013] [Indexed: 02/06/2023] Open
Abstract
Modern combinatorial chemistry is used to discover compounds with desired function by an alternative strategy, in which the biological target is directly involved in the choice of ligands assembled from a pool of smaller fragments. Herein, we present the first experimental result where the use of in situ click chemistry has been successfully applied to probe the ligand-binding site of Abl and the ability of this enzyme to form its inhibitor. Docking studies show that Abl is able to allow the in situ click chemistry between specific azide and alkyne fragments by binding to Abl-active sites. This report allows medicinal chemists to use protein-directed in situ click chemistry for exploring the conformational space of a ligand-binding pocket and the ability of the protein to guide its inhibitor. This approach can be a novel, valuable tool to guide drug design synthesis in the field of tyrosine kinases.
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Affiliation(s)
- Cristina Peruzzotti
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi
19, 20133 Milano, Italy
| | - Stella Borrelli
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi
19, 20133 Milano, Italy
| | - Micol Ventura
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi
19, 20133 Milano, Italy
| | - Rebecca Pantano
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi
19, 20133 Milano, Italy
| | - Gaia Fumagalli
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi
19, 20133 Milano, Italy
| | | | - Damiano Monticelli
- Dipartimento di Scienze Alta
Tecnologia, Università degli Studi dell’Insubria, Via Valleggio 11, 22100 Como, Italy
| | | | - Anna Lucia Fallacara
- Dipartimento Farmaco Chimico
Tecnologico, Università degli Studi di Siena, Via Alcide de Gasperi 2, I-53100, Siena, Italy
| | - Cristina Tintori
- Dipartimento Farmaco Chimico
Tecnologico, Università degli Studi di Siena, Via Alcide de Gasperi 2, I-53100, Siena, Italy
| | - Maurizio Botta
- Dipartimento Farmaco Chimico
Tecnologico, Università degli Studi di Siena, Via Alcide de Gasperi 2, I-53100, Siena, Italy
| | - Daniele Passarella
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi
19, 20133 Milano, Italy
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13
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Fang Z, Grütter C, Rauh D. Strategies for the selective regulation of kinases with allosteric modulators: exploiting exclusive structural features. ACS Chem Biol 2013; 8:58-70. [PMID: 23249378 DOI: 10.1021/cb300663j] [Citation(s) in RCA: 159] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The modulation of kinase function has become an important goal in modern drug discovery and chemical biology research. In cancer-targeted therapies, kinase inhibitors have been experiencing an upsurge, which can be measured by the increasing number of kinase inhibitors approved by the FDA in recent years. However, lack of efficacy, limited selectivity, and the emergence of acquired drug resistance still represent major bottlenecks in the clinic and challenge inhibitor development. Most known kinase inhibitors target the active kinase and are ATP competitive. A second class of small organic molecules, which address remote sites of the kinase and stabilize enzymatically inactive conformations, is rapidly moving to the forefront of kinase inhibitor research. Such allosteric modulators bind to sites that are less conserved across the kinome and only accessible upon conformational changes. These molecules are therefore thought to provide various advantages such as higher selectivity and extended drug target residence times. This review highlights various strategies that have been developed to utilizing exclusive structural features of kinases and thereby modulating their activity allosterically.
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Affiliation(s)
- Zhizhou Fang
- Technische Universität Dortmund, Fakultät
Chemie − Chemische Biologie, Otto-Hahn-Strasse
6, D-44227 Dortmund, Germany
| | - Christian Grütter
- Technische Universität Dortmund, Fakultät
Chemie − Chemische Biologie, Otto-Hahn-Strasse
6, D-44227 Dortmund, Germany
| | - Daniel Rauh
- Technische Universität Dortmund, Fakultät
Chemie − Chemische Biologie, Otto-Hahn-Strasse
6, D-44227 Dortmund, Germany
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14
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Li Y, Geng J, Liu Y, Yu S, Zhao G. Thiadiazole-a Promising Structure in Medicinal Chemistry. ChemMedChem 2012. [DOI: 10.1002/cmdc.201200355] [Citation(s) in RCA: 173] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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15
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Radi M, Evensen L, Dreassi E, Zamperini C, Caporicci M, Falchi F, Musumeci F, Schenone S, Lorens JB, Botta M. A combined targeted/phenotypic approach for the identification of new antiangiogenics agents active on a zebrafish model: from in silico screening to cyclodextrin formulation. Bioorg Med Chem Lett 2012; 22:5579-83. [PMID: 22853993 DOI: 10.1016/j.bmcl.2012.07.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 06/29/2012] [Accepted: 07/04/2012] [Indexed: 12/24/2022]
Abstract
A combined targeted/phenotypic approach for the rapid identification of novel antiangiogenics with in vivo efficacy is herein reported. Considering the important role played by the tyrosine kinase c-Src in the regulation of tumour angiogenesis, we submitted our in-house library of c-Src inhibitors to a sequential screening approach: in silico screening on VEGFR2, in vitro screening on HUVEC cells, ADME profiling, formulation and in vivo testing on a zebrafish model. A promising antiangiogenic candidate able to interfere with the vascular growth of a zebrafish model at low micromolar concentration was thus identified.
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Affiliation(s)
- Marco Radi
- Dipartimento Farmaco Chimico Tecnologico, University of Siena,Via Alcide de Gasperi 2, I-53100 Siena, Italy
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16
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Radi M, Brullo C, Crespan E, Tintori C, Musumeci F, Biava M, Schenone S, Dreassi E, Zamperini C, Maga G, Pagano D, Angelucci A, Bologna M, Botta M. Identification of potent c-Src inhibitors strongly affecting the proliferation of human neuroblastoma cells. Bioorg Med Chem Lett 2011; 21:5928-33. [DOI: 10.1016/j.bmcl.2011.07.079] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 07/21/2011] [Accepted: 07/22/2011] [Indexed: 01/08/2023]
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Arioli F, Borrelli S, Colombo F, Falchi F, Filippi I, Crespan E, Naldini A, Scalia G, Silvani A, Maga G, Carraro F, Botta M, Passarella D. N-[2-Methyl-5-(triazol-1-yl)phenyl]pyrimidin-2-amine as a Scaffold for the Synthesis of Inhibitors of Bcr-Abl. ChemMedChem 2011; 6:2009-18. [DOI: 10.1002/cmdc.201100304] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 08/02/2011] [Indexed: 11/10/2022]
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