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Cao L, Wu Y, Gong Y, Zhou Q. Small molecule modulators of cystic fibrosis transmembrane conductance regulator (CFTR): Structure, classification, and mechanisms. Eur J Med Chem 2024; 265:116120. [PMID: 38194776 DOI: 10.1016/j.ejmech.2023.116120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/28/2023] [Accepted: 12/31/2023] [Indexed: 01/11/2024]
Abstract
The advent of small molecule modulators targeting the cystic fibrosis transmembrane conductance regulator (CFTR) has revolutionized the treatment of persons with cystic fibrosis (CF) (pwCF). Presently, these small molecule CFTR modulators have gained approval for usage in approximately 90 % of adult pwCF. Ongoing drug development endeavors are focused on optimizing the therapeutic benefits while mitigating potential adverse effects associated with this treatment approach. Based on their mode of interaction with CFTR, these drugs can be classified into two distinct categories: specific CFTR modulators and non-specific CFTR modulators. Specific CFTR modulators encompass potentiators and correctors, whereas non-specific CFTR modulators encompass activators, proteostasis modulators, stabilizers, reader-through agents, and amplifiers. Currently, four small molecule modulators, all classified as potentiators and correctors, have obtained marketing approval. Furthermore, numerous novel small molecule modulators, exhibiting diverse mechanisms of action, are currently undergoing development. This review aims to explore the classification, mechanisms of action, molecular structures, developmental processes, and interrelationships among small molecule CFTR modulators.
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Affiliation(s)
- Luyang Cao
- China Pharmaceutical University, Nanjing, 210009, PR China
| | - Yong Wu
- Jiangsu Vcare PharmaTech Co., Ltd., Huakang Road 136, Biotech and Pharmaceutical Valley, Jiangbei New Area, Nanjing, 211800, PR China
| | - Yanchun Gong
- Jiangsu Vcare PharmaTech Co., Ltd., Huakang Road 136, Biotech and Pharmaceutical Valley, Jiangbei New Area, Nanjing, 211800, PR China.
| | - Qingfa Zhou
- China Pharmaceutical University, Nanjing, 210009, PR China.
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Jadhao NL, Musale HB, Gajbhiye JM, Humne VT. Copper-mediated [3 + 2] oxidative cyclization of oxime acetate and its utility in the formal synthesis of fentiazac. Org Biomol Chem 2024; 22:521-528. [PMID: 38087933 DOI: 10.1039/d3ob01882b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
A new protocol for the direct synthesis of 2-aminothiazole has been developed from oxime acetate and readily available sodium thiocyanate using a copper catalyst. The present transformation has good functional group tolerance. Various thiazoles were smoothly synthesized in good to excellent yields. The applicability of the present method has been extended to the formal synthesis of the non-steroidal and anti-inflammatory drug, fentiazac via the Sandmeyer reaction and Suzuki coupling.
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Affiliation(s)
- Nitin L Jadhao
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Pune, 411008, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Harish B Musale
- Department of Chemistry, Shri R. R. Lahoti Science College, Morshi, 444905, India.
| | - Jayant M Gajbhiye
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Pune, 411008, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vivek T Humne
- Department of Chemistry, Shri R. R. Lahoti Science College, Morshi, 444905, India.
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Baroni D, Scarano N, Ludovico A, Brandas C, Parodi A, Lunaccio D, Fossa P, Moran O, Cichero E, Millo E. In Silico and In Vitro Evaluation of the Mechanism of Action of Three VX809-Based Hybrid Derivatives as Correctors of the F508del CFTR Protein. Pharmaceuticals (Basel) 2023; 16:1702. [PMID: 38139828 PMCID: PMC10748060 DOI: 10.3390/ph16121702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Cystic fibrosis (CF), the most common autosomal recessive fatal genetic disease in the Caucasian population, is caused by mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR), an anion channel that regulates salt and water transport across a variety of secretory epithelia. Deletion of phenylalanine at position 508, F508del, the most common CF-causing mutation, destabilises the CFTR protein, causing folding and trafficking defects that lead to a dramatic reduction in its functional expression. Small molecules called correctors have been developed to rescue processing-defective F508del CFTR. We have combined in silico and in vitro approaches to investigate the mechanism of action and potential as CFTR correctors of three hybrid derivatives (2a, 7a, and 7m) obtained by merging the amino-arylthiazole core with the benzodioxole carboxamide moiety characterising the corrector lumacaftor. Molecular modelling analyses suggested that the three hybrids interact with a putative region located at the MSD1/NBD1 interface. Biochemical analyses confirmed these results, showing that the three molecules affect the expression and stability of the F508del NBD1. Finally, the YFP assay was used to evaluate the influence of the three hybrid derivatives on F508del CFTR function, assessing that their effect is additive to that of the correctors VX661 and VX445. Our study shows that the development and testing of optimised compounds targeting different structural and functional defects of mutant CFTR is the best strategy to provide more effective correctors that could be used alone or in combination as a valuable therapeutic option to treat an even larger cohort of people affected by CF.
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Affiliation(s)
- Debora Baroni
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche (CNR), Via De Marini, 6, 16149 Genova, Italy; (A.L.); (O.M.)
| | - Naomi Scarano
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genova, Viale Benedetto XV, 3, 16132 Genoa, Italy; (N.S.); (P.F.)
| | - Alessandra Ludovico
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche (CNR), Via De Marini, 6, 16149 Genova, Italy; (A.L.); (O.M.)
| | - Chiara Brandas
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche (CNR), Via De Marini, 6, 16149 Genova, Italy; (A.L.); (O.M.)
| | - Alice Parodi
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genova, Italy; (A.P.); (D.L.); (E.M.)
| | - Dario Lunaccio
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genova, Italy; (A.P.); (D.L.); (E.M.)
| | - Paola Fossa
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genova, Viale Benedetto XV, 3, 16132 Genoa, Italy; (N.S.); (P.F.)
| | - Oscar Moran
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche (CNR), Via De Marini, 6, 16149 Genova, Italy; (A.L.); (O.M.)
| | - Elena Cichero
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genova, Viale Benedetto XV, 3, 16132 Genoa, Italy; (N.S.); (P.F.)
| | - Enrico Millo
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genova, Italy; (A.P.); (D.L.); (E.M.)
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Mahesh P, Akshinthala P, Ankireddy AR, Katari NK, Gupta LK, Srivastava D, Jonnalagadda SB, Gundla R. Convenient synthesis, characterization and biological evaluation of novel 1-phenylcyclopropane carboxamide derivatives. Heliyon 2023; 9:e13111. [PMID: 36747540 PMCID: PMC9898299 DOI: 10.1016/j.heliyon.2023.e13111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
Small, strained ring molecules of phenylcyclopropane carboxamide have rigid, defined conformations and unique electronic properties. For these reasons many groups, seek to use these subunits to form biologically active compounds. Herein we report a generally applicable approach for preparing a small cyclopropane ring containing 1-phenylcyclopropane carboxamide derivatives to a wide range of the different aromatic compounds by α-alkylation of 2-phenyl acetonitrile derivatives with 1, 2-dibromo ethane in good yields followed by the conversion of cyano group to acid group by the reaction with concentrated hydrochloric acid. This obtained acid derivative undergoes acid amine coupling with various Methyl 2-(aminophenoxy)acetate to form 1-Phenylcyclopropane Carboxamide. These compounds possess distinct effective inhibition on the proliferation of U937, pro-monocytic, human myeloid leukaemia cell line while these compounds did not show cytotoxic activity on these cells. The structure-activity relationships of these compounds are discussed.
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Affiliation(s)
- Panasa Mahesh
- Department of Chemistry, GITAM School of Science, GITAM Deemed to be University, Hyderabad, Telangana, 502329, India
| | - Parameswari Akshinthala
- Department of Science and Humanities, MLR Institute of Technology, Dundigal, Medchal, Hyderabad, 500 043, India
| | - Ashok Reddy Ankireddy
- Department of Chemistry, GITAM School of Science, GITAM Deemed to be University, Hyderabad, Telangana, 502329, India
| | - Naresh Kumar Katari
- Department of Chemistry, GITAM School of Science, GITAM Deemed to be University, Hyderabad, Telangana, 502329, India,School of Chemistry & Physics, College of Agriculture, Engineering & Science, University of KwaZulu-Natal, Westville Campus, P Bag X 54001, Durban, 4000, South Africa,Corresponding author. Department of Chemistry, GITAM School of Science, GITAM Deemed to be University, Hyderabad, Telangana, 502329, India
| | - Lavleen Kumar Gupta
- Drug Discovery Division, IgYImmunologix India Pvt Ltd, Hyderabad, Telangana, 500089 India
| | - Deepali Srivastava
- Drug Discovery Division, IgYImmunologix India Pvt Ltd, Hyderabad, Telangana, 500089 India
| | - Sreekantha Babu Jonnalagadda
- School of Chemistry & Physics, College of Agriculture, Engineering & Science, University of KwaZulu-Natal, Westville Campus, P Bag X 54001, Durban, 4000, South Africa,Corresponding author.
| | - Rambabu Gundla
- Department of Chemistry, GITAM School of Science, GITAM Deemed to be University, Hyderabad, Telangana, 502329, India,Corresponding author.
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Parodi A, Righetti G, Pesce E, Salis A, Tomati V, Pastorino C, Tasso B, Benvenuti M, Damonte G, Pedemonte N, Cichero E, Millo E. Journey on VX-809-Based Hybrid Derivatives towards Drug-like F508del-CFTR Correctors: From Molecular Modeling to Chemical Synthesis and Biological Assays. Pharmaceuticals (Basel) 2022; 15:ph15030274. [PMID: 35337072 PMCID: PMC8955485 DOI: 10.3390/ph15030274] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 02/01/2023] Open
Abstract
Cystic fibrosis (CF) is a genetic disease affecting the lungs and pancreas and causing progressive damage. CF is caused by mutations abolishing the function of CFTR, a protein whose role is chloride’s mobilization in the epithelial cells of various organs. Recently a therapy focused on small molecules has been chosen as a main approach to contrast CF, designing and synthesizing compounds acting as misfolding (correctors) or defective channel gating (potentiators). Multi-drug therapies have been tested with different combinations of the two series of compounds. Previously, we designed and characterized two series of correctors, namely, hybrids, which were conceived including the aminoarylthiazole (AAT) core, merged with the benzodioxole carboxamide moiety featured by VX-809. In this paper, we herein proceeded with molecular modeling studies guiding the design of a new third series of hybrids, featuring structural variations at the thiazole moiety and modifications on position 4. These derivatives were tested in different assays including a YFP functional assay on models F508del-CFTR CFBE41o-cells, alone and in combination with VX-445, and by using electrophysiological techniques on human primary bronchial epithelia to demonstrate their F508del-CFTR corrector ability. This study is aimed (i) at identifying three molecules (9b, 9g, and 9j), useful as novel CFTR correctors with a good efficacy in rescuing the defect of F508del-CFTR; and (ii) at providing useful information to complete the structure–activity study within all the three series of hybrids as possible CFTR correctors, supporting the development of pharmacophore modelling studies, taking into account all the three series of hybrids. Finally, in silico evaluation of the hybrids pharmacokinetic (PK) properties contributed to highlight hybrid developability as drug-like correctors.
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Affiliation(s)
- Alice Parodi
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV, 1, 16132 Genoa, Italy; (A.P.); (A.S.); (M.B.); (G.D.)
| | - Giada Righetti
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy; (G.R.); (B.T.)
| | - Emanuela Pesce
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (E.P.); (V.T.); (N.P.)
| | - Annalisa Salis
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV, 1, 16132 Genoa, Italy; (A.P.); (A.S.); (M.B.); (G.D.)
| | - Valeria Tomati
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (E.P.); (V.T.); (N.P.)
| | - Cristina Pastorino
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DI-NOGMI), University of Genoa, 16132 Genoa, Italy;
| | - Bruno Tasso
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy; (G.R.); (B.T.)
| | - Mirko Benvenuti
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV, 1, 16132 Genoa, Italy; (A.P.); (A.S.); (M.B.); (G.D.)
| | - Gianluca Damonte
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV, 1, 16132 Genoa, Italy; (A.P.); (A.S.); (M.B.); (G.D.)
| | - Nicoletta Pedemonte
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (E.P.); (V.T.); (N.P.)
| | - Elena Cichero
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy; (G.R.); (B.T.)
- Correspondence: (E.C.); (E.M.)
| | - Enrico Millo
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV, 1, 16132 Genoa, Italy; (A.P.); (A.S.); (M.B.); (G.D.)
- Correspondence: (E.C.); (E.M.)
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Sabbadini R, Pesce E, Parodi A, Mustorgi E, Bruzzone S, Pedemonte N, Casale M, Millo E, Cichero E. Probing Allosteric Hsp70 Inhibitors by Molecular Modelling Studies to Expedite the Development of Novel Combined F508del CFTR Modulators. Pharmaceuticals (Basel) 2021; 14:ph14121296. [PMID: 34959696 PMCID: PMC8709398 DOI: 10.3390/ph14121296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/07/2021] [Accepted: 12/09/2021] [Indexed: 11/16/2022] Open
Abstract
Cystic fibrosis (CF) is caused by different mutations related to the cystic fibrosis transmembrane regulator protein (CFTR), with F508del being the most common. Pioneering the development of CFTR modulators, thanks to the development of effective correctors or potentiators, more recent studies deeply encouraged the administration of triple combination therapeutics. However, combinations of molecules interacting with other proteins involved in functionality of the CFTR channel recently arose as a promising approach to address a large rescue of F508del-CFTR. In this context, the design of compounds properly targeting the molecular chaperone Hsp70, such as the allosteric inhibitor MKT-077, proved to be effective for the development of indirect CFTR modulators, endowed with ability to amplify the accumulation of the rescued protein. Herein we performed structure-based studies of a number of allosteric HSP70 inhibitors, considering the recent X-ray crystallographic structure of the human enzyme. This allowed us to point out the main interaction supporting the binding mode of MKT-077, as well as of the related analogues. In particular, cation-π and π-π stacking with the conserve residue Tyr175 deeply stabilized inhibitor binding at the HSP70 cavity. Molecular docking studies had been followed by QSAR analysis and then by virtual screening of aminoaryl thiazoles (I-IIIa) as putative HSP70 inhibitors. Their effectiveness as CFTR modulators has been verified by biological assays, in combination with VX-809, whose positive results confirmed the reliability of the whole applied computational method. Along with this, the "in-silico" prediction of absorption, distribution, metabolism, and excretion (ADME) properties highlighted, once more, that AATs may represent a chemical class to be further investigated for the rational design of novel combination of compounds for CF treatment.
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Affiliation(s)
- Roberto Sabbadini
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy;
| | - Emanuela Pesce
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini, 5, 16147 Genova, Italy; (E.P.); (N.P.)
| | - Alice Parodi
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy; (A.P.); (S.B.)
| | - Eleonora Mustorgi
- Department of Pharmacy, Section of Chemistry and Food and Pharmaceutical Technologies, University of Genoa, Viale Cembrano, 4, 16148 Genoa, Italy; (E.M.); (M.C.)
| | - Santina Bruzzone
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy; (A.P.); (S.B.)
| | - Nicoletta Pedemonte
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini, 5, 16147 Genova, Italy; (E.P.); (N.P.)
| | - Monica Casale
- Department of Pharmacy, Section of Chemistry and Food and Pharmaceutical Technologies, University of Genoa, Viale Cembrano, 4, 16148 Genoa, Italy; (E.M.); (M.C.)
| | - Enrico Millo
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy; (A.P.); (S.B.)
- Correspondence: (E.M.); (E.C.); Tel.: +10-335-3032-3033 (E.M.); +39-010-353-8350 (E.C.)
| | - Elena Cichero
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy;
- Correspondence: (E.M.); (E.C.); Tel.: +10-335-3032-3033 (E.M.); +39-010-353-8350 (E.C.)
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Abstract
INTRODUCTION Cystic fibrosis (CF) is a life-threatening inherited disease caused by mutations in the gene encoding the CF transmembrane conductance regulator (CFTR) protein, an anion channel expressed at the apical membrane of secretory epithelia. CF leads to multiorgan dysfunction with progressive deterioration of lung function being the major cause of untimely death. Conventional CF therapies target only symptoms and consequences downstream of the primary genetic defect and the current life expectancy and quality of life of these individuals are still very limited. AREA COVERED CFTR modulator drugs are novel-specialized therapies that enhance or even restore functional expression of CFTR mutants and have been approved for clinical use for individuals with specific CF genotypes. This review summarizes classical approaches used for the pre-clinical development of CFTR correctors and potentiators as well as emerging strategies aiming to accelerate modulator development and expand theratyping efforts. EXPERT OPINION Highly effective CFTR modulator drugs are expected to deeply modify the disease course for the majority of individuals with CF. A multitude of experimental approaches have been established to accelerate the development of novel modulators. CF patient-derived specimens are valuable cell models to predict therapeutic effectiveness of existing (and novel) modulators in a precision medicine approach.
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Affiliation(s)
| | | | - Guido Veit
- Department of Physiology, McGill University, Montréal, Canada
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Righetti G, Casale M, Tonelli M, Liessi N, Fossa P, Pedemonte N, Millo E, Cichero E. New Insights into the Binding Features of F508del CFTR Potentiators: A Molecular Docking, Pharmacophore Mapping and QSAR Analysis Approach. Pharmaceuticals (Basel) 2020; 13:ph13120445. [PMID: 33291847 PMCID: PMC7762081 DOI: 10.3390/ph13120445] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 11/27/2020] [Accepted: 12/01/2020] [Indexed: 02/06/2023] Open
Abstract
Cystic fibrosis (CF) is the autosomal recessive disorder most recurrent in Caucasian populations. To combat this disease, many life-prolonging therapies are required and deeply investigated, including the development of the so-called cystic fibrosis transmembrane conductance regulator (CFTR) modulators, such as correctors and potentiators. Combination therapy with the two series of drugs led to the approval of several multi-drug effective treatments, such as Orkambi, and to the recent promising evaluation of the triple-combination Elexacaftor-Tezacaftor-Ivacaftor. This scenario enlightened the effectiveness of the multi-drug approach to pave the way for the discovery of novel therapeutic agents to contrast CF. The recent X-crystallographic data about the human CFTR in complex with the well-known potentiator Ivacaftor (VX-770) opened the possibility to apply a computational study aimed to explore the key features involved in the potentiator binding. Herein, we discussed molecular docking studies performed onto the chemotypes so far discussed in the literature as CFTR potentiator, reporting the most relevant interactions responsible for their mechanism of action, involving Van der Waals interactions and π–π stacking with F236, Y304, F305 and F312, as well as H-bonding F931, Y304, S308 and R933. This kind of positioning will stabilize the effective potentiator at the CFTR channel. These data have been accompanied by pharmacophore analyses, which promoted the design of novel derivatives endowed with a main (hetero)aromatic core connected to proper substituents, featuring H-bonding moieties. A highly predictive quantitative-structure activity relationship (QSAR) model has been developed, giving a cross-validated r2 (r2cv) = 0.74, a non-cross validated r2 (r2ncv) = 0.90, root mean square error (RMSE) = 0.347, and a test set r2 (r2pred) = 0.86. On the whole, the results are expected to gain useful information to guide the further development and optimization of new CFTR potentiators.
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Affiliation(s)
- Giada Righetti
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV 3, 16132 Genoa, Italy; (G.R.); (M.T.)
| | - Monica Casale
- Department of Pharmacy, Section of Chemistry and Food and Pharmaceutical Technologies, University of Genoa, Viale Cembrano 4, 16148 Genoa, Italy;
| | - Michele Tonelli
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV 3, 16132 Genoa, Italy; (G.R.); (M.T.)
| | - Nara Liessi
- Center of Excellence for Biomedical Research (CEBR), University of Genoa, Viale Benedetto XV 9, 16132 Genoa, Italy; (N.L.); (E.M.)
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy
| | - Paola Fossa
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV 3, 16132 Genoa, Italy; (G.R.); (M.T.)
- Correspondence: (P.F.); (E.C.); Tel.: +39-010-353-8238 (P.F.); +39-010-353-8370 (E.C.); Fax: +39-010-353-8399 (P.F.); +39-010-353-8399 (E.C.)
| | | | - Enrico Millo
- Center of Excellence for Biomedical Research (CEBR), University of Genoa, Viale Benedetto XV 9, 16132 Genoa, Italy; (N.L.); (E.M.)
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy
| | - Elena Cichero
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV 3, 16132 Genoa, Italy; (G.R.); (M.T.)
- Correspondence: (P.F.); (E.C.); Tel.: +39-010-353-8238 (P.F.); +39-010-353-8370 (E.C.); Fax: +39-010-353-8399 (P.F.); +39-010-353-8399 (E.C.)
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Parodi A, Righetti G, Pesce E, Salis A, Tasso B, Urbinati C, Tomati V, Damonte G, Rusnati M, Pedemonte N, Cichero E, Millo E. Discovery of novel VX-809 hybrid derivatives as F508del-CFTR correctors by molecular modeling, chemical synthesis and biological assays. Eur J Med Chem 2020; 208:112833. [DOI: 10.1016/j.ejmech.2020.112833] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/04/2020] [Accepted: 09/05/2020] [Indexed: 11/21/2022]
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Righetti G, Casale M, Liessi N, Tasso B, Salis A, Tonelli M, Millo E, Pedemonte N, Fossa P, Cichero E. Molecular Docking and QSAR Studies as Computational Tools Exploring the Rescue Ability of F508del CFTR Correctors. Int J Mol Sci 2020; 21:E8084. [PMID: 33138251 DOI: 10.3390/ijms21218084] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 12/11/2022] Open
Abstract
Cystic fibrosis (CF) is the autosomal recessive disorder most recurrent in Caucasian populations. Different mutations involving the cystic fibrosis transmembrane regulator protein (CFTR) gene, which encodes the CFTR channel, are involved in CF. A number of life-prolonging therapies have been conceived and deeply investigated to combat this disease. Among them, the administration of the so-called CFTR modulators, such as correctors and potentiators, have led to quite beneficial effects. Recently, based on QSAR (quantitative structure activity relationship) studies, we reported the rational design and synthesis of compound 2, an aminoarylthiazole-VX-809 hybrid derivative exhibiting promising F508del-CFTR corrector ability. Herein, we explored the docking mode of the prototype VX-809 as well as of the aforementioned correctors in order to derive useful guidelines for the rational design of further analogues. In addition, we refined our previous QSAR analysis taking into account our first series of in-house hybrids. This allowed us to optimize the QSAR model based on the chemical structure and the potency profile of hybrids as F508del-CFTR correctors, identifying novel molecular descriptors explaining the SAR of the dataset. This study is expected to speed up the discovery process of novel potent CFTR modulators.
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Pibiri I, Melfi R, Tutone M, Di Leonardo A, Pace A, Lentini L. Targeting Nonsense: Optimization of 1,2,4-Oxadiazole TRIDs to Rescue CFTR Expression and Functionality in Cystic Fibrosis Cell Model Systems. Int J Mol Sci 2020; 21:ijms21176420. [PMID: 32899265 PMCID: PMC7504161 DOI: 10.3390/ijms21176420] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/26/2020] [Accepted: 09/01/2020] [Indexed: 02/07/2023] Open
Abstract
Cystic fibrosis (CF) patients develop a severe form of the disease when the cystic fibrosis transmembrane conductance regulator (CFTR) gene is affected by nonsense mutations. Nonsense mutations are responsible for the presence of a premature termination codon (PTC) in the mRNA, creating a lack of functional protein. In this context, translational readthrough-inducing drugs (TRIDs) represent a promising approach to correct the basic defect caused by PTCs. By using computational optimization and biological screening, we identified three new small molecules showing high readthrough activity. The activity of these compounds has been verified by evaluating CFTR expression and functionality after treatment with the selected molecules in cells expressing nonsense–CFTR–mRNA. Additionally, the channel functionality was measured by the halide sensitive yellow fluorescent protein (YFP) quenching assay. All three of the new TRIDs displayed high readthrough activity and low toxicity and can be considered for further evaluation as a therapeutic approach toward the second major cause of CF.
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Affiliation(s)
- Ivana Pibiri
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; (R.M.); (M.T.); (A.D.L.); (A.P.)
- Correspondence: (I.P.); (L.L.); Tel.: +39-091-238-97545 (I.P.); +39-091-238-97341 (L.L.)
| | - Raffaella Melfi
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; (R.M.); (M.T.); (A.D.L.); (A.P.)
| | - Marco Tutone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; (R.M.); (M.T.); (A.D.L.); (A.P.)
| | - Aldo Di Leonardo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; (R.M.); (M.T.); (A.D.L.); (A.P.)
- Centro di OncoBiologia Sperimentale (COBS), via San Lorenzo Colli, 90145 Palermo, Italy
| | - Andrea Pace
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; (R.M.); (M.T.); (A.D.L.); (A.P.)
| | - Laura Lentini
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; (R.M.); (M.T.); (A.D.L.); (A.P.)
- Correspondence: (I.P.); (L.L.); Tel.: +39-091-238-97545 (I.P.); +39-091-238-97341 (L.L.)
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12
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Pesce E, Pedemonte N, Leoni A, Locatelli A, Morigi R. Synthesis and biological evaluation of thiazole derivatives on basic defects underlying cystic fibrosis. Bioorg Med Chem Lett 2020; 30:127473. [PMID: 32784089 DOI: 10.1016/j.bmcl.2020.127473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/24/2020] [Accepted: 08/04/2020] [Indexed: 12/14/2022]
Abstract
Cystic fibrosis is a genetic disease caused by loss-of-function mutations in the cystic fibrosis transmembrane conductance regulator gene, encoding for CFTR protein. The most frequent mutation is the deletion of phenylalanine at position 508 (F508del), which leads to distinct defects in channel gating and cellular processing. In last years, several thiazole containing small molecules, endowed with dual F508del-CFTR modulator activity, proved to be able to target these defects. In search of new chemical entities able to restore CFTR function, we designed and synthesized a small series of sixteen thiazole derivatives. The designed compounds were studied as correctors and potentiators of F508del-CFTR. Although none of the molecules showed significant corrector activity, compounds 10 and 11 exhibited potentiator effects, thus allowing to determine some basic structural features which enable to obtain F508del-CFTR potentiator activity. In silico ADME studies showed that these derivatives obey Lipinski's rule of five and are expected to be orally bioavailable. Therefore, these molecules may represent a good starting point for the design of analogues endowed with improved CFTR potentiator activity and a good pharmacokinetic profile.
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Affiliation(s)
- Emanuela Pesce
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy
| | - Nicoletta Pedemonte
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy
| | - Alberto Leoni
- Dipartimento di Farmacia e Biotecnologie, Università di Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Alessandra Locatelli
- Dipartimento di Farmacia e Biotecnologie, Università di Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Rita Morigi
- Dipartimento di Farmacia e Biotecnologie, Università di Bologna, Via Belmeloro 6, 40126 Bologna, Italy.
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13
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Akella M, Malla R. Molecular modeling and in vitro study on pyrocatechol as potential pharmacophore of CD151 inhibitor. J Mol Graph Model 2020; 100:107681. [PMID: 32738620 DOI: 10.1016/j.jmgm.2020.107681] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/25/2020] [Accepted: 06/24/2020] [Indexed: 11/24/2022]
Abstract
CD151 has been recognized as a prognostic marker, the therapeutic target of breast cancers, but less explored for small molecule inhibitors due to lack of a validated model. The 3-D structure of CD151 large extracellular loop (LEL) was modeled using the LOMETS server and validated by the Ramachandran plot. The validated structure was employed for molecular docking and structure-based pharmacophore analysis. Druglikeness was evaluated by the ADMET description protocol. Antiproliferative activity was evaluated by MTT, BrdU incorporation, flow cytometry, and cell death ELISAPLUS assay. This study predicted the best model for CD151-LEL with 94.1% residues in favored regions and Z score -2.79 kcal/mol using the threading method. The web-based receptor cavity method identified one functional target site, which was suitable for the binding of aromatic and heterocyclic compounds. Molecular docking study identified pyrocatechol (PCL) and 5-fluorouracil (FU) as potential leads of CD151-LEL. The pharmacophore model identified interaction points of modeled CD151-LEL with PCL and FU. Also, the analysis of ADMET properties revealed the drug-likeness of PCL and FU. The viability of MDA-MB 231 cells was significantly reduced with PCL and FU but less affected MCF-12A, normal healthy breast epithelial cell line. With 50% toxic concentration, both PCL and FU significantly inhibited 82.46 and 87.12% proliferation, respectively, of MDA-MB 231 cells by altering morphology and inducing G1 cell cycle arrest and apoptosis. In addition, PCL and FU inhibited the CD151 expression by 4.5-and 4.8-folds, respectively. This study suggests the further assessment of pyrocatechol as a potential lead of CD151 in breast cancer at the molecular level.
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Affiliation(s)
- Manasa Akella
- Cancer Biology Lab, Dept. of Biochemistry and Bioinformatics, Institute of Science, GITAM (Deemed to Be University), Visakhapatnam, 530045, Andhra Pradesh, India
| | - RamaRao Malla
- Cancer Biology Lab, Dept. of Biochemistry and Bioinformatics, Institute of Science, GITAM (Deemed to Be University), Visakhapatnam, 530045, Andhra Pradesh, India.
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Tutone M, Pibiri I, Perriera R, Campofelice A, Culletta G, Melfi R, Pace A, Almerico AM, Lentini L. Pharmacophore-Based Design of New Chemical Scaffolds as Translational Readthrough-Inducing Drugs (TRIDs). ACS Med Chem Lett 2020; 11:747-753. [PMID: 32435380 DOI: 10.1021/acsmedchemlett.9b00609] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/18/2020] [Indexed: 12/31/2022] Open
Abstract
Translational readthrough-inducing drugs (TRIDs) rescue the functional full-length protein expression in genetic diseases, such as cystic fibrosis, caused by premature termination codons (PTCs). Small molecules have been developed as TRIDs to trick the ribosomal machinery during recognition of the PTC. Herein we report a computational study to identify new TRID scaffolds. A pharmacophore approach was carried out on compounds that showed readthrough activity. The pharmacophore model applied to screen different libraries containing more than 87000 compounds identified four hit-compounds presenting scaffolds with diversity from the oxadiazole lead. These compounds have been synthesized and tested using the Fluc reporter harboring the UGA PTC. Moreover, the cytotoxic effect and the expression of the CFTR protein were evaluated. These compounds, a benzimidazole derivative (NV2899), a benzoxazole derivative (NV2913), a thiazole derivative (NV2909), and a benzene-1,3-disulfonate derivative (NV2907), were shown to be potential new lead compounds as TRIDs, boosting further efforts to address the optimization of the chemical scaffolds.
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Affiliation(s)
- Marco Tutone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, via Archirafi, 90123-Palermo, Italy
| | - Ivana Pibiri
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, via Archirafi, 90123-Palermo, Italy
| | - Riccardo Perriera
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, via Archirafi, 90123-Palermo, Italy
| | - Ambra Campofelice
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, via Archirafi, 90123-Palermo, Italy
| | - Giulia Culletta
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, via Archirafi, 90123-Palermo, Italy
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, viale Annunziata, 98168-Messina, Italy
| | - Raffaella Melfi
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, via Archirafi, 90123-Palermo, Italy
| | - Andrea Pace
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, via Archirafi, 90123-Palermo, Italy
| | - Anna Maria Almerico
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, via Archirafi, 90123-Palermo, Italy
| | - Laura Lentini
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, via Archirafi, 90123-Palermo, Italy
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Santos KLBD, Cruz JN, Silva LB, Ramos RS, Neto MFA, Lobato CC, Ota SSB, Leite FHA, Borges RS, Silva CHTPD, Campos JM, Santos CBR. Identification of Novel Chemical Entities for Adenosine Receptor Type 2A Using Molecular Modeling Approaches. Molecules 2020; 25:E1245. [PMID: 32164183 DOI: 10.3390/molecules25051245] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/01/2020] [Accepted: 03/06/2020] [Indexed: 12/20/2022] Open
Abstract
Adenosine Receptor Type 2A (A2AAR) plays a role in important processes, such as anti-inflammatory ones. In this way, the present work aimed to search for compounds by pharmacophore-based virtual screening. The pharmacokinetic/toxicological profiles of the compounds, as well as a robust QSAR, predicted the binding modes via molecular docking. Finally, we used molecular dynamics to investigate the stability of interactions from ligand-A2AAR. For the search for A2AAR agonists, the UK-432097 and a set of 20 compounds available in the BindingDB database were studied. These compounds were used to generate pharmacophore models. Molecular properties were used for construction of the QSAR model by multiple linear regression for the prediction of biological activity. The best pharmacophore model was used by searching for commercial compounds in databases and the resulting compounds from the pharmacophore-based virtual screening were applied to the QSAR. Two compounds had promising activity due to their satisfactory pharmacokinetic/toxicological profiles and predictions via QSAR (Diverset 10002403 pEC50 = 7.54407; ZINC04257548 pEC50 = 7.38310). Moreover, they had satisfactory docking and molecular dynamics results compared to those obtained for Regadenoson (Lexiscan®), used as the positive control. These compounds can be used in biological assays (in vitro and in vivo) in order to confirm the potential activity agonist to A2AAR.
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Liessi N, Pesce E, Salis A, Damonte G, Tasso B, Cichero E, Pedemonte N, Millo E. Synthesis and Structure-activity Relationship of Aminoarylthiazole Derivatives as Potential Potentiators of the Chloride Transport Defect in Cystic Fibrosis. Med Chem 2020; 17:646-657. [PMID: 32141420 DOI: 10.2174/1573406416666200306114300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/29/2020] [Accepted: 01/29/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Cystic fibrosis (CF) is the autosomal recessive disorder most common in Caucasian populations. It is caused by mutations in the cystic fibrosis transmembrane regulator protein (CFTR). CFTR is predominantly expressed at the apical plasma membranes of the epithelial cells lining several organs, and functions as a cAMP-regulated chloride/bicarbonate channel. To address the underlying causes of cystic fibrosis, two biomolecular activities are required, namely correctors to increase CFTR levels at the cell surface, and potentiators to allow the effective opening of the CFTR channel. OBJECTIVE In our previous data, we demonstrated that some aminoarylthiazoles (AATs) have peculiar activity acting as correctors and as potentiator-like molecules. Curiously, a compound called 1 has been shown to be markedly active as a potentiator. Now, we have further modified its scaffold at different portions, for the identification of molecules with improved potency and effectiveness on mutant CFTR. METHODS Starting from this active compound, we synthesized a small library trying to improve the activity as potentiators. To extrapolate the contribution of a particular structural portion to bioactivity, we selectively modified one portion at a time. RESULTS Our study has provided a structure-activity relationship (SAR) on AATs and led to the identification of some compounds, with a particular ability to act as CFTR potentiators. CONCLUSION Two compounds 2 and 13 appear to be promising molecules and could be used for the future development of potentiators of the chloride transport defect in cystic fibrosis.
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Affiliation(s)
- Nara Liessi
- Center of Excellence for Biomedical Research (CEBR), University of Genoa, Viale Benedetto XV 9, 16132 Genoa, Italy
| | - Emanuela Pesce
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Annalisa Salis
- Center of Excellence for Biomedical Research (CEBR), University of Genoa, Viale Benedetto XV 9, 16132 Genoa, Italy
| | - Gianluca Damonte
- Center of Excellence for Biomedical Research (CEBR), University of Genoa, Viale Benedetto XV 9, 16132 Genoa, Italy
| | - Bruno Tasso
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy
| | - Elena Cichero
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy
| | | | - Enrico Millo
- Center of Excellence for Biomedical Research (CEBR), University of Genoa, Viale Benedetto XV 9, 16132 Genoa, Italy
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17
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Wang J, Peng W, Li X, Fan W, Wei D, Wu B, Fan L, Wu C, Li L. Towards to potential 2-cyano-pyrimidines cathepsin-K inhibitors: An in silico design and screening research based on comprehensive application of quantitative structure–activity relationships, molecular docking and ADMET prediction. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.06.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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18
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Jadhav BS, Yamgar RS, Kenny RS, Mali SN, Chaudhari HK, Mandewale MC. Synthesis, In silico and Biological Studies of Thiazolyl-2h-chromen-2-one Derivatives as Potent Antitubercular Agents. Curr Comput Aided Drug Des 2019; 16:511-522. [PMID: 31438831 DOI: 10.2174/1386207322666190722162100] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/26/2019] [Accepted: 06/28/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND A series of new six thiazolyl-2-amine-based Schiff base derivatives (4a-4f) were synthesized by a sequential multistep reaction starting with Salicylaldehyde. METHODS All the Schiff base derivatives were screened in-vitro for their antibacterial activity against Mycobacterium tuberculosis (H37RV strain) ATCC No-27294. The synthesized compounds were characterized by FTIR, 1H-NMR, 13C-NMR and Mass spectrometry. RESULTS Among the compounds tested, 4c and 4f derivatives exhibited potent antitubercular activity against M. tuberculosis at MIC 6.25 μg/mL. CONCLUSION We extended our study to explore the inhibition mechanism by conducting molecular docking analysis by using Schrodinger's molecular modeling software. All the newly synthesized compounds were found to be in-silico AMES test non-toxic and non-carcinogens. The good Qikprop's Absorption, Distribution, Metabolism and Excretion (ADMET) would definitely help the researchers in order to make more potent Anti-TB agents.
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Affiliation(s)
- Bhagwat S Jadhav
- Department of Chemistry, Government of Maharashtra, Ismail Yusuf College of Arts, Science and Commerce, Jogeshwari (East), Mumbai-400 060, India
| | - Ramesh S Yamgar
- Department of Chemistry, Chikitsak Samuha’s Patkar-Varde College of Arts, Science and Commerce, Goregaon (West), Mumbai 400 062, India
| | - Rajesh S Kenny
- Department of Chemistry, Chikitsak Samuha’s Patkar-Varde College of Arts, Science and Commerce, Goregaon (West), Mumbai 400 062, India
| | - Suraj N Mali
- Institute of Chemical Technology, Matunga, Mumbai 400019, India
| | | | - Mustapha C Mandewale
- Department of Chemistry, Government of Maharashtra, Ismail Yusuf College of Arts, Science and Commerce, Jogeshwari (East), Mumbai-400 060, India
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Abstract
Cystic fibrosis (CF), a life-threatening multiorgan genetic disease, is facing a new era of research and development using innovative gene-directed personalized therapies. The priority organ to cure is the lung, which suffers recurrent and chronic bacterial infection and inflammation since infancy, representing the main cause of morbidity and precocious mortality of these individuals. After the disappointing failure of gene-replacement approaches using gene therapy vectors, no single drug is presently available to repair all the CF gene defects. The impressive number of different CF gene mutations is now tackled with different chemical and biotechnological tools tailored to the specific molecular derangements, thanks to the extensive knowledge acquired over many years on the mechanisms of CF cell and organ pathology. This review provides an overview and recalls both the successes and limitations of the different experimental approaches, such as high-throughput screening on chemical libraries to discover CF gene correctors and potentiators, dual-acting compounds, read-through molecules, splicing defect repairing tools, cystic fibrosis transmembrane conductance regulator (CFTR) "amplifiers," CFTR interactome modulators and the first gene editing attempts.
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Affiliation(s)
- Giulio Cabrini
- Laboratory of Molecular Pathology, University Hospital, Verona, Italy. .,Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy.
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20
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Spanò V, Montalbano A, Carbone A, Scudieri P, Galietta LJV, Barraja P. An overview on chemical structures as ΔF508-CFTR correctors. Eur J Med Chem 2019; 180:430-448. [PMID: 31326599 DOI: 10.1016/j.ejmech.2019.07.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 10/26/2022]
Abstract
Deletion of phenylalanine at position 508 (F508del) in the CFTR protein, is the most common mutation causing cystic fibrosis (CF). F508del causes misfolding and rapid degradation of CFTR protein a defect that can be targeted with pharmacological agents termed "correctors". Correctors belong to various chemical classes but are generally small molecules based on nitrogen sulfur or oxygen heterocycles. The mechanism of action of correctors is generally unknown but there is experimental evidence that some of them can directly act on mutant CFTR improving folding and stability. Here we overview the characteristics of the various F508del correctors described so far to obtain indications on key chemical structures and modifications that are required for mutant protein rescue.
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Affiliation(s)
- Virginia Spanò
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123, Palermo, Italy
| | - Alessandra Montalbano
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123, Palermo, Italy
| | - Anna Carbone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123, Palermo, Italy
| | - Paolo Scudieri
- Telethon Institute of Genetics and Medicine (TIGEM), Campi Flegrei 34, 80078, Pozzuoli, NA, Italy
| | - Luis J V Galietta
- Telethon Institute of Genetics and Medicine (TIGEM), Campi Flegrei 34, 80078, Pozzuoli, NA, Italy; Department of Translational Medical Sciences (DISMET), University of Naples, "Federico II", 80131, Naples, Italy
| | - Paola Barraja
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123, Palermo, Italy.
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Evren AE, Yurttas L, Ekselli B, Akalin-Ciftci G. Synthesis and biological evaluation of 5-methyl-4-phenyl thiazole derivatives as anticancer agents. PHOSPHORUS SULFUR 2019. [DOI: 10.1080/10426507.2018.1550642] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Asaf E. Evren
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Anadolu University, Eskişehir, Turkey
| | - Leyla Yurttas
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Anadolu University, Eskişehir, Turkey
| | - Büşra Ekselli
- Faculty of Pharmacy, Department of Biochemistry, Anadolu University, Eskişehir, Turkey
| | - Gülşen Akalin-Ciftci
- Faculty of Pharmacy, Department of Biochemistry, Anadolu University, Eskişehir, Turkey
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22
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Wang JL, Li L, Hu MB, Wu B, Fan WX, Peng W, Wei DN, Wu CJ. In silico drug design of inhibitor of nuclear factor kappa B kinase subunit beta inhibitors from 2-acylamino-3-aminothienopyridines based on quantitative structure–activity relationships and molecular docking. Comput Biol Chem 2019; 78:297-305. [DOI: 10.1016/j.compbiolchem.2018.12.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 12/11/2018] [Accepted: 12/26/2018] [Indexed: 11/17/2022]
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Peng Y, Alexov E, Basu S. Structural Perspective on Revealing and Altering Molecular Functions of Genetic Variants Linked with Diseases. Int J Mol Sci 2019; 20:ijms20030548. [PMID: 30696058 PMCID: PMC6386852 DOI: 10.3390/ijms20030548] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 01/25/2019] [Accepted: 01/26/2019] [Indexed: 12/25/2022] Open
Abstract
Structural information of biological macromolecules is crucial and necessary to deliver predictions about the effects of mutations-whether polymorphic or deleterious (i.e., disease causing), wherein, thermodynamic parameters, namely, folding and binding free energies potentially serve as effective biomarkers. It may be emphasized that the effect of a mutation depends on various factors, including the type of protein (globular, membrane or intrinsically disordered protein) and the structural context in which it occurs. Such information may positively aid drug-design. Furthermore, due to the intrinsic plasticity of proteins, even mutations involving radical change of the structural and physico⁻chemical properties of the amino acids (native vs. mutant) can still have minimal effects on protein thermodynamics. However, if a mutation causes significant perturbation by either folding or binding free energies, it is quite likely to be deleterious. Mitigating such effects is a promising alternative to the traditional approaches of designing inhibitors. This can be done by structure-based in silico screening of small molecules for which binding to the dysfunctional protein restores its wild type thermodynamics. In this review we emphasize the effects of mutations on two important biophysical properties, stability and binding affinity, and how structures can be used for structure-based drug design to mitigate the effects of disease-causing variants on the above biophysical properties.
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Affiliation(s)
- Yunhui Peng
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA.
| | - Emil Alexov
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA.
| | - Sankar Basu
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA.
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Pibiri I, Lentini L, Melfi R, Tutone M, Baldassano S, Ricco Galluzzo P, Di Leonardo A, Pace A. Rescuing the CFTR protein function: Introducing 1,3,4-oxadiazoles as translational readthrough inducing drugs. Eur J Med Chem 2018; 159:126-142. [PMID: 30278331 DOI: 10.1016/j.ejmech.2018.09.057] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 12/20/2022]
Abstract
Nonsense mutations in the CFTR gene prematurely terminate translation of the CFTR mRNA leading to the production of a truncated protein that lacks normal function causing a more severe form of the cystic fibrosis (CF) disease. About 10% of patients affected by CF show a nonsense mutation. A potential treatment of this alteration is to promote translational readthrough of premature termination codons (PTCs) by Translational Readthrough Inducing Drugs (TRIDs) such as PTC124. In this context we aimed to compare the activity of PTC124 with analogues differing in the heteroatoms position in the central heterocyclic core. By a validated protocol consisting of computational screening, synthesis and biological tests we identified a new small molecule (NV2445) with 1,3,4-oxadiazole core showing a high readthrough activity. Moreover, we evaluated the CFTR functionality after NV2445 treatment in CF model systems and in cells expressing a nonsense-CFTR-mRNA. Finally, we studied the supramolecular interactions between TRIDs and CFTR-mRNA to assess the biological target/mechanism and compared the predicted ADME properties of NV2445 and PTC124.
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Affiliation(s)
- Ivana Pibiri
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy.
| | - Laura Lentini
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy.
| | - Raffaella Melfi
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy
| | - Marco Tutone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy
| | - Sara Baldassano
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy
| | - Paola Ricco Galluzzo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy
| | - Aldo Di Leonardo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy; Centro di OncoBiologia Sperimentale (COBS), via San Lorenzo Colli, 90145, Palermo, Italy
| | - Andrea Pace
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy
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Khairullina VR, Gimadieva AR, Gerchikov AY, Mustafin AG, Zarudii FS. Quantitative structure-activity relationship of the thymidylate synthase inhibitors of Mus musculus in the series of quinazolin-4-one and quinazolin-4-imine derivatives. J Mol Graph Model 2018; 85:198-211. [PMID: 30227365 DOI: 10.1016/j.jmgm.2018.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 07/19/2018] [Accepted: 09/02/2018] [Indexed: 02/03/2023]
Abstract
A quantitative structure-activity relationship analysis of the 2-methylquinazolin-4-one and quinazolin-4-imine derivatives, well-known antifolate thymidylate synthase (TYMS) inhibitors, has been performed in the range IC50 = 0.4÷380000.0 nmoL/L using the GUSAR 2013 program. Based on the MNA and QNA descriptors using the self-consistent regression, 6 statistically significant consensus models for predicting the IC50 numerical values have been constructed. These models demonstrate high and moderate prognostic accuracies for the training and external validation test sets, respectively. The molecular fragments of TYMS inhibitors regulating their antitumor activity are identified. The obtained data open opportunities for developing novel promising inhibitors of TYMS.
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Affiliation(s)
| | - Alfiya R Gimadieva
- Ufa Institute of Chemistry - Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 71 prospect Oktyabrya, Ufa, 450054, Russian Federation
| | | | - Akhat G Mustafin
- Bashkir State University, 32 Z. Validi str., Ufa, 450076, Russian Federation; Ufa Institute of Chemistry - Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 71 prospect Oktyabrya, Ufa, 450054, Russian Federation
| | - Felix S Zarudii
- Bashkir State Medical University, 3 Lenina str, Ufa, 450000, Russian Federation
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Dechecchi MC, Tamanini A, Cabrini G. Molecular basis of cystic fibrosis: from bench to bedside. Ann Transl Med 2018; 6:334. [PMID: 30306073 PMCID: PMC6174194 DOI: 10.21037/atm.2018.06.48] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 06/26/2018] [Indexed: 12/21/2022]
Abstract
Cystic fibrosis (CF), is an autosomal recessive disease affecting different organs. The lung disease, characterized by recurrent and chronic bacterial infection and inflammation since infancy, is the main cause of morbidity and precocious mortality of these individuals. The innovative therapies directed to repair the defective CF gene should account for the presence of more than 200 disease-causing mutations of the CF transmembrane conductance regulator (CFTR) gene. The review will recall the different experimental approaches in discovering CFTR protein targeted molecules, such as the high throughput screening on chemical libraries to discover correctors and potentiators of CFTR protein, dual-acting compounds, read-through molecules, splicing defects repairing tools, CFTR "amplifiers".
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Affiliation(s)
- Maria Cristina Dechecchi
- Laboratory of Analysis, Section of Molecular Pathology, University Hospital of Verona, Verona, Italy
| | - Anna Tamanini
- Laboratory of Analysis, Section of Molecular Pathology, University Hospital of Verona, Verona, Italy
| | - Giulio Cabrini
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
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Cruz JV, Neto MFA, Silva LB, da S Ramos R, da S Costa J, Brasil DSB, Lobato CC, da Costa GV, Bittencourt JAHM, da Silva CHTP, Leite FHA, Santos CBR. Identification of Novel Protein Kinase Receptor Type 2 Inhibitors Using Pharmacophore and Structure-Based Virtual Screening. Molecules 2018; 23:E453. [PMID: 29463017 DOI: 10.3390/molecules23020453] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 01/26/2018] [Accepted: 02/01/2018] [Indexed: 12/31/2022] Open
Abstract
The Protein Kinase Receptor type 2 (RIPK2) plays an important role in the pathogenesis of inflammatory diseases; it signals downstream of the NOD1 and NOD2 intracellular sensors and promotes a productive inflammatory response. However, excessive NOD2 signaling has been associated with various diseases, including sarcoidosis and inflammatory arthritis; the pharmacological inhibition of RIPK2 is an affinity strategy that demonstrates an increased expression of pro-inflammatory secretion activity. In this study, a pharmacophoric model based on the crystallographic pose of ponatinib, a potent RIPK2 inhibitor, and 30 other ones selected from the BindingDB repository database, was built. Compounds were selected based on the available ZINC compounds database and in silico predictions of their pharmacokinetic, toxicity and potential biological activity. Molecular docking was performed to identify the probable interactions of the compounds as well as their binding affinity with RIPK2. The compounds were analyzed to ponatinib and WEHI-345, which also used as a control. At least one of the compounds exhibited suitable pharmacokinetic properties, low toxicity and an interesting binding affinity and high fitness compared with the crystallographic pose of WEHI-345 in complex with RIPK2. This compound also possessed suitable synthetic accessibility, rendering it a potential and very promising RIPK2 inhibitor to be further investigated in regards to different diseases, particularly inflammatory ones.
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